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

Science.gov (United States)

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.

Exploring Energy Landscapes

Science.gov (United States)

Wales, David J.

2018-04-01

Recent advances in the potential energy landscapes approach are highlighted, including both theoretical and computational contributions. Treating the high dimensionality of molecular and condensed matter systems of contemporary interest is important for understanding how emergent properties are encoded in the landscape and for calculating these properties while faithfully representing barriers between different morphologies. The pathways characterized in full dimensionality, which are used to construct kinetic transition networks, may prove useful in guiding such calculations. The energy landscape perspective has also produced new procedures for structure prediction and analysis of thermodynamic properties. Basin-hopping global optimization, with alternative acceptance criteria and generalizations to multiple metric spaces, has been used to treat systems ranging from biomolecules to nanoalloy clusters and condensed matter. This review also illustrates how all this methodology, developed in the context of chemical physics, can be transferred to landscapes defined by cost functions associated with machine learning.

Direct design of an energy landscape with bistable DNA origami mechanisms.

Science.gov (United States)

Zhou, Lifeng; Marras, Alexander E; Su, Hai-Jun; Castro, Carlos E

2015-03-11

Structural DNA nanotechnology provides a feasible technique for the design and fabrication of complex geometries even exhibiting controllable dynamic behavior. Recently we have demonstrated the possibility of implementing macroscopic engineering design approaches to construct DNA origami mechanisms (DOM) with programmable motion and tunable flexibility. Here, we implement the design of compliant DNA origami mechanisms to extend from prescribing motion to prescribing an energy landscape. Compliant mechanisms facilitate motion via deformation of components with tunable stiffness resulting in well-defined mechanical energy stored in the structure. We design, fabricate, and characterize a DNA origami nanostructure with an energy landscape defined by two stable states (local energy minima) separated by a designed energy barrier. This nanostructure is a four-bar bistable mechanism with two undeformed states. Traversing between those states requires deformation, and hence mechanical energy storage, in a compliant arm of the linkage. The energy barrier for switching between two states was obtained from the conformational distribution based on a Boltzmann probability function and closely follows a predictive mechanical model. Furthermore, we demonstrated the ability to actuate the mechanism into one stable state via additional DNA inputs and then release the actuation via DNA strand displacement. This controllable multistate system establishes a foundation for direct design of energy landscapes that regulate conformational dynamics similar to biomolecular complexes.

Technology assessment in energy landscapes. Agent-based modeling of energy conflicts

International Nuclear Information System (INIS)

Scheffran, Juergen; Link, P. Michael; Shaaban, Mostafa; Suesser, Diana

2017-01-01

The risks and conflicts of the fossil-nuclear age are in contrast to the effects of renewable energies which appear in a largely positive light. However, the transformation towards a low-carbon energy supply creates new energy landscapes with a high demand for suitable land areas - which may also provoke energy conflicts. Technology assessment can contribute to reducing such energy conflicts and increasing public acceptance by using spatial agent-based models that represent dynamic decisions and interactions of stakeholders regarding energy alternatives and land-use options. Northern Germany serves as a case study region where farmers and communities are local actors of the energy transition.

Energy landscapes, landscapes in transition. How to prepare one's territory to the deployment of renewable energies

International Nuclear Information System (INIS)

2014-06-01

This guide first defines the notion of landscape, outlines what is at stake with decentralised renewable energy production, and presents the various important aspects of a deployment of decentralised renewable energy production. It describes how to define a general strategy for the integration of this production: relationship between energy and landscape, project implementation, partnership, tools to anticipate changes, evolution of social demand through dialogue, conciliation of technical and financial constraints and landscape ambitions. An appendix proposes legal and bibliographical information: legal relationships between energy and landscape, possible arrangements for PLU (plan local d'urbanisme, local urban plan) and SCOT (schema de coherence territoriale, territorial planning document)

Relationship between energy landscape and low-temperature dynamics of ±J spin glasses

International Nuclear Information System (INIS)

Kobe, S.; Krawczyk, J.

2004-01-01

Clusters and valleys in the exact low-energy landscape of finite Edwards-Anderson ±J spin glasses are related to the distribution of spin domains and free spins in the ground states. The time evolution of the spin correlation function reflects a walk through the landscape at a given temperature and shows typical glassy behaviour

Competing Wind Energy Discourses, Contested Landscapes

Directory of Open Access Journals (Sweden)

Antje Otto

2014-10-01

Full Text Available The impairment of landscapes is a concern constantly raised against wind energy developments in Germany as in other countries. Often, landscapes or landscape types are treated in the literature as essentialist or at least as uncontested categories. We analyse two examples of local controversies about wind energy, in which “landscape” is employed by supporters and opponents alike, from a poststructuralist and discourse theoretical angle. The aim is to identify and compare landscape constructs produced in the micro discourses of wind energy objectors and proponents at local level (a within each case, (b between the two cases and (c with landscape constructs that were previously found in macro discourses. One major finding is that several different landscapes can exist at one and the same place. Furthermore there seems to be a relatively stable set of competing landscape concepts which is reproduced in specific controversies. The paper concludes by highlighting practical consequences and by identifying promising avenues of further research.

Badlands: A parallel basin and landscape dynamics model

Directory of Open Access Journals (Sweden)

T. Salles

2016-01-01

Full Text Available 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.

Energy landscape reveals that the budding yeast cell cycle is a robust and adaptive multi-stage process.

Directory of Open Access Journals (Sweden)

Cheng Lv

2015-03-01

Full Text Available Quantitatively understanding the robustness, adaptivity and efficiency of cell cycle dynamics under the influence of noise is a fundamental but difficult question to answer for most eukaryotic organisms. Using a simplified budding yeast cell cycle model perturbed by intrinsic noise, we systematically explore these issues from an energy landscape point of view by constructing an energy landscape for the considered system based on large deviation theory. Analysis shows that the cell cycle trajectory is sharply confined by the ambient energy barrier, and the landscape along this trajectory exhibits a generally flat shape. We explain the evolution of the system on this flat path by incorporating its non-gradient nature. Furthermore, we illustrate how this global landscape changes in response to external signals, observing a nice transformation of the landscapes as the excitable system approaches a limit cycle system when nutrients are sufficient, as well as the formation of additional energy wells when the DNA replication checkpoint is activated. By taking into account the finite volume effect, we find additional pits along the flat cycle path in the landscape associated with the checkpoint mechanism of the cell cycle. The difference between the landscapes induced by intrinsic and extrinsic noise is also discussed. In our opinion, this meticulous structure of the energy landscape for our simplified model is of general interest to other cell cycle dynamics, and the proposed methods can be applied to study similar biological systems.

New interaction paths in the energy landscape: the role of local energy initiatives

OpenAIRE

de Boer, Jessica; Zuidema, Christian; Gugerell, Katharina

2018-01-01

Energy transition is an encompassing process which not only involves the energy system but also the landscape in which the energy system is embedded. Renewable energy is triggering new interactions with local landscapes in physical, socio-economic and institutional senses. We capture these interactions using the energy landscape concept, which expresses the interdependence of the energy system with the landscape. We aim to understand whether and how local energy initiatives facilitate this in...

Arid landscape dynamics along a precipitation gradient: addressing vegetation - landscape structure - resource interactions at different time scales

NARCIS (Netherlands)

Buis, E.

2008-01-01

This research is entitled ‘Arid landscape dynamics along a precipitation gradient: addressing
vegetation – landscape structure – resource interactions at different time scales’ with as subtitle
‘A case study for the Northern Negev Desert of Israel’. Landscape dynamics describes the

Energy landscapes shape animal movement ecology.

Science.gov (United States)

Shepard, Emily L C; Wilson, Rory P; Rees, W Gareth; Grundy, Edward; Lambertucci, Sergio A; Vosper, Simon B

2013-09-01

The metabolic costs of animal movement have been studied extensively under laboratory conditions, although frequently these are a poor approximation of the costs of operating in the natural, heterogeneous environment. Construction of "energy landscapes," which relate animal locality to the cost of transport, can clarify whether, to what extent, and how movement properties are attributable to environmental heterogeneity. Although behavioral responses to aspects of the energy landscape are well documented in some fields (notably, the selection of tailwinds by aerial migrants) and scales (typically large), the principles of the energy landscape extend across habitat types and spatial scales. We provide a brief synthesis of the mechanisms by which environmentally driven changes in the cost of transport can modulate the behavioral ecology of animal movement in different media, develop example cost functions for movement in heterogeneous environments, present methods for visualizing these energy landscapes, and derive specific predictions of expected outcomes from individual- to population- and species-level processes. Animals modulate a suite of movement parameters (e.g., route, speed, timing of movement, and tortuosity) in relation to the energy landscape, with the nature of their response being related to the energy savings available. Overall, variation in movement costs influences the quality of habitat patches and causes nonrandom movement of individuals between them. This can provide spatial and/or temporal structure to a range of population- and species-level processes, ultimately including gene flow. Advances in animal-attached technology and geographic information systems are opening up new avenues for measuring and mapping energy landscapes that are likely to provide new insight into their influence in animal ecology.

Characterizing structural transitions using localized free energy landscape analysis.

Directory of Open Access Journals (Sweden)

Nilesh K Banavali

Full Text Available Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

Modeling Coupled Landscape Evolution and Soil Organic Carbon Dynamics in Intensively Management Landscapes

Science.gov (United States)

Yan, Q.; Kumar, P.

2017-12-01

Soil is the largest reservoir of carbon in the biosphere but in agricultural areas it is going through rapid erosion due disturbance arising from crop harvest, tillage, and tile drainage. Identifying whether the production of soil organic carbon (SOC) from the crops can compensate for the loss due to erosion is critical to ensure our food security and adapt to climate change. In the U.S. Midwest where large areas of land are intensively managed for agriculture practices, predicting soil quantity and quality are critical for maintaining crop yield and other Critical Zone services. This work focuses on modeling the coupled landscape evolutions soil organic carbon dynamics in agricultural fields. It couples landscape evolution, surface water runoff, organic matter transformation, and soil moisture dynamics to understand organic carbon gain and loss due to natural forcing and farming practices, such as fertilizer application and tillage. A distinctive feature of the model is the coupling of surface ad subsurface processes that predicts both surficial changes and transport along with the vertical transport and dynamics. Our results show that landscape evolution and farming practices play dominant roles in soil organic carbon (SOC) dynamics both above- and below-ground. Contrary to the common assumption that a vertical profile of SOC concentration decreases exponentially with depth, we find that in many situations SOC concentration below-ground could be higher than that at the surface. Tillage plays a complex role in organic matter dynamics. On one hand, tillage would accelerate the erosion rate, on the other hand, it would improve carbon storage by burying surface SOC into below ground. Our model consistently reproduces the observed above- and below-ground patterns of SOC in the field sites of Intensively Managed Landscapes Critical Zone Observatory (IMLCZO). This model bridges the gaps between the landscape evolution, below- and above-ground hydrologic cycle, and

Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.

Directory of Open Access Journals (Sweden)

Paul C Whitford

Full Text Available Functional rearrangements in biomolecular assemblies result from diffusion across an underlying energy landscape. While bulk kinetic measurements rely on discrete state-like approximations to the energy landscape, single-molecule methods can project the free energy onto specific coordinates. With measures of the diffusion, one may establish a quantitative bridge between state-like kinetic measurements and the continuous energy landscape. We used an all-atom molecular dynamics simulation of the 70S ribosome (2.1 million atoms; 1.3 microseconds to provide this bridge for specific conformational events associated with the process of tRNA translocation. Starting from a pre-translocation configuration, we identified sets of residues that collectively undergo rotary rearrangements implicated in ribosome function. Estimates of the diffusion coefficients along these collective coordinates for translocation were then used to interconvert between experimental rates and measures of the energy landscape. This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation. While this analysis was performed for a particular kinetic scheme of translocation, the quantitative framework is general and may be applied to energetic and kinetic descriptions that include any number of intermediates and transition states.

Energy landscape of social balance.

Science.gov (United States)

Marvel, Seth A; Strogatz, Steven H; Kleinberg, Jon M

2009-11-06

We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion of social "balance" allows us to define an energy landscape for such networks. Its structure is complex: numerical experiments reveal a landscape dimpled with local minima of widely varying energy levels. We derive rigorous bounds on the energies of these local minima and prove that they have a modular structure that can be used to classify them.

Energy Landscape of Social Balance

Science.gov (United States)

Marvel, Seth A.; Strogatz, Steven H.; Kleinberg, Jon M.

2009-11-01

We model a close-knit community of friends and enemies as a fully connected network with positive and negative signs on its edges. Theories from social psychology suggest that certain sign patterns are more stable than others. This notion of social “balance” allows us to define an energy landscape for such networks. Its structure is complex: numerical experiments reveal a landscape dimpled with local minima of widely varying energy levels. We derive rigorous bounds on the energies of these local minima and prove that they have a modular structure that can be used to classify them.

Energy forest cultivation and the landscape

International Nuclear Information System (INIS)

Bell, Simon

1994-01-01

The place of energy forestry in the landscape is discussed, principally with reference to Britain and Europe. The importance of design as a means of ensuring an attractive appearance, while meeting functional and economic requirements, is stressed. Simple design principles which help energy forests, mainly short rotation arable coppice, to fit into the landscape are suggested. (author)

The relative importance of physical and biological energy in landscape evolution

Science.gov (United States)

Turowski, J. M.; Schwanghart, W.

2017-12-01

Landscapes are formed by the interplay of uplift and geomorphic processes, including interacting and competing physical and biological processes. For example, roots re-inforce soil and thereby stabilize hillslopes and the canopy cover of the forest may mediate the impact of precipitation. Furthermore, plants and animals act as geomorphic agents, directly altering landscape response and dynamics by their actions: tree roots may crack rocks, thus changing subsurface water flows and exposing fresh material for denudation; fungi excrete acids that accelerate rates of chemical weathering, and burrowing animals displace soil and rocks while digging holes for shelter or in search of food. Energetically, landscapes can be viewed as open systems in which topography stores potential energy above a base level. Tectonic processes add energy to the system by uplift and mechanically altering rock properties. Especially in unvegetated regions, erosion and transport by wind can be an important geomorphic process. Advection of atmospheric moisture in high altitudes provides potential energy that is converted by water fluxes through catchments. At the same time, the conversion of solar energy through atmospheric and biological processes drives primary production of living organisms. If we accept that biota influence geomorphic processes, then what is their energetic contribution to landscape evolution relative to physical processes? Using two case studies, we demonstrate that all components of energy input are negligible apart from biological production, quantified by net primary productivity (NPP) and potential energy conversion by water that is placed high up in the landscape as rainfall and leaves it as runoff. Assuming that the former is representative for biological energy and the latter for physical energy, we propose that the ratio of these two values can be used as a proxy for the relative importance of biological and physical processes in landscape evolution. All necessary

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

Science.gov (United States)

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.

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

Science.gov (United States)

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.

Sustainable energy landscapes : designing, planning, and development

NARCIS (Netherlands)

Stremke, S.; Dobbelsteen, van den A.

2013-01-01

In the near future the appearance and spatial organization of urban and rural landscapes will be strongly influenced by the generation of renewable energy. One of the critical tasks will be the re-integration of these sustainable energy landscapes into the existing environment—which people value and

The significance of the amorphous potential energy landscape for dictating glassy dynamics and driving solid-state crystallisation.

Science.gov (United States)

Ruggiero, Michael T; Krynski, Marcin; Kissi, Eric Ofosu; Sibik, Juraj; Markl, Daniel; Tan, Nicholas Y; Arslanov, Denis; van der Zande, Wim; Redlich, Britta; Korter, Timothy M; Grohganz, Holger; Löbmann, Korbinian; Rades, Thomas; Elliott, Stephen R; Zeitler, J Axel

2017-11-15

The fundamental origins surrounding the dynamics of disordered solids near their characteristic glass transitions continue to be fiercely debated, even though a vast number of materials can form amorphous solids, including small-molecule organic, inorganic, covalent, metallic, and even large biological systems. The glass-transition temperature, T g , can be readily detected by a diverse set of techniques, but given that these measurement modalities probe vastly different processes, there has been significant debate regarding the question of why T g can be detected across all of them. Here we show clear experimental and computational evidence in support of a theory that proposes that the shape and structure of the potential-energy surface (PES) is the fundamental factor underlying the glass-transition processes, regardless of the frequency that experimental methods probe. Whilst this has been proposed previously, we demonstrate, using ab initio molecular-dynamics (AIMD) simulations, that it is of critical importance to carefully consider the complete PES - both the intra-molecular and inter-molecular features - in order to fully understand the entire range of atomic-dynamical processes in disordered solids. Finally, we show that it is possible to utilise this dependence to directly manipulate and harness amorphous dynamics in order to control the behaviour of such solids by using high-powered terahertz pulses to induce crystallisation and preferential crystal-polymorph growth in glasses. Combined, these findings provide compelling evidence that the PES landscape, and the corresponding energy barriers, are the ultimate controlling feature behind the atomic and molecular dynamics of disordered solids, regardless of the frequency at which they occur.

Trp-cage: Folding free energy landscape in explicit water

Science.gov (United States)

Zhou, Ruhong

2003-11-01

Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å C-RMSD (C-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.

Learning free energy landscapes using artificial neural networks.

Science.gov (United States)

Sidky, Hythem; Whitmer, Jonathan K

2018-03-14

Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

Learning free energy landscapes using artificial neural networks

Science.gov (United States)

Sidky, Hythem; Whitmer, Jonathan K.

2018-03-01

Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

New interaction paths in the energy landscape: the role of local energy initiatives

NARCIS (Netherlands)

de Boer, Jessica; Zuidema, Christian; Gugerell, Katharina

2018-01-01

Energy transition is an encompassing process which not only involves the energy system but also the landscape in which the energy system is embedded. Renewable energy is triggering new interactions with local landscapes in physical, socio-economic and institutional senses. We capture these

Reliable protein folding on non-funneled energy landscapes: the free energy reaction path

OpenAIRE

Lois, Gregg; Blawzdziewicz, Jerzy; O'Hern, Corey S.

2008-01-01

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical denaturant or pH, are adjusted to induce folding. A theory based on this insight predicts that (1) proteins with non-funneled energy landscapes can fold reliably to their native state, (2) reliable folding can occur as an equilibrium or out-of-equilibrium pro...

Energy-landscape Nexus: Advancing a conceptual framework for the design of sustainable energy landscapes

NARCIS (Netherlands)

Stremke, S.

2013-01-01

For some time now, the concept of “energy landscape” is discussed in academia while more and more practising landscape architects contribute to the siting, designing, and assessment of renewable energy technologies (see Stremke et al. 2012). Yet, there remains some ambiguity what exactly is meant

Dynamics of the flood response to slow-fast landscape-climate feedbacks

Directory of Open Access Journals (Sweden)

R. A. P. Perdigão

2015-06-01

Full Text Available The dynamical evolution of the flood response to landscape-climate feedbacks is evaluated in a joint nonlinear statistical-dynamical approach. For that purpose, a spatiotemporal sensitivity analysis is conducted on hydrological data from 1976–2008 over 804 catchments throughout Austria, and a general, data-independent nonlinear dynamical model is built linking floods with climate (via precipitation, landscape (via elevation 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. The results show that floods are more responsive to spatial (regional than to temporal (decadal variability. Catchments from dry lowlands and high wetlands exhibit similarity between the spatial and temporal sensitivities (spatiotemporal symmetry and low landscape-climate codependence, suggesting they are not coevolving significantly. However, intermediate regions show differences between those sensitivities (symmetry breaks and higher landscape-climate codependence, suggesting undergoing coevolution. The break of symmetry is an emergent behaviour from nonlinear feedbacks within the system. A new 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 interplay between slow and fast dynamics, represented respectively by spatial and temporal characteristics. The dynamical model captures emerging features of the flood dynamics and nonlinear landscape-climate feedbacks, supporting the nonlinear statistical assessment of spatiotemporally asymmetric flood change. Moreover, it enables the dynamical estimation of flood changes in space and time from the given knowledge at different spatiotemporal conditions. This study ultimately brings to light emerging signatures of

Impacts of renewable energy on landscape. Alternative of offshore wind in marine areas

Directory of Open Access Journals (Sweden)

Francesca Moraci

2014-01-01

Full Text Available The effects determined in the landscape by plants powered by renewable sources represent some unresolved issues in terms of visual and landscape impact mitigation in general. These aspects relate to the landscape are recognized in all types of impact with due attention to the various components and dynamics involved identifiable in the landscape of reference.The wind power plants, in particular, while making unquestionable environmental benefits thanks to the production of energy from renewable sources, but imposes a significant cost to the landscape with the installation of wind turbines in contexts necessarily favorable to impact,  interrupting the skyline, creating territorial discontinuities, "subtracting" and altering the landscape in the absence of effective mitigation works.The environmental compatibility of the proposed solutions depends primarily on the location of wind farms.Is necessary indicate  an overall strategy, a shared model of planning and land management, as in other European countries such as Denmark, Germany, France and the United Kingdom where the choice of locating wind farms has resulted in a new draft territory, construction and redesign of the landscape.

A deterministic method for estimating free energy genetic network landscapes with applications to cell commitment and reprogramming paths.

Science.gov (United States)

Olariu, Victor; Manesso, Erica; Peterson, Carsten

2017-06-01

Depicting developmental processes as movements in free energy genetic landscapes is an illustrative tool. However, exploring such landscapes to obtain quantitative or even qualitative predictions is hampered by the lack of free energy functions corresponding to the biochemical Michaelis-Menten or Hill rate equations for the dynamics. Being armed with energy landscapes defined by a network and its interactions would open up the possibility of swiftly identifying cell states and computing optimal paths, including those of cell reprogramming, thereby avoiding exhaustive trial-and-error simulations with rate equations for different parameter sets. It turns out that sigmoidal rate equations do have approximate free energy associations. With this replacement of rate equations, we develop a deterministic method for estimating the free energy surfaces of systems of interacting genes at different noise levels or temperatures. Once such free energy landscape estimates have been established, we adapt a shortest path algorithm to determine optimal routes in the landscapes. We explore the method on three circuits for haematopoiesis and embryonic stem cell development for commitment and reprogramming scenarios and illustrate how the method can be used to determine sequential steps for onsets of external factors, essential for efficient reprogramming.

Mitigation/Adaptation: landscape architecture meets sustainable energy transition

NARCIS (Netherlands)

Stremke, S.

2009-01-01

Mitigation of climate change and adaptation to renewable energy sources are among the emerging fields of activity in landscape architecture. If landscape architects recognize the need for sustainable development on the basis of renewable energy sources, then how can we contribute to sustainable and

Random versus Deterministic Descent in RNA Energy Landscape Analysis

Directory of Open Access Journals (Sweden)

Luke Day

2016-01-01

Full Text Available Identifying sets of metastable conformations is a major research topic in RNA energy landscape analysis, and recently several methods have been proposed for finding local minima in landscapes spawned by RNA secondary structures. An important and time-critical component of such methods is steepest, or gradient, descent in attraction basins of local minima. We analyse the speed-up achievable by randomised descent in attraction basins in the context of large sample sets where the size has an order of magnitude in the region of ~106. While the gain for each individual sample might be marginal, the overall run-time improvement can be significant. Moreover, for the two nongradient methods we analysed for partial energy landscapes induced by ten different RNA sequences, we obtained that the number of observed local minima is on average larger by 7.3% and 3.5%, respectively. The run-time improvement is approximately 16.6% and 6.8% on average over the ten partial energy landscapes. For the large sample size we selected for descent procedures, the coverage of local minima is very high up to energy values of the region where the samples were randomly selected from the partial energy landscapes; that is, the difference to the total set of local minima is mainly due to the upper area of the energy landscapes.

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

Science.gov (United States)

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...

Potential energy landscape of TIP4P/2005 water

Science.gov (United States)

Handle, Philip H.; Sciortino, Francesco

2018-04-01

We report a numerical study of the statistical properties of the potential energy landscape of TIP4P/2005, one of the most accurate rigid water models. We show that, in the region where equilibrated configurations can be generated, a Gaussian landscape description is able to properly describe the model properties. We also find that the volume dependence of the landscape properties is consistent with the existence of a locus of density maxima in the phase diagram. The landscape-based equation of state accurately reproduces the TIP4P/2005 pressure-vs-volume curves, providing a sound extrapolation of the free-energy at low T. A positive-pressure liquid-liquid critical point is predicted by the resulting free-energy.

Free energy landscapes of electron transfer system in dipolar environment below and above the rotational freezing temperature

International Nuclear Information System (INIS)

Suzuki, Yohichi; Tanimura, Yoshitaka

2007-01-01

Electron transfer reaction in a polar solvent is modeled by a solute dipole surrounded by dipolar molecules with simple rotational dynamics posted on the three-dimensional distorted lattice sites. The interaction energy between the solute and solvent dipoles as a reaction coordinate is adopted and free energy landscapes are calculated by generating all possible states for a 26 dipolar system and by employing Wang-Landau sampling algorithm for a 92 dipolar system. For temperatures higher than the energy scale of dipole-dipole interactions, the free energy landscapes for the small reaction coordinate region have quadratic shape as predicted by Marcus [Rev. Mod. Phys. 65, 599 (1993)] whereas for the large reaction coordinate region, the landscapes exhibit a nonquadratic shape. When the temperature drops, small notched structures appear on the free energy profiles because of the frustrated interactions among dipoles. The formation of notched structure is analyzed with statistical approach and it is shown that the amplitude of notched structure depend upon the segment size of the reaction coordinate and is characterized by the interaction energy among the dipoles. Using simulated free energy landscapes, the authors calculate the reaction rates as a function of the energy gap for various temperatures. At high temperature, the reactions rates follow a bell shaped (inverted parabolic) energy gap law in the small energy gap regions, while it becomes steeper than the parabolic shape in a large energy gap regions due to the nonquadratic shape of the free energy landscape. The peak position of parabola also changes as the function of temperature. At low temperature, the profile of the reaction rates is no longer smooth because of the many local minima of the free energy landscape

Probing the Free Energy Landscape of the FBP28 WW Domain Using Multiple Techniques

NARCIS (Netherlands)

Periole, Xavier; Allen, Lucy R.; Tamiola, Kamil; Mark, Alan E.; Paci, Emanuele

The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent.

Global optimization of proteins using a dynamical lattice model: Ground states and energy landscapes

OpenAIRE

Dressel, F.; Kobe, S.

2004-01-01

A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in agreement with experimental data. All possible model structures of small proteins are available below a certain energy threshold. The exact lowenergy landscapes for the trp cage protein (1L2Y) is presented showing the connectivity of all states and energy barriers.

Accelerated weight histogram method for exploring free energy landscapes

Energy Technology Data Exchange (ETDEWEB)

Lindahl, V.; Lidmar, J.; Hess, B. [Department of Theoretical Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm (Sweden)

2014-07-28

Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies from these simulations remains a major challenge. Fully exploring the free energy landscape of, say, a biological macromolecule typically requires sampling large conformational changes and slow transitions. Often, the only feasible way to study such a system is to simulate it using an enhanced sampling method. The accelerated weight histogram (AWH) method is a new, efficient extended ensemble sampling technique which adaptively biases the simulation to promote exploration of the free energy landscape. The AWH method uses a probability weight histogram which allows for efficient free energy updates and results in an easy discretization procedure. A major advantage of the method is its general formulation, making it a powerful platform for developing further extensions and analyzing its relation to already existing methods. Here, we demonstrate its efficiency and general applicability by calculating the potential of mean force along a reaction coordinate for both a single dimension and multiple dimensions. We make use of a non-uniform, free energy dependent target distribution in reaction coordinate space so that computational efforts are not wasted on physically irrelevant regions. We present numerical results for molecular dynamics simulations of lithium acetate in solution and chignolin, a 10-residue long peptide that folds into a β-hairpin. We further present practical guidelines for setting up and running an AWH simulation.

[Dynamic evolution of landscape spatial pattern in Taihu Lake basin, China].

Science.gov (United States)

Wang, Fang; Xie, Xiao Ping; Chen, Zhi Cong

2017-11-01

Based on the land-use satellite image datasets of 2000, 2010 and 2015, the landscape index, dynamic change model, landscape transfer matrix and CLUE-S model were integrated to analyze the dynamic evolution of the landscape spatial pattern of Taihu Lake basin. The results showed that the landscape type of the basin was dominated by cultivated land and construction land, and the degree of landscape fragmentation was strengthened from 2000 to 2015, and the distribution showed a uniform trend. From the point of transfer dynamic change, the cultivated land and construction land changed significantly, which was reduced by 6761 km 2 (2.1%) and increased by 6615.33 km 2 (8.4%), respectively. From the landscape transfer, it could be seen that the main change direction of the cultivated land reduction was the construction land, and the cultivated land with 7866.30 km 2 was converted into construction land, accounting for 91.6% of the cultivated land change, and the contribution to the construction land was 96.5%. The trend of dynamic changes of cultivated and construction land in the counties and cities was the same as that of the whole Taihu Lake basin. For Shanghai Central Urban, as well as Pudong District, Lin'an City, Baoshan District, Minhang District, Jiading District and Changzhou City, the area of the cultivated land and construction land changed more prominently. However, compared with the CLUE-S model for the landscape pattern change in 2030, the change of cultivated and construction lands would be the largest in the natural development scenario. Under the ecological protection scenario, the area of grassland would increase and the dynamic degree would reach 54.5%. Under the situation of cultivated land protection, the conversion of cultivated land to construction land would be decreased.

A spherical model with directional interactions: II. Dynamics and landscape properties

International Nuclear Information System (INIS)

Mayer, Christian; Sciortino, Francesco; Tartaglia, Piero; Zaccarelli, Emanuela

2010-01-01

We study a binary non-additive hard-sphere mixture with square well interactions only between dissimilar particles. An appropriate choice of the inter-particle potential parameters favors the formation of equilibrium structures with tetrahedral ordering (Zaccarelli et al 2007 J. Chem. Phys. 127 174501). By performing extensive event-driven molecular dynamics simulations, we monitor the dynamics of the system, locating the iso-diffusivity lines in the phase diagram, and discuss their location with respect to the gas-liquid phase separation. We observe the formation of an ideal gel which continuously crosses towards an attractive glass upon increasing the density. Moreover, we evaluate the statistical properties of the potential energy landscape for this model. We find that the configurational entropy, for densities within the optimal network-forming region, is finite even in the ground state and obeys a logarithmic dependence on the energy.

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

Science.gov (United States)

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.

Strong field-matching effects in superconducting YBa2Cu3O7-δ films with vortex energy landscapes engineered via masked ion irradiation

Science.gov (United States)

Swiecicki, I.; Ulysse, C.; Wolf, T.; Bernard, R.; Bergeal, N.; Briatico, J.; Faini, G.; Lesueur, J.; Villegas, Javier E.

2012-06-01

We have developed a masked ion irradiation technique to engineer the energy landscape for vortices in oxide superconductors. This approach associates the possibility to design the landscape geometry at the nanoscale with the unique capability to adjust the depth of the energy wells for vortices. This enabled us to unveil the key role of vortex channeling in modulating the amplitude of the field matching effects with the artificial energy landscape, and to make the latter govern flux dynamics over an unusually wide range of temperatures and applied fields for high-temperature superconducting films.

Mind the gap: modelling event-based and millennial-scale landscape dynamics

NARCIS (Netherlands)

Baartman, J.E.M.

2012-01-01

This research looks at landscape dynamics – erosion and deposition – from two different perspectives: long-term landscape evolution over millennial timescales on the one hand and short-term event-based erosion and deposition at the other hand. For the first, landscape evolution models (LEMs) are

Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy.

Science.gov (United States)

Heenan, Patrick R; Yu, Hao; Siewny, Matthew G W; Perkins, Thomas T

2018-03-28

Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG 0 ) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG 0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.

Science.gov (United States)

Nayar, Divya; Chakravarty, Charusita

2015-08-27

Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.

Evaluating the landscape impact of renewable energy plants

Science.gov (United States)

Ioannidis, Romanos; Koutsoyiannis, Demetris

2017-04-01

Different types of renewable energy have been on an ongoing competition with each other. There has been a lot of research comparing the most common types of renewable energy plants in relation with their efficiency, cost and environmental impact. However, few papers so far have attempted to analyse their impact on landscape and there has never been in depth research on which type of renewable energy causes the least impact on the natural, cultural and aesthetic characteristics of a landscape. This seems to be a significant omission given the vast areas of land already covered with renewable energy plants and the worldwide plans for many more renewable energy projects in the future. Meanwhile, the low aesthetic quality of renewable energy plants has already been an obstacle to their further development, with several relevant examples from countries such as Spain and the Netherlands. There have even been cases where aesthetic degradation is the primary or even the single argument of the opposition to proposed plants. In any case, the aesthetic design and the integration of renewable energy plants into the landscape should really be important design parameters if we plan those projects to truly be sustainable and to be considered complete works of engineering. To initiate dialogue over those aspects of renewable energy, we provide a first comparison on hydro, solar and wind energy. To materialize this comparison, we use data from existing dams, photovoltaic and wind farms. Initially, the average area per MW covered by each type of energy plant is calculated and then evaluated qualitatively from a landscape-impact perspective. Although the area affected is comparable in these three cases, the analysis of the data suggests that dams offer a considerable amount of advantages compared to the other two types of plants. This conclusion arises from the fact that dams, whose basic impact to the landscape is the creation of an artificial lake, contribute much less to the

Potential energy landscape signatures of slow dynamics in glass forming liquids

DEFF Research Database (Denmark)

Sastry, S.; Debenedetti, P. G.; Stillinger, F. H.

1999-01-01

We study the properties of local potential energy minima (‘inherent structures’) sampled by liquids at low temperatures as an approach to elucidating the mechanisms of the observed dynamical slowing down observed as the glass transition temperature is approached. This onset of slow dynamics...

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

2014-08-28

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

The potential energy landscape in the Lennard-Jones binary mixture model

International Nuclear Information System (INIS)

Sampoli, M; Benassi, P; Eramo, R; Angelani, L; Ruocco, G

2003-01-01

The potential energy landscape in the Kob-Andersen Lennard-Jones binary mixture model has been studied carefully from the liquid down to the supercooled regime, from T = 2 down to 0.46. One thousand independent configurations along the time evolution locus have been examined at each temperature investigated. From the starting configuration, we searched for the nearest saddle (or quasi-saddle) and minimum of the potential energy. The vibrational densities of states for the starting and the two derived configurations have been evaluated. Besides the number of negative eigenvalues of the saddles other quantities show some signature of the approach of the dynamical arrest temperature

The mechanisms for filling carbon nanotubes with molten salts: carbon nanotubes as energy landscape filters

International Nuclear Information System (INIS)

Bishop, Clare L; Wilson, Mark

2009-01-01

The mechanisms for filling carbon nanotubes with molten salts are investigated using molecular dynamics computer simulation. Inorganic nanotubular structures, whose morphologies can be rationalized in terms of the folding, or the removal of sections from, planes of square nets are found to form. The formation mechanisms are found to follow a 'chain-by-chain' motif in which the structures build systematically from charge neutral M-X-M-Xc chains. The formation mechanisms are rationalized in terms of the ion-ion interactions (intra-chain and inter-chain terms). In addition, the mechanisms of filling are discussed in terms of a 'hopping' between basins on the underlying energy landscape. The role of the carbon nanotube as an energy landscape filter is discussed.

Energy Landscapes for the Self-Assembly of Supramolecular Polyhedra

Science.gov (United States)

Russell, Emily R.; Menon, Govind

2016-06-01

We develop a mathematical model for the energy landscape of polyhedral supramolecular cages recently synthesized by self-assembly (Sun et al. in Science 328:1144-1147, 2010). Our model includes two essential features of the experiment: (1) geometry of the organic ligands and metallic ions; and (2) combinatorics. The molecular geometry is used to introduce an energy that favors square-planar vertices (modeling {Pd}^{2+} ions) and bent edges with one of two preferred opening angles (modeling boomerang-shaped ligands of two types). The combinatorics of the model involve two-colorings of edges of polyhedra with four-valent vertices. The set of such two-colorings, quotiented by the octahedral symmetry group, has a natural graph structure and is called the combinatorial configuration space. The energy landscape of our model is the energy of each state in the combinatorial configuration space. The challenge in the computation of the energy landscape is a combinatorial explosion in the number of two-colorings of edges. We describe sampling methods based on the symmetries of the configurations and connectivity of the configuration graph. When the two preferred opening angles encompass the geometrically ideal angle, the energy landscape exhibits a very low-energy minimum for the most symmetric configuration at equal mixing of the two angles, even when the average opening angle does not match the ideal angle.

The effects of landscaping on the residential cooling energy

Science.gov (United States)

Misni, A.

2018-02-01

This paper examines the effectiveness of landscaping on the air-conditioning energy saving of houses in a tropical environment. This case study involved looking at the construction and landscaping of three single-family houses in three sections of Shah Alam, Selangor, Malaysia. The houses ranged in age from 5 to 30 years old, which provided different examples of construction and maturity levels of the surrounding landscaping. Landscaping affects the thermal performance as well as on the air-conditioning energy of houses, in how it provides shade, channels wind, and evapotranspiration. While the construction of the three houses was similar, they were different in size and design, including their landscape design. These houses were chosen because they are representative of single-family tropical houses and landscaping styles in Malaysia since 30 years ago. Three houses were chosen; the 30-year-old house, the 10-year-old house, and the 5-year-old house. In a tropical country, landscaping is used to reduce the effects of the hot and humid climate. The houses spent 15-45% of the electricity cost on cooling. These results were influenced by human factors and the surrounding landscaping. Every type of vegetation, such as trees, grass, shrubs, groundcover, and turf, contributes to reducing air temperatures near the house and providing evaporative cooling.

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

Science.gov (United States)

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

Exploring the conformational energy landscape of proteins

Energy Technology Data Exchange (ETDEWEB)

Nienhaus, G.U. [Univ. of Illinois, Urbana, IL (United States)]|[Universitaet Ulm (Germany); Mueller, J.D.; McMahon, B.H. [Univ. of Illinois, Urbana, IL (United States)] [and others

1997-04-01

Proteins possess a complex energy landscape with a large number of local minima called conformational substates that are arranged in a hierarchical fashion. Here we discuss experiments aimed at the elucidation of the energy landscape in carbonmonoxy myoglobin (MbCO). In the highest tier of the hierarchy, a few taxonomic substates exist. Because of their small number, these substates are accessible to detailed structural investigations. Spectroscopic experiments are discussed that elucidate the role of protonations of amino acid side chains in creating the substates. The lower tiers of the hierarchy contain a large number of statistical substates. Substate interconversions are observed in the entire temperature range from below 1 K up to the denaturation temperature, indicating a wide spectrum of energy barriers that separate the substates.

Potential energy landscapes of elemental and heterogeneous chalcogen clusters

International Nuclear Information System (INIS)

Mauro, John C.; Loucks, Roger J.; Balakrishnan, Jitendra; Varshneya, Arun K.

2006-01-01

We describe the potential energy landscapes of elemental S 8 , Se 8 , and Te 8 clusters using disconnectivity graphs. Inherent structures include both ring and chain configurations, with rings especially dominant in Se 8 . We also map the potential energy landscapes of heterogeneous Se n (S,Te) 8-n clusters, which offer insights into the structure of heterogeneous chalcogen glasses

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

Science.gov (United States)

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.

Energy Transition: Missed Opportunities and Emerging Challenges for Landscape Planning and Designing

Directory of Open Access Journals (Sweden)

Renée M. de Waal

2014-07-01

Full Text Available Making the shift from fossil fuels to renewable energy seems inevitable. Because energy transition poses new challenges and opportunities to the discipline of landscape architecture, the questions addressed in this paper are: (1 what landscape architects can learn from successful energy transitions in Güssing, Jühnde and Samsø; and (2 to what extent landscape architecture (or other spatial disciplines contributed to energy transition in the aforementioned cases. An exploratory, comparative case study was conducted to identify differences and similarities among the cases, to answer the research questions, and to formulate recommendations for further research and practice. The comparison indicated that the realized renewable energy systems are context-dependent and, therefore, specifically designed to meet the respective energy demand, making use of the available potentials for renewable energy generation and efficiency. Further success factors seemed to be the presence of (local frontrunners and a certain degree of citizen participation. The relatively smooth implementation of renewable energy technologies in Jühnde and on Samsø may indicate the importance of careful and (partly institutionalized consideration of landscape impact, siting and design. Comparing the cases against the literature demonstrated that landscape architects were not as involved as they, theoretically, could have been. However, particularly when the aim is sustainable development, rather than “merely” renewable energy provision, the integrative concept of “sustainable energy landscapes” can be the arena where landscape architecture and other disciplines meet to pursue global sustainability goals, while empowering local communities and safeguarding landscape quality.

Temporal disconnectivity of the energy landscape in glassy systems

Science.gov (United States)

Lempesis, Nikolaos; Boulougouris, Georgios C.; Theodorou, Doros N.

2013-03-01

An alternative graphical representation of the potential energy landscape (PEL) has been developed and applied to a binary Lennard-Jones glassy system, providing insight into the unique topology of the system's potential energy hypersurface. With the help of this representation one is able to monitor the different explored basins of the PEL, as well as how - and mainly when - subsets of basins communicate with each other via transitions in such a way that details of the prior temporal history have been erased, i.e., local equilibration between the basins in each subset has been achieved. In this way, apart from detailed information about the structure of the PEL, the system's temporal evolution on the PEL is described. In order to gather all necessary information about the identities of two or more basins that are connected with each other, we consider two different approaches. The first one is based on consideration of the time needed for two basins to mutually equilibrate their populations according to the transition rate between them, in the absence of any effect induced by the rest of the landscape. The second approach is based on an analytical solution of the master equation that explicitly takes into account the entire explored landscape. It is shown that both approaches lead to the same result concerning the topology of the PEL and dynamical evolution on it. Moreover, a "temporal disconnectivity graph" is introduced to represent a lumped system stemming from the initial one. The lumped system is obtained via a specially designed algorithm [N. Lempesis, D. G. Tsalikis, G. C. Boulougouris, and D. N. Theodorou, J. Chem. Phys. 135, 204507 (2011), 10.1063/1.3663207]. The temporal disconnectivity graph provides useful information about both the lumped and the initial systems, including the definition of "metabasins" as collections of basins that communicate with each other via transitions that are fast relative to the observation time. Finally, the two examined

Landscape of Future Accelerators at the Energy and Intensity Frontier

Energy Technology Data Exchange (ETDEWEB)

Syphers, M. J. [Northern Illinois U.; Chattopadhyay, S. [Northern Illinois U.

2016-11-21

An overview is provided of the currently envisaged landscape of charged particle accelerators at the energy and intensity frontiers to explore particle physics beyond the standard model via 1-100 TeV-scale lepton and hadron colliders and multi-Megawatt proton accelerators for short- and long- baseline neutrino experiments. The particle beam physics, associated technological challenges and progress to date for these accelerator facilities (LHC, HL-LHC, future 100 TeV p-p colliders, Tev-scale linear and circular electron-positron colliders, high intensity proton accelerator complex PIP-II for DUNE and future upgrade to PIP-III) are outlined. Potential and prospects for advanced “nonlinear dynamic techniques” at the multi-MW level intensity frontier and advanced “plasma- wakefield-based techniques” at the TeV-scale energy frontier and are also described.

Ideal glass transitions in thin films: An energy landscape perspective

Science.gov (United States)

Truskett, Thomas M.; Ganesan, Venkat

2003-07-01

We introduce a mean-field model for the potential energy landscape of a thin fluid film confined between parallel substrates. The model predicts how the number of accessible basins on the energy landscape and, consequently, the film's ideal glass transition temperature depend on bulk pressure, film thickness, and the strength of the fluid-fluid and fluid-substrate interactions. The predictions are in qualitative agreement with the experimental trends for the kinetic glass transition temperature of thin films, suggesting the utility of landscape-based approaches for studying the behavior of confined fluids.

Free energy landscape of a minimalist salt bridge model.

Science.gov (United States)

Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei

2016-01-01

Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.

Landscape seasons and air mass dynamics in Latvia

International Nuclear Information System (INIS)

Krauklis, A.; Draveniece, A.

2004-01-01

Latvia is located in the middle of an area where the boreal and nemoral zones and the regions of oceanic and continental climate meet, and it was studied as a model territory of the most typical variation of boreo-nemoral ecotone. The subject of this study was seasonal dynamics of the state of landscapes and diachronous links between seasons. It was found that landscapes undergo 12 seasonal states or seasons during the annual cycle of insulation and air mass occurrence. Each season may be distinguished by a definite amount of solar radiation, distinctive state of heat and water balance, phenological state of vegetation, and a distinctive occurrence of different air mass types and their particular 'association'. During each season these variables show a particular combination of numerical values and a distinctive landscape pattern

How animals distribute themselves in space: variable energy landscapes

OpenAIRE

Masello, Juan F.; Kato, Akiko; Sommerfeld, Julia; Mattern, Thomas; Quillfeldt, Petra

2017-01-01

Background Foraging efficiency determines whether animals will be able to raise healthy broods, maintain their own condition, avoid predators and ultimately increase their fitness. Using accelerometers and GPS loggers, features of the habitat and the way animals deal with variable conditions can be translated into energetic costs of movement, which, in turn, can be translated to energy landscapes.We investigated energy landscapes in Gentoo Penguins Pygoscelis papua from two colonies at New Is...

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

Science.gov (United States)

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.

Trends of Forest Dynamics in Tiger Landscapes Across Asia

Science.gov (United States)

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.

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

Science.gov (United States)

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

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

Science.gov (United States)

Ishida, Hisashi; Matsumoto, Atsushi

2014-01-01

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

Free-energy landscape of reverse tRNA translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Hisashi Ishida

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

Membranes: A Variety of Energy Landscapes for Many Transfer Opportunities.

Science.gov (United States)

Bacchin, Patrice

2018-02-22

A membrane can be represented by an energy landscape that solutes or colloids must cross. A model accounting for the momentum and the mass balances in the membrane energy landscape establishes a new way of writing for the Darcy law. The counter-pressure in the Darcy law is no longer written as the result of an osmotic pressure difference but rather as a function of colloid-membrane interactions. The ability of the model to describe the physics of the filtration is discussed in detail. This model is solved in a simplified energy landscape to derive analytical relationships that describe the selectivity and the counter-pressure from ab initio operating conditions. The model shows that the stiffness of the energy landscape has an impact on the process efficiency: a gradual increase in interactions (such as with hourglass pore shape) can reduce the separation energetic cost. It allows the introduction of a new paradigm to increase membrane efficiency: the accumulation that is inherent to the separation must be distributed across the membrane. Asymmetric interactions thus lead to direction-dependent transfer properties and the membrane exhibits diode behavior. These new transfer opportunities are discussed.

Integrated visions (part II): Envisioning Sustainable Energy Landscapes

NARCIS (Netherlands)

Stremke, S.; Koh, J.; Neven, C.T.; Boekel, A.

2012-01-01

ABSTRACT Climate change and resource depletion are driving the transition to renewable energy sources. Both the supply of renewables and the demand for energy are influenced by the physical environment and therefore concern spatial planning and landscape design. Envisioning the longterm development

Nonequilibrium landscape theory of neural networks.

Science.gov (United States)

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

2013-11-05

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

Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

Energy Technology Data Exchange (ETDEWEB)

Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States); Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States)

2016-01-28

The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

Energy transition: towards landscape devastation?

International Nuclear Information System (INIS)

Posokhow, Andre

2013-09-01

The author criticizes some aspects of the content of the French policy for energy transition. He states that the objective of reduction of greenhouse emissions is unreachable and moreover useless when China keeps on opening new coal-fired power stations. He states that temperatures do not increase any longer and that it is not sure that CO 2 emissions are responsible for past increases. He outlines that the power of wind turbines is only a quarter of their theoretical one, that replacing nuclear energy by wind energy would require the installation of 33.000 wind turbines. He states that objectives of energy saving are not credible, and that the energy mix predictions are fuzzy. He outlines contradictions about the nuclear power station life duration, states that the installation of 210 wind turbines per district would devastate the French landscape

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

International Nuclear Information System (INIS)

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

2010-01-01

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

Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding.

Science.gov (United States)

Malhotra, Pooja; Jethva, Prashant N; Udgaonkar, Jayant B

2017-08-08

To characterize experimentally the ruggedness of the free energy landscape of protein folding is challenging, because the distributed small free energy barriers are usually dominated by one, or a few, large activation free energy barriers. This study delineates changes in the roughness of the free energy landscape by making use of the observation that a decrease in ruggedness is accompanied invariably by an increase in folding cooperativity. Hydrogen exchange (HX) coupled to mass spectrometry was used to detect transient sampling of local energy minima and the global unfolded state on the free energy landscape of the small protein single-chain monellin. Under native conditions, local noncooperative openings result in interconversions between Boltzmann-distributed intermediate states, populated on an extremely rugged "uphill" energy landscape. The cooperativity of these interconversions was increased by selectively destabilizing the native state via mutations, and further by the addition of a chemical denaturant. The perturbation of stability alone resulted in seven backbone amide sites exchanging cooperatively. The size of the cooperatively exchanging and/or unfolding unit did not depend on the extent of protein destabilization. Only upon the addition of a denaturant to a destabilized mutant variant did seven additional backbone amide sites exchange cooperatively. Segmentwise analysis of the HX kinetics of the mutant variants further confirmed that the observed increase in cooperativity was due to the smoothing of the ruggedness of the free energy landscape of folding of the protein by the chemical denaturant.

Protein Folding Free Energy Landscape along the Committor - the Optimal Folding Coordinate.

Science.gov (United States)

Krivov, Sergei V

2018-06-06

Recent advances in simulation and experiment have led to dramatic increases in the quantity and complexity of produced data, which makes the development of automated analysis tools very important. A powerful approach to analyze dynamics contained in such data sets is to describe/approximate it by diffusion on a free energy landscape - free energy as a function of reaction coordinates (RC). For the description to be quantitatively accurate, RCs should be chosen in an optimal way. Recent theoretical results show that such an optimal RC exists; however, determining it for practical systems is a very difficult unsolved problem. Here we describe a solution to this problem. We describe an adaptive nonparametric approach to accurately determine the optimal RC (the committor) for an equilibrium trajectory of a realistic system. In contrast to alternative approaches, which require a functional form with many parameters to approximate an RC and thus extensive expertise with the system, the suggested approach is nonparametric and can approximate any RC with high accuracy without system specific information. To avoid overfitting for a realistically sampled system, the approach performs RC optimization in an adaptive manner by focusing optimization on less optimized spatiotemporal regions of the RC. The power of the approach is illustrated on a long equilibrium atomistic folding simulation of HP35 protein. We have determined the optimal folding RC - the committor, which was confirmed by passing a stringent committor validation test. It allowed us to determine a first quantitatively accurate protein folding free energy landscape. We have confirmed the recent theoretical results that diffusion on such a free energy profile can be used to compute exactly the equilibrium flux, the mean first passage times, and the mean transition path times between any two points on the profile. We have shown that the mean squared displacement along the optimal RC grows linear with time as for

Conference on landscape impacts of wind energy and local acceptance: France-Germany crossed views

International Nuclear Information System (INIS)

Bouscatel, Jerome; Olagne, Regis; Derkenne, Chantal; Galiano, Mila; Mayer, Joerg; Ratzbor, Guenter; Laborgne, Pia; Nadai, Alain; Ratouis, Marie-Odile; Schoebel-Rutschmann, Soeren; Petit, Jean-Francois; Guennewig, Dieter; Portales, David

2008-01-01

The French-German office for Renewable energies (OFAEnR) organised a conference on the landscape impacts of wind energy. In the framework of this French-German exchange of experience, more than 100 participants exchanged views on the environmental impact of wind farms and the opinion of residents. This document brings together the available presentations (slides) made during this event: 1 - French people and wind energy (Mila Galiano); 2 - Wind energy acceptance in Germany: an essential factor for the wind industry development (Joerg Mayer); 3 - Taking into account landscapes and residents in the development of wind farms: a France-Germany comparison (Pia Laborgne, Alain Nadai); 3 - Wind energy development supervision thanks to territorial planning in Germany (Guenter Ratzbor); 4 - Landscape challenges in wind energy development: point of view and role of a state decentralised department (Marie-Odile Ratouis); 5 - Park or landscape - Wind turbines as elements of the cultural landscape (Soeren Schoebel-Rutschmann); 6 - How should a developer approach the 'landscape' aspect when foreseeing a wind energy project installation (Jean-Francois Petit); 7 - More consensual wind energy projects along highways, railways and overhead power lines? (Dieter Guennewig); 8 - The 'wings top': un example of participatory and citizen's project (David Portales)

Ideal glass transitions in thin films: An energy landscape perspective

OpenAIRE

Truskett, Thomas M.; Ganesan, Venkat

2003-01-01

We introduce a mean-field model for the potential energy landscape of a thin fluid film confined between parallel substrates. The model predicts how the number of accessible basins on the energy landscape and, consequently, the film's ideal glass transition temperature depend on bulk pressure, film thickness, and the strength of the fluid-fluid and fluid-substrate interactions. The predictions are in qualitative agreement with the experimental trends for the kinetic glass transition temperatu...

The changing geopolitical landscape of energy

International Nuclear Information System (INIS)

Lesourne, Jacques

2011-08-01

The author first discusses the impact of the financial crisis of 2008, and of the large-scale exploitation of shale gases in the USA on energy policies and on the geopolitical landscape of energy. Then, he discusses the influence that events which occurred in 2011 had on these issues: firstly, the Copenhagen and Cancun Conferences, secondly, the Fukushima accident, thirdly, the nuclear phasing-out by Germany and incidentally by Italy, and fourthly, the Arab Spring. In the next parts, he comments the consequences for the European energy policy, and the perspectives for the struggle against climate change

Importance of ecotone type to landscape dynamics at biome transition zones

Science.gov (United States)

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...

Polyomaviridae Assembly Polymorphism from an Energy Landscape Perspective

Directory of Open Access Journals (Sweden)

Karim M. ElSawy

2008-01-01

Full Text Available Polyomaviridae assemble in vitro into different aggregates depending on experimental conditions. We use an energy landscape approach using empirical energy calculations to quantify how the formation of these different aggregates depends on pH, the presence of bound calcium ions and disulfide linkages. Computations are carried out for SV40, a member of the Polyomaviridae family and are based on the binding free energy landscape of three distinct trimers of pentamers that correspond to the different bonding configurations between the capsid proteins observed in its crystal structure. Our computational analysis shows that the energetics of one of these environments is pivotal for the polymorphic assembly behaviour of SV40, whilst the binding energy landscapes of the other two environments are broadly funnel-shaped and thus contribute little to the formation of particles other than virus-like particles (VLP. We have quantified how the existence of bound calcium ions in the absence of disulfide linkages enhances the binding free energies of all three environments and hence, favours the assembly of VLPs. Moreover, estimation of the relative binding free energies of the three environments at pH 5 and pH 8 reveals that they are destabilized at pH 5 relative to pH 8. The extent of this destabilization is dependent on the presence of disulfide linkages and bound calcium ions and accounts for the experimentally observed polymorphic behaviour of VP1 proteins at pH 5. Interestingly, concurrent existence of bound calcium ions and disulfide linkages is found to be destabilizing and thus may disrupt the assembly of VLPs at pH 8.

Climate change impact on landscape fire and forest biomass dynamics

International Nuclear Information System (INIS)

Li, C.

2004-01-01

The aim of this study was to improve current understandings of fire regimes. The estimation of biomass dynamics at the stand scale is essential for understanding landscape scale biomass dynamics, particularly in order to understand the potential effects of fire regimes. This study presented a synthesis of research results obtained from stand scale studies together with fire behaviour and weather variables. Landscape structure, topography and climate conditions were also considered. Integration of the data was conducted with the SEM-LAND model, a spatially explicit model for landscape dynamics. Equations for the model were presented, including fire initiation and spread, as well as a lightning fire process and simulated fire suppression. Results indicated that fire suppression could alter the distribution of fire sizes. The effect of tree and stand mortality on forest biomass estimates was also discussed along with the impact of climate change on fire regimes. Results indicate that fire activities are likely to increase. Results also demonstrate that fire frequency and size distribution are correlated without human intervention. Theoretical negative exponential forest age distribution is not always supported by empirical observations. Point-based fire frequency and fire cycle definitions are special cases from a computational perspective. Detection of quantitative interrelationships may simplify preconditions for estimating fire regimes, and serve as a means to address incomplete empirical observations. 12 refs., 3 figs

Activated aging dynamics and effective trap model description in the random energy model

Science.gov (United States)

Baity-Jesi, M.; Biroli, G.; Cammarota, C.

2018-01-01

We study the out-of-equilibrium aging dynamics of the random energy model (REM) ruled by a single spin-flip Metropolis dynamics. We focus on the dynamical evolution taking place on time-scales diverging with the system size. Our aim is to show to what extent the activated dynamics displayed by the REM can be described in terms of an effective trap model. We identify two time regimes: the first one corresponds to the process of escaping from a basin in the energy landscape and to the subsequent exploration of high energy configurations, whereas the second one corresponds to the evolution from a deep basin to the other. By combining numerical simulations with analytical arguments we show why the trap model description does not hold in the former but becomes exact in the second.

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

Science.gov (United States)

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...

Landscape Dynamics on the Island of La Gonave, Haiti, 1990–2010

Directory of Open Access Journals (Sweden)

Lisa M. Kennedy

2013-09-01

Full Text Available The island of La Gonave lies northwest of Port-au-Prince and is representative of the subsistence Haitian lifestyle. Little is known about the land cover changes and conversion rates on La Gonave. Using Landsat images from 1990 to 2010, this research investigates landscape dynamics through image classification, change detection, and landscape pattern analysis. Five land cover classes were considered: Agriculture, Forest/Dense Vegetation (DV, Shrub, Barren/Eroded, and Nonforested Wetlands. Overall image classification accuracy was 87%. Results of land cover change analysis show that all major land cover types experienced substantial changes from 1990 to 2010. The area percent change was −39.7, −22.7, 87.4, and −7.0 for Agriculture, Forest/Dense Vegetation, Shrub, and Barren/Eroded. Landscape pattern analysis illustrated the encroachment of Shrub cover in core Forest/DV patches and the decline of Agricultural patch integrity. Agricultural abandonment, deforestation, and forest regrowth combined to generate a dynamic island landscape, resulting in higher levels of land cover fragmentation.

Landscape genetics highlights the role of bank vole metapopulation dynamics in the epidemiology of Puumala hantavirus.

Science.gov (United States)

Guivier, E; Galan, M; Chaval, Y; Xuéreb, A; Ribas Salvador, A; Poulle, M-L; Voutilainen, L; Henttonen, H; Charbonnel, N; Cosson, J F

2011-09-01

Rodent host dynamics and dispersal are thought to be critical for hantavirus epidemiology as they determine pathogen persistence and transmission within and between host populations. We used landscape genetics to investigate how the population dynamics of the bank vole Myodes glareolus, the host of Puumala hantavirus (PUUV), vary with forest fragmentation and influence PUUV epidemiology. We sampled vole populations within the Ardennes, a French PUUV endemic area. We inferred demographic features such as population size, isolation and migration with regard to landscape configuration. We next analysed the influence of M. glareolus population dynamics on PUUV spatial distribution. Our results revealed that the global metapopulation dynamics of bank voles were strongly shaped by landscape features, including suitable patch size and connectivity. Large effective size in forest might therefore contribute to the higher observed levels of PUUV prevalence. By contrast, populations from hedge networks highly suffered from genetic drift and appeared strongly isolated from all other populations. This might result in high probabilities of local extinction for both M. glareolus and PUUV. Besides, we detected signatures of asymmetric bank vole migration from forests to hedges. These movements were likely to sustain PUUV in fragmented landscapes. In conclusion, our study provided arguments in favour of source-sink dynamics shaping PUUV persistence and spread in heterogeneous, Western European temperate landscapes. It illustrated the potential contribution of landscape genetics to the understanding of the epidemiological processes occurring at this local scale. © 2011 Blackwell Publishing Ltd.

The dynamical landscape of marine phytoplankton diversity

Science.gov (United States)

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

Nonequilibrium landscape theory of neural networks

Science.gov (United States)

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

2013-01-01

The brain map project aims to map out the neuron connections of the human brain. Even with all of the wirings mapped out, the global and physical understandings of the function and behavior are still challenging. Hopfield quantified the learning and memory process of symmetrically connected neural networks globally through equilibrium energy. The energy basins of attractions represent memories, and the memory retrieval dynamics is determined by the energy gradient. However, the realistic neural networks are asymmetrically connected, and oscillations cannot emerge from symmetric neural networks. Here, we developed a nonequilibrium landscape–flux theory for realistic asymmetrically connected neural networks. We uncovered the underlying potential landscape and the associated Lyapunov function for quantifying the global stability and function. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. We applied our theory to rapid-eye movement sleep cycle. We identified the key regulation factors for function through global sensitivity analysis of landscape topography against wirings, which are in good agreements with experiments. PMID:24145451

Numerical evaluation of the statistical properties of a potential energy landscape

International Nuclear Information System (INIS)

Nave, E La; Sciortino, F; Tartaglia, P; Michele, C De; Mossa, S

2003-01-01

The techniques which allow the numerical evaluation of the statistical properties of the potential energy landscape for models of simple liquids are reviewed and critically discussed. Expressions for the liquid free energy and its vibrational and configurational components are reported. Finally, a possible model for the statistical properties of the landscape, which appears to describe correctly fragile liquids in the region where equilibrium simulations are feasible, is discussed

Deciphering hierarchical features in the energy landscape of adenylate kinase folding/unfolding

Science.gov (United States)

Taylor, J. Nicholas; Pirchi, Menahem; Haran, Gilad; Komatsuzaki, Tamiki

2018-03-01

Hierarchical features of the energy landscape of the folding/unfolding behavior of adenylate kinase, including its dependence on denaturant concentration, are elucidated in terms of single-molecule fluorescence resonance energy transfer (smFRET) measurements in which the proteins are encapsulated in a lipid vesicle. The core in constructing the energy landscape from single-molecule time-series across different denaturant concentrations is the application of rate-distortion theory (RDT), which naturally considers the effects of measurement noise and sampling error, in combination with change-point detection and the quantification of the FRET efficiency-dependent photobleaching behavior. Energy landscapes are constructed as a function of observation time scale, revealing multiple partially folded conformations at small time scales that are situated in a superbasin. As the time scale increases, these denatured states merge into a single basin, demonstrating the coarse-graining of the energy landscape as observation time increases. Because the photobleaching time scale is dependent on the conformational state of the protein, possible nonequilibrium features are discussed, and a statistical test for violation of the detailed balance condition is developed based on the state sequences arising from the RDT framework.

Specificity and affinity quantification of flexible recognition from underlying energy landscape topography.

Directory of Open Access Journals (Sweden)

Xiakun Chu

2014-08-01

Full Text Available Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less flexibility leads to weaker (stronger coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition.

Conservation of butterfly populations in dynamic landscapes: The role of farming practices and landscape mosaic

Czech Academy of Sciences Publication Activity Database

Aviron, S.; Kindlmann, Pavel; Burel, F.

2007-01-01

Roč. 205, 1-2 (2007), s. 135-145 ISSN 0304-3800 R&D Projects: GA AV ČR IAA6087301; GA MŠk LC06073; GA ČR(CZ) GEDIV/06/E013 Institutional research plan: CEZ:AV0Z60870520 Keywords : Connectivity * Landscape dynamics * Resource disturbance * Movement * Simulation model Subject RIV: EH - Ecology, Behaviour Impact factor: 2.077, year: 2007

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

Directory of Open Access Journals (Sweden)

Han Yan

Full Text Available 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

Incorporating Renewable Energy Science in Regional Landscape Design: Results from a Competition in The Netherlands

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Renée M. de Waal

2015-04-01

Full Text Available Energy transition is expected to make an important contribution to sustainable development. Although it is argued that landscape design could foster energy transition, there is scant empirical research on how practitioners approach this new challenge. The research question central to this study is: To what extent and how is renewable energy science incorporated in regional landscape design? To address this knowledge gap, a case study of a regional landscape design competition in the Netherlands, held from 2010–2012, is presented. Its focus was on integral, strategic landscape transformation with energy transition as a major theme. Content analysis of the 36 competition entries was supplemented and triangulated with a survey among the entrants, observation of the process and a study of the competition documents and website. Results indicated insufficient use of key-strategies elaborated by renewable energy science. If landscape design wants to adopt a supportive role towards energy transition, a well-informed and evidence-based approach is highly recommended. Nevertheless, promising strategies for addressing the complex process of ensuring sustainable energy transition also emerged. They include the careful cultivation of public support by developing inclusive and bottom-up processes, and balancing energy-conscious interventions with other land uses and interests.

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

Science.gov (United States)

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.

Energy landscapes for a machine learning application to series data

Energy Technology Data Exchange (ETDEWEB)

Ballard, Andrew J.; Stevenson, Jacob D.; Das, Ritankar; Wales, David J., E-mail: dw34@cam.ac.uk [University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW (United Kingdom)

2016-03-28

Methods developed to explore and characterise potential energy landscapes are applied to the corresponding landscapes obtained from optimisation of a cost function in machine learning. We consider neural network predictions for the outcome of local geometry optimisation in a triatomic cluster, where four distinct local minima exist. The accuracy of the predictions is compared for fits using data from single and multiple points in the series of atomic configurations resulting from local geometry optimisation and for alternative neural networks. The machine learning solution landscapes are visualised using disconnectivity graphs, and signatures in the effective heat capacity are analysed in terms of distributions of local minima and their properties.

Energy landscapes for a machine learning application to series data

International Nuclear Information System (INIS)

Ballard, Andrew J.; Stevenson, Jacob D.; Das, Ritankar; Wales, David J.

2016-01-01

Methods developed to explore and characterise potential energy landscapes are applied to the corresponding landscapes obtained from optimisation of a cost function in machine learning. We consider neural network predictions for the outcome of local geometry optimisation in a triatomic cluster, where four distinct local minima exist. The accuracy of the predictions is compared for fits using data from single and multiple points in the series of atomic configurations resulting from local geometry optimisation and for alternative neural networks. The machine learning solution landscapes are visualised using disconnectivity graphs, and signatures in the effective heat capacity are analysed in terms of distributions of local minima and their properties.

Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments.

Science.gov (United States)

Gorter, Florien A; Aarts, Mark G M; Zwaan, Bas J; de Visser, J Arjan G M

2018-01-01

The fitness landscape is a concept that is widely used for understanding and predicting evolutionary adaptation. The topography of the fitness landscape depends critically on the environment, with potentially far-reaching consequences for evolution under changing conditions. However, few studies have assessed directly how empirical fitness landscapes change across conditions, or validated the predicted consequences of such change. We previously evolved replicate yeast populations in the presence of either gradually increasing, or constant high, concentrations of the heavy metals cadmium (Cd), nickel (Ni), and zinc (Zn), and analyzed their phenotypic and genomic changes. Here, we reconstructed the local fitness landscapes underlying adaptation to each metal by deleting all repeatedly mutated genes both by themselves and in combination. Fitness assays revealed that the height, and/or shape, of each local fitness landscape changed considerably across metal concentrations, with distinct qualitative differences between unconditionally (Cd) and conditionally toxic metals (Ni and Zn). This change in topography had particularly crucial consequences in the case of Ni, where a substantial part of the individual mutational fitness effects changed in sign across concentrations. Based on the Ni landscape analyses, we made several predictions about which mutations had been selected when during the evolution experiment. Deep sequencing of population samples from different time points generally confirmed these predictions, demonstrating the power of landscape reconstruction analyses for understanding and ultimately predicting evolutionary dynamics, even under complex scenarios of environmental change. Copyright © 2018 by the Genetics Society of America.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

Science.gov (United States)

Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

2015-10-26

The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

A Multi-Scalar Approach to Theorizing Socio-Ecological Dynamics of Urban Residential Landscapes

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Rinku Roy Chowdhury

2011-01-01

Full Text Available Urban residential expansion increasingly drives land use, land cover and ecological changes worldwide, yet social science theories explaining such change remain under-developed. Existing theories often focus on processes occurring at one scale, while ignoring other scales. Emerging evidence from four linked U.S. research sites suggests it is essential to examine processes at multiple scales simultaneously when explaining the evolution of urban residential landscapes. Additionally, focusing on urbanization dynamics across multiple sites with a shared research design may yield fruitful comparative insights. The following processes and social-hierarchical scales significantly influence the spatial configurations of residential landscapes: household-level characteristics and environmental attitudes; formal and informal institutions at the neighborhood scale; and municipal-scale land-use governance. While adopting a multi-scale and multi-site approach produces research challenges, doing so is critical to advancing understanding of coupled socio-ecological systems and associated vulnerabilities in a dynamic and environmentally important setting: residential landscapes.

Colonizing Dynamic Alluvial and Coastal Landscapes in the Holocene

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Kidder, T.; Liu, X.; Ervin, K.

2017-12-01

Throughout the Holocene humans have had to adapt to dynamic, rapidly changing alluvial and coastal landscapes. Understanding when people inhabit a given environment is an important starting point for exploring human adaptations, but increasingly we need to consider how, and especially why certain environments are used—or not used— so we can understand the consequences of these human actions. Using four case studies—one from the Yellow River Valley, China, one from coastal Jiangsu, China, one from the Mississippi River Valley (Mississippi, USA) and one from the Mississippi River delta (Louisiana , USA)—we develop a model of how humans at various stages of cultural development colonize new environments. Using archaeological data and ecological modeling we investigate the relationship between the timing of landscape colonization and the ecological richness and predictability of any given environment. As new landscapes emerge and mature humans adopt different strategies for exploiting these novel environments that begins with episodic use and increasingly shifts to stable, long-term habitation. The early phase of landscape colonization appears to be the most significant period because it shapes human environmental practices and sets each culture on a trajectory of socio-cultural development. Thus, human-environment interaction is a critical part of the emergence of cultural patterns that shapes the past, present, and even the future.

Modelling sediment dynamics due to hillslope-river interactions : incorporating fluvial behaviour in landscape evolution model LAPSUS

NARCIS (Netherlands)

Baartman, Jantiene E. M.; van Gorp, Wouter; Temme, Arnaud J. A. M.; Schoorl, Jeroen M.

Landscape evolution models (LEMs) simulate the three-dimensional development of landscapes over time. Different LEMs have different foci, e.g. erosional behaviour, river dynamics, the fluvial domain, hillslopes or a combination. LEM LAPSUS is a relatively simple cellular model operating on

Integrating Future Land Use Scenarios to Evaluate the Spatio-Temporal Dynamics of Landscape Ecological Security

Directory of Open Access Journals (Sweden)

Yi Lu

2016-11-01

Full Text Available Urban ecological security is the basic principle of national ecological security. However, analyses of the spatial and temporal dynamics of ecological security remain limited, especially those that consider different scenarios of urban development. In this study, an integrated method is proposed that combines the Conversion of Land Use and its Effects (CLUE-S model with the Pressure–State–Response (P-S-R framework to assess landscape ecological security (LES in Huangshan City, China under two scenarios. Our results suggest the following conclusions: (1 the spatial and temporal dynamics of ecological security are closely related to the urbanization process; (2 although the average values of landscape ecological security are similar under different scenarios, the areas of relatively high security levels vary considerably; and (3 spatial heterogeneity in ecological security exists between different districts and counties, and the city center and its vicinity may face relatively serious declines in ecological security in the future. Overall, the proposed method not only illustrates the spatio-temporal dynamics of landscape ecological security under different scenarios but also reveals the anthropogenic effects on ecosystems by differentiating between causes, effects, and human responses at the landscape scale. This information is of great significance to decision-makers for future urban planning and management.

Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations

OpenAIRE

Ono, S.; Kuroda, M.; Higo, J.; Kamiya, N.; Nakajima, N.; Nakamura, H.

2002-01-01

Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was cal...

Free energy landscape and transition pathways from Watson–Crick to Hoogsteen base pairing in free duplex DNA

Science.gov (United States)

Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-01-01

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson–Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine–thymine (A–T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. PMID:26250116

Simulation Based Exploration of Critical Zone Dynamics in Intensively Managed Landscapes

Science.gov (United States)

Kumar, P.

2017-12-01

The advent of high-resolution measurements of topographic and (vertical) vegetation features using areal LiDAR are enabling us to resolve micro-scale ( 1m) landscape structural characteristics over large areas. Availability of hyperspectral measurements is further augmenting these LiDAR data by enabling the biogeochemical characterization of vegetation and soils at unprecedented spatial resolutions ( 1-10m). Such data have opened up novel opportunities for modeling Critical Zone processes and exploring questions that were not possible before. We show how an integrated 3-D model at 1m grid resolution can enable us to resolve micro-topographic and ecological dynamics and their control on hydrologic and biogeochemical processes over large areas. We address the computational challenge of such detailed modeling by exploiting hybrid CPU and GPU computing technologies. We show results of moisture, biogeochemical, and vegetation dynamics from studies in the Critical Zone Observatory for Intensively managed Landscapes (IMLCZO) in the Midwestern United States.

Modeling long-term changes in forested landscapes and their relation to the Earth's energy balance

Science.gov (United States)

Shugart, H. H.; Emanuel, W. R.; Solomon, A. M.

1984-01-01

The dynamics of the forested parts of the Earth's surface on time scales from decades to centuries are discussed. A set of computer models developed at Oak Ridge National Laboratory and elsewhere are applied as tools. These models simulate a landscape by duplicating the dynamics of growth, death and birth of each tree living on a 0.10 ha element of the landscape. This spatial unit is generally referred to as a gap in the case of the forest models. The models were tested against and applied to a diverse array of forests and appear to provide a reasonable representation for investigating forest-cover dynamics. Because of the climate linkage, one important test is the reconstruction of paleo-landscapes. Detailed reconstructions of changes in vegetation in response to changes in climate are crucial to understanding the association of the Earth's vegetation and climate and the response of the vegetation to climate change.

Renewable energy policy and landscape management in Andalusia, Spain: The facts

International Nuclear Information System (INIS)

Prados, Maria-Jose

2010-01-01

Renewable energy has developed spectacularly in Spain since the European Union started a process of energy policy reform. A review of Spanish State legislation on renewable energies confirms that the success in installing renewable energy is attributable to public aid. Andalusia is one of the autonomous communities, which has simultaneously developed the legal framework and very successfully implemented the introduction of renewable power. When implementing the central government's policy, the Andalusian regional government prioritised increases in both surface cover by wind and solar plants (thermal and photovoltaic energy) and in the number of companies involved. However, this development of renewable energies took place without any proper integration into regional spatial and landscape planning. This paper explores renewable power implementation in Andalusia through regulatory measures put in place over the last decade to develop renewable energy systems and the way they can be managed alongside planning issues. The location of large-scale renewable plants has had consequences for territory in the socio-political context of renewable energy promotion. The main findings focus on renewable energy plant sprawl throughout rural areas in Andalusia with no clear effect on landscape management and no firm backing from the local population.

Energy landscapes in proteins and glasses

Science.gov (United States)

Singh, Sadanand

Soft materials are ubiquitous in our day-to-day life. They include liquids, colloids, polymers, foams, gels, granular systems, and a number of biological materials. While these materials exhibit a wide range of textures and morphologies, many of their properties have common physicochemical origins. A better understanding of such origins would lead to rational design and engineering of functional soft materials. A common feature of soft materials is the wide range of time and length scales that characterizes their behavior. Unfortunately, available molecular modeling techniques are often ill-suited for problems that exhibit multiple length and time scales. In this thesis, we introduce and implement new simulation methods that have enabled molecular-level studies of soft materials. Such methods permit calculation of free energy surfaces, and we demonstrate their usefulness in the context of proteins and glasses, both of which exhibit rugged free energy landscapes. A first application is concerned with human amylin, a protein associated with Type II diabetes. Patients with Type II diabetes exhibit fibrillar deposits of human amylin protein in the pancreas. By applying the advanced simulation methods and algorithms developed in this work, we investigate the structure and folding dynamics of human amylin. A detailed mechanism is presented at the atomic-level for the nucleation and aggregation of the peptide. The results presented in this work could help in development of therapeutic strategies for Type II diabetes. The second application is concerned with the study of vapor-deposited ultrastable glasses. These stable glasses have, far below the conventional glass transition temperature, the properties expected from the equilibrium supercooled liquid state. Our results indicate that optimal stability is attained when deposition occurs near the Kauzmann temperature. We also show that the extraordinary stability of model vapor deposited glasses is associated with distinct

Measuring urban tree loss dynamics across residential landscapes.

Science.gov (United States)

Ossola, Alessandro; Hopton, Matthew E

2018-01-15

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

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

Science.gov (United States)

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

Alternating access mechanisms of LeuT-fold transporters: trailblazing towards the promised energy landscapes.

Science.gov (United States)

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

2017-08-01

Secondary active transporters couple the uphill translocation of substrates to electrochemical ion gradients. Transporter conformational motion, generically referred to as alternating access, enables a central ligand binding site to change its orientation relative to the membrane. Here we review themes of alternating access and the transduction of ion gradient energy to power this process in the LeuT-fold class of transporters where crystallographic, computational and spectroscopic approaches have converged to yield detailed models of transport cycles. Specifically, we compare findings for the Na + -coupled amino acid transporter LeuT and the Na + -coupled hydantoin transporter Mhp1. Although these studies have illuminated multiple aspects of transporter structures and dynamics, a number of questions remain unresolved that so far hinder understanding transport mechanisms in an energy landscape perspective. Copyright © 2016 Elsevier Ltd. All rights reserved.

Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.

Science.gov (United States)

Ghaemi, Zhaleh; Guzman, Irisbel; Gnutt, David; Luthey-Schulten, Zaida; Gruebele, Martin

2017-09-14

U1A protein-stem loop 2 RNA association is a basic step in the assembly of the spliceosomal U1 small nuclear ribonucleoprotein. Long-range electrostatic interactions due to the positive charge of U1A are thought to provide high binding affinity for the negatively charged RNA. Short range interactions, such as hydrogen bonds and contacts between RNA bases and protein side chains, favor a specific binding site. Here, we propose that electrostatic interactions are as important as local contacts in biasing the protein-RNA energy landscape toward a specific binding site. We show by using molecular dynamics simulations that deletion of two long-range electrostatic interactions (K22Q and K50Q) leads to mutant-specific alternative RNA bound states. One of these states preserves short-range interactions with aromatic residues in the original binding site, while the other one does not. We test the computational prediction with experimental temperature-jump kinetics using a tryptophan probe in the U1A-RNA binding site. The two mutants show the distinct predicted kinetic behaviors. Thus, the stem loop 2 RNA has multiple binding sites on a rough RNA-protein binding landscape. We speculate that the rough protein-RNA binding landscape, when biased to different local minima by electrostatics, could be one way that protein-RNA interactions evolve toward new binding sites and novel function.

Energy Landscape of Pentapeptides in a Higher-Order (ϕ,ψ Conformational Subspace

Directory of Open Access Journals (Sweden)

Karim M. ElSawy

2016-01-01

Full Text Available The potential energy landscape of pentapeptides was mapped in a collective coordinate principal conformational subspace derived from principal component analysis of a nonredundant representative set of protein structures from the PDB. Three pentapeptide sequences that are known to be distinct in terms of their secondary structure characteristics, (Ala5, (Gly5, and Val.Asn.Thr.Phe.Val, were considered. Partitioning the landscapes into different energy valleys allowed for calculation of the relative propensities of the peptide secondary structures in a statistical mechanical framework. The distribution of the observed conformations of pentapeptide data showed good correspondence to the topology of the energy landscape of the (Ala5 sequence where, in accord with reported trends, the α-helix showed a predominant propensity at 298 K. The topography of the landscapes indicates that the stabilization of the α-helix in the (Ala5 sequence is enthalpic in nature while entropic factors are important for stabilization of the β-sheet in the Val.Asn.Thr.Phe.Val sequence. The results indicate that local interactions within small pentapeptide segments can lead to conformational preference of one secondary structure over the other where account of conformational entropy is important in order to reveal such preference. The method, therefore, can provide critical structural information for ab initio protein folding methods.

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

Science.gov (United States)

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-06-15

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).

Control of the Effective Free-Energy Landscape in a Frustrated Magnet by a Field Pulse

Science.gov (United States)

Wan, Yuan; Moessner, Roderich

2017-10-01

Thermal fluctuations can lift the degeneracy of a ground state manifold, producing a free-energy landscape without accidentally degenerate minima. In a process known as order by disorder, a subset of states incorporating symmetry breaking may be selected. Here, we show that such a free-energy landscape can be controlled in a nonequilibrium setting as the slow motion within the ground state manifold is governed by the fast modes out of it. For the paradigmatic case of the classical pyrochlore X Y antiferromagnet, we show that a uniform magnetic field pulse can excite these fast modes to generate a tunable effective free-energy landscape with minima at thermodynamically unstable portions of the ground state manifold.

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

Science.gov (United States)

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

Physical mechanism of mind changes and tradeoffs among speed, accuracy, and energy cost in brain decision making: Landscape, flux, and path perspectives

International Nuclear Information System (INIS)

Yan Han; Wang Jin; Zhang Kun

2016-01-01

Cognitive behaviors are determined by underlying neural networks. Many brain functions, such as learning and memory, have been successfully described by attractor dynamics. For decision making in the brain, a quantitative description of global attractor landscapes has not yet been completely given. Here, we developed a theoretical framework to quantify the landscape associated with the steady state probability distributions and associated steady state curl flux, measuring the degree of non-equilibrium through the degree of detailed balance breaking for decision making. We quantified the decision-making processes with optimal paths from the undecided attractor states to the decided attractor states, which are identified as basins of attractions, on the landscape. Both landscape and flux determine the kinetic paths and speed. The kinetics and global stability of decision making are explored by quantifying the landscape topography through the barrier heights and the mean first passage time. Our theoretical predictions are in agreement with experimental observations: more errors occur under time pressure. We quantitatively explored two mechanisms of the speed-accuracy tradeoff with speed emphasis and further uncovered the tradeoffs among speed, accuracy, and energy cost. Our results imply that there is an optimal balance among speed, accuracy, and the energy cost in decision making. We uncovered the possible mechanisms of changes of mind and how mind changes improve performance in decision processes. Our landscape approach can help facilitate an understanding of the underlying physical mechanisms of cognitive processes and identify the key factors in the corresponding neural networks. (paper)

New Energy Landscapes of Pennsylvania: Forests to Farms to Fracking

Science.gov (United States)

Johnson, Deborah A.

This dissertation adds to the literature on energy needed by industry, government, and citizens for decision-making. The pursuit to access or create new energy resources spawns new landscapes of energy in the early 21st century. The combination of hydraulic fracturing and horizontal drilling technologies---popularly called "fracking"---enables entry into previously inaccessible natural gas reserves such as the Marcellus shale much of which lies beneath Pennsylvania. Although this unconventional method offers a promising source of domestic energy and job growth, the potential for negative impacts raises concerns and questions. The questions include: What is the controversy about fracking in Pennsylvania? What are the impacts of fracking? What costs is Pennsylvania paying as it shifts to shale gas extraction? Are there activities taking place or material signs that point to the emerging new landscapes? Are the individuals and organizations that resist shale gas extraction---the so-called "Green Forces"---and others who live within the region of development more or less attuned to these costs? A mixed methods approach consists of landscape and stakeholder analyses including visual examination of GIS-generated maps, satellite images, and photos taken in the field specifically from four counties: Washington, Warren, McKean, and Bradford. Research captures stakeholders' voices across the public, government, and private sectors at different scales. A stakeholder matrix facilitates data organization and analysis. Data include 114 individual statements from an EPA Public Meeting, texts from 40 online-newspaper articles or blogs, and face-to-face interviews or focus group participation of 36 individuals. Further data come from a public health conference, industry convention, and public protest. The new energy landscape covers spaces in Pennsylvania where oil and gas development previously had not been present. It obscures as well as exposes the legacy of past energy

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

Science.gov (United States)

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

2014-11-01

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

Free energy landscape and transition pathways from Watson-Crick to Hoogsteen base pairing in free duplex DNA.

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Yang, Changwon; Kim, Eunae; Pak, Youngshang

2015-09-18

Houghton (HG) base pairing plays a central role in the DNA binding of proteins and small ligands. Probing detailed transition mechanism from Watson-Crick (WC) to HG base pair (bp) formation in duplex DNAs is of fundamental importance in terms of revealing intrinsic functions of double helical DNAs beyond their sequence determined functions. We investigated a free energy landscape of a free B-DNA with an adenosine-thymine (A-T) rich sequence to probe its conformational transition pathways from WC to HG base pairing. The free energy landscape was computed with a state-of-art two-dimensional umbrella molecular dynamics simulation at the all-atom level. The present simulation showed that in an isolated duplex DNA, the spontaneous transition from WC to HG bp takes place via multiple pathways. Notably, base flipping into the major and minor grooves was found to play an important role in forming these multiple transition pathways. This finding suggests that naked B-DNA under normal conditions has an inherent ability to form HG bps via spontaneous base opening events. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

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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...

Inflation, Dark Matter, and Dark Energy in the String Landscape

OpenAIRE

Liddle, Andrew R; Ureña-López, L Arturo

2006-01-01

We consider the conditions needed to unify the description of dark matter, dark energy and inflation in the context of the string landscape. We find that incomplete decay of the inflaton field gives the possibility that a single field is responsible for all three phenomena. By contrast, unifying dark matter and dark energy into a single field, separate from the inflaton, appears rather difficult.

Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects

Science.gov (United States)

Alakent, Burak; Camurdan, Mehmet C.; Doruker, Pemra

2005-10-01

Time series analysis tools are employed on the principal modes obtained from the Cα trajectories from two independent molecular-dynamics simulations of α-amylase inhibitor (tendamistat). Fluctuations inside an energy minimum (intraminimum motions), transitions between minima (interminimum motions), and relaxations in different hierarchical energy levels are investigated and compared with those encountered in vacuum by using different sampling window sizes and intervals. The low-frequency low-indexed mode relationship, established in vacuum, is also encountered in water, which shows the reliability of the important dynamics information offered by principal components analysis in water. It has been shown that examining a short data collection period (100ps) may result in a high population of overdamped modes, while some of the low-frequency oscillations (memory: future conformations are less dependent on previous conformations due to the lowering of energy barriers in hierarchical levels of the energy landscape. In short-time dynamics (sight contradicts. However, this comes about because water enhances the transitions between minima and forces the protein to reduce its already inherent inability to maintain oscillations observed in vacuum. Some of the frequencies lower than 10cm-1 are found to be overdamped, while those higher than 20cm-1 are slightly increased. As for the long-time dynamics in water, it is found that random-walk motion is maintained for approximately 200ps (about five times of that in vacuum) in the low-indexed modes, showing the lowering of energy barriers between the higher-level minima.

Regional and landscape-scale variability of Landsat-observed vegetation dynamics in northwest Siberian tundra

International Nuclear Information System (INIS)

Frost, Gerald V; Epstein, Howard E; Walker, Donald A

2014-01-01

Widespread increases in Arctic tundra productivity have been documented for decades using coarse-scale satellite observations, but finer-scale observations indicate that changes have been very uneven, with a high degree of landscape- and regional-scale heterogeneity. Here we analyze time-series of the Normalized Difference Vegetation Index (NDVI) observed by Landsat (1984–2012), to assess landscape- and regional-scale variability of tundra vegetation dynamics in the northwest Siberian Low Arctic, a little-studied region with varied soils, landscape histories, and permafrost attributes. We also estimate spatio-temporal rates of land-cover change associated with expansion of tall alder (Alnus) shrublands, by integrating Landsat time-series with very-high-resolution imagery dating to the mid-1960s. We compiled Landsat time-series for eleven widely-distributed landscapes, and performed linear regression of NDVI values on a per-pixel basis. We found positive net NDVI trends (‘greening’) in nine of eleven landscapes. Net greening occurred in alder shrublands in all landscapes, and strong greening tended to correspond to shrublands that developed since the 1960s. Much of the spatial variability of greening within landscapes was linked to landscape physiography and permafrost attributes, while between-landscape variability largely corresponded to differences in surficial geology. We conclude that continued increases in tundra productivity in the region are likely in upland tundra landscapes with fine-textured, cryoturbated soils; these areas currently tend to support discontinuous vegetation cover, but are highly susceptible to rapid increases in vegetation cover, as well as land-cover changes associated with the development of tall shrublands. (paper)

Energy landscape for martensitic phase transformation in shape memory NiTi

International Nuclear Information System (INIS)

Kibey, S.; Sehitoglu, H.; Johnson, D.D.

2009-01-01

First-principles calculations are presented for parent B2 phase and martensitic B19 and B19' phases in NiTi. The results indicate that both B19 and B19' are energetically more stable than the parent B2 phase. By means of ab initio density functional theory, the complete distortion-shuffle energy landscape associated with B2 → B19 transformation in NiTi is then determined. In addition to accounting for the Bain-type deformation through the Cauchy-Born rule, the study explicitly accounts for the shuffle displacements experienced by the internal ions in NiTi. The energy landscape allows the energy barrier associated with the B2 → B19 transformation pathway to be identified. The results indicate that a barrier of 0.48 mRyd atom -1 (relative to the B2 phase) must be overcome to transform the parent B2 NiTi to orthorhombic B19 martensite

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.

Science.gov (United States)

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.

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

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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 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 amphibian declines and extinctions are far more likely to occur as a result of permanent habitat loss resulting from development than from the temporary degradation of habitat caused by current forestry practices.

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

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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

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

International Nuclear Information System (INIS)

Wu, Wei; Wang, Jin

2014-01-01

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

Thermal Infrared Remote Sensing for Analysis of Landscape Ecological Processes: Methods and Applications

Science.gov (United States)

Quattrochi, Dale A.; Luvall, Jeffrey C.

1998-01-01

Thermal Infrared (TIR) remote sensing data can provide important measurements of surface energy fluxes and temperatures, which are integral to understanding landscape processes and responses. One example of this is the successful application of TIR remote sensing data to estimate evapotranspiration and soil moisture, where results from a number of studies suggest that satellite-based measurements from TIR remote sensing data can lead to more accurate regional-scale estimates of daily evapotranspiration. With further refinement in analytical techniques and models, the use of TIR data from airborne and satellite sensors could be very useful for parameterizing surface moisture conditions and developing better simulations of landscape energy exchange over a variety of conditions and space and time scales. Thus, TIR remote sensing data can significantly contribute to the observation, measurement, and analysis of energy balance characteristics (i.e., the fluxes and redistribution of thermal energy within and across the land surface) as an implicit and important aspect of landscape dynamics and landscape functioning. The application of TIR remote sensing data in landscape ecological studies has been limited, however, for several fundamental reasons that relate primarily to the perceived difficulty in use and availability of these data by the landscape ecology community, and from the fragmentation of references on TIR remote sensing throughout the scientific literature. It is our purpose here to provide evidence from work that has employed TIR remote sensing for analysis of landscape characteristics to illustrate how these data can provide important data for the improved measurement of landscape energy response and energy flux relationships. We examine the direct or indirect use of TIR remote sensing data to analyze landscape biophysical characteristics, thereby offering some insight on how these data can be used more robustly to further the understanding and modeling of

The impact of land use change and hydroclimatic variability on landscape connectivity dynamics across surface water networks at subcontinental scale

Science.gov (United States)

Tulbure, M. G.; Bishop-Taylor, R.; Broich, M.

2017-12-01

Land use (LU) change and hydroclimatic variability affect spatiotemporal landscape connectivity dynamics, important for species movement and dispersal. Despite the fact that LU change can strongly influence dispersal potential over time, prior research has only focused on the impacts of dynamic changes in the distribution of potential habitats. We used 8 time-steps of historical LU together with a Landsat-derived time-series of surface water habitat dynamics (1986-2011) over the Murray-Darling Basin (MDB), a region with extreme hydroclimatic variability, impacted by LU changes. To assess how changing LU and hydroclimatic variability affect landscape connectivity across time, we compared 4 scenarios, namely one where both climate and LU are dynamic over time, one where climate is kept steady (i.e. a median surface water extent layer), and two scenarios where LU is kept steady (i.e. resistance values associated with the most recent or the first LU layer). We used circuit theory to assign landscape features with `resistance' costs and graph theory network analysis, with surface water habitats as `nodes' connected by dispersal paths or `edges' Findings comparing a dry and an average season show high differences in number of nodes (14581 vs 21544) and resistance distances. The combined effect of LU change and landscape wetness was lower than expected, likely a function of the large, MDB-wide, aggregation scale. Spatially explicit analyses are expected to identify areas where the synergistic effect of LU change and landscape wetness greatly reduce or increase landscape connectivity, as well as areas where the two effects cancel each other out.

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

Science.gov (United States)

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.

Landscape dynamics analysis in Iasi Metropolitan Area (Romania using remote sensing data

Directory of Open Access Journals (Sweden)

CÃTÃLIN CÎMPIANU

2013-08-01

Full Text Available The present paper focuses on the observation and quantification of land cover changes in Iasi Metropolitan Area during 1993-2009. The analysis is centered upon the built-up space dynamics and includes the detection of its extension directions and the measurement of its structural changes by landscape metrics. In order to obtain the land cover data, some remote sensing images were processed by supervised classification and Normalized Difference Vegetation Index (NDVI. In the end of the study, a synthetic statistical analysis of the change dynamics is performed at commune level, in order to compare the administrative units by the intensity of land cover dynamics.

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

Science.gov (United States)

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.

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

Science.gov (United States)

Mueller, Thomas; Olson, K.A.; Dressler, G.; Leimgruber, Peter; Fuller, Todd K.; Nicholson, Craig; Novaro, A.J.; Bolgeri, M.J.; Wattles, David W.; 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�

Comparison of Recent Oil and Gas, Wind Energy, and Other Anthropogenic Landscape Alteration Factors in Texas Through 2014.

Science.gov (United States)

Pierre, Jon Paul; Wolaver, Brad D; Labay, Benjamin J; LaDuc, Travis J; Duran, Charles M; Ryberg, Wade A; Hibbitts, Toby J; Andrews, John R

2018-05-01

Recent research assessed how hydrocarbon and wind energy expansion has altered the North American landscape. Less understood, however, is how this energy development compares to other anthropogenic land use changes. Texas leads U.S. hydrocarbon production and wind power generation and has a rapidly expanding population. Thus, for ~47% of Texas (~324,000 km 2 ), we mapped the 2014 footprint of energy activities (~665,000 oil and gas wells, ~5700 wind turbines, ~237,000 km oil and gas pipelines, and ~2000 km electrical transmission lines). We compared the footprint of energy development to non-energy-related activities (agriculture, roads, urbanization) and found direct landscape alteration from all factors affects ~23% of the study area (~76,000 km 2 ), led by agriculture (~16%; ~52,882 km 2 ). Oil and gas activities altered turbine pads and ~10 km 2 from power transmission lines. We found that edge effects of widely-distributed energy infrastructure caused more indirect landscape alteration than larger, more concentrated urbanization and agriculture. This study presents a novel technique to quantify and compare anthropogenic activities causing both direct and indirect landscape alteration. We illustrate this landscape-mapping framework in Texas for the Spot-tailed Earless Lizard (Holbrookia lacerata); however, the approach can be applied to a range of species in developing regions globally.

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

Science.gov (United States)

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

2015-04-01

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

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

Science.gov (United States)

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

Multiscale coarse-graining of the protein energy landscape.

Directory of Open Access Journals (Sweden)

Ronald D Hills

2010-06-01

Full Text Available A variety of coarse-grained (CG models exists for simulation of proteins. An outstanding problem is the construction of a CG model with physically accurate conformational energetics rivaling all-atom force fields. In the present work, atomistic simulations of peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop and test a CG interaction potential of general utility for the simulation of proteins of arbitrary sequence. The reduced representation relies on multiple interaction sites to maintain the anisotropic packing and polarity of individual sidechains. CG energy landscapes computed from replica exchange simulations of the folding of Trpzip, Trp-cage and adenylate kinase resemble those of other reduced representations; non-native structures are observed with energies similar to those of the native state. The artifactual stabilization of misfolded states implies that non-native interactions play a deciding role in deviations from ideal funnel-like cooperative folding. The role of surface tension, backbone hydrogen bonding and the smooth pairwise CG landscape is discussed. Ab initio folding aside, the improved treatment of sidechain rotamers results in stability of the native state in constant temperature simulations of Trpzip, Trp-cage, and the open to closed conformational transition of adenylate kinase, illustrating the potential value of the CG force field for simulating protein complexes and transitions between well-defined structural states.

Protein energy landscapes determined by five-dimensional crystallography

International Nuclear Information System (INIS)

Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

2013-01-01

Barriers of activation within the photocycle of a photoactive protein were extracted from comprehensive time courses of time resolved crystallographic data collected at multiple temperature settings. Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012 ▶), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001 ▶), Chem. Rev.101, 1569–1581; Schmidt et al. (2005 ▶), Methods Mol. Biol.305, 115–154; Schmidt (2008 ▶), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallography, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010 ▶), Acta Cryst. A66, 198–206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallographic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes

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

Science.gov (United States)

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.

Understanding landscape dynamics over thousand years : combining field and model work : with case study in the Drakensberg foothill, KwaZulu-Natal, South Africa

NARCIS (Netherlands)

Temme, A.J.A.M.

2008-01-01

The title of this thesis is “Understanding landscape dynamics over thousands of years : combining field and model work, with a case study in the Drakensberg Foothills, KwaZulu-Natal, South Africa”. As the title clearly states, the overall objective is an increased knowledge of landscape dynamics

Potential energy landscape and robustness of a gene regulatory network: toggle switch.

Directory of Open Access Journals (Sweden)

Keun-Young Kim

2007-03-01

Full Text Available Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers. It leads to the robustness of the biological basins of the gene switches. The technique used here is general and can be applied to explore the potential energy landscape of the gene networks.

Energy landscape of all-atom protein-protein interactions revealed by multiscale enhanced sampling.

Directory of Open Access Journals (Sweden)

Kei Moritsugu

2014-10-01

Full Text Available Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape.

Quantitative analysis of the publishing landscape in high-energy physics

International Nuclear Information System (INIS)

Mele, Salvatore; Dallman, David; Vigen, Jens; Yeomans, Joanne

2006-01-01

World-wide collaboration in high-energy physics (HEP) is a tradition which dates back several decades, with scientific publications mostly coauthored by scientists from different countries. This coauthorship phenomenon makes it difficult to identify precisely the 'share' of each country in HEP scientific production. One year's worth of HEP scientific articles published in peer-reviewed journals is analysed and their authors are uniquely assigned to countries. This method allows the first correct estimation on a pro rata basis of the share of HEP scientific publishing among several countries and institutions. The results provide an interesting insight into the geographical collaborative patterns of the HEP community. The HEP publishing landscape is further analysed to provide information on the journals favoured by the HEP community and on the geographical variation of their author bases. These results provide quantitative input to the ongoing debate on the possible transition of HEP publishing to an Open Access model. Foreword. This paper reports the results of a recent detailed study of the publishing landscape in high energy physics. We thought that because of its direct relevance to the high energy physics community, this important quantitative input to the debate on the transition to Open Access naturally finds its place in our journal. Marc Henneaux, JHEP Scientific Director

Identifying Greater Sage-Grouse source and sink habitats for conservation planning in an energy development landscape.

Science.gov (United States)

Kirol, Christopher P; Beck, Jeffrey L; Huzurbazar, Snehalata V; Holloran, Matthew J; Miller, Scott N

2015-06-01

Conserving a declining species that is facing many threats, including overlap of its habitats with energy extraction activities, depends upon identifying and prioritizing the value of the habitats that remain. In addition, habitat quality is often compromised when source habitats are lost or fragmented due to anthropogenic development. Our objective was to build an ecological model to classify and map habitat quality in terms of source or sink dynamics for Greater Sage-Grouse (Centrocercus urophasianus) in the Atlantic Rim Project Area (ARPA), a developing coalbed natural gas field in south-central Wyoming, USA. We used occurrence and survival modeling to evaluate relationships between environmental and anthropogenic variables at multiple spatial scales and for all female summer life stages, including nesting, brood-rearing, and non-brooding females. For each life stage, we created resource selection functions (RSFs). We weighted the RSFs and combined them to form a female summer occurrence map. We modeled survival also as a function of spatial variables for nest, brood, and adult female summer survival. Our survival-models were mapped as survival probability functions individually and then combined with fixed vital rates in a fitness metric model that, when mapped, predicted habitat productivity (productivity map). Our results demonstrate a suite of environmental and anthropogenic variables at multiple scales that were predictive of occurrence and survival. We created a source-sink map by overlaying our female summer occurrence map and productivity map to predict habitats contributing to population surpluses (source habitats) or deficits (sink habitat) and low-occurrence habitats on the landscape. The source-sink map predicted that of the Sage-Grouse habitat within the ARPA, 30% was primary source, 29% was secondary source, 4% was primary sink, 6% was secondary sink, and 31% was low occurrence. Our results provide evidence that energy development and avoidance of

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

Science.gov (United States)

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

Calculation of the Local Free Energy Landscape in the Restricted Region by the Modified Tomographic Method.

Science.gov (United States)

Chen, Changjun

2016-03-31

The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.

A new approach to quantify semiochemical effects on insects based on energy landscapes.

Directory of Open Access Journals (Sweden)

Rory P Wilson

Full Text Available Our ability to document insect preference for semiochemicals is pivotal in pest control as these agents can improve monitoring and be deployed within integrated pest management programmes for more efficacious control of pest species. However, methods used to date have drawbacks that limit their utility. We present and test a new concept for determining insect motivation to move towards, or away from, semiochemicals by noting direction and speed of movement as animals work against a defined energy landscape (environmentally dependent variation in the cost of transport requiring different powers to negotiate. We conducted trials with the pine weevils Hylobius abietis and peach-potato aphids Myzus persicae exposed to various attractants and repellents and placed so that they either moved up defined slopes against gravity or had to travel over variously rough surfaces.Linear Mixed Models demonstrated clear reductions in travel speed by insects moving along increasingly energetically taxing energy landscapes but also that responses varied according to different semiochemicals, thus highlighting the value of energy landscapes as a new concept to help measure insect motivation to access or avoid different attractants or repellents across individuals.New sensitive, detailed indicators of insect motivation derived from this approach should prove important in pest control across the world.

Exploring the energy landscape of the charge transport levels in organic semiconductors at the molecular scale.

Science.gov (United States)

Cornil, J; Verlaak, S; Martinelli, N; Mityashin, A; Olivier, Y; Van Regemorter, T; D'Avino, G; Muccioli, L; Zannoni, C; Castet, F; Beljonne, D; Heremans, P

2013-02-19

strongly interacting electron-hole pairs can potentially escape from their Coulomb well, a process that is at the heart of photoconversion or molecular doping. Yet they do, with near-quantitative yield in some cases. Limited screening by the low dielectric medium in organic materials leads to subtle static and dynamic electronic polarization effects that strongly impact the energy landscape for charges, which offers a rationale for this apparent inconsistency. In this Account, we use different theoretical approaches to predict the energy landscape of charge carriers at the molecular level and review a few case studies highlighting the role of electrostatic interactions in conjugated organic molecules. We describe the pros and cons of different theoretical approaches that provide access to the energy landscape defining the motion of charge carriers. We illustrate the applications of these approaches through selected examples involving OFETs, OLEDs, and solar cells. The three selected examples collectively show that energetic disorder governs device performances and highlights the relevance of theoretical tools to probe energy landscapes in molecular assemblies.

Detectability of landscape effects on recolonization increases with regional population density.

Science.gov (United States)

Liman, Anna-Sara; Dalin, Peter; Björkman, Christer

2015-07-01

Variation in population size over time can influence our ability to identify landscape-moderated differences in community assembly. To date, however, most studies at the landscape scale only cover snapshots in time, thereby overlooking the temporal dynamics of populations and communities. In this paper, we present data that illustrate how temporal variation in population density at a regional scale can influence landscape-moderated variation in recolonization and population buildup in disturbed habitat patches. Four common insect species, two omnivores and two herbivores, were monitored over 8 years in 10 willow short-rotation coppice bio-energy stands with a four-year disturbance regime (coppice cycle). The population densities in these regularly disturbed stands were compared to densities in 17 undisturbed natural Salix cinerea (grey willow) stands in the same region. A time series approach was used, utilizing the natural variation between years to statistically model recolonization as a function of landscape composition under two different levels of regional density. Landscape composition, i.e. relative amount of forest vs. open agricultural habitats, largely determined the density of re-colonizing populations following willow coppicing in three of the four species. However, the impact of landscape composition was not detectable in years with low regional density. Our results illustrate that landscape-moderated recolonization can change over time and that considering the temporal dynamics of populations may be crucial when designing and evaluating studies at landscape level.

Landscape management for sustainable supplies of bio energy feedstock and enhanced soil quality

International Nuclear Information System (INIS)

Douglas, K.; Muth, D.

2013-01-01

Agriculture can simultaneously address global food, feed, fiber, and energy challenges provided our soil, water, and air resources are not compromised in doing so. Our objective is to present a landscape management concept as an approach for integrating multiple bio energy feedstock sources into current crop production systems. This is done to show how multiple, increasing global challenges can be met in a sustainable manner. We discuss how collaborative research among Usda-Agricultural Research Service (ARS), US Department of Energy (DOE) Idaho National Laboratory (INL), several university extension and research partners, and industry representatives [known as the Renewable Energy Assessment Project (Reap) team] has led to the development of computer-based decision aids for guiding sustainable bio energy feedstock production. The decision aids, known initially as the Corn Stover Tool and more recently as the Landscape Environmental Assessment Framework (Leaf) are tools designed to recognize the importance of nature s diversity and can therefore be used to guide sustainable feedstock production without having negative impacts on critical ecosystem services. Using a 57 ha farm site in central Iowa, USA, we show how producer decisions regarding corn (Zea mays L.) stover harvest within the US Corn Belt can be made in a more sustainable manner. This example also supports Reap team conclusions that stover should not be harvested if average grain yields are less than 11 Mg ha-1 unless more balanced landscape management practices are implemented. The tools also illustrate the importance of sub-field management and site-specific stover harvest strategies

Relaxation height in energy landscapes : an application to multiple metastable states

NARCIS (Netherlands)

Cirillo, E.N.M.; Nardi, F.R.

2012-01-01

The study of systems with multiple (not necessarily degenerate) metastable states presents subtle difficulties from the mathematical point of view related to the variational problem that has to be solved in these cases. We introduce the notion of relaxation height in a general energy landscape and

Landscape sensitivity in a dynamic environment

Science.gov (United States)

Lin, Jiun-Chuan; Jen, Chia-Horn

2010-05-01

Landscape sensitivity at different scales and topics is presented in this study. Methodological approach composed most of this paper. According to the environmental records in the south eastern Asia, the environment change is highly related with five factors, such as scale of influence area, background of environment characters, magnitude and frequency of events, thresholds of occurring hazards and influence by time factor. This paper tries to demonstrate above five points from historical and present data. It is found that landscape sensitivity is highly related to the degree of vulnerability of the land and the processes which put on the ground including human activities. The scale of sensitivity and evaluation of sensitivities is demonstrated in this paper by the data around east Asia. The methods of classification are mainly from the analysis of environmental data and the records of hazards. From the trend of rainfall records, rainfall intensity and change of temperature, the magnitude and frequency of earthquake, dust storm, days of draught, number of hazards, there are many coincidence on these factors with landscape sensitivities. In conclusion, the landscape sensitivities could be classified as four groups: physical stable, physical unstable, unstable, extremely unstable. This paper explain the difference.

Strategies for the exploration of free energy landscapes: Unity in diversity and challenges ahead

Directory of Open Access Journals (Sweden)

Fabio Pietrucci

2017-11-01

Full Text Available Computer simulations play an important role in the study of transformation processes of condensed matter, including phase transitions, chemical reactions, and conformational changes of biomolecules. In principle, atomic trajectories, such as those generated using the molecular dynamics approach, contain detailed structural, thermodynamic, and kinetic information about activated processes. In practice, due to free energy barriers, there is often a wide gap between the time scale of the transformation and the time scale accessible with simulations. This review offers a practical guide to the ingenious methods aimed to accelerate the exploration and reconstruction of free energy landscapes of complex systems. The focus is on basic unifying concepts, successful strategies, and pitfalls, illustrated with examples of application to scientific problems from different disciplines. The current challenges in the field consist mainly in the cumbersome identification of optimal reaction coordinates and in the extensive recourse to expert human supervision and fine tuning of the algorithms. The full achievement of wide-spectrum formulations and easy reproducibility of results would constitute the breakthrough necessary to enter the era of routine use of enhanced sampling simulations.

Autonomously folding protein fragments reveal differences in the energy landscapes of homologous RNases H.

Directory of Open Access Journals (Sweden)

Laura E Rosen

Full Text Available An important approach to understanding how a protein sequence encodes its energy landscape is to compare proteins with different sequences that fold to the same general native structure. In this work, we compare E. coli and T. thermophilus homologs of the protein RNase H. Using protein fragments, we create equilibrium mimics of two different potential partially-folded intermediates (I(core and I(core+1 hypothesized to be present on the energy landscapes of these two proteins. We observe that both T. thermophilus RNase H (ttRNH fragments are folded and have distinct stabilities, indicating that both regions are capable of autonomous folding and that both intermediates are present as local minima on the ttRNH energy landscape. In contrast, the two E. coli RNase H (ecRNH fragments have very similar stabilities, suggesting that the presence of additional residues in the I(core+1 fragment does not affect the folding or structure as compared to I(core. NMR experiments provide additional evidence that only the I(core intermediate is populated by ecRNH. This is one of the biggest differences that has been observed between the energy landscapes of these two proteins. Additionally, we used a FRET experiment in the background of full-length ttRNH to specifically monitor the formation of the I(core+1 intermediate. We determine that the ttRNH I(core+1 intermediate is likely the intermediate populated prior to the rate-limiting barrier to global folding, in contrast to E. coli RNase H for which I(core is the folding intermediate. This result provides new insight into the nature of the rate-limiting barrier for the folding of RNase H.

Coupling movement and landscape ecology for animal conservation in production landscapes.

Science.gov (United States)

Doherty, Tim S; Driscoll, Don A

2018-01-10

Habitat conversion in production landscapes is among the greatest threats to biodiversity, not least because it can disrupt animal movement. Using the movement ecology framework, we review animal movement in production landscapes, including areas managed for agriculture and forestry. We consider internal and external drivers of altered animal movement and how this affects navigation and motion capacities and population dynamics. Conventional management approaches in fragmented landscapes focus on promoting connectivity using structural changes in the landscape. However, a movement ecology perspective emphasizes that manipulating the internal motivations or navigation capacity of animals represents untapped opportunities to improve movement and the effectiveness of structural connectivity investments. Integrating movement and landscape ecology opens new opportunities for conservation management in production landscapes. © 2018 The Authors.

Characterizing European cultural landscapes

DEFF Research Database (Denmark)

Tieskens, Koen F.; Schulp, Catharina J E; Levers, Christian

2017-01-01

intensification and land abandonment. To prevent the loss of cultural landscapes, knowledge on the location of different types of cultural landscapes is needed. In this paper, we present a characterization of European cultural landscapes based on the prevalence of three key dimensions of cultural landscapes......Almost all rural areas in Europe have been shaped or altered by humans and can be considered cultural landscapes, many of which now are considered to entail valuable cultural heritage. Current dynamics in land management have put cultural landscapes under a huge pressure of agricultural...... the three dimensions into a continuous “cultural landscape index” that allows for a characterization of Europe's rural landscapes. The characterization identifies hotspots of cultural landscapes, where all three dimensions are present, such as in the Mediterranean. On the other hand, Eastern and Northern...

Landscape encodings enhance optimization.

Directory of Open Access Journals (Sweden)

Konstantin Klemm

Full Text Available Hard combinatorial optimization problems deal with the search for the minimum cost solutions (ground states of discrete systems under strong constraints. A transformation of state variables may enhance computational tractability. It has been argued that these state encodings are to be chosen invertible to retain the original size of the state space. Here we show how redundant non-invertible encodings enhance optimization by enriching the density of low-energy states. In addition, smooth landscapes may be established on encoded state spaces to guide local search dynamics towards the ground state.

Landscape Encodings Enhance Optimization

Science.gov (United States)

Klemm, Konstantin; Mehta, Anita; Stadler, Peter F.

2012-01-01

Hard combinatorial optimization problems deal with the search for the minimum cost solutions (ground states) of discrete systems under strong constraints. A transformation of state variables may enhance computational tractability. It has been argued that these state encodings are to be chosen invertible to retain the original size of the state space. Here we show how redundant non-invertible encodings enhance optimization by enriching the density of low-energy states. In addition, smooth landscapes may be established on encoded state spaces to guide local search dynamics towards the ground state. PMID:22496860

Free energy landscape of dissociative adsorption of methane on ideal and defected graphene from ab initio simulations

Science.gov (United States)

Wlazło, M.; Majewski, J. A.

2018-03-01

We study the dissociative adsorption of methane at the surface of graphene. Free energy profiles, which include activation energies for different steps of the reaction, are computed from constrained ab initio molecular dynamics. At 300 K, the reaction barriers are much lower than experimental bond dissociation energies of gaseous methane, strongly indicating that the graphene surface acts as a catalyst of methane decomposition. On the other hand, the barriers are still much higher than on the nickel surface. Methane dissociation therefore occurs at a higher rate on nickel than on graphene. This reaction is a prerequisite for graphene growth from a precursor gas. Thus, the growth of the first monolayer should be a fast and efficient process while subsequent layers grow at a diminished rate and in a more controllable manner. Defects may also influence reaction energetics. This is evident from our results, in which simple defects (Stone-Wales defect and nitrogen substitution) lead to different free energy landscapes at both dissociation and adsorption steps of the process.

Dynamic monitoring of landscape patterns and ecological processes

Indian Academy of Sciences (India)

Landscape patterns and ecological processes have been in long-term research focus in the field of landscape ecology, but how to measure their quantitative relations is still open. This work chooses the Hulunbeier grassland as the study area where ecosystem shows high vulnerability, frequent evolvement of landscape ...

Responding to Landscape Change: Stakeholder Participation and Social Capital in Five European Landscapes

Directory of Open Access Journals (Sweden)

Thanasis Kizos

2018-01-01

Full Text Available The concept of landscape has been increasingly used, in the last decades, in policy and land use planning, both in regard to so-called “special” and to “ordinary” or “everyday” landscapes. This has raised the importance of local and public participation in all issues that refer to landscapes and the definition of the groups that “have a stake” in the landscape. In this paper, we provide insights into how stakeholders perceive the dynamics of local processes of landscape change (and continuity and which processes of landscape change they perceive as important, in positive and negative ways, from five communities within the European Union. These landscapes involve different landscape issues “at stake”, different national and local planning and decision-making traditions and practices, and varying degrees of engagement. The understanding of these complexities and the unraveling of the insights is done through the concept of social capital and its different forms. We report on three series of workshops that have been organized to discuss landscape issues and approaches or ideas for landscape management. We witnessed interactions between the different stakeholders and gained insights into how social capital affects landscape change. We found that despite differences, similarities emerged concerning the interplay between “expert” and “local” knowledge and between “insideness” and “outsideness”. Social capital plays an important part, as it provides the template for personal and collective evaluation of landscape changes, who should manage these changes and how they should be managed. These findings are important to develop in-depth insights on dynamics and values of cultural landscapes and visions for re-coupling social and ecological components in cultural landscapes and translate them into policy and management options.

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

Science.gov (United States)

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.

Relationship between energy systems and landscapes. Guidelines and tools for design and management

Directory of Open Access Journals (Sweden)

Elisabetta Ginelli

2014-10-01

Full Text Available Landscapes undergoing conservation, valorisation, management and reconstruction policies, become a fundamental factor for the local/global development of natural, cultural, human and social potentials of territories. With the contribution of technological design culture, the research, having a strong multidisciplinary character, focuses on managing the relationship between energy systems and landscapes with the general aim of subverting and transforming apparent conflicts in synergies, in order to overcome a sectorial and segmented approach barely based on energy performances. Through the introduction of a complex multidimensional methodology of analysis and evaluation the goal of this work, is to develop standards of acceptability, meta-design criteria and guidelines for design, intro- ducing a methodology for multidimen- sional complex analysis and evaluation, to support Public Authorities.

Sources to the landscape - detailed spatiotemporal analysis of 200 years Danish landscape dynamics using unexploited historical maps and aerial photos

DEFF Research Database (Denmark)

Svenningsen, Stig Roar; Christensen, Andreas Aagaard; Dupont, Henrik

to declassification of military maps and aerial photos from the cold war, only relatively few sources have been made available to researchers due to lacking efforts in digitalization and related services. And even though the digitizing of cartographic material has been accelerated, the digitally available materials...... or to the commercial photo series from the last 20 years. This poster outlines a new research project focusing on the potential of unexploited cartographic sources for detailed analysis of the dynamic of the Danish landscape between 1800 – 2000. The project draws on cartographic sources available in Danish archives...... of material in landscape change studies giving a high temporal and spatial resolution. The project also deals with the opportunity and constrain of comparing different cartographic sources with diverse purpose and time of production, e.g. different scale and quality of aerial photos or the difference between...

Homogenization techniques for population dynamics in strongly heterogeneous landscapes.

Science.gov (United States)

Yurk, Brian P; Cobbold, Christina A

2018-12-01

An important problem in spatial ecology is to understand how population-scale patterns emerge from individual-level birth, death, and movement processes. These processes, which depend on local landscape characteristics, vary spatially and may exhibit sharp transitions through behavioural responses to habitat edges, leading to discontinuous population densities. Such systems can be modelled using reaction-diffusion equations with interface conditions that capture local behaviour at patch boundaries. In this work we develop a novel homogenization technique to approximate the large-scale dynamics of the system. We illustrate our approach, which also generalizes to multiple species, with an example of logistic growth within a periodic environment. We find that population persistence and the large-scale population carrying capacity is influenced by patch residence times that depend on patch preference, as well as movement rates in adjacent patches. The forms of the homogenized coefficients yield key theoretical insights into how large-scale dynamics arise from the small-scale features.

Monitoring Forest Change in Landscapes Under-Going Rapid Energy Development: Challenges and New Perspectives

Directory of Open Access Journals (Sweden)

Paul D. Pickell

2014-07-01

Full Text Available The accelerated development of energy resources around the world has substantially increased forest change related to oil and gas activities. In some cases, oil and gas activities are the primary catalyst of land-use change in forested landscapes. We discuss the challenges associated with characterizing ecological change related to energy resource development using North America as an exemplar. We synthesize the major impacts of energy development to forested ecosystems and offer new perspectives on how to detect and monitor anthropogenic disturbance during the Anthropocene. The disturbance of North American forests for energy development has resulted in persistent linear corridors, suppression of historical disturbance regimes, novel ecosystems, and the eradication of ecological memory. Characterizing anthropogenic disturbances using conventional patch-based disturbance measures will tend to underestimate the ecological impacts of energy development. Suitable indicators of anthropogenic impacts in forests should be derived from the integration of multi-scalar Earth observations. Relating these indicators to ecosystem condition will be a capstone in the progress toward monitoring forest change in landscapes undergoing rapid energy development.

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

Science.gov (United States)

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...

Non-equilibrium physics of neural networks for leaning, memory and decision making: landscape and flux perspectives

Science.gov (United States)

Wang, Jin

Cognitive behaviors are determined by underlying neural networks. Many brain functions, such as learning and memory, can be described by attractor dynamics. We developed a theoretical framework for global dynamics by quantifying the landscape associated with the steady state probability distributions and steady state curl flux, measuring the degree of non-equilibrium through detailed balance breaking. We found the dynamics and oscillations in human brains responsible for cognitive processes and physiological rhythm regulations are determined not only by the landscape gradient but also by the flux. We found that the flux is closely related to the degrees of the asymmetric connections in neural networks and is the origin of the neural oscillations. The neural oscillation landscape shows a closed-ring attractor topology. The landscape gradient attracts the network down to the ring. The flux is responsible for coherent oscillations on the ring. We suggest the flux may provide the driving force for associations among memories. Both landscape and flux determine the kinetic paths and speed of decision making. The kinetics and global stability of decision making are explored by quantifying the landscape topography through the barrier heights and the mean first passage time. The theoretical predictions are in agreement with experimental observations: more errors occur under time pressure. We quantitatively explored two mechanisms of the speed-accuracy tradeoff with speed emphasis and further uncovered the tradeoffs among speed, accuracy, and energy cost. Our results show an optimal balance among speed, accuracy, and the energy cost in decision making. We uncovered possible mechanisms of changes of mind and how mind changes improve performance in decision processes. Our landscape approach can help facilitate an understanding of the underlying physical mechanisms of cognitive processes and identify the key elements in neural networks.

Free energy landscape and multiple folding pathways of an H-type RNA pseudoknot.

Directory of Open Access Journals (Sweden)

Yunqiang Bian

Full Text Available How RNA sequences fold to specific tertiary structures is one of the key problems for understanding their dynamics and functions. Here, we study the folding process of an H-type RNA pseudoknot by performing a large-scale all-atom MD simulation and bias-exchange metadynamics. The folding free energy landscapes are obtained and several folding intermediates are identified. It is suggested that the folding occurs via multiple mechanisms, including a step-wise mechanism starting either from the first helix or the second, and a cooperative mechanism with both helices forming simultaneously. Despite of the multiple mechanism nature, the ensemble folding kinetics estimated from a Markov state model is single-exponential. It is also found that the correlation between folding and binding of metal ions is significant, and the bound ions mediate long-range interactions in the intermediate structures. Non-native interactions are found to be dominant in the unfolded state and also present in some intermediates, possibly hinder the folding process of the RNA.

The landscape of nonlinear structural dynamics: an introduction.

Science.gov (United States)

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

2015-09-28

Nonlinear behaviour is ever-present in vibrations and other dynamical motions of engineering structures. Manifestations of nonlinearity include amplitude-dependent natural frequencies, buzz, squeak and rattle, self-excited oscillation and non-repeatability. This article primarily serves as an extended introduction to a theme issue in which such nonlinear phenomena are highlighted through diverse case studies. More ambitiously though, there is another goal. Both the engineering context and the mathematical techniques that can be used to identify, analyse, control or exploit these phenomena in practice are placed in the context of a mind-map, which has been created through expert elicitation. This map, which is available in software through the electronic supplementary material, attempts to provide a practitioner's guide to what hitherto might seem like a vast and complex research landscape. © 2015 The Authors.

Comparing the Folding and Misfolding Energy Landscapes of Phosphoglycerate Kinase

OpenAIRE

Agocs, Gergely; Szabo, Bence T.; Koehler, Gottfried; Osvath, Szabolcs

2012-01-01

Partitioning of polypeptides between protein folding and amyloid formation is of outstanding pathophysiological importance. Using yeast phosphoglycerate kinase as model, here we identify the features of the energy landscape that decide the fate of the protein: folding or amyloidogenesis. Structure formation was initiated from the acid-unfolded state, and monitored by fluorescence from 10 ms to 20 days. Solvent conditions were gradually shifted between folding and amyloidogenesis, and the prop...

Statistical topography of fitness landscapes

OpenAIRE

Franke, Jasper

2011-01-01

Fitness landscapes are generalized energy landscapes that play an important conceptual role in evolutionary biology. These landscapes provide a relation between the genetic configuration of an organism and that organism’s adaptive properties. In this work, global topographical features of these fitness landscapes are investigated using theoretical models. The resulting predictions are compared to empirical landscapes. It is shown that these landscapes allow, at least with respe...

An energy landscape based approach for studying supercooled liquid and glassy thin films

Science.gov (United States)

Shah, Pooja; Mittal, Jeetain; Truskett, Thomas M.

2004-03-01

Materials in confined spaces are important in science and technology. Examples include biological fluids in membranes, liquids trapped in porous rocks, and thin-film materials used in high-resolution patterning technologies. However, few reliable rules exist to predict how the properties of materials will be affected by thin-film confinement. We have recently shown that the potential energy landscape formalism can be used to study, by both theory [1] and simulation [2], how the behavior of thin-film materials depends on sample dimensions and film-substrate interactions. Our landscape-based mean-field theory [1] can be used to study both the thermodynamic properties and the ideal glass transition of thin films. It predicts that, in the case of neutral or repulsive walls, the ideal glass transition temperature is lowered by decreasing film thickness. This is in qualitative agreement with experimental trends for the kinetic glass transition in confined fluids. Landscape-based approaches are also valuable for understanding the structural and mechanical properties of thin-film glasses. We demonstrate how the concept of an "equation of state of the energy landscape" [3] can be generalized to thin films [1, 2], where it gives insights into potential molecular mechanisms of tensile strength. [1] T. M. Truskett and V. Ganesan, J. Chem. Phys. 119, 1897-1900(2003); J. Mittal, P. Shah and T. M. Truskett, to be submitted to Langmuir. [2] P. Shah and T. M. Truskett, to be submitted to J. Phys. Chem. B. [3] S. Sastry, P. G. Debenedetti and F. H. Stillinger, Phys. Rev. E 56, 5533 (1997)

Discrete kinetic models from funneled energy landscape simulations.

Directory of Open Access Journals (Sweden)

Nicholas P Schafer

Full Text Available A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK. In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.

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

Energy Technology Data Exchange (ETDEWEB)

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.

Increasing connectivity between metapopulation ecology and landscape ecology.

Science.gov (United States)

Howell, Paige E; Muths, Erin; Hossack, Blake R; Sigafus, Brent H; Chandler, Richard B

2018-05-01

Metapopulation ecology and landscape ecology aim to understand how spatial structure influences ecological processes, yet these disciplines address the problem using fundamentally different modeling approaches. Metapopulation models describe how the spatial distribution of patches affects colonization and extinction, but often do not account for the heterogeneity in the landscape between patches. Models in landscape ecology use detailed descriptions of landscape structure, but often without considering colonization and extinction dynamics. We present a novel spatially explicit modeling framework for narrowing the divide between these disciplines to advance understanding of the effects of landscape structure on metapopulation dynamics. Unlike previous efforts, this framework allows for statistical inference on landscape resistance to colonization using empirical data. We demonstrate the approach using 11 yr of data on a threatened amphibian in a desert ecosystem. Occupancy data for Lithobates chiricahuensis (Chiricahua leopard frog) were collected on the Buenos Aires National Wildlife Refuge (BANWR), Arizona, USA from 2007 to 2017 following a reintroduction in 2003. Results indicated that colonization dynamics were influenced by both patch characteristics and landscape structure. Landscape resistance increased with increasing elevation and distance to the nearest streambed. Colonization rate was also influenced by patch quality, with semi-permanent and permanent ponds contributing substantially more to the colonization of neighboring ponds relative to intermittent ponds. Ponds that only hold water intermittently also had the highest extinction rate. Our modeling framework can be widely applied to understand metapopulation dynamics in complex landscapes, particularly in systems in which the environment between habitat patches influences the colonization process. © 2018 by the Ecological Society of America.

The free energy landscape of small molecule unbinding.

Directory of Open Access Journals (Sweden)

Danzhi Huang

2011-02-01

Full Text Available The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide and eleven (5-diethylamino-2-pentanone non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics of ligand unbinding.

Control landscapes for observable preparation with open quantum systems

International Nuclear Information System (INIS)

Wu Rebing; Pechen, Alexander; Rabitz, Herschel; Hsieh, Michael; Tsou, Benjamin

2008-01-01

A quantum control landscape is defined as the observable as a function(al) of the system control variables. Such landscapes were introduced to provide a basis to understand the increasing number of successful experiments controlling quantum dynamics phenomena. This paper extends the concept to encompass the broader context of the environment having an influence. For the case that the open system dynamics are fully controllable, it is shown that the control landscape for open systems can be lifted to the analysis of an equivalent auxiliary landscape of a closed composite system that contains the environmental interactions. This inherent connection can be analyzed to provide relevant information about the topology of the original open system landscape. Application to the optimization of an observable expectation value reveals the same landscape simplicity observed in former studies on closed systems. In particular, no false suboptimal traps exist in the system control landscape when seeking to optimize an observable, even in the presence of complex environments. Moreover, a quantitative study of the control landscape of a system interacting with a thermal environment shows that the enhanced controllability attainable with open dynamics significantly broadens the range of the achievable observable values over the control landscape

Dynamic Disturbance Processes Create Dynamic Lek Site Selection in a Prairie Grouse.

Directory of Open Access Journals (Sweden)

Torre J Hovick

Full Text Available It is well understood that landscape processes can affect habitat selection patterns, movements, and species persistence. These selection patterns may be altered or even eliminated as a result of changes in disturbance regimes and a concomitant management focus on uniform, moderate disturbance across landscapes. To assess how restored landscape heterogeneity influences habitat selection patterns, we examined 21 years (1991, 1993-2012 of Greater Prairie-Chicken (Tympanuchus cupido lek location data in tallgrass prairie with restored fire and grazing processes. Our study took place at The Nature Conservancy's Tallgrass Prairie Preserve located at the southern extent of Flint Hills in northeastern Oklahoma. We specifically addressed stability of lek locations in the context of the fire-grazing interaction, and the environmental factors influencing lek locations. We found that lek locations were dynamic in a landscape with interacting fire and grazing. While previous conservation efforts have treated leks as stable with high site fidelity in static landscapes, a majority of lek locations in our study (i.e., 65% moved by nearly one kilometer on an annual basis in this dynamic setting. Lek sites were in elevated areas with low tree cover and low road density. Additionally, lek site selection was influenced by an interaction of fire and patch edge, indicating that in recently burned patches, leks were located near patch edges. These results suggest that dynamic and interactive processes such as fire and grazing that restore heterogeneity to grasslands do influence habitat selection patterns in prairie grouse, a phenomenon that is likely to apply throughout the Greater Prairie-Chicken's distribution when dynamic processes are restored. As conservation moves toward restoring dynamic historic disturbance patterns, it will be important that siting and planning of anthropogenic structures (e.g., wind energy, oil and gas and management plans not view lek

Multivariable extrapolation of grand canonical free energy landscapes

Science.gov (United States)

Mahynski, Nathan A.; Errington, Jeffrey R.; Shen, Vincent K.

2017-12-01

We derive an approach for extrapolating the free energy landscape of multicomponent systems in the grand canonical ensemble, obtained from flat-histogram Monte Carlo simulations, from one set of temperature and chemical potentials to another. This is accomplished by expanding the landscape in a Taylor series at each value of the order parameter which defines its macrostate phase space. The coefficients in each Taylor polynomial are known exactly from fluctuation formulas, which may be computed by measuring the appropriate moments of extensive variables that fluctuate in this ensemble. Here we derive the expressions necessary to define these coefficients up to arbitrary order. In principle, this enables a single flat-histogram simulation to provide complete thermodynamic information over a broad range of temperatures and chemical potentials. Using this, we also show how to combine a small number of simulations, each performed at different conditions, in a thermodynamically consistent fashion to accurately compute properties at arbitrary temperatures and chemical potentials. This method may significantly increase the computational efficiency of biased grand canonical Monte Carlo simulations, especially for multicomponent mixtures. Although approximate, this approach is amenable to high-throughput and data-intensive investigations where it is preferable to have a large quantity of reasonably accurate simulation data, rather than a smaller amount with a higher accuracy.

Linking habitat selection to fitness-related traits in herbivores: the role of the energy landscape

Science.gov (United States)

Ryan A. Long; R. T. Bowyer; Warren P. Porter; Paul Mathewson; Kevin L. Monteith; Scott L. Findholt; Brian L. Dick; John G. Kie

2016-01-01

Animals may partially overcome environmental constraints on fitness by behaviorally adjusting their exposure to costs and supplies of energy. Few studies, however, have linked spatiotemporal variation in the energy landscape to behaviorally mediated measures of performance that ostensibly influence individual fitness. We hypothesized that strength of selection by North...

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

Science.gov (United States)

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. © 2015 John Wiley & Sons Ltd.

A Tale of Two Regions: Landscape Ecological Planning for Shale Gas Energy Futures

Science.gov (United States)

Murtha, T., Jr.; Schroth, O.; Orland, B.; Goldberg, L.; Mazurczyk, T.

2015-12-01

As we increasingly embrace deep shale gas deposits to meet global energy demands new and dispersed local and regional policy and planning challenges emerge. Even in regions with long histories of energy extraction, such as coal, shale gas and the infrastructure needed to produce the gas and transport it to market offers uniquely complex transformations in land use and landcover not previously experienced. These transformations are fast paced, dispersed and can overwhelm local and regional planning and regulatory processes. Coupled to these transformations is a structural confounding factor. While extraction and testing are carried out locally, regulation and decision-making is multilayered, often influenced by national and international factors. Using a geodesign framework, this paper applies a set of geospatial landscape ecological planning tools in two shale gas settings. First, we describe and detail a series of ongoing studies and tools that we have developed for communities in the Marcellus Shale region of the eastern United States, specifically the northern tier of Pennsylvania. Second, we apply a subset of these tools to potential gas development areas of the Fylde region in Lancashire, United Kingdom. For the past five years we have tested, applied and refined a set of place based and data driven geospatial models for forecasting, envisioning, analyzing and evaluating shale gas activities in northern Pennsylvania. These models are continuously compared to important landscape ecological planning challenges and priorities in the region, e.g. visual and cultural resource preservation. Adapting and applying these tools to a different landscape allow us to not only isolate and define important regulatory and policy exigencies in each specific setting, but also to develop and refine these models for broader application. As we continue to explore increasingly complex energy solutions globally, we need an equally complex comparative set of landscape ecological

Biodiversity and ecosystem functioning in dynamic landscapes

Science.gov (United States)

Brose, Ulrich; Hillebrand, Helmut

2016-01-01

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

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

Science.gov (United States)

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

A data-driven analysis of energy balance closure across FLUXNET research sites: The role of landscape scale heterogeneity

DEFF Research Database (Denmark)

Stoy, Paul C.; Mauder, Matthias; Foken, Thomas

2013-01-01

approached 1. These results suggest that landscape-level heterogeneity in vegetation and topography cannot be ignored as a contributor to incomplete energy balance closure at the flux network level, although net radiation measurements, biological energy assimilation, unmeasured storage terms......The energy balance at most surface-atmosphere flux research sites remains unclosed. The mechanisms underlying the discrepancy between measured energy inputs and outputs across the global FLUXNET tower network are still under debate. Recent reviews have identified exchange processes and turbulent...... motions at large spatial and temporal scales in heterogeneous landscapes as the primary cause of the lack of energy balance closure at some intensively-researched sites, while unmeasured storage terms cannot be ruled out as a dominant contributor to the lack of energy balance closure at many other sites...

Vacuum selection on axionic landscapes

International Nuclear Information System (INIS)

Wang, Gaoyuan; Battefeld, Thorsten

2016-01-01

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

Free energy landscape and molecular pathways of gas hydrate nucleation

Energy Technology Data Exchange (ETDEWEB)

Bi, Yuanfei; Porras, Anna; Li, Tianshu, E-mail: tsli@gwu.edu [Department of Civil and Environmental Engineering, George Washington University, Washington DC 20052 (United States)

2016-12-07

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p{sub B} histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p{sub B} histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

Free energy landscape and molecular pathways of gas hydrate nucleation

International Nuclear Information System (INIS)

Bi, Yuanfei; Porras, Anna; Li, Tianshu

2016-01-01

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

Free energy landscape and molecular pathways of gas hydrate nucleation.

Science.gov (United States)

Bi, Yuanfei; Porras, Anna; Li, Tianshu

2016-12-07

Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

Geomorpho-Landscapes

Science.gov (United States)

Farabollini, Piero; Lugeri, Francesca; Amadio, Vittorio

2014-05-01

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

Conserving agrobiodiversity amid global change, migration, and nontraditional livelihood networks: the dynamic uses of cultural landscape knowledge

Directory of Open Access Journals (Sweden)

Karl S. Zimmerer

2014-06-01

Full Text Available I examined agrobiodiversity in smallholder cultural landscapes with the goal of offering new insights into management and policy options for the resilience-based in situ conservation and social-ecological sustainability of local, food-producing crop types, i.e., landraces. I built a general, integrative approach to focus on both land use and livelihood functions of crop landraces in the context of nontraditional, migration-related livelihoods amid global change. The research involved a multimethod, case-study design focused on a cultural landscape of maize, i.e., corn, growing in the Andes of central Bolivia, which is a global hot spot for this crop's agrobiodiversity. Central questions included the following: (1 What are major agroecological functions and food-related services of the agrobiodiversity of Andean maize landraces, and how are they related to cultural landscapes and associated knowledge systems? (2 What are new migration-related livelihood groups, and how are their dynamic livelihoods propelled through global change, in particular international and national migration, linked to the use and cultural landscapes of agrobiodiversity? (3 What are management and policy options derived from the previous questions? Combined social-ecological services as both cultivation and food resources are found to function in relation to the cultural landscape. Results demonstrated major variations of maturation-based, phenologic traits and food-use properties that are cornerstones of the landrace-level agrobiodiversity of Andean maize. Knowledge of these parameters is widespread. Linkage of these production and consumption functions yields a major insight into dynamics of Andean maize agrobiodiversity. Concurrently, this smallholder cultural landscape has become increasingly dependent on new rural conditions, especially increased livelihood diversification and migration amid growing peri-urban influences. Viability of landrace-level maize

Is the fenamate group a polymorphophore?: contrasting the crystal energy landscapes of fenamic and tolfenamic acids

NARCIS (Netherlands)

Uzoh, O.G.; Cruz-Cabeza, A.J.; Price, S. L.

2012-01-01

The concept of a polymorphophore was investigated by contrasting the crystal energy landscapes of monomorphic fenamic acid (2-(phenylamino)-benzoic acid, FA) and one of its highly polymorphic derivatives, tolfenamic acid (2-[(3-chloro-2-methylphenyl)amino]-benzoic acid, TA). The crystal energy

Soil Redox Dynamics Vary with Landscape Position and Hydroperiod in the Pantanal Wetland Ecosystem

Science.gov (United States)

Couto, E. G.; Johnson, M. S.; Pinto-jr, O.; Leite, N. K.

2012-12-01

The Pantanal wetland ecosystem of central South America is the largest tropical wetland complex in the world. Nevertheless, biogeochemistry in the Pantanal is quite limited. A unimodal precipitation regime averages approximately 1200 mm y-1 during the six-month rainy season, leading to seasonal flooding on much, but not all, of the landscape. We investigated the impact of landscape position and hydroperiod on soil redox potential (Eh) in four research locations in the Northern Pantanal near Poconé, Mato Grosso: two locations subject to flooding (a flooded forest and a flooded scrub forest) and two locations with infrequent surface flooding (tree islands known as cordilheiras). Redox sensors were installed at 10 cm and 30 cm depths at each of the four locations with half-hourly data recorded over all hydro-periods (dry season, rising water, flood and falling water). Here we summarize results to date in this ongoing study. Reducing conditions were observed in response to both precipitation events saturating soil from the surface downward, as well as in response to regional flooding dynamics that saturate soil from below. These are helping to guide design of a study on methane dynamics in the Pantanal wetland complex.

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

Science.gov (United States)

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.

Past and future landscape dynamics in pasture-woodlands of the Swiss Jura Mountains under climate change

Directory of Open Access Journals (Sweden)

Alexander Peringer

2013-09-01

We present a refined version of the spatially explicit, dynamic simulation model WoodPaM with improved climate sensitivity of simulated vegetation. We investigate pasture-woodland dynamics by applying an innovative combination of retrospective simulations starting in the Middle Ages with prospective simulations following two climate change scenarios. The retrospective simulations demonstrate the strong dependency of the landscape mosaic on both climate and management. In high elevation mountain pastures, climate cooling during the Little Ice Age hindered simulated tree regeneration and reduced forage production of grasslands. Both led to an increase in open grassland and to a structural simplification of the landscape. In turn, climate warming afterwards showed the opposite effect. At lower elevations, high cattle stocking rates generally dominate simulated succession, leading to a slow development of quite homogenous landscapes whose structures are hardly affected by historical climate variability. Aerial photographs suggest that logging and windstorms critically shaped the current landscape, both homogenizing mosaic structures that emerge from selective grazing. Simulations of climate change scenarios suggest delayed but inevitable structural changes in the landscape mosaic and a temporary breakdown of the ecosystem service wood production. The population of currently dominating Norway spruce collapses due to simulated drought. Spruce is only slowly replaced either by beech under moderate warming or by Scots pine under extreme warming. In general, the shift in tree species dominance results in landscapes of less structural richness than today. In order to maintain the mosaic structure of pasture-woodlands, we recommend a future increase in cattle stocking on mountain pastures. The (re- introduction of mixed herds (cattle with horses, sheep, and goats could mitigate the simulated trend towards structural homogenization of the forest-grassland mosaic because

Landscape moderation of biodiversity patterns and processes - eight hypotheses.

Science.gov (United States)

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

2012-08-01

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

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

Science.gov (United States)

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. Copyright © 2017 Southern Society for Clinical Investigation. Published by Elsevier Inc. All rights reserved.

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

Science.gov (United States)

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.

Landscape predictions from cosmological vacuum selection

Energy Technology Data Exchange (ETDEWEB)

Bousso, Raphael; Bousso, Raphael; Yang, Sheng

2007-04-23

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

Landscape predictions from cosmological vacuum selection

International Nuclear Information System (INIS)

Bousso, Raphael; Yang, I-S.

2007-01-01

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

Energy landscapes shape microbial communities in hydrothermal systems on the Arctic Mid-Ocean Ridge.

Science.gov (United States)

Dahle, Håkon; Økland, Ingeborg; Thorseth, Ingunn H; Pederesen, Rolf B; Steen, Ida H

2015-07-01

Methods developed in geochemical modelling combined with recent advances in molecular microbial ecology provide new opportunities to explore how microbial communities are shaped by their chemical surroundings. Here, we present a framework for analyses of how chemical energy availability shape chemotrophic microbial communities in hydrothermal systems through an investigation of two geochemically different basalt-hosted hydrothermal systems on the Arctic Mid-Ocean Ridge: the Soria Moria Vent field (SMVF) and the Loki's Castle Vent Field (LCVF). Chemical energy landscapes were evaluated through modelling of the Gibbs energy from selected redox reactions under different mixing ratios between seawater and hydrothermal fluids. Our models indicate that the sediment-influenced LCVF has a much higher potential for both anaerobic and aerobic methane oxidation, as well as aerobic ammonium and hydrogen oxidation, than the SMVF. The modelled energy landscapes were used to develop microbial community composition models, which were compared with community compositions in environmental samples inside or on the exterior of hydrothermal chimneys, as assessed by pyrosequencing of partial 16S rRNA genes. We show that modelled microbial communities based solely on thermodynamic considerations can have a high predictive power and provide a framework for analyses of the link between energy availability and microbial community composition.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

Energy Technology Data Exchange (ETDEWEB)

Yang, Y. Isaac [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (China); Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871 (China); Biodynamic Optical Imaging Center, Peking University, Beijing 100871 (China)

2016-03-07

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ − ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

One-dimensional arrays of oscillators: Energy localization in thermal equilibrium

International Nuclear Information System (INIS)

Reigada, R.; Romero, A.H.; Sarmiento, A.; Lindenberg, K.

1999-01-01

All systems in thermal equilibrium exhibit a spatially variable energy landscape due to thermal fluctuations. Thus at any instant there is naturally a thermodynamically driven localization of energy in parts of the system relative to other parts of the system. The specific characteristics of the spatial landscape such as, for example, the energy variance, depend on the thermodynamic properties of the system and vary from one system to another. The temporal persistence of a given energy landscape, that is, the way in which energy fluctuations (high or low) decay toward the thermal mean, depends on the dynamical features of the system. We discuss the spatial and temporal characteristics of spontaneous energy localization in 1D anharmonic chains in thermal equilibrium. copyright 1999 American Institute of Physics

Quantum Adiabatic Optimization and Combinatorial Landscapes

Science.gov (United States)

Smelyanskiy, V. N.; Knysh, S.; Morris, R. D.

2003-01-01

In this paper we analyze the performance of the Quantum Adiabatic Evolution (QAE) algorithm on a variant of Satisfiability problem for an ensemble of random graphs parametrized by the ratio of clauses to variables, gamma = M / N. We introduce a set of macroscopic parameters (landscapes) and put forward an ansatz of universality for random bit flips. We then formulate the problem of finding the smallest eigenvalue and the excitation gap as a statistical mechanics problem. We use the so-called annealing approximation with a refinement that a finite set of macroscopic variables (verses only energy) is used, and are able to show the existence of a dynamic threshold gamma = gammad, beyond which QAE should take an exponentially long time to find a solution. We compare the results for extended and simplified sets of landscapes and provide numerical evidence in support of our universality ansatz.

Organic fields sustain weed metacommunity dynamics in farmland landscapes.

Science.gov (United States)

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.

LANDSCAPE ECOLOGICAL METHOD TO STUDY AGRICULTURAL VEGETATION: SOME EXAMPLES FROM THE PO VALLEY

Directory of Open Access Journals (Sweden)

E. GIGLIO

2006-01-01

Full Text Available Vegetation is the most important landscape component, as regards to its ability to catch solar energy and to transform it, but also to shape the landscape, to structure the space, to create the fit environment for different animal species, to contribute to the maintenance of a correct metastability level for the landscape, etc. It is a biological system which acts under the constraints of the principles of the System Theory and owns the same properties of any other living system: so, it is a complex adaptive, hierarchical, dynamic, dissipative, self-organizing, self-transcendent, autocatalytic, self-maintaining system and follows the non-equilibrium thermodynamic. Its ecological state can be investigated through the comparison between “gathered data” (pathology and “normal data” (physiology for analogous types of vegetation. The Biological Integrated School of Landscape Ecology provides an integrated methodology to define ecological threshold limits of the different Agricultural Landscape types and applies to agricultural vegetation the specific part of the new methodology already tested to studying forests (the Landscape Biological Survey of Vegetation. Ecological quality, better and worst parameters, biological territorial capacity of vegetated corridors, agricultural field, poplar groves, orchards and woody remnant patches are investigated. Some examples from diverse agricultural landscapes of the Po Valley will be discussed. KEY WORDS: agricultural landscape, vegetation, landscape ecology, landscape health, Biological Integrated Landscape Ecology, Landscape Biological Survey of vegetation.

LANDSCAPE ECOLOGICAL METHOD TO STUDY AGRICULTURAL VEGETATION: SOME EXAMPLES FROM THE PO VALLEY

Directory of Open Access Journals (Sweden)

E. GIGLIO

2006-05-01

Full Text Available Vegetation is the most important landscape component, as regards to its ability to catch solar energy and to transform it, but also to shape the landscape, to structure the space, to create the fit environment for different animal species, to contribute to the maintenance of a correct metastability level for the landscape, etc. It is a biological system which acts under the constraints of the principles of the System Theory and owns the same properties of any other living system: so, it is a complex adaptive, hierarchical, dynamic, dissipative, self-organizing, self-transcendent, autocatalytic, self-maintaining system and follows the non-equilibrium thermodynamic. Its ecological state can be investigated through the comparison between “gathered data” (pathology and “normal data” (physiology for analogous types of vegetation. The Biological Integrated School of Landscape Ecology provides an integrated methodology to define ecological threshold limits of the different Agricultural Landscape types and applies to agricultural vegetation the specific part of the new methodology already tested to studying forests (the Landscape Biological Survey of Vegetation. Ecological quality, better and worst parameters, biological territorial capacity of vegetated corridors, agricultural field, poplar groves, orchards and woody remnant patches are investigated. Some examples from diverse agricultural landscapes of the Po Valley will be discussed. KEY WORDS: agricultural landscape, vegetation, landscape ecology, landscape health, Biological Integrated Landscape Ecology, Landscape Biological Survey of vegetation.

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

Science.gov (United States)

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.

Algorithm for dealing with depressions in dynamic landscape evolution models

NARCIS (Netherlands)

Temme, A.J.A.M.; Schoorl, J.M.; Veldkamp, A.

2006-01-01

Depressions in landscapes function as buffers for water and sediment. A landscape with depressions has less runoff, less erosion and more sedimentation than a landscape without depressions. Sinks in digital elevation models (DEMs) can be existing features that correctly represent depressions in

Are there Traps in Quantum Control Landscapes?

International Nuclear Information System (INIS)

Pechen, Alexander N.; Tannor, David J.

2011-01-01

There has been great interest in recent years in quantum control landscapes. Given an objective J that depends on a control field ε the dynamical landscape is defined by the properties of the Hessian δ 2 J/δε 2 at the critical points δJ/δε=0. We show that contrary to recent claims in the literature the dynamical control landscape can exhibit trapping behavior due to the existence of special critical points and illustrate this finding with an example of a 3-level Λ system. This observation can have profound implications for both theoretical and experimental quantum control studies.

Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.

Science.gov (United States)

Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

2016-12-13

In recent work, we demonstrated that it is possible to obtain approximate representations of high-dimensional free energy surfaces with variationally enhanced sampling ( Shaffer, P.; Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci. , 2016 , 113 , 17 ). The high-dimensional spaces considered in that work were the set of backbone dihedral angles of a small peptide, Chignolin, and the high-dimensional free energy surface was approximated as the sum of many two-dimensional terms plus an additional term which represents an initial estimate. In this paper, we build on that work and demonstrate that we can calculate high-dimensional free energy surfaces of very high accuracy by incorporating additional terms. The additional terms apply to a set of collective variables which are more coarse than the base set of collective variables. In this way, it is possible to build hierarchical free energy surfaces, which are composed of terms that act on different length scales. We test the accuracy of these free energy landscapes for the proteins Chignolin and Trp-cage by constructing simple coarse-grained models and comparing results from the coarse-grained model to results from atomistic simulations. The approach described in this paper is ideally suited for problems in which the free energy surface has important features on different length scales or in which there is some natural hierarchy.

Cognitive radio networks dynamic resource allocation schemes

CERN Document Server

Wang, Shaowei

2014-01-01

This SpringerBrief presents a survey of dynamic resource allocation schemes in Cognitive Radio (CR) Systems, focusing on the spectral-efficiency and energy-efficiency in wireless networks. It also introduces a variety of dynamic resource allocation schemes for CR networks and provides a concise introduction of the landscape of CR technology. The author covers in detail the dynamic resource allocation problem for the motivations and challenges in CR systems. The Spectral- and Energy-Efficient resource allocation schemes are comprehensively investigated, including new insights into the trade-off

Characterizing European cultural landscapes: Accounting for structure, management intensity and value of agricultural and forest landscapes

NARCIS (Netherlands)

Tieskens, Koen F.; Schulp, Catharina J.E.; Levers, Christian; Lieskovský, Juraj; Kuemmerle, Tobias; Plieninger, Tobias; Verburg, Peter H.

Abstract Almost all rural areas in Europe have been shaped or altered by humans and can be considered cultural landscapes, many of which now are considered to entail valuable cultural heritage. Current dynamics in land management have put cultural landscapes under a huge pressure of agricultural

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

Science.gov (United States)

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

2012-05-01

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

Hessian eigenvalue distribution in a random Gaussian landscape

Science.gov (United States)

Yamada, Masaki; Vilenkin, Alexander

2018-03-01

The energy landscape of multiverse cosmology is often modeled by a multi-dimensional random Gaussian potential. The physical predictions of such models crucially depend on the eigenvalue distribution of the Hessian matrix at potential minima. In particular, the stability of vacua and the dynamics of slow-roll inflation are sensitive to the magnitude of the smallest eigenvalues. The Hessian eigenvalue distribution has been studied earlier, using the saddle point approximation, in the leading order of 1/ N expansion, where N is the dimensionality of the landscape. This approximation, however, is insufficient for the small eigenvalue end of the spectrum, where sub-leading terms play a significant role. We extend the saddle point method to account for the sub-leading contributions. We also develop a new approach, where the eigenvalue distribution is found as an equilibrium distribution at the endpoint of a stochastic process (Dyson Brownian motion). The results of the two approaches are consistent in cases where both methods are applicable. We discuss the implications of our results for vacuum stability and slow-roll inflation in the landscape.

Digital landscapes of imagination

OpenAIRE

Starlight Vattano

2014-01-01

Urban landscapes that exist in the expression of an imaginative sequence define their shape through the digital representation. These hyperreal dimensions, combine imagination and representation as constituents a new reality, which follows the utopian, suprematist and constructivist theories, where the two-dimensional dynamics is transformed into an infinite space in which the imagination creates new forms. Although interpretations of the urban landscape film, put in place a correspondence be...

Exploring the fitness landscape of poliovirus

Science.gov (United States)

Bianco, Simone; Acevedo, Ashely; Andino, Raul; Tang, Chao

2012-02-01

RNA viruses are known to display extraordinary adaptation capabilities to different environments, due to high mutation rates. Their very dynamical evolution is captured by the quasispecies concept, according to which the viral population forms a swarm of genetic variants linked through mutation, which cooperatively interact at a functional level and collectively contribute to the characteristics of the population. The description of the viral fitness landscape becomes paramount towards a more thorough understanding of the virus evolution and spread. The high mutation rate, together with the cooperative nature of the quasispecies, makes it particularly challenging to explore its fitness landscape. I will present an investigation of the dynamical properties of poliovirus fitness landscape, through both the adoption of new experimental techniques and theoretical models.

Determining landscape extent for succession and disturbance simulation modeling

Science.gov (United States)

Eva C. Karau; Robert E. Keane

2007-01-01

Dividing regions into manageable landscape units presents special problems in landscape ecology and land management. Ideally, a landscape should be large enough to capture a broad range of vegetation, environmental and disturbance dynamics, but small enough to be useful for focused management objectives. The purpose of this study was to determine the optimal landscape...

Impacts on the environment and landscape of new energy productions on farm parcels and buildings, Final report

International Nuclear Information System (INIS)

Pointereau, Ph.; Bochu, J.L.; Couturier, Ch.; Coulon, F.; Arnal, A.; Giorgis, S.

2009-01-01

This study aims at identifying positive and negative impacts of new energy productions implemented in farms on the environment (water, soil, biodiversity, space occupancy) and on landscapes, and at proposing techniques and regulations to strengthen positive consequences and to limit possible problems created by these energy productions. The considered productions are: trees apart from forest (hedges and copses), new farm energetic crops (Miscanthus for example), solar equipment (photovoltaic mounted on buildings or on ground, solar hot water and solar dryers), biogas production equipment, hydraulic micro-plants. The authors addressed the following environmental impacts: water (in quantity and quality), soils (quality, erosion risks), biodiversity, space occupancy (with respect to other activities), and landscape

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch

Science.gov (United States)

Cragnolini, Tristan; Chakraborty, Debayan; Šponer, Jiří; Derreumaux, Philippe; Pasquali, Samuela; Wales, David J.

2017-10-01

We explore the energy landscape for a four-fold telomere repeat, obtaining interconversion pathways between six experimentally characterised G-quadruplex topologies. The results reveal a multi-funnel system, with a variety of intermediate configurations and misfolded states. This organisation is identified with the intrinsically multi-functional nature of the system, suggesting a new paradigm for the classification of such biomolecules and clarifying issues regarding apparently conflicting experimental results.

Dynamic Gene-Resource Landscape Management of Norway Spruce: Combining Utilization and Conservation

Directory of Open Access Journals (Sweden)

Milan Lstibůrek

2017-10-01

Full Text Available Traditional gene-resource management programs for forest trees are long-term endeavors requiring sustained organizational commitment covering extensive landscapes. While successful in maintaining adaptation, genetic diversity and capturing traditional growth attributes gains, these programs are dependent on rigid methods requiring elaborate mating schemes, thus making them slow in coping with climate change challenges. Here, we review the significance of Norway spruce in the boreal region and its current management practices. Next, we discuss opportunities offered by novel technologies and, with the use of computer simulations, we propose and evaluate a dynamic landscape gene-resource management in Norway. Our suggested long-term management approach capitalizes on: (1 existing afforestation activities, natural crosses, and DNA-based pedigree assembly to create structured pedigree for evaluation, thus traditional laborious control crosses are avoided and (2 landscape level genetic evaluation, rather than localized traditional progeny trials, allowing for screening of adapted individuals across multiple environmental gradients under changing climate. These advantages lead to greater genetic response to selection in adaptive traits without the traditional breeding and testing scheme, facilitating conservation of genetic resources within the breeding population of the most important forest tree species in Norway. The use of in situ selection from proven material exposed to realistic conditions over vast territories has not been conducted in forestry before. Our proposed approach is in contrast to worldwide current programs, where genetic evaluation is constrained by the range of environments where testing is conducted, which may be insufficient to capture the broad environmental variation necessary to tackle adaptation under changing climate.

A Community Landscape Model of Pro-Environmental Behavior: The Effects of Landscape and Community Interaction on Residential Energy Behaviors in Two Pennsylvania Towns

Science.gov (United States)

Mainzer, Stephen P.

We are using more energy every year. Between 2001 and 2011, Pennsylvania residential electricity sales increased by two and a half times the number of new customers, accounting for almost one third of the state's total electricity consumption. Our ability to meet demand by acquiring new energy sources faces several challenges. Confusion surrounds the physical and economic accessibility of remaining fossil fuel sources. Immense land use requirements and subsequent environmental impacts challenge a total shift to renewable energy sources. The laws of thermodynamics limit the potential for new technology to efficiently convert raw energy to consumable sources. As a result, any rational strategy to meet future energy demands must involve conservation. Conservation is a pro-environmental behavior, an act intended to benefit the environment surrounding a person. I posit that a transdisciplinary model, the community landscape model of the pro-environmental behavior, unifies the conceptually analogous - yet disparate - fields of landscape, community, and behavior towards explaining residential energy conservation actions. Specifically, the study attempted to describe links between the physical environment, social environment, and conservation behaviors through a mixed-method framework. Two Pennsylvania townships - Spring and East Buffalo townships - were selected from an analysis of housing, electricity consumption, and land cover trends. Key informants from both townships informed the design of a survey instrument that captured the utility consumption, residential conservation actions, energy and environmental values, types and levels of community engagement, perceived barriers, and socio-demographic information from 107 randomly selected households. A mixed-method analysis produced evidence that place-based values and intention to participate in the community were significantly linked to lower utility consumption in households. People who cared deeply about their town

Food web assembly at the landscape scale : Using stable isotopes to reveal changes in trophic structure during succession

NARCIS (Netherlands)

Schrama, Maarten; Jouta, Jeltje; Berg, Matty P.; Olff, Han

Food webs are increasingly evaluated at the landscape scale, accounting for spatial interactions involving different nutrient and energy channels. Also, while long viewed as static, food webs are increasingly seen as dynamic entities that assemble during vegetation succession. The next necessary

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

Science.gov (United States)

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

2017-11-01

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.

Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.

Science.gov (United States)

Mansbach, Rachael A; Ferguson, Andrew L

2015-03-14

The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

What determines area burned in large landscapes? Insights from a decade of comparative landscape-fire modelling

Science.gov (United States)

Geoffrey J. Cary; Robert E. Keane; Mike D. Flannigan; Ian D. Davies; Russ A. Parsons

2015-01-01

Understanding what determines area burned in large landscapes is critical for informing wildland fire management in fire-prone environments and for representing fire activity in Dynamic Global Vegetation Models. For the past ten years, a group of landscape-fire modellers have been exploring the relative influence of key determinants of area burned in temperate and...

Modelling landslide dynamics in forested landscapes

NARCIS (Netherlands)

Claessens, L.F.G.

2005-01-01

The research resulting in this thesis covers the geological, geomorphological and landscape ecology related themes of the project 'Podzolisation under Kauri (Agathis australis): for better or worse?' supported by theNetherlands Organisation

Exploring the energy landscape of biopolymers using single molecule force spectroscopy and molecular simulations

OpenAIRE

Hyeon, Changbong

2010-01-01

In recent years, single molecule force techniques have opened a new avenue to decipher the folding landscapes of biopolymers by allowing us to watch and manipulate the dynamics of individual proteins and nucleic acids. In single molecule force experiments, quantitative analyses of measurements employing sound theoretical models and molecular simulations play central role more than any other field. With a brief description of basic theories for force mechanics and molecular simulation techniqu...

Understanding coupled natural and human systems on fire prone landscapes: integrating wildfire simulation into an agent based planning system.

Science.gov (United States)

Barros, Ana; Ager, Alan; Preisler, Haiganoush; Day, Michelle; Spies, Tom; Bolte, John

2015-04-01

Agent-based models (ABM) allow users to examine the long-term effects of agent decisions in complex systems where multiple agents and processes interact. This framework has potential application to study the dynamics of coupled natural and human systems where multiple stimuli determine trajectories over both space and time. We used Envision, a landscape based ABM, to analyze long-term wildfire dynamics in a heterogeneous, multi-owner landscape in Oregon, USA. Landscape dynamics are affected by land management policies, actors decisions, and autonomous processes such as vegetation succession, wildfire, or at a broader scale, climate change. Key questions include: 1) How are landscape dynamics influenced by policies and institutions, and 2) How do land management policies and actor decisions interact to produce intended and unintended consequences with respect to wildfire on fire-prone landscapes. Applying Envision to address these questions required the development of a wildfire module that could accurately simulate wildfires on the heterogeneous landscapes within the study area in terms of replicating historical fire size distribution, spatial distribution and fire intensity. In this paper we describe the development and testing of a mechanistic fire simulation system within Envision and application of the model on a 3.2 million fire prone landscape in central Oregon USA. The core fire spread equations use the Minimum Travel Time algorithm developed by M Finney. The model operates on a daily time step and uses a fire prediction system based on the relationship between energy release component and historical fires. Specifically, daily wildfire probabilities and sizes are generated from statistical analyses of historical fires in relation to daily ERC values. The MTT was coupled with the vegetation dynamics module in Envision to allow communication between the respective subsystem and effectively model fire effects and vegetation dynamics after a wildfire. Canopy and

Electrostatics, structure prediction, and the energy landscapes for protein folding and binding.

Science.gov (United States)

Tsai, Min-Yeh; Zheng, Weihua; Balamurugan, D; Schafer, Nicholas P; Kim, Bobby L; Cheung, Margaret S; Wolynes, Peter G

2016-01-01

While being long in range and therefore weakly specific, electrostatic interactions are able to modulate the stability and folding landscapes of some proteins. The relevance of electrostatic forces for steering the docking of proteins to each other is widely acknowledged, however, the role of electrostatics in establishing specifically funneled landscapes and their relevance for protein structure prediction are still not clear. By introducing Debye-Hückel potentials that mimic long-range electrostatic forces into the Associative memory, Water mediated, Structure, and Energy Model (AWSEM), a transferable protein model capable of predicting tertiary structures, we assess the effects of electrostatics on the landscapes of thirteen monomeric proteins and four dimers. For the monomers, we find that adding electrostatic interactions does not improve structure prediction. Simulations of ribosomal protein S6 show, however, that folding stability depends monotonically on electrostatic strength. The trend in predicted melting temperatures of the S6 variants agrees with experimental observations. Electrostatic effects can play a range of roles in binding. The binding of the protein complex KIX-pKID is largely assisted by electrostatic interactions, which provide direct charge-charge stabilization of the native state and contribute to the funneling of the binding landscape. In contrast, for several other proteins, including the DNA-binding protein FIS, electrostatics causes frustration in the DNA-binding region, which favors its binding with DNA but not with its protein partner. This study highlights the importance of long-range electrostatics in functional responses to problems where proteins interact with their charged partners, such as DNA, RNA, as well as membranes. © 2015 The Protein Society.

Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

Directory of Open Access Journals (Sweden)

Bhattacharyya Moitrayee

2010-08-01

Full Text Available Abstract Background One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results In this study, we have explored the ligand induced conformational changes in H.pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H.pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co-operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in

From climate-smart agriculture to climate-smart landscapes

Directory of Open Access Journals (Sweden)

Scherr Sara J

2012-08-01

Full Text Available Abstract Background For agricultural systems to achieve climate-smart objectives, including improved food security and rural livelihoods as well as climate change adaptation and mitigation, they often need to be take a landscape approach; they must become ‘climate-smart landscapes’. Climate-smart landscapes operate on the principles of integrated landscape management, while explicitly incorporating adaptation and mitigation into their management objectives. Results An assessment of climate change dynamics related to agriculture suggests that three key features characterize a climate-smart landscape: climate-smart practices at the field and farm scale; diversity of land use across the landscape to provide resilience; and management of land use interactions at landscape scale to achieve social, economic and ecological impacts. To implement climate-smart agricultural landscapes with these features (that is, to successfully promote and sustain them over time, in the context of dynamic economic, social, ecological and climate conditions requires several institutional mechanisms: multi-stakeholder planning, supportive landscape governance and resource tenure, spatially-targeted investment in the landscape that supports climate-smart objectives, and tracking change to determine if social and climate goals are being met at different scales. Examples of climate-smart landscape initiatives in Madagascar’s Highlands, the African Sahel and Australian Wet Tropics illustrate the application of these elements in contrasting contexts. Conclusions To achieve climate-smart landscape initiatives widely and at scale will require strengthened technical capacities, institutions and political support for multi-stakeholder planning, governance, spatial targeting of investments and multi-objective impact monitoring.

Persistence and diversity of directional landscape connectivity improves biomass pulsing in expanding and contracting wetlands

Science.gov (United States)

Yurek, Simeon; DeAngelis, Don; Trexler, Joel C.; Klassen, Stephen; Larsen, Laurel G.

2016-01-01

In flood-pulsed ecosystems, hydrology and landscape structure mediate transfers of energy up the food chain by expanding and contracting in area, enabling spatial expansion and growth of fish populations during rising water levels, and subsequent concentration during the drying phase. Connectivity of flooded areas is dynamic as waters rise and fall, and is largely determined by landscape geomorphology and anisotropy. We developed a methodology for simulating fish dispersal and concentration on spatially-explicit, dynamic floodplain wetlands with pulsed food web dynamics, to evaluate how changes in connectivity through time contribute to the concentration of fish biomass that is essential for higher trophic levels. The model also tracks a connectivity index (DCI) over different compass directions to see if fish biomass dynamics can be related in a simple way to topographic pattern. We demonstrate the model for a seasonally flood-pulsed, oligotrophic system, the Everglades, where flow regimes have been greatly altered. Three dispersing populations of functional fish groups were simulated with empirically-based dispersal rules on two landscapes, and two twelve-year time series of managed water levels for those areas were applied. The topographies of the simulations represented intact and degraded ridge-and-slough landscapes (RSL). Simulation results showed large pulses of biomass concentration forming during the onset of the drying phase, when water levels were falling and fish began to converge into the sloughs. As water levels fell below the ridges, DCI declined over different directions, closing down dispersal lanes, and fish density spiked. Persistence of intermediate levels of connectivity on the intact RSL enabled persistent concentration events throughout the drying phase. The intact landscape also buffered effects of wet season population growth. Water level reversals on both landscapes negatively affected fish densities by depleting fish populations without

Forest dynamics.

Science.gov (United States)

Frelich, Lee

2016-01-01

Forest dynamics encompass changes in stand structure, species composition, and species interactions with disturbance and environment over a range of spatial and temporal scales. For convenience, spatial scale is defined as individual tree, neighborhood, stand, and landscape. Whether a given canopy-leveling disturbance will initiate a sequence of development in structure with little change in composition or initiate an episode of succession depends on a match or mismatch, respectively, with traits of the dominant tree species that allow the species to survive disturbance. When these match, certain species-disturbance type combinations lock in a pattern of stand and landscape dynamics that can persist for several generations of trees; thus, dominant tree species regulate, as well as respond to, disturbance. A complex interaction among tree species, neighborhood effects, disturbance type and severity, landform, and soils determines how stands of differing composition form and the mosaic of stands that compose the landscape. Neighborhood effects (e.g., serotinous seed rain, sprouting, shading, leaf-litter chemistry, and leaf-litter physical properties) operate at small spatial extents of the individual tree and its neighbors but play a central role in forest dynamics by contributing to patch formation at stand scales and dynamics of the entire landscape. Dominance by tree species with neutral to negative neighborhood effects leads to unstable landscape dynamics in disturbance-prone regions, wherein most stands are undergoing succession; stability can only occur under very low-severity disturbance regimes. Dominance by species with positive effects leads to stable landscape dynamics wherein only a small proportion of stands undergo succession at any one time. Positive neighborhood effects are common in temperate and boreal zones, whereas negative effects are more common in tropical climates. Landscapes with positive dynamics have alternate categories of dynamics

Management effectiveness and land cover change in dynamic cultural landscapes-assessing a central European biosphere reserve

DEFF Research Database (Denmark)

Ohnesorge, B.; Plieninger, Tobias; Hostert, P.

2013-01-01

Protected areas are a central pillar of efforts to safeguard biodiversity and ecosystem services, but their contribution to the conservation and management of European cultural landscapes that have complex spatial-temporal dynamics is unclear. The conservation strategy of biosphere reserves aims...... at integrating biodiversity and ecosystem service conservation with economic development by designating zones of differing protection and use intensities. It is applied worldwide to protect and manage valuable cultural landscapes. Using the example of a German biosphere reserve, we developed a framework...... in the reserve's core, buffer, and transition zones and in a surrounding reference area by means of a geographical information system. (Un-)desirable key processes related to management aims were defined and compared for the various zones. We found that-despite an overall land cover persistence of approximately...

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

Science.gov (United States)

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.

Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin.

Science.gov (United States)

Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

2016-02-02

The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin.

Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

Science.gov (United States)

Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

2016-01-01

The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin. PMID:26787868

Co-designing energy landscapes: Application of participatory mapping and geographic information systems in the exploration of low carbon futures

NARCIS (Netherlands)

Stremke, S.; Picchi, Paolo

2017-01-01

The chapter begins with a literature review of energy potential mapping, ecosystem services (ES) assessment and participatory mapping (PM). PM is a key technique to conduct tradeoff analysis while co-designing sustainable energy landscapes (SEL) with local communities. Stakeholders, among others,

Funneled potential and flux landscapes dictate the stabilities of both the states and the flow: Fission yeast cell cycle.

Directory of Open Access Journals (Sweden)

Xiaosheng Luo

2017-09-01

Full Text Available Using fission yeast cell cycle as an example, we uncovered that the non-equilibrium network dynamics and global properties are determined by two essential features: the potential landscape and the flux landscape. These two landscapes can be quantified through the decomposition of the dynamics into the detailed balance preserving part and detailed balance breaking non-equilibrium part. While the funneled potential landscape is often crucial for the stability of the single attractor networks, we have uncovered that the funneled flux landscape is crucial for the emergence and maintenance of the stable limit cycle oscillation flow. This provides a new interpretation of the origin for the limit cycle oscillations: There are many cycles and loops existed flowing through the state space and forming the flux landscapes, each cycle with a probability flux going through the loop. The limit cycle emerges when a loop stands out and carries significantly more probability flux than other loops. We explore how robustness ratio (RR as the gap or steepness versus averaged variations or roughness of the landscape, quantifying the degrees of the funneling of the underlying potential and flux landscapes. We state that these two landscapes complement each other with one crucial for stabilities of states on the cycle and the other crucial for the stability of the flow along the cycle. The flux is directly related to the speed of the cell cycle. This allows us to identify the key factors and structure elements of the networks in determining the stability, speed and robustness of the fission yeast cell cycle oscillations. We see that the non-equilibriumness characterized by the degree of detailed balance breaking from the energy pump quantified by the flux is the cause of the energy dissipation for initiating and sustaining the replications essential for the origin and evolution of life. Regulating the cell cycle speed is crucial for designing the prevention and curing

Golf-course and funnel energy landscapes: Protein folding concepts in martensites

Science.gov (United States)

Shankaraiah, N.

2017-06-01

We use protein folding energy landscape concepts such as golf course and funnel to study re-equilibration in athermal martensites under systematic temperature quench Monte Carlo simulations. On quenching below a transition temperature, the seeded high-symmetry parent-phase austenite that converts to the low-symmetry product-phase martensite, through autocatalytic twinning or elastic photocopying, has both rapid conversions and incubation delays in the temperature-time-transformation phase diagram. We find the rapid (incubation delays) conversions at low (high) temperatures arises from the presence of large (small) size of golf-course edge that has the funnel inside for negative energy states. In the incubating state, the strain structure factor enters into the Brillouin-zone golf course through searches for finite transitional pathways which close off at the transition temperature with Vogel-Fulcher divergences that are insensitive to Hamiltonian energy scales and log-normal distributions, as signatures of dominant entropy barriers. The crossing of the entropy barrier is identified through energy occupancy distributions, Monte Carlo acceptance fractions, heat emission, and internal work.

Conjugate gradient filtering of instantaneous normal modes, saddles on the energy landscape, and diffusion in liquids.

Science.gov (United States)

Chowdhary, J; Keyes, T

2002-02-01

Instantaneous normal modes (INM's) are calculated during a conjugate-gradient (CG) descent of the potential energy landscape, starting from an equilibrium configuration of a liquid or crystal. A small number (approximately equal to 4) of CG steps removes all the Im-omega modes in the crystal and leaves the liquid with diffusive Im-omega which accurately represent the self-diffusion constant D. Conjugate gradient filtering appears to be a promising method, applicable to any system, of obtaining diffusive modes and facilitating INM theory of D. The relation of the CG-step dependent INM quantities to the landscape and its saddles is discussed.

The landscape genetics of infectious disease emergence and spread.

Science.gov (United States)

Biek, Roman; Real, Leslie A

2010-09-01

The spread of parasites is inherently a spatial process often embedded in physically complex landscapes. It is therefore not surprising that infectious disease researchers are increasingly taking a landscape genetics perspective to elucidate mechanisms underlying basic ecological processes driving infectious disease dynamics and to understand the linkage between spatially dependent population processes and the geographic distribution of genetic variation within both hosts and parasites. The increasing availability of genetic information on hosts and parasites when coupled to their ecological interactions can lead to insights for predicting patterns of disease emergence, spread and control. Here, we review research progress in this area based on four different motivations for the application of landscape genetics approaches: (i) assessing the spatial organization of genetic variation in parasites as a function of environmental variability, (ii) using host population genetic structure as a means to parameterize ecological dynamics that indirectly influence parasite populations, for example, gene flow and movement pathways across heterogeneous landscapes and the concurrent transport of infectious agents, (iii) elucidating the temporal and spatial scales of disease processes and (iv) reconstructing and understanding infectious disease invasion. Throughout this review, we emphasize that landscape genetic principles are relevant to infection dynamics across a range of scales from within host dynamics to global geographic patterns and that they can also be applied to unconventional 'landscapes' such as heterogeneous contact networks underlying the spread of human and livestock diseases. We conclude by discussing some general considerations and problems for inferring epidemiological processes from genetic data and try to identify possible future directions and applications for this rapidly expanding field.

The importance of on-site evaluation for placing renewable energy in the landscape: A case study of the Búrfell wind farm (Iceland

Directory of Open Access Journals (Sweden)

Frantál Bohumil

2017-12-01

Full Text Available Using a case study of the Búrfell wind farm project, a large wind farm proposed in the Central Highlands of Iceland, the authors attempt to provide new insights into the factors shaping subjective landscape perceptions and attitudes to renewable energy developments, and into alternative methods that may be used for their assessment. The research was based on an on-site visit and actual experience of the place, investigated using a combination of mental mapping, the technique of the semantic differential and a questionnaire survey. The results show that participants visiting a landscape and using all sensory organs in combination with mental mapping, can reveal more important information than using only ‘laboratory’ methods with static photographs. The results suggest that the perception of landscape is highly subjective. Those perceiving the landscape as more open, homogenous, industrial, unfamiliar and resilient also consider it more compatible with wind turbines. The perception of the landscape’s compatibility with wind turbines proved to be a dominant factor shaping attitudes towards the project. The acceptance of wind turbines is not, however, inconsistent with the perception of landscape as beautiful, wild and unique. Participants from more densely populated countries and countries with a developed wind energy industry were more tolerant of wind turbines in the Icelandic landscape.

Approximate scaling properties of RNA free energy landscapes

Science.gov (United States)

Baskaran, S.; Stadler, P. F.; Schuster, P.

1996-01-01

RNA free energy landscapes are analysed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size distribution, and the scaling of the curve length measured with different yard stick lengths are used to describe the structure of these "time series". Although they are stationary by construction, we find that their local behavior is consistent with both AR(1) and self-affine processes. Random walks confined to excursion sets (i.e., with the restriction that the fitness value exceeds a certain threshold at each step) exhibit essentially the same statistics as free random walks. We find that an AR(1) time series is in general approximately self-affine on timescales up to approximately the correlation length. We present an empirical relation between the correlation parameter rho of the AR(1) model and the exponents characterizing self-affinity.

Simple solvable energy-landscape model that shows a thermodynamic phase transition and a glass transition.

Science.gov (United States)

Naumis, Gerardo G

2012-06-01

When a liquid melt is cooled, a glass or phase transition can be obtained depending on the cooling rate. Yet, this behavior has not been clearly captured in energy-landscape models. Here, a model is provided in which two key ingredients are considered in the landscape, metastable states and their multiplicity. Metastable states are considered as in two level system models. However, their multiplicity and topology allows a phase transition in the thermodynamic limit for slow cooling, while a transition to the glass is obtained for fast cooling. By solving the corresponding master equation, the minimal speed of cooling required to produce the glass is obtained as a function of the distribution of metastable states.

Shifts in wind energy potential following land-use driven vegetation dynamics in complex terrain.

Science.gov (United States)

Fang, Jiannong; Peringer, Alexander; Stupariu, Mihai-Sorin; Pǎtru-Stupariu, Ileana; Buttler, Alexandre; Golay, Francois; Porté-Agel, Fernando

2018-10-15

Many mountainous regions with high wind energy potential are characterized by multi-scale variabilities of vegetation in both spatial and time dimensions, which strongly affect the spatial distribution of wind resource and its time evolution. To this end, we developed a coupled interdisciplinary modeling framework capable of assessing the shifts in wind energy potential following land-use driven vegetation dynamics in complex mountain terrain. It was applied to a case study area in the Romanian Carpathians. The results show that the overall shifts in wind energy potential following the changes of vegetation pattern due to different land-use policies can be dramatic. This suggests that the planning of wind energy project should be integrated with the land-use planning at a specific site to ensure that the expected energy production of the planned wind farm can be reached over its entire lifetime. Moreover, the changes in the spatial distribution of wind and turbulence under different scenarios of land-use are complex, and they must be taken into account in the micro-siting of wind turbines to maximize wind energy production and minimize fatigue loads (and associated maintenance costs). The proposed new modeling framework offers, for the first time, a powerful tool for assessing long-term variability in local wind energy potential that emerges from land-use change driven vegetation dynamics over complex terrain. Following a previously unexplored pathway of cause-effect relationships, it demonstrates a new linkage of agro- and forest policies in landscape development with an ultimate trade-off between renewable energy production and biodiversity targets. Moreover, it can be extended to study the potential effects of micro-climatic changes associated with wind farms on vegetation development (growth and patterning), which could in turn have a long-term feedback effect on wind resource distribution in mountainous regions. Copyright © 2018 Elsevier B.V. All rights

Evidence and opportunities for integrating landscape ecology into natural resource planning across multiple-use landscapes

Science.gov (United States)

Trammel, E. Jamie; Carter, Sarah; Haby, Travis S.; Taylor, Jason J.

2018-01-01

Enhancing natural resource management has been a focus of landscape ecology since its inception, but numerous authors argue that landscape ecology has not yet been effective in achieving the underlying goal of planning and designing sustainable landscapes. We developed nine questions reflecting the application of fundamental research topics in landscape ecology to the landscape planning process and reviewed two recent landscape-scale plans in western North America for evidence of these concepts in plan decisions. Both plans considered multiple resources, uses, and values, including energy development, recreation, conservation, and protection of cultural and historic resources. We found that land use change and multiscale perspectives of resource uses and values were very often apparent in planning decisions. Pattern-process relationships, connectivity and fragmentation, ecosystem services, landscape history, and climate change were reflected less frequently. Landscape sustainability was considered only once in the 295 decisions reviewed, and outputs of landscape models were not referenced. We suggest six actionable opportunities for further integrating landscape ecology concepts into landscape planning efforts: 1) use landscape sustainability as an overarching goal, 2) adopt a broad ecosystem services framework, 3) explore the role of landscape history more comprehensively, 4) regularly consider and accommodate potential effects of climate change, 5) use landscape models to support plan decisions, and 6) promote a greater presence of landscape ecologists within agencies that manage large land bases and encourage active involvement in agency planning efforts. Together these actions may improve the defensibility, durability, and sustainability of landscape plan decisions.

A cavitation transition in the energy landscape of simple cohesive liquids and glasses

International Nuclear Information System (INIS)

Altabet, Y. Elia; Debenedetti, Pablo G.; Stillinger, Frank H.

2016-01-01

In particle systems with cohesive interactions, the pressure-density relationship of the mechanically stable inherent structures sampled along a liquid isotherm (i.e., the equation of state of an energy landscape) will display a minimum at the Sastry density ρ S . The tensile limit at ρ S is due to cavitation that occurs upon energy minimization, and previous characterizations of this behavior suggested that ρ S is a spinodal-like limit that separates all homogeneous and fractured inherent structures. Here, we revisit the phenomenology of Sastry behavior and find that it is subject to considerable finite-size effects, and the development of the inherent structure equation of state with system size is consistent with the finite-size rounding of an athermal phase transition. What appears to be a continuous spinodal-like point at finite system sizes becomes discontinuous in the thermodynamic limit, indicating behavior akin to a phase transition. We also study cavitation in glassy packings subjected to athermal expansion. Many individual expansion trajectories averaged together produce a smooth equation of state, which we find also exhibits features of finite-size rounding, and the examples studied in this work give rise to a larger limiting tension than for the corresponding landscape equation of state.

Dynamic Changes of Landscape Pattern and Vulnerability Analysis in Qingyi River Basin

Science.gov (United States)

Li, Ziwei; Xie, Chaoying; He, Xiaohui; Guo, Hengliang; Wang, Li

2017-11-01

Environmental vulnerability research is one of the core areas of global environmental change research. Over the past 10 years, ecologically fragile zones or transition zones had been significantly affected by environmental degradation and climate change and human activities. In this paper, we analyzed the spatial and temporal changes of landscape pattern and landscape vulnerability degree in Qingyi River Basin by calculating the landscape sensitivity index and landscape restoration degree index based on Landsat images of 2005, 2010 and 2015. The results showed that: (1) The top conversion area was farmland, woodland and grassland area decreased, city land and rural residential land increased fastest. (2) The fragility of the landscape pattern along the Qingyi River gradually increased between 2005 and 2015, the downstream area was influenced by the influence of human activities. (3) Landscape pattern changes and fragility are mainly affected by urbanization. These findings are helpful for understanding the evolution of landscape pattern as well as urban ecology, which both have significant implications for urban planning and minimize the potential environmental impacts of urbanization in Qingyi River Basin.

Smart Landscape. The architecture of the "micro smart grid" as a resilience strategy for landscape

OpenAIRE

Garbarini, Giulia

2018-01-01

“Smart Landscape”, starting from energy devices for the management and distribution of electricity resources, tends to define a possible vision of landscape. The main structure and process are based on the architecture of a “micro smart grid”, which is generally associated with urban energy grids and districts, but may become a figurative reference for new forms of landscape, such as “Smart Landscape”. The output of the research would be to show how the main strategies of “Smart Landsc...

Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

Energy Technology Data Exchange (ETDEWEB)

Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)

2015-01-14

We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.

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

Science.gov (United States)

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.

The environmental benefits of cellulosic energy crops at a landscape scale

International Nuclear Information System (INIS)

Graham, R.L.; Liu, W.; English, B.C.

1995-01-01

The objective of this paper is to present a broad overview of the potential environmental impacts of biomass energy from energy crops--particularly the cellulosic energy crops current under development. For this discussion, the term energy crop refers to a crop grown primarily to create feedstock for either making biofuels such as ethanol or burning in a heat or electricity generation facility. Cellulosic energy crops are designed to be used in cellulose-based ethanol conversion processes (as opposed to starch or sugar-based ethanol conversion processes). As more cellulose can be produced per hectare of land than can sugar or starch, the cellulose-based ethanol conversion process is a more efficient sue of land for ethanol production. Assessing the environmental impacts of biomass energy from energy crops is complex because the environmental impact of using biomass for energy must be considered in the context of alternative energy options while the environmental impact of producing biomass from energy crops must be considered in the context of alternative land-uses. Using biomass-derived energy can reduce greenhouse gas emissions or increase them; growing biomass energy crops can enhance soil fertility or degrade it. Without knowing the context of the biomass energy, one can say little about its specific environmental impacts. The primary focus of this paper is an evaluation of the environmental impacts of growing cellulosic energy crops especially at the landscape or regional scale. However, to set the stage for this discussion, the authors begin by comparing the environmental advantages and disadvantages of biomass-derived energy relative to other energy alternatives such as coal, hydropower, nuclear power, oil/gasoline, natural gas and photovoltaics

Landscape genetics of high mountain frog metapopulations

Science.gov (United States)

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

2010-01-01

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

Role of renewable energy policies in energy dependency in Finland: System dynamics approach

International Nuclear Information System (INIS)

Aslani, Alireza; Helo, Petri; Naaranoja, Marja

2014-01-01

Highlights: • A system dynamics model for evaluating renewable energy policies on dependency is proposed. • The model considers the role of diversification on dependency and security of energy supply in Finland. • Dependency on imported sources will decrease depends on the defined scenarios in Finland. - Abstract: Objective: We discuss the role of diversification on dependency and security of energy supply. A system dynamics model with especial focus on the role of renewable energy resources (as a portfolio) on Finland’s energy dependency is developed. The purpose is also to cover a part of research gap exists in the system dynamics modeling of energy security investigations. Methods: A causal loops diagram and a system dynamics model evaluate Finnish scenarios of renewable energy policies. The analysis describes the relationship between dynamic factors such as RE encouragement packages, dependency, and energy demand. Results: A causal loops diagram and a system dynamics model evaluate three different Finnish scenarios of renewable energy policies by 2020. Conclusion: Analysis shows that despite 7% electricity/heat consumption growth by 2020 in Finland, dependency on imported sources will decrease between 1% and 7% depend on the defined scenarios. Practice Implications: The proposed model not only helps decision makers to test their scenarios related to renewable energy polices, it can be implemented by other countries

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

Science.gov (United States)

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

Sustaining ecosystem services in cultural landscapes

Directory of Open Access Journals (Sweden)

Tobias Plieninger

2014-06-01

Full Text Available Classical conservation approaches focus on the man-made degradation of ecosystems and tend to neglect the social-ecological values that human land uses have imprinted on many environments. Throughout the world, ingenious land-use practices have generated unique cultural landscapes, but these are under pressure from agricultural intensification, land abandonment, and urbanization. In recent years, the cultural landscapes concept has been broadly adopted in science, policy, and management. The interest in both outstanding and vernacular landscapes finds expression in the UNESCO World Heritage Convention, the European Landscape Convention, and the IUCN Protected Landscape Approach. These policies promote the protection, management, planning, and governance of cultural landscapes. The ecosystem services approach is a powerful framework to guide such efforts, but has rarely been applied in landscape research and management. With this paper, we introduce a special feature that aims to enhance the theoretical, empirical and practical knowledge of how to safeguard the resilience of ecosystem services in cultural landscapes. It concludes (1 that the usefulness of the ecosystem services approach to the analysis and management of cultural landscapes should be reviewed more critically; (2 that conventional ecosystem services assessment needs to be complemented by socio-cultural valuation; (3 that cultural landscapes are inherently changing, so that a dynamic view on ecosystem services and a focus on drivers of landscape change are needed; and (4 that managing landscapes for ecosystem services provision may benefit from a social-ecological resilience perspective.

Investigation of the Structures and Energy Landscapes of Thiocyanate-Water Clusters

Directory of Open Access Journals (Sweden)

Lewis C. Smeeton

2017-03-01

Full Text Available The Basin Hopping search method is used to find the global minima (GM and map the energy landscapes of thiocyanate-water clusters, (SCN−(H2On with 3–50 water molecules, with empirical potentials describing the ion-water and water-water interactions. (It should be noted that beyond n = 23, the lowest energy structures were only found in 1 out of 8 searches so they are unlikely to be the true GM but are indicative low energy structures. As for pure water clusters, the low energy isomers of thiocyanate-water clusters show a preponderance of fused water cubes and pentagonal prisms, with the weakly solvated thiocyanate ion lying on the surface, replacing two water molecules along an edge of a water polyhedron and with the sulfur atom in lower coordinated sites than nitrogen. However, by comparison with Density Functional Theory (DFT calculations, the empirical potential is found to overestimate the strength of the thiocyanate-water interaction, especially O–H⋯S, with low energy DFT structures having lower coordinate N and (especially S atoms than for the empirical potential. In the case of these finite ion-water clusters, the chaotropic (“disorder-making” thiocyanate ion weakens the water cluster structure but the water molecule arrangement is not significantly changed.

Sinks without borders: Snowshoe hare dynamics in a complex landscape

Science.gov (United States)

Griffin, Paul C.; Mills, L. Scott

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.

Landscapes of human evolution: models and methods of tectonic geomorphology and the reconstruction of hominin landscapes.

Science.gov (United States)

Bailey, Geoffrey N; Reynolds, Sally C; King, Geoffrey C P

2011-03-01

This paper examines the relationship between complex and tectonically active landscapes and patterns of human evolution. We show how active tectonics can produce dynamic landscapes with geomorphological and topographic features that may be critical to long-term patterns of hominin land use, but which are not typically addressed in landscape reconstructions based on existing geological and paleoenvironmental principles. We describe methods of representing topography at a range of scales using measures of roughness based on digital elevation data, and combine the resulting maps with satellite imagery and ground observations to reconstruct features of the wider landscape as they existed at the time of hominin occupation and activity. We apply these methods to sites in South Africa, where relatively stable topography facilitates reconstruction. We demonstrate the presence of previously unrecognized tectonic effects and their implications for the interpretation of hominin habitats and land use. In parts of the East African Rift, reconstruction is more difficult because of dramatic changes since the time of hominin occupation, while fossils are often found in places where activity has now almost ceased. However, we show that original, dynamic landscape features can be assessed by analogy with parts of the Rift that are currently active and indicate how this approach can complement other sources of information to add new insights and pose new questions for future investigation of hominin land use and habitats. Copyright © 2010 Elsevier Ltd. All rights reserved.

Time Series Analysis of Energy Production and Associated Landscape Fragmentation in the Eagle Ford Shale Play

Science.gov (United States)

Pierre, Jon Paul; Young, Michael H.; Wolaver, Brad D.; Andrews, John R.; Breton, Caroline L.

2017-11-01

Spatio-temporal trends in infrastructure footprints, energy production, and landscape alteration were assessed for the Eagle Ford Shale of Texas. The period of analysis was over four 2-year periods (2006-2014). Analyses used high-resolution imagery, as well as pipeline data to map EF infrastructure. Landscape conditions from 2006 were used as baseline. Results indicate that infrastructure footprints varied from 94.5 km2 in 2008 to 225.0 km2 in 2014. By 2014, decreased land-use intensities (ratio of land alteration to energy production) were noted play-wide. Core-area alteration by period was highest (3331.6 km2) in 2008 at the onset of play development, and increased from 582.3 to 3913.9 km2 by 2014, though substantial revegetation of localized core areas was observed throughout the study (i.e., alteration improved in some areas and worsened in others). Land-use intensity in the eastern portion of the play was consistently lower than that in the western portion, while core alteration remained relatively constant east to west. Land alteration from pipeline construction was 65 km2 for all time periods, except in 2010 when alteration was recorded at 47 km2. Percent of total alteration from well-pad construction increased from 27.3% in 2008 to 71.5% in 2014. The average number of wells per pad across all 27 counties increased from 1.15 to 1.7. This study presents a framework for mapping landscape alteration from oil and gas infrastructure development. However, the framework could be applied to other energy development programs, such as wind or solar fields, or any other regional infrastructure development program.

Quasi-potential and Two-Scale Large Deviation Theory for Gillespie Dynamics

KAUST Repository

Li, Tiejun

2016-01-07

The construction of energy landscape for bio-dynamics is attracting more and more attention recent years. In this talk, I will introduce the strategy to construct the landscape from the connection to rare events, which relies on the large deviation theory for Gillespie-type jump dynamics. In the application to a typical genetic switching model, the two-scale large deviation theory is developed to take into account the fast switching of DNA states. The comparison with other proposals are also discussed. We demonstrate different diffusive limits arise when considering different regimes for genetic translation and switching processes.

Structure prediction of nanoclusters; a direct or a pre-screened search on the DFT energy landscape?

Science.gov (United States)

Farrow, M R; Chow, Y; Woodley, S M

2014-10-21

The atomic structure of inorganic nanoclusters obtained via a search for low lying minima on energy landscapes, or hypersurfaces, is reported for inorganic binary compounds: zinc oxide (ZnO)n, magnesium oxide (MgO)n, cadmium selenide (CdSe)n, and potassium fluoride (KF)n, where n = 1-12 formula units. The computational cost of each search is dominated by the effort to evaluate each sample point on the energy landscape and the number of required sample points. The effect of changing the balance between these two factors on the success of the search is investigated. The choice of sample points will also affect the number of required data points and therefore the efficiency of the search. Monte Carlo based global optimisation routines (evolutionary and stochastic quenching algorithms) within a new software package, viz. Knowledge Led Master Code (KLMC), are employed to search both directly and after pre-screening on the DFT energy landscape. Pre-screening includes structural relaxation to minimise a cheaper energy function - based on interatomic potentials - and is found to improve significantly the search efficiency, and typically reduces the number of DFT calculations required to locate the local minima by more than an order of magnitude. Although the choice of functional form is important, the approach is robust to small changes to the interatomic potential parameters. The computational cost of initial DFT calculations of each structure is reduced by employing Gaussian smearing to the electronic energy levels. Larger (KF)n nanoclusters are predicted to form cuboid cuts from the rock-salt phase, but also share many structural motifs with (MgO)n for smaller clusters. The transition from 2D rings to 3D (bubble, or fullerene-like) structures occur at a larger cluster size for (ZnO)n and (CdSe)n. Differences between the HOMO and LUMO energies, for all the compounds apart from KF, are in the visible region of the optical spectrum (2-3 eV); KF lies deep in the UV region

A methodology for creating greenways through multidisciplinary sustainable landscape planning.

Science.gov (United States)

Pena, Selma Beatriz; Abreu, Maria Manuela; Teles, Rui; Espírito-Santo, Maria Dalila

2010-01-01

This research proposes a methodology for defining greenways via sustainable planning. This approach includes the analysis and discussion of culture and natural processes that occur in the landscape. The proposed methodology is structured in three phases: eco-cultural analysis; synthesis and diagnosis; and proposal. An interdisciplinary approach provides an assessment of the relationships between landscape structure and landscape dynamics, which are essential to any landscape management or land use. The landscape eco-cultural analysis provides a biophysical, dynamic (geomorphologic rate), vegetation (habitats from directive 92/43/EEC) and cultural characterisation. The knowledge obtained by this analysis then supports the definition of priority actions to stabilise the landscape and the management measures for the habitats. After the analysis and diagnosis phases, a proposal for the development of sustainable greenways can be achieved. This methodology was applied to a study area of the Azambuja Municipality in the Lisbon Metropolitan Area (Portugal). The application of the proposed methodology to the study area shows that landscape stability is crucial for greenway users in order to appreciate the landscape and its natural and cultural elements in a sustainable and healthy way, both by cycling or by foot. A balanced landscape will increase the value of greenways and in return, they can develop socio-economic activities with benefits for rural communities. Copyright 2009 Elsevier Ltd. All rights reserved.

DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates.

Directory of Open Access Journals (Sweden)

Ignacia Echeverria

2015-02-01

Full Text Available DNA molecules are highly charged semi-flexible polymers that are involved in a wide variety of dynamical processes such as transcription and replication. Characterizing the binding landscapes around DNA molecules is essential to understanding the energetics and kinetics of various biological processes. We present a curvilinear coordinate system that fully takes into account the helical symmetry of a DNA segment. The latter naturally allows to characterize the spatial organization and motions of ligands tracking the minor or major grooves, in a motion reminiscent of sliding. Using this approach, we performed umbrella sampling (US molecular dynamics (MD simulations to calculate the three-dimensional potentials of mean force (3D-PMFs for a Na+ cation and for methyl guanidinium, an arginine analog. The computed PMFs show that, even for small ligands, the free energy landscapes are complex. In general, energy barriers of up to ~5 kcal/mol were measured for removing the ligands from the minor groove, and of ~1.5 kcal/mol for sliding along the minor groove. We shed light on the way the minor groove geometry, defined mainly by the DNA sequence, shapes the binding landscape around DNA, providing heterogeneous environments for recognition by various ligands. For example, we identified the presence of dissociation points or "exit ramps" that naturally would terminate sliding. We discuss how our findings have important implications for understanding how proteins and ligands associate and slide along DNA.

A PM7 dynamic residue-ligand interactions energy landscape of the BACE1 inhibitory pathway by hydroxyethylamine compounds. Part I: The flap closure process.

Science.gov (United States)

Gueto-Tettay, Carlos; Martinez-Consuegra, Alejandro; Zuchniarz, Joshua; Gueto-Tettay, Luis Roberto; Drosos-Ramírez, Juan Carlos

2017-09-01

BACE1 is an enzyme of scientific interest because it participates in the progression of Alzheimer's disease. Hydroxyethylamines (HEAs) are a family of compounds which exhibit inhibitory activity toward BACE1 at a nanomolar level, favorable pharmacokinetic properties and oral bioavailability. The first step in the inhibition of BACE1 by HEAs consists of their entrance into the protease active site and the resultant conformational change in the protein, from Apo to closed form. These two conformations differ in the position of an antiparallel loop (called the flap) which covers the entrance to the catalytic site. For BACE1, closure of this flap is vital to its catalytic activity and to inhibition of the enzyme due to the new interactions thereby formed with the ligand. In the present study a dynamic energy landscape of residue-ligand interaction energies (ReLIE) measured for 112 amino acids in the BACE1 active site and its immediate vicinity during the closure of the flap induced by 8 HEAs of different inhibitory power is presented. A total of 6.272 million ReLIE calculations, based on the PM7 semiempirical method, provided a deep and quantitative view of the first step in the inhibition of the aspartyl protease. The information suggests that residues Asp93, Asp289, Thr292, Thr293, Asn294 and Arg296 are anchor points for the ligand, accounting for approximately 45% of the total protein-ligand interaction. Additionally, flap closure improved the BACE1-HEA interaction by around 25%. Furthermore, the inhibitory activity of HEAs could be related to the capacity of these ligands to form said anchor point interactions and maintain them over time: the lack of some of these anchor interactions delayed flap closure or impeded it completely, or even caused the flap to reopen. The methodology employed here could be used as a tool to evaluate future structural modifications which lead to improvements in the favorability and stability of BACE1-HEA ReLIEs, aiding in the design of

Conserving Coherence and Storing Energy during Internal Conversion: Photoinduced Dynamics of cis- and trans-Azobenzene Radical Cations

KAUST Repository

Munkerup, Kristin

2017-10-24

Light harvesting via energy storage in azobenzene has been a key topic for decades, and the process of energy distribution over the molecular degrees of freedom following photoexcitation remains to be understood. Dynamics of a photoexcited system can exhibit high degrees of non-ergodicity when it is driven by just a few degrees of freedom. Typically, an internal conversion leads to the loss of such localization of dynamics, as the intramolecular energy becomes statistically redistributed over all molecular degrees of freedom. Here, we present a unique case where the excitation energy remains localized even subsequent to internal conversion. Strong-field ionization is used to prepare cis- and trans-azobenzene radical cations on the D1 surface with little excess energy, at the equilibrium neutral geometry. These D1 ions are preferably formed because in this case D1 and D0 switch place in the presence of the strong laser field. The post-ionization dynamics is dictated by the potential energy landscape. The D1 surface is steep downhill along the cis/trans isomerization coordinate and towards a common minimum shared by the two isomers in the region of D1/D0 conical intersection. Coherent cis/trans torsional motion along this coordinate is manifested in the ion transients by a cosine modulation. In this scenario, D0 becomes populated with molecules that are energized mainly along the cis-trans isomerization coordinate, with the kinetic energy above the cis-trans inter-conversion barrier. These activated azobenzene molecules easily cycle back and forth along the D0 surface, and give rise to several periods of modulated signal before coherence is lost. This persistent localization of the internal energy during internal conversion is provided by the steep downhill potential energy surface, small initial internal energy content, and a strong hole-lone pair interaction that drives the molecule along the cis-trans isomerization coordinate to facilitate the transition between

Sustaining ecosystem services in cultural landscapes

DEFF Research Database (Denmark)

Plieninger, Tobias; van der Horst, Dan; Schleyer, Christian

2014-01-01

Classical conservation approaches focus on the man-made degradation of ecosystems and tend to neglect the socialecological values that human land uses have imprinted on many environments. Throughout the world, ingenious land-use practices have generated unique cultural landscapes...... research and management. With this paper, we introduce a special feature that aims to enhance the theoretical, empirical and practical knowledge of how to safeguard the resilience of ecosystem services in cultural landscapes. It concludes (1) that the usefulness of the ecosystem services approach...... to the analysis and management of cultural landscapes should be reviewed more critically; (2) that conventional ecosystem services assessment needs to be complemented by socio-cultural valuation; (3) that cultural landscapes are inherently changing, so that a dynamic view on ecosystem services and a focus...

Tensor modes on the string theory landscape

International Nuclear Information System (INIS)

Westphal, Alexander

2012-06-01

We attempt an estimate for the distribution of the tensor mode fraction r over the landscape of vacua in string theory. The dynamics of eternal inflation and quantum tunneling lead to a kind of democracy on the landscape, providing no bias towards large-field or small-field inflation regardless of the class of measure. The tensor mode fraction then follows the number frequency distributions of inflationary mechanisms of string theory over the landscape. We show that an estimate of the relative number frequencies for small-field vs large-field inflation, while unattainable on the whole landscape, may be within reach as a regional answer for warped Calabi-Yau flux compactifications of type IIB string theory.

Tensor modes on the string theory landscape

Energy Technology Data Exchange (ETDEWEB)

Westphal, Alexander

2012-06-15

We attempt an estimate for the distribution of the tensor mode fraction r over the landscape of vacua in string theory. The dynamics of eternal inflation and quantum tunneling lead to a kind of democracy on the landscape, providing no bias towards large-field or small-field inflation regardless of the class of measure. The tensor mode fraction then follows the number frequency distributions of inflationary mechanisms of string theory over the landscape. We show that an estimate of the relative number frequencies for small-field vs large-field inflation, while unattainable on the whole landscape, may be within reach as a regional answer for warped Calabi-Yau flux compactifications of type IIB string theory.

Soil erosion dynamics response to landscape pattern

NARCIS (Netherlands)

Ouyang, W.; Skidmore, A.K.; Hao, F.; Wang, T.

2010-01-01

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

Contingent Diversity on Anthropic Landscapes

Directory of Open Access Journals (Sweden)

William Balée

2010-02-01

Full Text Available Behaviorally modern human beings have lived in Amazonia for thousands of years. Significant dynamics in species turnovers due to human-mediated disturbance were associated with the ultimate emergence and expansion of agrarian technologies in prehistory. Such disturbances initiated primary and secondary landscape transformations in various locales of the Amazon region. Diversity in these locales can be understood by accepting the initial premise of contingency, expressed as unprecedented human agency and human history. These effects can be accessed through the archaeological record and in the study of living languages. In addition, landscape transformation can be demonstrated in the study of traditional knowledge (TK. One way of elucidating TK distinctions between anthropic and nonanthropic landscapes concerns elicitation of differential labeling of these landscapes and more significantly, elicitation of the specific contents, such as trees, occurring in these landscapes. Freelisting is a method which can be used to distinguish the differential species compositions of landscapes resulting from human-mediated disturbance vs. those which do not evince records of human agency and history. The TK of the Ka’apor Indians of Amazonian Brazil as revealed in freelisting exercises shows differentiation of anthropogenic from high forests as well as a recognition of diversity in the anthropogenic forests. This suggests that the agents of human-mediated disturbance and landscape transformation in traditional Amazonia encode diversity and contingency into their TK, which encoding reflects past cultural influence on landscape and society over time.

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

Science.gov (United States)

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...

Obsolete or resurgent? The International Energy Agency in a changing global landscape

International Nuclear Information System (INIS)

Van de Graaf, Thijs

2012-01-01

Founded in response to the 1973 oil shock, the International Energy Agency (IEA) is arguably still the most important multilateral organization for energy-importing countries. Yet, the global geopolitical landscape has changed considerably since the IEA's creation. The rise of new energy consumers, new energy-related challenges and new international energy forums prompt a rethink of the agency's current role and institutional design. This article seeks to contribute to the recent debate on the future role of the IEA by examining specific drivers, avenues and constraints for institutional reform. The method used is SWOT analysis, which allows to summarize the key factors emanating from an assessment of an organization's internal characteristics (strengths and weaknesses) and its external environment (opportunities and threats). Building on this SWOT analysis, the article formulates a strategy for the IEA to remain the focal point in global energy governance. Key elements of this strategy include: stronger engagement with new consumers, rapprochement with OPEC, becoming a leading voice in the energy transition, and changing the agency's internal governance practices. - Highlights: ► The IEA is challenged by the rise of new consumers, threats and organizations. ► Assessment of the agency’s internal characteristics and external environment. ► The IEA needs to step up its outreach policy and fully embrace sustainable energy.

Visualizing Energy on Target: Molecular Dynamics Simulations

Science.gov (United States)

2017-12-01

ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

The dynamic landscape of gene regulation during Bombyx mori oogenesis.

Science.gov (United States)

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.

Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.

Science.gov (United States)

Meng, Yilin; Roux, Benoît

2015-08-11

The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost.

Accounting for Landscape Heterogeneity Improves Spatial Predictions of Tree Vulnerability to Drought

Science.gov (United States)

Schwantes, A. M.; Parolari, A.; Swenson, J. J.; Johnson, D. M.; Domec, J. C.; Jackson, R. B.; Pelak, N. F., III; Porporato, A. M.

2017-12-01

Globally, as climate change continues, forest vulnerability to droughts and heatwaves is increasing, but vulnerability differs regionally and locally depending on landscape position. However, most models used in forecasting forest responses to heatwaves and droughts do not incorporate relevant spatial processes. To improve predictions of spatial tree vulnerability, we employed a non-linear stochastic model of soil moisture dynamics across a landscape, accounting for spatial differences in aspect, topography, and soils. Our unique approach integrated plant hydraulics and landscape processes, incorporating effects from lateral redistribution of water using a topographic index and radiation and temperature differences attributable to aspect. Across a watershed in central Texas we modeled dynamic water stress for a dominant tree species, Juniperus ashei. We compared our results to a detailed spatial dataset of drought-impacted areas (>25% canopy loss) derived from remote sensing during the severe 2011 drought. We then projected future dynamic water stress through the 21st century using climate projections from 10 global climate models under two scenarios, and compared models with and without landscape heterogeneity. Within this watershed, 42% of J. ashei dominated systems were impacted by the 2011 drought. Modeled dynamic water stress tracked these spatial patterns of observed drought-impacted areas. Total accuracy increased from 59%, when accounting only for soil variability, to 73% when including lateral redistribution of water and radiation and temperature effects. Dynamic water stress was projected to increase through the 21st century, with only minimal buffering from the landscape. During the hotter and more severe droughts projected in the 21st century, up to 90% of the watershed crossed a dynamic water stress threshold associated with canopy loss in 2011. Favorable microsites may exist across a landscape where trees can persist; however, if future droughts are

Dynamics of one-dimensional domain walls interacting with disorder potential

International Nuclear Information System (INIS)

Krusin-Elbaum, L.; Shibauchi, T.; Argyle, B.; Gignac, L.; Zabel, T.; Weller, D.

2001-01-01

Dynamics of 1D perpendicular-anisotropy domain walls in a few monolayer-thin Co films is imaged by polar Kerr microscopy. When domain walls, driven by a square-pulsed magnetic fields, travel through a random disordered potential landscape, they display Gaussian-distributed roughness characteristic of this landscape. Average velocity of the domain wall driven by a constant magnetic field strongly depends on a strain field which modifies (increases) the elastic energy of the wall and reduces the wall velocity

Tuning Surface Energy Landscapes in Metallic Quantum Films using Alkali Adsorbates

Science.gov (United States)

Khajetoorians, Alexander; Qin, Shengyong; Zhu, Wenguang; Eisele, Holger; Zhang, Zhenyu; Shih, Chih-Kang

2008-03-01

Quantum confinement shows a strong interplay with growth and kinetics in thin metal systems where the Fermi wavelength has a special relationship to the surface normal lattice constant. In the case of Pb/Si(111) systems, this relationship reveals an interesting thickness-dependent bilayer oscillation in the density of states and surface energy up to a phase. In this paper, we report on a novel effect: tuning of the energy landscape of a flat-top quantum Pb mesa using Cs adsorbates. Using STM/STS, we show that depositing Cs adsorbates on a thin Pb mesa promotes quantum stable Pb nanoislands on preferentially unstable thicknesses. Thickness-dependent nanoisland densities show a strong bilayer oscillation correlating with quantum stability. By modifying the Cs coverage on the mesa surface, we can tune the lateral size distribution of the nanoislands and the overall amplitude of the island density oscillation. Nanoisland formation is linked to a step decoration of Cs adatoms along the step edge of the nanoisland.

Landscape Sustainability in a Sonoran Desert City

Directory of Open Access Journals (Sweden)

Chris A. Martin

2008-01-01

Full Text Available The objective of this paper is to discuss concepts of landscape sustainability in the Phoenix metropolitan area. Phoenix is situated in the greater Salt River Valley of the lower Sonoran Desert in the southwest United States. In this paper I use the ecological frameworks of ecosystem services and resiliency as a metric for understanding landscape sustainability. An assessment of landscape sustainability performance benchmarks were made by surveying research findings of scientists affiliated with the Central Arizona Phoenix Long Term Ecological Research Project (CAP LTER. In Phoenix, present day emphases on cultural, aesthetic, and habitat formation ecosystem services within an arid ecoregion of low natural resilience coupled to a complex matrix of socioeconomic stratification, excessive landscape water use and pruning practices has had the undesired effect of degrading landscape sustainability. This has been measured as mixed patterns of plant diversity and human-altered patterns of carbon regulation, microclimate control, and trophic dynamics. In the future, sustainable residential landscaping in desert cities such as Phoenix may be fostered through use of water-conserving irrigation technologies, oasis-style landscape design motifs, recycling of landscape green waste, and conservative plant pruning strategies.

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

Science.gov (United States)

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

2017-08-01

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. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Free energy landscape and cooperatively rearranging region in a hard sphere glass

Science.gov (United States)

Yoshidome, Takashi; Yoshimori, Akira; Odagaki, Takashi

2007-08-01

Exploiting the density functional theory, we calculate the free energy landscape (FEL) of the hard sphere glass in three dimensions. From the FEL, we estimate the number of the particles in the cooperatively rearranging region (CRR). We find that the density dependence of the number of the particles in the CRR is expressed as a power law function of the density. Analyzing the relaxation process in the CRR, we also find that the string motion is the elementary process for the structural relaxation, which leads to the natural definition of the simultaneously rearranging region as the particles displaced in the string motion.

Soil fertility dynamics in a semiarid basin: impact of scale level in weighing the effect of the landscape variables

International Nuclear Information System (INIS)

Ruiz-Navarro, A.; Barbera, G. G.; Albaladejo, J.

2009-01-01

Arid and semi-arid Mediterranean soils are particularly sensitive to degradation processes, and soil fertility could play important role in restoration/conservation practices. Our objective was to study the relationships between soil and landscape at different scales in order to understand the main drivers of soil fertility on a semiarid catchment. A stratified sampling plan was carried out to take soil and landscape representative variability. Multivariate statistic techniques were used to elucidate the relationship between both. The results showed that soil fertility are positively related with density of vegetation and topographical conditions favourable to soil moisture at small scale, while negatively with topographical factors that contributed erosion dynamic on ero debility lithologies at medium and large scale. (Author) 8 refs.

Computational design of RNAs with complex energy landscapes.

Science.gov (United States)

Höner zu Siederdissen, Christian; Hammer, Stefan; Abfalter, Ingrid; Hofacker, Ivo L; Flamm, Christoph; Stadler, Peter F

2013-12-01

RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computed efficiently, RNA molecules are amenable not only to in vitro and in vivo selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state structure has received considerable attention for nearly two decades, there have been few efforts to design RNAs that can switch between distinct prescribed conformations. We introduce a user-friendly tool for designing RNA sequences that fold into multiple target structures. The underlying algorithm makes use of a combination of graph coloring and heuristic local optimization to find sequences whose energy landscapes are dominated by the prescribed conformations. A flexible interface allows the specification of a wide range of design goals. We demonstrate that bi- and tri-stable "switches" can be designed easily with moderate computational effort for the vast majority of compatible combinations of desired target structures. RNAdesign is freely available under the GPL-v3 license. Copyright © 2013 Wiley Periodicals, Inc.

Global attractors and extinction dynamics of cyclically competing species.

Science.gov (United States)

Rulands, Steffen; Zielinski, Alejandro; Frey, Erwin

2013-05-01

Transitions to absorbing states are of fundamental importance in nonequilibrium physics as well as ecology. In ecology, absorbing states correspond to the extinction of species. We here study the spatial population dynamics of three cyclically interacting species. The interaction scheme comprises both direct competition between species as in the cyclic Lotka-Volterra model, and separated selection and reproduction processes as in the May-Leonard model. We show that the dynamic processes leading to the transient maintenance of biodiversity are closely linked to attractors of the nonlinear dynamics for the overall species' concentrations. The characteristics of these global attractors change qualitatively at certain threshold values of the mobility and depend on the relative strength of the different types of competition between species. They give information about the scaling of extinction times with the system size and thereby the stability of biodiversity. We define an effective free energy as the negative logarithm of the probability to find the system in a specific global state before reaching one of the absorbing states. The global attractors then correspond to minima of this effective energy landscape and determine the most probable values for the species' global concentrations. As in equilibrium thermodynamics, qualitative changes in the effective free energy landscape indicate and characterize the underlying nonequilibrium phase transitions. We provide the complete phase diagrams for the population dynamics and give a comprehensive analysis of the spatio-temporal dynamics and routes to extinction in the respective phases.

Fort Collins Science Center Ecosystem Dynamics Branch

Science.gov (United States)

Wilson, Jim; Melcher, C.; Bowen, Z.

2009-01-01

Complex natural resource issues require understanding a web of interactions among ecosystem components that are (1) interdisciplinary, encompassing physical, chemical, and biological processes; (2) spatially complex, involving movements of animals, water, and airborne materials across a range of landscapes and jurisdictions; and (3) temporally complex, occurring over days, weeks, or years, sometimes involving response lags to alteration or exhibiting large natural variation. Scientists in the Ecosystem Dynamics Branch of the U.S. Geological Survey, Fort Collins Science Center, investigate a diversity of these complex natural resource questions at the landscape and systems levels. This Fact Sheet describes the work of the Ecosystems Dynamics Branch, which is focused on energy and land use, climate change and long-term integrated assessments, herbivore-ecosystem interactions, fire and post-fire restoration, and environmental flows and river restoration.

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

Science.gov (United States)

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...

Using graph approach for managing connectivity in integrative landscape modelling

Science.gov (United States)

Rabotin, Michael; Fabre, Jean-Christophe; Libres, Aline; Lagacherie, Philippe; Crevoisier, David; Moussa, Roger

2013-04-01

In cultivated landscapes, a lot of landscape elements such as field boundaries, ditches or banks strongly impact water flows, mass and energy fluxes. At the watershed scale, these impacts are strongly conditionned by the connectivity of these landscape elements. An accurate representation of these elements and of their complex spatial arrangements is therefore of great importance for modelling and predicting these impacts.We developped in the framework of the OpenFLUID platform (Software Environment for Modelling Fluxes in Landscapes) a digital landscape representation that takes into account the spatial variabilities and connectivities of diverse landscape elements through the application of the graph theory concepts. The proposed landscape representation consider spatial units connected together to represent the flux exchanges or any other information exchanges. Each spatial unit of the landscape is represented as a node of a graph and relations between units as graph connections. The connections are of two types - parent-child connection and up/downstream connection - which allows OpenFLUID to handle hierarchical graphs. Connections can also carry informations and graph evolution during simulation is possible (connections or elements modifications). This graph approach allows a better genericity on landscape representation, a management of complex connections and facilitate development of new landscape representation algorithms. Graph management is fully operational in OpenFLUID for developers or modelers ; and several graph tools are available such as graph traversal algorithms or graph displays. Graph representation can be managed i) manually by the user (for example in simple catchments) through XML-based files in easily editable and readable format or ii) by using methods of the OpenFLUID-landr library which is an OpenFLUID library relying on common open-source spatial libraries (ogr vector, geos topologic vector and gdal raster libraries). Open

Governing Forest Landscape Restoration: Cases from Indonesia

Directory of Open Access Journals (Sweden)

Cora van Oosten

2014-05-01

Full Text Available Forest landscape restoration includes both the planning and implementation of measures to restore degraded forests within the perspective of the wider landscape. Governing forest landscape restoration requires fundamental considerations about the conceptualisation of forested landscapes and the types of restoration measures to be taken, and about who should be engaged in the governance process. A variety of governance approaches to forest landscape restoration exist, differing in both the nature of the object to be governed and the mode of governance. This paper analyses the nature and governance of restoration in three cases of forest landscape restoration in Indonesia. In each of these cases, both the original aim for restoration and the initiators of the process differ. The cases also differ in how deeply embedded they are in formal spatial planning mechanisms at the various political scales. Nonetheless, the cases show similar trends. All cases show a dynamic process of mobilising the landscape’s stakeholders, plus a flexible process of crafting institutional space for conflict management, negotiation and decision making at the landscape level. As a result, the landscape focus changed over time from reserved forests to forested mosaic lands. The cases illustrate that the governance of forest landscape restoration should not be based on strict design criteria, but rather on a flexible governance approach that stimulates the creation of novel public-private institutional arrangements at the landscape level.

Drawing time : The representation of change and dynamics in Dutch landscape architectural practice after 1985

NARCIS (Netherlands)

van Dooren, N.

2017-01-01

Landscape architect design involves drawings. The relation between drawing and new landscape seems evident, but is complex and fascinating, due to the particularities of drawings, of landscape and of landscape architecture. Landscape is essentially a time-based medium -think of the seasons (cyclical

Energy Efficient Routing Algorithms in Dynamic Optical Core Networks with Dual Energy Sources

DEFF Research Database (Denmark)

Wang, Jiayuan; Fagertun, Anna Manolova; Ruepp, Sarah Renée

2013-01-01

This paper proposes new energy efficient routing algorithms in optical core networks, with the application of solar energy sources and bundled links. A comprehensive solar energy model is described in the proposed network scenarios. Network performance in energy savings, connection blocking...... probability, resource utilization and bundled link usage are evaluated with dynamic network simulations. Results show that algorithms proposed aiming for reducing the dynamic part of the energy consumption of the network may raise the fixed part of the energy consumption meanwhile....

Microtopographic patterns in an arctic baydjarakh field: do fine-grain patterns enforce landscape stability?

International Nuclear Information System (INIS)

Gamon, John A; Kershaw, G Peter; Williamson, Scott; Hik, David S

2012-01-01

Recent observations suggest that while some arctic landscapes are undergoing rapid change, others are apparently more resilient. In this study, we related surface cover and energy balance to microtopography in a degraded polygonal peat plateau (baydjarakh field) near Churchill, Manitoba in mid-summer 2010. The landscape consists of remnant high-centered polygons divided by troughs of varying widths. Historical aerial photos indicate these topographical features have been stable for over 80 years. Our goal was to explore patterns that might explain the apparent stability of this landscape over this time period and to evaluate remote sensing methods for characterizing microtopographic patterns that might resist change in the face of climate warming. Summertime surface albedo measurements were combined with several years of winter snow depth, snow heat flux, summer thaw depth and annual surface temperature, all of which had striking contrasts between wet troughs and high polygon centers. Measurements of albedo and the snowpack heat transfer coefficient were lowest for wet troughs (areas of standing water) dominated by graminoids, and were significantly higher for high polygon centers, dominated by dwarf shrubs and lichens. Snow depth, surface temperature and thaw depth were all significantly higher for wet troughs than high polygon centers. Together these patterns of cover and energy balance associated with microtopographic variation can contribute to the stability of this landscape through differential heat transfer and storage. We hypothesize that local thermal feedback effects, involving greater heat trapping in the troughs than on the baydjarakh tops, and effective insulation on the baydjarakh edges, have ensured landscape stability over most of the past century. These results suggest that high-resolution remote sensing, combined with detailed field monitoring, could provide insights into the dynamics or stability of arctic landscapes, where cover often varies

Dynamic energy spectrum and energy deposition in solid target by intense pulsed ion beams

Institute of Scientific and Technical Information of China (English)

Xiao Yu; Xiao-Yun Le; Zheng Liu; Jie Shen; Yu I.Isakova; Hao-Wen Zhong; Jie Zhang; Sha Yan; Gao-Long Zhang; Xiao-Fu Zhang

2017-01-01

A method for analyzing the dynamic energy spectrum of intense pulsed ion beam (IPIB) was proposed.Its influence on beam energy deposition in metal target was studied with IPIB produced by two types of magnetically insulated diodes (MID).The emission of IPIB was described with space charge limitation model,and the dynamic energy spectrum was further analyzed with time-of-flight method.IPIBs generated by pulsed accelerators of BIPPAB-450 (active MID) and TEMP-4M (passive MID) were studied.The dynamic energy spectrum was used to deduce the power density distribution of IPIB in the target with Monte Carlo simulation and infrared imaging diagnostics.The effect on the distribution and evolution of thermal field induced by the characteristics of IPIB dynamic energy spectrum was discussed.

AN EVALUATION OF THE SPATIAL DIMENSION OF LANDSCAPE ...

African Journals Online (AJOL)

Osondu

2012-03-30

Mar 30, 2012 ... with adequate landscaping, - using landscape elements, to create a ... air, water and energy cycles that replenish and rejuvenate ... First, using the street map of. Ogbomoso ... swimming pools, etc, were regarded as conscious.

DINÂMICA DA PAISAGEM NA PRAIA DE VALHA-ME DEUS, CURURUPU-MA / LANDSCAPE DYNAMICS OF THE BEACH OF VALHA-ME DEUS IN CURURUPU – MA

Directory of Open Access Journals (Sweden)

Francisco Wendell Dias Costa

2017-08-01

Full Text Available The landscape dynamics in Valha-me Deus beach, located in the county of Cururupu, in the state of Maranhão, Brazil. The study was carried out based on the geosystemic theory and considering the following methodological procedures: bibliographical and cartographic research and analysis of the area of study, field search intended to measure the climatic parameters and the observations according to the dynamics integrated in the landscape, involving the behavior of the morphogenetic agents of climatic, oceanographic, biotic and anthropic origin. The results show that the area is formed an unconsolidated sedimentary formation, constituted of quartz-like sand with fine and very fine size, submitted to climatic and oceanographic agents and processes which determine intense alterations of the morphology, allowing it to infer a high degree of vulnerability of the natural landscape, despite the low interference from men as the morphogenetic agent. The thermo averages and the wind speed are higher in the dry season if compared to the rain season, and the action of the waves and the ocean currents determines the morphodymanic pattern of the beach.

Shedding Light on Protein Folding, Structural and Functional Dynamics by Single Molecule Studies

Directory of Open Access Journals (Sweden)

Krutika Bavishi

2014-11-01

Full Text Available The advent of advanced single molecule measurements unveiled a great wealth of dynamic information revolutionizing our understanding of protein dynamics and behavior in ways unattainable by conventional bulk assays. Equipped with the ability to record distribution of behaviors rather than the mean property of a population, single molecule measurements offer observation and quantification of the abundance, lifetime and function of multiple protein states. They also permit the direct observation of the transient and rarely populated intermediates in the energy landscape that are typically averaged out in non-synchronized ensemble measurements. Single molecule studies have thus provided novel insights about how the dynamic sampling of the free energy landscape dictates all aspects of protein behavior; from its folding to function. Here we will survey some of the state of the art contributions in deciphering mechanisms that underlie protein folding, structural and functional dynamics by single molecule fluorescence microscopy techniques. We will discuss a few selected examples highlighting the power of the emerging techniques and finally discuss the future improvements and directions.

Control over Structure and Function of Peptide Amphiphile Supramolecular Assemblies through Molecular Design and Energy Landscapes

Science.gov (United States)

Tantakitti, Faifan

Supramolecular chemistry is a powerful tool to create a material of a defined structure with tunable properties. This strategy has led to catalytically active, bioactive, and environment-responsive materials, among others, that are valuable in applications ranging from sensor technology to energy and medicine. Supramolecular polymers formed by peptide amphiphiles (PAs) have been especially relevant in tissue regeneration due to their ability to form biocompatible structures and mimic many important signaling molecules in biology. These supramolecular polymers can form nanofibers that create networks which mimic natural extracellular matrices. PA materials have been shown to induce growth of blood vessels, bone, cartilage, and nervous tissue, among others. The work described in this thesis not only studied the relationship between molecular structure and functions of PA assemblies, but also uncovered a powerful link between the energy landscape of their supramolecular self-assembly and the ability of PA materials to interact with cells. In chapter 2, it is argued that fabricating fibrous nanostructures with defined mechanical properties and decoration with bioactive molecules is not sufficient to create a material that can effectively communicate with cells. By systemically placing the fibronectin-derived RGDS epitope at increasing distances from the surface of PA nanofibers through a linker of one to five glycine residues, integrin-mediated RGDS signaling was enhanced. The results suggested that the spatial presentation of an epitope on PA nanofibers strongly influences the bioactivity of the PA substrates. In further improving functionality of a PA-based scaffold to effectively direct cell growth and differentiation, chapter 3 explored the use of a cell microcarrier to compartmentalize and simultaneously tune insoluble and soluble signals in a single matrix. PA nanofibers were incorporated at the surface of the microcarrier in order to promote cell adhesion, while

Landscape dynamics of aspen and conifer forests

Science.gov (United States)

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...

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction.

Science.gov (United States)

Akhter, Nasrin; Shehu, Amarda

2018-01-19

Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction

Directory of Open Access Journals (Sweden)

Nasrin Akhter

2018-01-01

Full Text Available Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.

Landscape anthropogenic disturbance in the Mediterranean ecosystem: is the current landscape sustainable?

Science.gov (United States)

Biondi, Guido; D'Andrea, Mirko; Fiorucci, Paolo; Franciosi, Chiara; Lima, Marco

2013-04-01

Mediterranean landscape during the last centuries has been subject to strong anthropogenic disturbances who shifted natural vegetation cover in a cultural landscape. Most of the natural forest were destroyed in order to allow cultivation and grazing activities. In the last century, fast growing conifer plantations were introduced in order to increase timber production replacing slow growing natural forests. In addition, after the Second World War most of the grazing areas were changed in unmanaged mediterranean conifer forest frequently spread by fires. In the last decades radical socio economic changes lead to a dramatic abandonment of the cultural landscape. One of the most relevant result of these human disturbances, and in particular the replacement of deciduous forests with coniferous forests, has been the increasing in the number of forest fires, mainly human caused. The presence of conifers and shrubs, more prone to fire, triggered a feedback mechanism that makes difficult to return to the stage of potential vegetation causing huge economic, social and environmental damages. The aim of this work is to investigate the sustainability of the current landscape. A future landscape scenario has been simulated considering the natural succession in absence of human intervention assuming the current fire regime will be unaltered. To this end, a new model has been defined, implementing an ecological succession model coupled with a simply Forest Fire Model. The ecological succession model simulates the vegetation dynamics using a rule-based approach discrete in space and time. In this model Plant Functional Types (PFTs) are used to describe the landscape. Wildfires are randomly ignited on the landscape, and their propagation is simulated using a stochastic cellular automata model. The results show that the success of the natural succession toward a potential vegetation cover is prevented by the frequency of fire spreading. The actual landscape is then unsustainable

Shapes of tree representations of spin-glass landscapes

International Nuclear Information System (INIS)

Hordijk, Wim; Fontanari, Jose F; Stadler, Peter F

2003-01-01

Much of the information about the multi-valley structure of disordered spin systems can be convened in a simple tree structure - a barrier tree - the leaves and internal nodes of which represent, respectively, the local minima and the lowest energy saddles connecting those minima. Here we apply several statistics used in the study of phylogenetic trees to barrier trees that result from the energy landscapes of p-spin models. These statistics give information about the shape of these barrier trees, in particular about balance and symmetry. We then ask if they can be used to classify different types of landscapes, compare them with results obtained from random trees, and investigate the structure of subtrees of the barrier trees. We conclude that at least one of the used statistics is capable of distinguishing different types of landscapes, that the barrier trees from p-spin energy landscapes are quite different from random trees, and that subtrees of barrier trees do not reflect the overall tree structure, but their structure is correlated with their 'depth' in the tree

Energy capture and storage in asymmetrically multistable modular structures inspired by skeletal muscle

Science.gov (United States)

Kidambi, Narayanan; Harne, Ryan L.; Wang, K. W.

2017-08-01

The remarkable versatility and adaptability of skeletal muscle that arises from the assembly of its nanoscale cross-bridges into micro-scale assemblies known as sarcomeres provides great inspiration for the development of advanced adaptive structures and material systems. Motivated by the capability of cross-bridges to capture elastic strain energy to improve the energetic efficiency of sudden movements and repeated motions, and by models of cross-bridge power stroke motions and sarcomere contractile behaviors that incorporate asymmetric, bistable potential energy landscapes, this research develops and studies modular mechanical structures that trap and store energy in higher-energy configurations. Modules exhibiting tailorable asymmetric bistability are first designed and fabricated, revealing how geometric parameters influence the asymmetry of the resulting double-well energy landscapes. These experimentally-observed characteristics are then investigated with numerical and analytical methods to characterize the dynamics of asymmetrically bistable modules. The assembly of such modules into greater structures generates complex, multi-well energy landscapes with stable system configurations exhibiting different quantities of stored elastic potential energy. Dynamic analyses illustrate the ability of these structures to capture a portion of the initial kinetic energy due to impulsive excitations as recoverable strain potential energy, and reveal how stiffness parameters, damping, and the presence of thermal noise in micro- and nano-scale applications influence energy capture behaviors. The insights gained could foster the development of advanced structural/material systems inspired by skeletal muscle, including actuators that effectively capture, store, and release energy, as well as adaptive, robust, and reusable armors and protective devices.

Oil and Gas Development in Southwestern Wyoming - Energy Data and Services for the Wyoming Landscape Conservation Initiative (WLCI)

Science.gov (United States)

Biewick, Laura

2009-01-01

The purpose of this report is to explore current oil and gas energy development in the area encompassing the Wyoming Landscape Conservation Initiative. The Wyoming Landscape Conservation Initiative is a long-term science-based effort to ensure southwestern Wyoming's wildlife and habitat remain viable in areas facing development pressure. Wyoming encompasses some of the highest quality wildlife habitats in the Intermountain West. At the same time, this region is an important source of natural gas. Using Geographic Information System technology, energy data pertinent to the conservation decision-making process have been assembled to show historical oil and gas exploration and production in southwestern Wyoming. In addition to historical data, estimates of undiscovered oil and gas are included from the 2002 U.S. Geological Survey National Assessment of Oil and Gas in the Southwestern Wyoming Province. This report is meant to facilitate the integration of existing data with new knowledge and technologies to analyze energy resources development and to assist in habitat conservation planning. The well and assessment data can be accessed and shared among many different clients including, but not limited to, an online web-service for scientists and resource managers engaged in the Initiative.

Mesoscale Simulation and Machine Learning of Asphaltene Aggregation Phase Behavior and Molecular Assembly Landscapes.

Science.gov (United States)

Wang, Jiang; Gayatri, Mohit A; Ferguson, Andrew L

2017-05-11

Asphaltenes constitute the heaviest fraction of the aromatic group in crude oil. Aggregation and precipitation of asphaltenes during petroleum processing costs the petroleum industry billions of dollars each year due to downtime and production inefficiencies. Asphaltene aggregation proceeds via a hierarchical self-assembly process that is well-described by the Yen-Mullins model. Nevertheless, the microscopic details of the emergent cluster morphologies and their relative stability under different processing conditions remain poorly understood. We perform coarse-grained molecular dynamics simulations of a prototypical asphaltene molecule to establish a phase diagram mapping the self-assembled morphologies as a function of temperature, pressure, and n-heptane:toluene solvent ratio informing how to control asphaltene aggregation by regulating external processing conditions. We then combine our simulations with graph matching and nonlinear manifold learning to determine low-dimensional free energy surfaces governing asphaltene self-assembly. In doing so, we introduce a variant of diffusion maps designed to handle data sets with large local density variations, and report the first application of many-body diffusion maps to molecular self-assembly to recover a pseudo-1D free energy landscape. Increasing pressure only weakly affects the landscape, serving only to destabilize the largest aggregates. Increasing temperature and toluene solvent fraction stabilizes small cluster sizes and loose bonding arrangements. Although the underlying molecular mechanisms differ, the strikingly similar effect of these variables on the free energy landscape suggests that toluene acts upon asphaltene self-assembly as an effective temperature.

Recent developments in computer modeling add ecological realism to landscape genetics

Science.gov (United States)

Background / Question / Methods A factor limiting the rate of progress in landscape genetics has been the shortage of spatial models capable of linking life history attributes such as dispersal behavior to complex dynamic landscape features. The recent development of new models...

Diel predator activity drives a dynamic landscape of fear

Science.gov (United States)

Kohl, Michel T.; Stahler, Daniel R.; Metz, Matthew C.; Forester, James D.; Kauffman, Matthew J.; Varley, Nathan; White, P.J.; Smith, Douglas W.; MacNulty, Daniel R.

2017-01-01

A "landscape of fear" (LOF) is a map that describes continuous spatial variation in an animal's perception of predation risk. The relief on this map reflects, for example, places that an animal avoids to minimize risk. Although the LOF concept is a potential unifying theme in ecology that is often invoked to explain the ecological and conservation significance of fear, quantified examples of a LOF over large spatial scales are lacking as is knowledge about the daily dynamics of a LOF. Despite theory and data to the contrary, investigators often assume, implicitly or explicitly, that a LOF is a static consequence of a predator's mere presence. We tested the prediction that a LOF in a large-scale, free-living system is a highly-dynamic map with "peaks" and "valleys" that alternate across the diel (24-hour) cycle in response to daily lulls in predator activity. We did so with extensive data from the case study of Yellowstone elk (Cervus elaphus) and wolves (Canis lupus) that was the original basis for the LOF concept. We quantified the elk LOF, defined here as spatial allocation of time away from risky places and times, across nearly 1000-km2 of northern Yellowstone National Park and found that it fluctuated with the crepuscular activity pattern of wolves, enabling elk to use risky places during wolf downtimes. This may help explain evidence that wolf predation risk has no effect on elk stress levels, body condition, pregnancy, or herbivory. The ability of free-living animals to adaptively allocate habitat use across periods of high and low predator activity within the diel cycle is an underappreciated aspect of animal behavior that helps explain why strong antipredator responses may trigger weak ecological effects, and why a LOF may have less conceptual and practical importance than direct killing.

Improving Vibration Energy Harvesting Using Dynamic Magnifier

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Almuatasim Alomari

2016-01-01

Full Text Available This paper reports on the design and evaluation of vibration-based piezoelectric energy-harvesting devices based on a polyvinylidene fluoride unimorph cantilever beam attached to the front of a dynamic magnifier. Experimental studies of the electromechanical frequency response functions are studied for the first three resonance frequencies. An analytical analysis is undertaken by applying the chain matrix in order to predict output voltage and output power with respect to the vibration frequency. The proposed harvester was modeled using MATLAB software and COMSOL multi- physics to study the mode shapes and electrical output parameters. The voltage and power output of the energy harvester with a dynamic magnifier was 2.62 V and 13.68 mW, respectively at the resonance frequency of the second mode. The modeling approach provides a basis to design energy harvesters exploiting dynamic magnification for improved performance and bandwidth. The potential application of such energy harvesting devices in the transport sector include autonomous structural health monitoring systems that often include embedded sensors, data acquisition, wireless communication, and energy harvesting systems.

The elastic free energy of a tandem modular protein under force.

Science.gov (United States)

Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

2015-05-01

Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins. Copyright © 2015. Published by Elsevier Inc.

Digital landscapes of imagination

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Starlight Vattano

2014-05-01

Full Text Available Urban landscapes that exist in the expression of an imaginative sequence define their shape through the digital representation. These hyperreal dimensions, combine imagination and representation as constituents a new reality, which follows the utopian, suprematist and constructivist theories, where the two-dimensional dynamics is transformed into an infinite space in which the imagination creates new forms. Although interpretations of the urban landscape film, put in place a correspondence between reality and virtuality, into the modeling of spatial movements, from which do not arise contraries, but only interdependencies. It is a particular type of representation that takes shape via the digital in motion and provides new tools for urban representation.

Dynamic modeling, simulation and control of energy generation

CERN Document Server

Vepa, Ranjan

2013-01-01

This book addresses the core issues involved in the dynamic modeling, simulation and control of a selection of energy systems such as gas turbines, wind turbines, fuel cells and batteries. The principles of modeling and control could be applied to other non-convention methods of energy generation such as solar energy and wave energy.A central feature of Dynamic Modeling, Simulation and Control of Energy Generation is that it brings together diverse topics in thermodynamics, fluid mechanics, heat transfer, electro-chemistry, electrical networks and electrical machines and focuses on their appli

Dynamic colloidal assembly pathways via low dimensional models

Energy Technology Data Exchange (ETDEWEB)

Yang, Yuguang; Bevan, Michael A., E-mail: mabevan@jhu.edu [Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Thyagarajan, Raghuram; Ford, David M. [Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003 (United States)

2016-05-28

Here we construct a low-dimensional Smoluchowski model for electric field mediated colloidal crystallization using Brownian dynamic simulations, which were previously matched to experiments. Diffusion mapping is used to infer dimensionality and confirm the use of two order parameters, one for degree of condensation and one for global crystallinity. Free energy and diffusivity landscapes are obtained as the coefficients of a low-dimensional Smoluchowski equation to capture the thermodynamics and kinetics of microstructure evolution. The resulting low-dimensional model quantitatively captures the dynamics of different assembly pathways between fluid, polycrystal, and single crystals states, in agreement with the full N-dimensional data as characterized by first passage time distributions. Numerical solution of the low-dimensional Smoluchowski equation reveals statistical properties of the dynamic evolution of states vs. applied field amplitude and system size. The low-dimensional Smoluchowski equation and associated landscapes calculated here can serve as models for predictive control of electric field mediated assembly of colloidal ensembles into two-dimensional crystalline objects.

The effects of landscape modifications on the long-term persistence of animal populations.

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Jacob Nabe-Nielsen

Full Text Available BACKGROUND: The effects of landscape modifications on the long-term persistence of wild animal populations is of crucial importance to wildlife managers and conservation biologists, but obtaining experimental evidence using real landscapes is usually impossible. To circumvent this problem we used individual-based models (IBMs of interacting animals in experimental modifications of a real Danish landscape. The models incorporate as much as possible of the behaviour and ecology of four species with contrasting life-history characteristics: skylark (Alauda arvensis, vole (Microtus agrestis, a ground beetle (Bembidion lampros and a linyphiid spider (Erigone atra. This allows us to quantify the population implications of experimental modifications of landscape configuration and composition. METHODOLOGY/PRINCIPAL FINDINGS: Starting with a real agricultural landscape, we progressively reduced landscape complexity by (i homogenizing habitat patch shapes, (ii randomizing the locations of the patches, and (iii randomizing the size of the patches. The first two steps increased landscape fragmentation. We assessed the effects of these manipulations on the long-term persistence of animal populations by measuring equilibrium population sizes and time to recovery after disturbance. Patch rearrangement and the presence of corridors had a large effect on the population dynamics of species whose local success depends on the surrounding terrain. Landscape modifications that reduced population sizes increased recovery times in the short-dispersing species, making small populations vulnerable to increasing disturbance. The species that were most strongly affected by large disturbances fluctuated little in population sizes in years when no perturbations took place. SIGNIFICANCE: Traditional approaches to the management and conservation of populations use either classical methods of population analysis, which fail to adequately account for the spatial configurations

Urban landscape as palimpsest

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Daniel-Gabriel Vâlceanu

2014-12-01

Full Text Available The current urban morphology and the identity building of the city construction can be designed as a palimpsest; the spatial development stages of urban systems represent the result of their evolution over time. The characteristics of urban palimpsest depend mainly on the emergent factors that influenced the territorial dynamics and the configuration of urban bodies. Urban life and its quality are directly influenced by spatial and temporal factors of the city evolution. For this reason the study aims to achieve a research to explain the concept of urban palimpsest and the current morphology of urban tissue because they are products of landscape transformations along the history. The current knowledge on urban palimpsest characteristics is very important and useful to plan the current and future evolution of urban systems. The case study presents a vast view on the history of spatial development and urban system as well as a dynamics of the landscape interconditioned by the elements of such development in the context of reference historical eras

Anthropogenic Influences in Land Use/Land Cover Changes in Mediterranean Forest Landscapes in Sicily

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Donato S. La Mela Veca

2016-01-01

Full Text Available This paper analyzes and quantifies the land use/land cover changes of the main forest and semi-natural landscape types in Sicily between 1955 and 2012. We analyzed seven representative forest and shrubland landscapes in Sicily. These study areas were chosen for their importance in the Sicilian forest panorama. We carried out a diachronic survey on historical and current aerial photos; all the aerial images used to survey the land use/land cover changes were digitalized and georeferenced in the UTM WGS84 system. In order to classify land use, the Regional Forest Inventory 2010 legend was adopted for the more recent images, and the CORINE Land Cover III level used for the older, lower resolution images. This study quantifies forest landscape dynamics; our results show for almost all study areas an increase of forest cover and expansion, whereas a regressive dynamic is found in rural areas due to intensive agricultural and pasturage uses. Understanding the dynamics of forest landscapes could enhance the role of forestry policy as a tool for landscape management and regional planning.

Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization.

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Gianvito Grasso

Full Text Available The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety of these polymers is a challenge and in need of improvement. With the aim of designing more effective polycationic-based gene carriers, many parameters such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity ratio need to be taken into consideration. In the present work, the binding mechanism of three cationic polymers (polyarginine, polylysine and polyethyleneimine to a model siRNA target is computationally investigated at the atomistic level. In order to better understand the polycationic carrier-siRNA interactions, replica exchange molecular dynamic simulations were carried out to provide an exhaustive exploration of all the possible binding sites, taking fully into account the siRNA flexibility together with the presence of explicit solvent and ions. Moreover, well-tempered metadynamics simulations were employed to elucidate how molecular geometry, polycation flexibility, and charge neutralization affect the siRNA-polycations free energy landscape in term of low-energy binding modes and unbinding free energy barriers. Significant differences among polymer binding modes have been detected, revealing the advantageous binding properties of polyarginine and polylysine compared to polyethyleneimine.

Application of Spaceborne Scatterometer for Mapping Freeze-Thaw State in Northern Landscapes as a Measure of Ecological and Hydrological Processes

Science.gov (United States)

McDonald, Kyle; Kimball, John; Zimmermann, Reiner; Way, JoBea; Frolking, Steve; Running, Steve

1999-01-01

Landscape freeze/thaw transitions coincide with marked shifts in albedo, surface energy and mass exchange, and associated snow dynamics. Monitoring landscape freeze/thaw dynamics would improve our ability to quantify the interannual variability of boreal hydrology and river runoff/flood dynamics. The annual duration of frost-free period also bounds the period of photosynthetic activity in boreal and arctic regions thus affecting the annual carbon budget and the interannual variability of regional carbon fluxes. In this study, we use the NASA scatterometer (NSCAT) to monitor the temporal change in the radar backscatter signature across selected ecoregions of the boreal zone. We have measured vegetation tissue temperatures, soil temperature profiles, and micrometeorological parameters in situ at selected sites along a north-south transect extending across Alaska from Prudhoe Bay to the Kenai Peninsula and in Siberia near the Yenisey River. Data from these stations have been used to quantify the scatterometer's sensitivity to freeze/thaw state under a variety of terrain and landcover conditions. Analysis of the NSCAT temporal response over the 1997 spring thaw cycle shows a 3 to 5 dB change in measured backscatter that is well correlated with the landscape springtime thaw process. Having verified the instrument's capability to monitor freeze/thaw transitions, regional scale mosaicked data are applied to derive temporal series of freeze/thaw transition maps for selected circumpolar high latitude regions. These maps are applied to derive areal extent of frozen and thawed landscape and demonstrate the utility of spaceborne radar for operational monitoring of seasonal freeze-thaw dynamics and associated biophysical processes for the circumpolar high latitudes.

Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA.

Science.gov (United States)

Chakraborty, Debayan; Wales, David J

2018-01-04

The recent discovery that Hoogsteen (HG) base pairs are widespread in DNA across diverse sequences and positional contexts could have important implications for understanding DNA replication and DNA-protein recognition. While evidence is emerging that the Hoogsteen conformation could be a thermodynamically accessible conformation of the DNA duplex and provide a means to expand its functionality, relatively little is known about the molecular mechanism underlying the Watson-Crick (WC) to HG transition. In this Perspective, we describe pathways and kinetics for this transition at an atomic level of detail, using the energy landscape perspective. We show that competition between the duplex conformations results in a double funnel landscape, which explains some recent experimental observations. The interconversion pathways feature a number of intermediates, with a variable number of WC and HG base pairs. The relatively slow kinetics, with possible deviations from two-state behavior, suggest that this conformational switch is likely to be a challenging target for both simulation and experiment.

A landscape analysis plan

Science.gov (United States)

Nancy E. Fleenor

2002-01-01

A Landscape Analysis Plan (LAP) sets out broad guidelines for project development within boundaries of the Kings River Sustainable Forest Ecosystems Project. The plan must be a dynamic, living document, subject to change as new information arises over the course of this very long-term project (several decades). Two watersheds, each of 32,000 acres, were dedicated to...

Coupled Landscape and Channel Dynamics in the Ganges-Brahmaputra Tidal Deltaplain, Southwest Bangladesh

Science.gov (United States)

Bomer, J.; Wilson, C.; Hale, R. P.

2017-12-01

In the Ganges-Brahmaputra Delta (GBD) and other tide-dominated systems, periodic flooding of the land surface during the tidal cycle promotes sediment accretion and surface elevation gain over time. However, over the past several decades, anthropogenic modification of the GBD tidal deltaplain through embankment construction has precluded sediment delivery to catchment areas, leading to widespread channel siltation and subsidence in poldered landscapes. Amongst the current discussion on GBD sustainability, the relationship between tidal inundation period and resultant sedimentation in natural and embanked settings remains unclear. Moreover, an evaluation of how riparian sedimentology and stratigraphic architecture changes across the GBD tidal-fluvial spectrum is notably absent, despite its critical importance in assessing geomorphic change in human-impacted transitional environments. To provide local-scale, longitudinal trends of coupled landscape-channel dynamics, an array of surface elevation tables, groundwater piezometers, and sediment traps deployed in natural and embanked settings have been monitored seasonally over a time span of 4 years. This knowledge base will be extended across the GBD tidal-fluvial transition by collecting sediment cores from carefully selected point bars along the Gorai River. Sediments will be analyzed for lithologic, biostratigraphic, and geochemical properties to provide an integrated framework for discerning depositional zones and associated facies assemblages across this complex transitional environment. Preliminary comparisons of accretion and hydroperiod data suggest that inundation duration strongly governs mass accumulation on the intertidal platform, though other factors such as mass extraction from sediment source and vegetation density may play secondary roles.

Strain-energy effects on dynamic fragmentation

International Nuclear Information System (INIS)

Glenn, L.A.; Chudnovsky, A.

1986-01-01

Grady's model of the dynamic fragmentation process, in which the average fragment size is determined by balancing the local kinetic energy and the surface energy, is modified to include the stored elastic (strain) energy. The revised model predicts that the strain energy should dominate for brittle materials, with low fracture toughness and high fracture-initiation stress. This conclusion is not borne out, however, by limited experimental data on brittle steels, even when the kinetic-energy density is small compared with the strain-energy density

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

Science.gov (United States)

Stukenbrock, Eva H; Dutheil, Julien Y

2018-03-01

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. Copyright © 2018 Stukenbrock and Dutheil.

Transformations of rural production landscapes in the global network society

DEFF Research Database (Denmark)

Swaffield, Simon; Primdahl, Jørgen

2010-01-01

The concept of the global network society provides a basis for examination of current trends and policy issues in rural landscape change across a range of developed countries. Drivers of change include the demand for food and fibre to support the growing urban populations in developing conutries......, the rationalization and centralisation of supply chains under the open market angenda, and the global integration of information and control systems. These dynamics frequently conflict with place specific socio-cultural values and environmental integrity. The regional and local institutions through which...... these dynamics are managed often express conflicting aims and means, despite clearly stated intentions of 'policy integration'. Comparative analysis has highlighted the way production landscapes continue to intensify, and clear indications are found that these landscapes are converging in character under...

Extinction Risk in Successional Landscapes Subject to Catastrophic Disturbances

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David Boughton

2002-12-01

Full Text Available We explore the thesis that stochasticity in successional-disturbance systems can be an agent of species extinction. The analysis uses a simple model of patch dynamics for seral stages in an idealized landscape; each seral stage is assumed to support a specialist biota. The landscape as a whole is characterized by a mean patch birth rate, mean patch size, and mean lifetime for each patch type. Stochasticity takes three forms: (1 patch stochasticity is randomness in the birth times and sizes of individual patches, (2 landscape stochasticity is variation in the annual means of birth rate and size, and (3 turnover mode is whether a patch is eliminated by disturbance or by successional change. Analytical and numerical analyses of the model suggest that landscape stochasticity is the most important agent. Landscape stochasticity increases the extinction risk to species by increasing the risk that the habitat will fluctuate to zero, by reducing the mean abundance of species, and by increasing the variance in species abundance. The highest risk was found to occur in species that inhabit patches with short lifetimes. The results of this general model suggest an important mechanism by which climate change threatens biodiversity: an increase in the frequency of extreme climate events will probably cause pulses of disturbance during some time periods; these in turn would cause wider fluctuations in annual disturbance rates and thus increase the overall level of landscape stochasticity. However, the model also suggests that humans can manipulate landscape stochasticity to reduce risk. In particular, if managed disturbances were more evenly distributed in time, attrition of the regional biota might be prevented. Other work on the connection between patch dynamics and extinction risk assumes the absence of landscape stochasticity and thus overlooks an important component of risk to biodiversity.

Carbonate landscapes evolution: Insights from 36Cl

Science.gov (United States)

Godard, Vincent; Thomas, Franck; Ollivier, Vincent; Bellier, Olivier; Shabanian, Esmaeil; Miramont, Cécile; Fleury, Jules; Benedetti, Lucilla; Guillou, Valéry; Aster Team

2017-04-01

Carbonate landscapes cover a significant fraction of the Earth surface, but their long-term dynamics is still poorly understood. When comparing with the situation in areas underlain by quartz-rich lithologies, where the routine use of 10Be-derived denudation rates has delivered fundamental insights on landscape evolution processes, this knowledge gap is particularly notable. Recent advances in the measurement of 36Cl and better understanding of its production pathways has opened the way to the development of a similar physically-based and quantitative analysis of landscape evolution in carbonate settings. However, beyond these methodological considerations, we still face fundamental geomorphological open questions, as for example the assessment of the importance of congruent carbonate dissolution in long-wavelength topographic evolution. Such unresolved problems concerning the relative importance of physical and chemical weathering processes lead to question the applicability of standard slope-dependent Geomorphic Transport Laws in carbonate settings. These issues have been addressed studying the geomorphological evolution of selected limestone ranges in Provence, SE France, where 36Cl concentration measurements in bedrock and stream sediment samples allow constraining denudation over 10 ka time-scale. We first identify a significant denudation contrast between the summit surface and the flanks of the ranges, pointing to a substantial contribution of gravity-driven processes to the landscape evolution, in addition to dissolution. Furthermore, a detailed analysis of the relationships between hillslope morphology and hilltop denudation allow to identify a fundamental transition between two regimes: (1) a dynamics where hillslope evolution is controlled by linear diffusive downslope regolith transport; and, (2) a domain where denudation is limited by the rate at which physical and chemical weathering processes can produce clasts and lower the hilltop. Such an abrupt

Using Landscape metrics to analyze the landscape evolution under land abandonment

Science.gov (United States)

Pelorosso, Raffaele; Della Chiesa, Stefano; Gobattoni, Federica; Leone, Antonio

2010-05-01

view, therefore, not all the abandoned land will be covered by woods also after a reasonable time (e.g 20-30 years); open areas patches can resist over time as a consequence of different (more o less natural) disturbances, pointing out a landscape mosaic and vegetation pattern almost never completely homogeneous. This spatial and temporal differentiation of landscape pattern, therefore, require both the individuation of disturbances and their effect on land abandonment process to be analyzed for each different landscape. Many types of analysis and models were developed and used to understand the reason of abandonment, its evolution, likelihood future landscape scenarios and the leading consequences on environment and population in order to establish right land-uses to obtain suitable and sustainable goods and services from landscape itself. One of these analysis recurs to landscape metrics. Landscape metrics have been widely applied in ecology and landscape ecology (Rainis, 2003; Romero-Calcerrada and Perry, 2004 ; Narumalani et al., 2004; Rocchini et al., 2006) because they allow an objective description of the temporal pattern of landscape change and a comparison with other landscapes (Turner et al., 2001). Furthermore, a description of the shape, size and spatial arrangement of patches of vegetation can be used to link the observed pattern with the ecological processes that may have generated it (Rocchini et al., 2006). So these metrics can be used to see how an abandoned landscape can evolve under the effects of different constrictions that, also if not completely knew, have been affecting the present assessment. Through historical and recent aerial photos (1954-1985-1999) and several landscape metrics, the evolution of marginal municipality of central Apennine under abandonment is presented here. Temporal evolution of landscape metrics was discussed to underline the importance of such descriptors of vegetation pattern dynamics and the key role played by these

Energy flow theory of nonlinear dynamical systems with applications

CERN Document Server

Xing, Jing Tang

2015-01-01

This monograph develops a generalised energy flow theory to investigate non-linear dynamical systems governed by ordinary differential equations in phase space and often met in various science and engineering fields. Important nonlinear phenomena such as, stabilities, periodical orbits, bifurcations and chaos are tack-led and the corresponding energy flow behaviors are revealed using the proposed energy flow approach. As examples, the common interested nonlinear dynamical systems, such as, Duffing’s oscillator, Van der Pol’s equation, Lorenz attractor, Rössler one and SD oscillator, etc, are discussed. This monograph lights a new energy flow research direction for nonlinear dynamics. A generalised Matlab code with User Manuel is provided for readers to conduct the energy flow analysis of their nonlinear dynamical systems. Throughout the monograph the author continuously returns to some examples in each chapter to illustrate the applications of the discussed theory and approaches. The book can be used as ...

Landscape dynamics and different climate forcings in eastern Mongolia

Science.gov (United States)

Moore, N. J.; John, R.; Chen, J.

2017-12-01

Central and Eastern Mongolia have witnessed significant decreasing greening from the period 2000-2012. This decline may be partially, directly due to increased grazing pressure from livestock. Our study objective is to understand how landscape change may be altering heat fluxes and precipitation. Using the RAMS 6.0 regional climate model, we simulated the spatiotemporal changes in growing-season precipitation and atmospheric behavior under: (a) observed vegetation, and (b) aggressively reduced vegetation, to prognose likely locations and changes of the regional climate that might have resulted from land cover changes (2001-2010). We simulated a dzud/drought year (using forcing from 2001) and a wet year (using forcing from 2003). Our simulations show increased cloud cover and reduced daily temperature ranges for northeastern Mongolia where forest growth has expanded. Localized differences of 60 W/m2 of sensible heat flux were found when degraded landscape cover replaced older, more dense cover. More importantly, the overall trend towards reduced vegetation cover was responsible for higher screen height temperatures and reduced soil moisture throughout much of the domain, together with a shift of moisture southward of Inner Mongolia. Thus, even with improved chances for convection, soil moisture reductions of 5-10% would lead to overall even drier conditions. In the steppe regions around the Gobi desert, more complex patterns are evident and landscape drivers are less clear.

Ecological Functions of Landscapes

Science.gov (United States)

Kiryushin, V. I.

2018-01-01

Ecological functions of landscapes are considered a system of processes ensuring the development, preservation, and evolution of ecosystems and the biosphere as a whole. The concept of biogeocenosis can be considered a model that integrates biotic and environmental functions. The most general biogeocenotic functions specify the biodiversity, biotic links, self-organization, and evolution of ecosystems. Close interaction between biocenosis and the biotope (ecotope) is ensured by the continuous exchange of matter, energy, and information. Ecotope determines the biocenosis. The group of ecotopic functions includes atmospheric (gas exchange, heat exchange, hydroatmospheric, climate-forming), lithospheric (geodynamic, geophysical, and geochemical), hydrologic and hydrogeologic functions of landscape and ecotopic functions of soils. Bioecological functions emerge as a result of the biotope and ecotope interaction; these are the bioproductive, destructive, organoaccumulative, biochemical (gas, concentration, redox, biochemical, biopedological), pedogenetic, and energy functions

Energy transfer dynamics in Light-Harvesting Dendrimers

Science.gov (United States)

Melinger, Joseph S.; McMorrow, Dale; Kleiman, Valeria D.

2002-03-01

We explore energy transfer dynamics in light-harvesting phenylacetylene symmetric and asymmetric dendrimers. Femtosecond pump-probe spectroscopy is used to probe the ultrafast dynamics of electronic excitations in these dendrimers. The backbone of the macromolecule consists of branches of increasing conjugation length, creating an energy gradient, which funnels energy to an accepting perylene trap. In the case of the symmetric dendrimer (nanostar), the energy transfer efficiency is known to approach nearly unity, although the nature and timescale of the energy transfer process is still unknown. For the asymmetric dendrimers, energy transfer efficiencies are very high, with the possibility of more complex transfer processes. We experimentally monitor the transport of excitons through the light-harvesting dendrimer. The transients show a number of components, with timescales ranging from <300fs to several tens of picoseconds, revealing the complex photophysics taking place in these macromolecules. We interpret our results in terms of the Förster mechanism in which energy transfer occurs through dipole-dipole interactions.

Energy Management Dynamic Control Topology In MANET

Science.gov (United States)

Madhusudan, G.; Kumar, TNR

2017-08-01

Topology management via per-node transmission power adjustment has been shown effective in extending network lifetime. The existing algorithms constructs static topologies which fail to take the residual energy of network nodes, and cannot balance energy consumption efficiently. To address this problem, a Light Weighted Distributed Topology Control algorithm EMDCT(Energy Management Dynamic Control Topology ) is proposed in this paper. Based on the link metric of the network, both the energy consumption rate level and residual energy levels at the two end nodes are considered. EMDCT generates a Dynamic Topology that changes with the variation of node energy without the aid of location information, each node determines its transmission power according to local network information, which reduces the overhead complexity of EMDCT greatly. The experiment results show that EMDCT preserves network connectivity and manitains minimum-cost property of the network also it can extend network lifetime more remarkably.

Recent advances in the theory and application of fitness landscapes

CERN Document Server

Engelbrecht, Andries

2014-01-01

This book is concerned with recent advances in fitness landscapes. The concept of fitness landscapes originates from theoretical biology and refers to a framework for analysing and visualizing the relationships between genotypes, phenotypes and fitness. These relationships lay at the centre of attempts to mathematically describe evolutionary processes and evolutionary dynamics.     The book addresses recent advances in the understanding of fitness landscapes in evolutionary biology and evolutionary computation. In the volume, experts in the field of fitness landscapes present these findings in an integrated way to make it accessible to a number of audiences: senior undergraduate and graduate students in computer science, theoretical biology, physics, applied mathematics and engineering, but also researcher looking for a reference or/and entry point into using fitness landscapes for analysing algorithms. Also practitioners wanting to employ fitness landscape techniques for evaluating bio- and nature-inspired...

Reheating-volume measure in the string theory landscape

International Nuclear Information System (INIS)

Winitzki, Sergei

2008-01-01

I recently proposed the ''reheating-volume'' (RV) prescription as a possible solution to the measure problem in ''multiverse'' cosmology. The goal of this work is to extend the RV measure to scenarios involving bubble nucleation, such as the string theory landscape. In the spirit of the RV prescription, I propose to calculate the distribution of observable quantities in a landscape that is conditioned in probability to nucleate a finite total number of bubbles to the future of an initial bubble. A general formula for the relative number of bubbles of different types can be derived. I show that the RV measure is well defined and independent of the choice of the initial bubble type, as long as that type supports further bubble nucleation. Applying the RV measure to a generic landscape, I find that the abundance of Boltzmann brains is always negligibly small compared with the abundance of ordinary observers in the bubbles of the same type. As an illustration, I present explicit results for a toy landscape containing four vacuum states, and for landscapes with a single high-energy vacuum and a large number of low-energy vacua.

RS- and GIS-based study on landscape pattern change in the Poyang Lake wetland area, China

Science.gov (United States)

Chen, Xiaoling; Li, Hui; Bao, Shuming; Wu, Zhongyi; Fu, Weijuan; Cai, Xiaobin; Zhao, Hongmei; Guo, Peng

2006-10-01

As wetland has been recognized as an important component of ecosystem, it is received ever-increasing attention worldwide. Poyang Lake wetlands, the international wetlands and the largest bird habitat in Asia, play an important role in biodiversity and ecologic protection. However, with the rapid economic growth and urbanization, landscape patterns in the wetlands have dramatically changed in the past three decades. To better understand the wetland landscape dynamics, remote sensing, geographic information system technologies, and the FRAGSTATS landscape analysis program were used to measure landscape patterns. Statistical approach was employed to illustrate the driving forces. In this study, Landsat images (TM and ETM+) from 1989 and 2000 were acquired for the wetland area. The landscapes in the wetland area were classified as agricultural land, urban, wetland, forest, grassland, unused land, and water body using a combination of supervised and unsupervised classification techniques integrated with Digital Elevation Model (DEM). Landscape indices, which are popular for the quantitative analysis of landscape pattern, were then employed to analyze the landscape pattern changes between the two dates in a GIS. From this analysis an understanding of the spatial-temporal patterns of landscape evolution was generated. The results show that wetland area was reduced while fragmentation was increased over the study period. Further investigation was made to examine the relationship between landscape metrics and some other parameters such as urbanization to address the driving forces for those changes. The urban was chosen as center to conduct buffer analysis in a GIS to study the impact of human-induced activities on landscape pattern dynamics. It was found that the selected parameters were significantly correlated with the landscape metrics, which may well indicate the impact of human-induced activities on the wetland landscape pattern dynamics and account for the driving

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

Directory of Open Access Journals (Sweden)

Forchhammer Mads C

2009-06-01

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

Landscape structure, groundwater dynamics, and soil water content influence soil respiration across riparian-hillslope transitions in the Tenderfoot Creek Experimental Forest, Montana

Science.gov (United States)

Vincent J. Pacific; Brian L. McGlynn; Diego A. Riveros-Iregui; Daniel L. Welsch; Howard E. Epstein

2011-01-01

Variability in soil respiration at various spatial and temporal scales has been the focus of much research over the last decade aimed to improve our understanding and parameterization of physical and environmental controls on this flux. However, few studies have assessed the control of landscape position and groundwater table dynamics on the spatiotemporal variability...

Driving the Landscape

Science.gov (United States)

Haff, P. K.

2012-12-01

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

Dynamic properties of energy affordability measures

International Nuclear Information System (INIS)

Heindl, Peter; Schuessler, Rudolf

2015-01-01

Measures of affordability and of fuel poverty are applied in practice to assess the affordability of energy services, for example, or of water or housing. The extensive body of literature on affordability measures has little overlap with the existing literature on poverty measurement. A comprehensive assessment of the response of affordability measures as a result of changes in the distribution of income or expenditure (the dynamic properties) is missing. This paper aims to fill this gap by providing a conceptual discussion on the ‘dynamics’ of both energy affordability measures and fuel poverty measures. Several types of measures are examined in a microsimulation framework. Our results indicate that some measures exhibit odd dynamic behavior. This includes measures used in practice, such as the low income/high cost measure and the double median of expenditure share indicator. Odd dynamic behavior causes the risk of drawing false policy recommendations from the measures. Thus, an appropriate response of affordability measures to changes in relevant variables is a prerequisite for defining meaningful measures that inform about affordability or deprivation in certain domains of consumption. - Highlights: • We investigate changes in fuel poverty measures as result from changes in income and expenditure. • More generally, we investigate dynamic behavior of affordability measures using microsimulation. • We propose axioms regarding dynamic behavior of affordability measures. • Some measures which are used in practice show unintuitive dynamic behavior. • Inappropriate dynamic behavior causes a risk of false policy implications.

Landscape equivalent of the shoving model

DEFF Research Database (Denmark)

Dyre, Jeppe; Olsen, Niels Boye

2004-01-01

It is shown that the shoving model expression for the average relaxation time of viscous liquids, according to which the activation energy is proportional to the instantaneous shear modulus, follows largely from a classical "landscape" estimation of barrier heights from curvature at energy minima...

Quantitative analysis of the publishing landscape in High-Energy Physics

CERN Document Server

Mele, S; Vigen, Jens; Yeomans, Joanne

2006-01-01

World-wide collaboration in high-energy physics (HEP) is a tradition which dates back several decades, with scientific publications mostly coauthored by scientists from different countries. This coauthorship phenomenon makes it difficult to identify precisely the "share" of each country in HEP scientific production. One year's worth of HEP scientific articles published in peer-reviewed journals is analysed and their authors are uniquely assigned to countries. This method allows the first correct estimation on a pro rata basis of the share of HEP scientific publishing among several countries and institutions. The results provide an interesting insight into the geographical collaborative patterns of the HEP community. The HEP publishing landscape is further analysed to provide information on the journals favoured by the HEP community and on the geographical variation of their author bases. These results provide quantitative input to the ongoing debate on the possible transition of HEP publishing to an Open Acce...

Land destruction and redevelopment - the use of computer based landscape evolution models for post-mining landscape reconstruction

Science.gov (United States)

Hancock, Greg; Willgoose, Garry

2017-04-01

Mining provides essential resources for the global economy as well as considerable employment and economic benefits for the community. Mining is necessary for the modern economy. However, in recent decades the scale and environmental impact of mining has grown in line with the global demand for resources. This requires ever increasing areas of land to be disturbed. In particular, open-cast mining removes topsoil, disrupts aquifers and removes uneconomic material to depths of many hundreds of metres. Post-mining, this highly disturbed landscape system requires rehabilitation. The first and most important component of this process is to construct an erosionally stable landform which then can ecologically integrate with the surrounding undisturbed landscape. The scale and importance of this process cannot be overstated as without planned rehabilitation it is likely that a degraded and highly erosional landscape system with result. Here we discuss computer based landform evolution models which provide essential information on the likely erosional stability of the reconstructed landscape. These models use a digital elevation model to represent the landscape and dynamically adjusts the surface in response to erosion and deposition. They provide information on soil erosion rates at the storm event time scale through to annual time scales. The models can also be run to assess landscape evolution at millennial time scales. They also provide information on the type of erosion (i.e. rilling, gullying) and likely gully depths (and if they will occur). Importantly, the latest models have vegetation, armouring and pedogenesis submodels incorporated into their formulation. This allows both the surface and subsurface landscape evolution to be assessed. These models have been widely used and have huge benefits for the assessment of reconstructed landscapes as well as other disturbed landscape systems. Here we outline the state of the art.

Our Common Landscapes For The Future

DEFF Research Database (Denmark)

Brandt, Jesper

2017-01-01

Foreword for Marc Antrop and Veerle van Eetvelde: Landscape Perspectives – The Holistic Nature of Landscapes Our common landscapes for the future by Jesper Brandt The solution of the ecological crisis through a transformation towards sustainable development is the most urgent challenge in our time....... It is not just a question of CO2 and conversion toward renewable energy. The reestablishment and conscious development of our common landscapes at all spatial scales for the combined benefits of biodiversity, our cultural heritage and the preservation and development of ecosystem services will probably...... be the most comprehensive and necessary social task in the future, if a conversion towards a sustainable development shall succeed in due time. This is so because it will be necessary to ensure that the potential material wealth of modern society will be transformed into a good, fruitful and healthy life...

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

Energy Technology Data Exchange (ETDEWEB)

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.

Assessment of Landscape Changes: Theoretical Starting Points for Study and the Research Reality

Czech Academy of Sciences Publication Activity Database

Kolejka, Jaromír; Trnka, P.

2008-01-01

Roč. 16, č. 3 (2008), s. 2-15 ISSN 1210-8812 Institutional research plan: CEZ:AV0Z30860518 Keywords : criteria of landscape changes * landscape structures * space- time - dynamics Subject RIV: DE - Earth Magnetism, Geodesy, Geography

PELE:  Protein Energy Landscape Exploration. A Novel Monte Carlo Based Technique.

Science.gov (United States)

Borrelli, Kenneth W; Vitalis, Andreas; Alcantara, Raul; Guallar, Victor

2005-11-01

Combining protein structure prediction algorithms and Metropolis Monte Carlo techniques, we provide a novel method to explore all-atom energy landscapes. The core of the technique is based on a steered localized perturbation followed by side-chain sampling as well as minimization cycles. The algorithm and its application to ligand diffusion are presented here. Ligand exit pathways are successfully modeled for different systems containing ligands of various sizes:  carbon monoxide in myoglobin, camphor in cytochrome P450cam, and palmitic acid in the intestinal fatty-acid-binding protein. These initial applications reveal the potential of this new technique in mapping millisecond-time-scale processes. The computational cost associated with the exploration is significantly less than that of conventional MD simulations.

Transdisciplinary Challenges for Sustainable Management of Mediterranean Landscapes in the Global Information Society

Directory of Open Access Journals (Sweden)

Zev Naveh

2009-11-01

Full Text Available The present chaotic transformation from the industrial to the global information society is accelerating the ecological, social and economic unsustainability. The rapidly growing unsustainable, fossil energy powered urbanindustrial technosphere and their detrimental impacts on nature and human well-being are threatening the solar energy powered natural and seminatural biosphere landscapes and their vital ecosystem services. A sustainability revolution is therefore urgently needed, requiring a shift from the „fossil age“ to the „solar age“ of a new world economy, coupled with more sustainable lifestyles and consumption patterns. The sustainable future of viable multifunctional biosphere landscapes of the Mediterranean Region and elsewhere and their biological and cultural richness can only be ensured by a post-industrial symbiosis between nature and human society. For this purpose a mindset shift of scientists and professionals from narrow disciplinarity to transdisciplinarity is necessary, dealing with holistic land use planning and management, in close cooperation with land users and stakeholders. To conserve and restore the rapidly vanishing and degrading Mediterranean uplands and highest biological ecological and cultural landscape ecodiversity, their dynamic homeorhetic flow equilibrium, has to be maintained by continuing or simulating all anthropogenic processes of grazing, browsing by wild and domesticated ungulates. Catastrophic wildfires can be prevented only by active fire and fuel management, converting highly inflammable pine forests and dense shrub thickets into floristically enriched, multi- layered open woodlands and recreation forests.

Precision cosmology and the landscape

International Nuclear Information System (INIS)

Bousso, Raphael; Bousso, Raphael

2006-01-01

After reviewing the cosmological constant problem--why is Lambda not huge?--I outline the two basic approaches that had emerged by the late 1980s, and note that each made a clear prediction. Precision cosmological experiments now indicate that the cosmological constant is nonzero. This result strongly favors the environmental approach, in which vacuum energy can vary discretely among widely separated regions in the universe. The need to explain this variation from first principles constitutes an observational constraint on fundamental theory. I review arguments that string theory satisfies this constraint, as it contains a dense discretuum of metastable vacua. The enormous landscape of vacua calls for novel, statistical methods of deriving predictions, and it prompts us to reexamine our description of spacetime on the largest scales. I discuss the effects of cosmological dynamics, and I speculate that weighting vacua by their entropy production may allow for prior-free predictions that do not resort to explicitly anthropic arguments

Flowscapes : Infrastructure as landscape, landscape as infrastructure. Graduation Lab Landscape Architecture 2012/2013

NARCIS (Netherlands)

Nijhuis, S.; Jauslin, D.; De Vries, C.

2012-01-01

Flowscapes explores infrastructure as a type of landscape and landscape as a type of infrastructure, and is focused on landscape architectonic design of transportation-, green- and water infrastructures. These landscape infrastructures are considered armatures for urban and rural development. With

Landscape metrics for three-dimension urban pattern recognition

Science.gov (United States)

Liu, M.; Hu, Y.; Zhang, W.; Li, C.

2017-12-01

Understanding how landscape pattern determines population or ecosystem dynamics is crucial for managing our landscapes. Urban areas are becoming increasingly dominant social-ecological systems, so it is important to understand patterns of urbanization. Most studies of urban landscape pattern examine land-use maps in two dimensions because the acquisition of 3-dimensional information is difficult. We used Brista software based on Quickbird images and aerial photos to interpret the height of buildings, thus incorporating a 3-dimensional approach. We estimated the feasibility and accuracy of this approach. A total of 164,345 buildings in the Liaoning central urban agglomeration of China, which included seven cities, were measured. Twelve landscape metrics were proposed or chosen to describe the urban landscape patterns in 2- and 3-dimensional scales. The ecological and social meaning of landscape metrics were analyzed with multiple correlation analysis. The results showed that classification accuracy compared with field surveys was 87.6%, which means this method for interpreting building height was acceptable. The metrics effectively reflected the urban architecture in relation to number of buildings, area, height, 3-D shape and diversity aspects. We were able to describe the urban characteristics of each city with these metrics. The metrics also captured ecological and social meanings. The proposed landscape metrics provided a new method for urban landscape analysis in three dimensions.

Forest dynamics [version 1; referees: 2 approved

Directory of Open Access Journals (Sweden)

Lee Frelich

2016-02-01

Full Text Available Forest dynamics encompass changes in stand structure, species composition, and species interactions with disturbance and environment over a range of spatial and temporal scales. For convenience, spatial scale is defined as individual tree, neighborhood, stand, and landscape. Whether a given canopy-leveling disturbance will initiate a sequence of development in structure with little change in composition or initiate an episode of succession depends on a match or mismatch, respectively, with traits of the dominant tree species that allow the species to survive disturbance. When these match, certain species-disturbance type combinations lock in a pattern of stand and landscape dynamics that can persist for several generations of trees; thus, dominant tree species regulate, as well as respond to, disturbance. A complex interaction among tree species, neighborhood effects, disturbance type and severity, landform, and soils determines how stands of differing composition form and the mosaic of stands that compose the landscape. Neighborhood effects (e.g., serotinous seed rain, sprouting, shading, leaf-litter chemistry, and leaf-litter physical properties operate at small spatial extents of the individual tree and its neighbors but play a central role in forest dynamics by contributing to patch formation at stand scales and dynamics of the entire landscape. Dominance by tree species with neutral to negative neighborhood effects leads to unstable landscape dynamics in disturbance-prone regions, wherein most stands are undergoing succession; stability can only occur under very low-severity disturbance regimes. Dominance by species with positive effects leads to stable landscape dynamics wherein only a small proportion of stands undergo succession at any one time. Positive neighborhood effects are common in temperate and boreal zones, whereas negative effects are more common in tropical climates. Landscapes with positive dynamics have alternate categories

Stable schemes for dissipative particle dynamics with conserved energy

Energy Technology Data Exchange (ETDEWEB)

Stoltz, Gabriel, E-mail: stoltz@cermics.enpc.fr

2017-07-01

This article presents a new numerical scheme for the discretization of dissipative particle dynamics with conserved energy. The key idea is to reduce elementary pairwise stochastic dynamics (either fluctuation/dissipation or thermal conduction) to effective single-variable dynamics, and to approximate the solution of these dynamics with one step of a Metropolis–Hastings algorithm. This ensures by construction that no negative internal energies are encountered during the simulation, and hence allows to increase the admissible timesteps to integrate the dynamics, even for systems with small heat capacities. Stability is only limited by the Hamiltonian part of the dynamics, which suggests resorting to multiple timestep strategies where the stochastic part is integrated less frequently than the Hamiltonian one.

The dynamic landscape of virtual space explored through a multidisciplinary kaleidoscope

Directory of Open Access Journals (Sweden)

C.-I. REZEANU

2017-07-01

Full Text Available A social life disconnected from space it`s difficult to conceive. However, in sociology, the concept of space is still underdeveloped, missing from theories, dictionaries, or encyclopaedias. For more than a century, sociologists have assumed space as a passive scene for social actions, and implied as material, static, continuous and linearly travelled. In the new context of information society, economic globalisation, and postmodern hyper-reality, scholars question the conventional definitions of space. We believe sociologists will arrive at a more nuanced understanding of space, by taking an interdisciplinary approach, and focusing on how space is lived. We use virtual space as a proxy for understanding how complex space can be, and frame it through the concept of “cultural landscape” to capture its relational, dynamic, and socially constructed dimensions. Our aim is to illustrate the dynamism, versatility, and fluidity of virtual space by moving from one discipline and theoretical perspective to the other and interpreting the newly configured landscapes. We show that virtual space is a discontinuous imaginary process, organised in networks with multiple layers, experienced as a journey into a narrative text or as a ”consensual hallucination”, where the evanescence of the body and the anonymity of the self boost the quest for authenticity, self-discovery, self-disclosure and intimacy. Nonetheless, virtual space, due to its potential to equalise statuses, minimise authority and multiply the audiences of messages, is becoming the enabler of Habermasian communicative rationality, rousing moral consciousness and triggering civic actions.

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

Science.gov (United States)

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.

Entropic algorithms and the lid method as exploration tools for complex landscapes

DEFF Research Database (Denmark)

Barettin, Daniele; Sibani, Paolo

2011-01-01

to a single valley, are key to understand the dynamical properties of such systems. In this paper we combine the lid algorithm, a tool for landscape exploration previously applied to a range of models, with the Wang-Swendsen algorithm. To test this improved exploration tool, we consider a paradigmatic complex...... system, the Edwards-Andersom model in two and three spatial dimension. We find a striking difference between the energy dependence of the local density of states in the two cases: nearly flat in the first case, and nearly exponential in the second. The lid dependence of the data is analyzed to estimate...

Do geographically isolated wetlands influence landscape functions?

OpenAIRE

Cohen, Matthew J.; Creed, Irena F.; Alexander, Laurie; Basu, Nandita B.; Calhoun, Aram J. K.; Craft, Christopher; D’Amico, Ellen; DeKeyser, Edward; Fowler, Laurie; Golden, Heather E.; Jawitz, James W.; Kalla, Peter; Kirkman, L. Katherine; Lane, Charles R.; Lang, Megan

2016-01-01

Geographically isolated wetlands (GIWs), those surrounded by uplands, exchange materials, energy, and organisms with other elements in hydrological and habitat networks, contributing to landscape functions, such as flow generation, nutrient and sediment retention, and biodiversity support. GIWs constitute most of the wetlands in many North American landscapes, provide a disproportionately large fraction of wetland edges where many functions are enhanced, and form complexes with other water bo...

An individual-based model of Zebrafish population dynamics accounting for energy dynamics

DEFF Research Database (Denmark)

Beaudouin, Remy; Goussen, Benoit; Piccini, Benjamin

2015-01-01

Developing population dynamics models for zebrafish is crucial in order to extrapolate from toxicity data measured at the organism level to biological levels relevant to support and enhance ecological risk assessment. To achieve this, a dynamic energy budget for individual zebrafish (DEB model...

Wildlife disease prevalence in human-modified landscapes.

Science.gov (United States)

Brearley, Grant; Rhodes, Jonathan; Bradley, Adrian; Baxter, Greg; Seabrook, Leonie; Lunney, Daniel; Liu, Yan; McAlpine, Clive

2013-05-01

Human-induced landscape change associated with habitat loss and fragmentation places wildlife populations at risk. One issue in these landscapes is a change in the prevalence of disease which may result in increased mortality and reduced fecundity. Our understanding of the influence of habitat loss and fragmentation on the prevalence of wildlife diseases is still in its infancy. What is evident is that changes in disease prevalence as a result of human-induced landscape modification are highly variable. The importance of infectious diseases for the conservation of wildlife will increase as the amount and quality of suitable habitat decreases due to human land-use pressures. We review the experimental and observational literature of the influence of human-induced landscape change on wildlife disease prevalence, and discuss disease transmission types and host responses as mechanisms that are likely to determine the extent of change in disease prevalence. It is likely that transmission dynamics will be the key process in determining a pathogen's impact on a host population, while the host response may ultimately determine the extent of disease prevalence. Finally, we conceptualize mechanisms and identify future research directions to increase our understanding of the relationship between human-modified landscapes and wildlife disease prevalence. This review highlights that there are rarely consistent relationships between wildlife diseases and human-modified landscapes. In addition, variation is evident between transmission types and landscape types, with the greatest positive influence on disease prevalence being in urban landscapes and directly transmitted disease systems. While we have a limited understanding of the potential influence of habitat loss and fragmentation on wildlife disease, there are a number of important areas to address in future research, particularly to account for the variability in increased and decreased disease prevalence. Previous studies

Energy conservation in molecular dynamics simulations of classical systems

DEFF Research Database (Denmark)

Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

2012-01-01

Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

Impacts of Landscape Context on Patterns of Wind Downfall Damage in a Fragmented Amazonian Landscape

Science.gov (United States)

Schwartz, N.; Uriarte, M.; DeFries, R. S.; Gutierrez-Velez, V. H.; Fernandes, K.; Pinedo-Vasquez, M.

2015-12-01

Wind is a major disturbance in the Amazon and has both short-term impacts and lasting legacies in tropical forests. Observed patterns of damage across landscapes result from differences in wind exposure and stand characteristics, such as tree stature, species traits, successional age, and fragmentation. Wind disturbance has important consequences for biomass dynamics in Amazonian forests, and understanding the spatial distribution and size of impacts is necessary to quantify the effects on carbon dynamics. In November 2013, a mesoscale convective system was observed over the study area in Ucayali, Peru, a highly human modified and fragmented forest landscape. We mapped downfall damage associated with the storm in order to ask: how does the severity of damage vary within forest patches, and across forest patches of different sizes and successional ages? We applied spectral mixture analysis to Landsat images from 2013 and 2014 to calculate the change in non-photosynthetic vegetation fraction after the storm, and combined it with C-band SAR data from the Sentinel-1 satellite to predict downfall damage measured in 30 field plots using random forest regression. We then applied this model to map damage in forests across the study area. Using a land cover classification developed in a previous study, we mapped secondary and mature forest, and compared the severity of damage in the two. We found that damage was on average higher in secondary forests, but patterns varied spatially. This study demonstrates the utility of using multiple sources of satellite data for mapping wind disturbance, and adds to our understanding of the sources of variation in wind-related damage. Ultimately, an improved ability to map wind impacts and a better understanding of their spatial patterns can contribute to better quantification of carbon dynamics in Amazonian landscapes.

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

Directory of Open Access Journals (Sweden)

Efrat Sheffer

Full Text Available 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

Landscape-scale forest disturbance regimes in southern Peruvian Amazonia.

Science.gov (United States)

Boyd, Doreen S; Hill, Ross A; Hopkinson, Chris; Baker, Timothy R

2013-10-01

Landscape-scale gap-size frequency distributions in tropical forests are a poorly studied but key ecological variable. Currently, a scale gap currently exists between local-scale field-based studies and those employing regional-scale medium-resolution satellite data. Data at landscape scales but of fine resolution would, however, facilitate investigation into a range of ecological questions relating to gap dynamics. These include whether canopy disturbances captured in permanent sample plots (PSPs) are representative of those in their surrounding landscape, and whether disturbance regimes vary with forest type. Here, therefore, we employ airborne LiDAR data captured over 142.5 km2 of mature, swamp, and regenerating forests in southeast Peru to assess the landscape-scale disturbance at a sampling resolution of up to 2 m. We find that this landscape is characterized by large numbers of small gaps; large disturbance events are insignificant and infrequent. Of the total number of gaps that are 2 m2 or larger in area, just 0.45% were larger than 100 m2, with a power-law exponent (alpha) value of the gap-size frequency distribution of 2.22. However, differences in disturbance regimes are seen among different forest types, with a significant difference in the alpha value of the gap-size frequency distribution observed for the swamp/regenerating forests compared with the mature forests at higher elevations. Although a relatively small area of the total forest of this region was investigated here, this study presents an unprecedented assessment of this landscape with respect to its gap dynamics. This is particularly pertinent given the range of forest types present in the landscape and the differences observed. The coupling of detailed insights into forest properties and growth provided by PSPs with the broader statistics of disturbance events using remote sensing is recommended as a strong basis for scaling-up estimates of landscape and regional-scale carbon balance.

Landscape metrics application in ecological and visual landscape assessment

Directory of Open Access Journals (Sweden)

Gavrilović Suzana

2017-01-01

Full Text Available The development of landscape-ecological approach application in spatial planning provides exact theoretical and empirical evidence for monitoring ecological consequences of natural and/or anthropogenic factors, particularly changes in spatial structures caused by them. Landscape pattern which feature diverse landscape values is the holder of the unique landscape character at different spatial levels and represents a perceptual domain for its users. Using the landscape metrics, the parameters of landscape composition and configuration are mathematical algorithms that quantify the specific spatial characteristics used for interpretation of landscape features and processes (physical and ecological aspect, as well as forms (visual aspect and the meaning (cognitive aspect of the landscape. Landscape metrics has been applied mostly in the ecological and biodiversity assessments as well as in the determination of the level of structural change of landscape, but more and more applied in the assessment of the visual character of the landscape. Based on a review of relevant literature, the aim of this work is to show the main trends of landscape metrics within the aspect of ecological and visual assessments. The research methodology is based on the analysis, classification and systematization of the research studies published from 2000 to 2016, where the landscape metrics is applied: (1 the analysis of landscape pattern and its changes, (2 the analysis of biodiversity and habitat function and (3 a visual landscape assessment. By selecting representative metric parameters for the landscape composition and configuration, for each category is formed the basis for further landscape metrics research and application for the integrated ecological and visual assessment of the landscape values. Contemporary conceptualization of the landscape is seen holistically, and the future research should be directed towards the development of integrated landscape assessment

Topological and statistical properties of quantum control transition landscapes

International Nuclear Information System (INIS)

Hsieh, Michael; Wu Rebing; Rabitz, Herschel; Rosenthal, Carey

2008-01-01

A puzzle arising in the control of quantum dynamics is to explain the relative ease with which high-quality control solutions can be found in the laboratory and in simulations. The emerging explanation appears to lie in the nature of the quantum control landscape, which is an observable as a function of the control variables. This work considers the common case of the observable being the transition probability between an initial and a target state. For any controllable quantum system, this landscape contains only global maxima and minima, and no local extrema traps. The probability distribution function for the landscape value is used to calculate the relative volume of the region of the landscape corresponding to good control solutions. The topology of the global optima of the landscape is analysed and the optima are shown to have inherent robustness to variations in the controls. Although the relative landscape volume of good control solutions is found to shrink rapidly as the system Hilbert space dimension increases, the highly favourable landscape topology at and away from the global optima provides a rationale for understanding the relative ease of finding high-quality, stable quantum optimal control solutions

Bioversity in Multi-Ownership Landscapes

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Thomas A. Spies; K. Norman Johnson

2005-01-01

Many landscapes in the West are a patchwork of federal, state, forest industry and nonindustrial private forestlands. Each of these owners has a particular set of goals and practices that shapes the structure, species and dynamics of forest vegetation on their lands. Consequently, the pattern of landownership can have a major effect on the distribution of plants and...

A Method for Extracting the Free Energy Surface and Conformational Dynamics of Fast-Folding Proteins from Single Molecule Photon Trajectories

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2015-01-01

Single molecule fluorescence spectroscopy holds the promise of providing direct measurements of protein folding free energy landscapes and conformational motions. However, fulfilling this promise has been prevented by technical limitations, most notably, the difficulty in analyzing the small packets of photons per millisecond that are typically recorded from individual biomolecules. Such limitation impairs the ability to accurately determine conformational distributions and resolve sub-millisecond processes. Here we develop an analytical procedure for extracting the conformational distribution and dynamics of fast-folding proteins directly from time-stamped photon arrival trajectories produced by single molecule FRET experiments. Our procedure combines the maximum likelihood analysis originally developed by Gopich and Szabo with a statistical mechanical model that describes protein folding as diffusion on a one-dimensional free energy surface. Using stochastic kinetic simulations, we thoroughly tested the performance of the method in identifying diverse fast-folding scenarios, ranging from two-state to one-state downhill folding, as a function of relevant experimental variables such as photon count rate, amount of input data, and background noise. The tests demonstrate that the analysis can accurately retrieve the original one-dimensional free energy surface and microsecond folding dynamics in spite of the sub-megahertz photon count rates and significant background noise levels of current single molecule fluorescence experiments. Therefore, our approach provides a powerful tool for the quantitative analysis of single molecule FRET experiments of fast protein folding that is also potentially extensible to the analysis of any other biomolecular process governed by sub-millisecond conformational dynamics. PMID:25988351

Exploring the level sets of quantum control landscapes

International Nuclear Information System (INIS)

Rothman, Adam; Ho, Tak-San; Rabitz, Herschel

2006-01-01

A quantum control landscape is defined by the value of a physical observable as a functional of the time-dependent control field E(t) for a given quantum-mechanical system. Level sets through this landscape are prescribed by a particular value of the target observable at the final dynamical time T, regardless of the intervening dynamics. We present a technique for exploring a landscape level set, where a scalar variable s is introduced to characterize trajectories along these level sets. The control fields E(s,t) accomplishing this exploration (i.e., that produce the same value of the target observable for a given system) are determined by solving a differential equation over s in conjunction with the time-dependent Schroedinger equation. There is full freedom to traverse a level set, and a particular trajectory is realized by making an a priori choice for a continuous function f(s,t) that appears in the differential equation for the control field. The continuous function f(s,t) can assume an arbitrary form, and thus a level set generally contains a family of controls, where each control takes the quantum system to the same final target value, but produces a distinct control mechanism. In addition, although the observable value remains invariant over the level set, other dynamical properties (e.g., the degree of robustness to control noise) are not specifically preserved and can vary greatly. Examples are presented to illustrate the continuous nature of level-set controls and their associated induced dynamical features, including continuously morphing mechanisms for population control in model quantum systems

High-energy outer radiation belt dynamic modeling

International Nuclear Information System (INIS)

Chiu, Y.T.; Nightingale, R.W.; Rinaldi, M.A.

1989-01-01

Specification of the average high-energy radiation belt environment in terms of phenomenological montages of satellite measurements has been available for some time. However, for many reasons both scientific and applicational (including concerns for a better understanding of the high-energy radiatino background in space), it is desirable to model the dynamic response of the high-energy radiation belts to sources, to losses, and to geomagnetic activity. Indeed, in the outer electron belt, this is the only mode of modeling that can handle the large intensity fluctuations. Anticipating the dynamic modeling objective of the upcoming Combined Release and Radiation Effects Satellite (CRRES) program, we have undertaken to initiate the study of the various essential elements in constructing a dynamic radiation belt model based on interpretation of satellite data according to simultaneous radial and pitch-angle diffusion theory. In order to prepare for the dynamic radiation belt modeling based on a large data set spanning a relatively large segment of L-values, such as required for CRRES, it is important to study a number of test cases with data of similar characteristics but more restricted in space-time coverage. In this way, models of increasing comprehensiveness can be built up from the experience of elucidating the dynamics of more restrictive data sets. The principal objectives of this paper are to discuss issues concerning dynamic modeling in general and to summarize in particular the good results of an initial attempt at constructing the dynamics of the outer electron radiation belt based on a moderately active data period from Lockheed's SC-3 instrument flown on board the SCATHA (P78-2) spacecraft. Further, we shall discuss the issues brought out and lessons learned in this test case

Spacecraft Dynamic Characterization by Strain Energies Method

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Bretagne, J.-M.; Fragnito, M.; Massier, S.

2002-01-01

In the last years the significant increase in satellite broadcasting demand, with the wide band communication dawn, has given a great impulse to the telecommunication satellite market. The big demand is translated from operators (such as SES/Astra, Eutelsat, Intelsat, Inmarsat, EuroSkyWay etc.) in an increase of orders of telecom satellite to the world industrials. The largest part of these telecom satellite orders consists of Geostationary platforms which grow more and more in mass (over 5 tons) due to an ever longer demanded lifetime (up to 20 years), and become more complex due to the need of implementing an ever larger number of repeaters, antenna reflectors and feeds, etc... In this frame, the mechanical design and verification of these large spacecraft become difficult and ambitious at the same time, driven by the dry mass limitation objective. By the Finite Element Method (FEM), and on the basis of the telecom satellite heritage of a world leader constructor such as Alcatel Space Industries it is nowadays possible to model these spacecraft in a realistic and confident way in order to identify the main global dynamic aspects such as mode shapes, mass participation and/or dynamic responses. But on the other hand, one of the main aims consists in identifying soon in a program the most critical aspects of the system behavior in the launch dynamic environment, such as possible dynamic coupling between the different subsystems and secondary structures of the spacecraft (large deployable reflectors, thrusters, etc.). To this aim a numerical method has been developed in the frame of the Alcatel SPACEBUS family program, using MSC/Nastran capabilities and it is presented in this paper. The method is based on Spacecraft sub-structuring and strain energy calculation. The method mainly consists of two steps : 1) subsystem modal strain energy ratio (with respect to the global strain energy); 2) subsystem strain energy calculation for each mode according to the base driven

Analyzing high resolution topography for advancing the understanding of mass and energy transfer through landscapes: A review

Science.gov (United States)

Passaiacquaa, Paola; Belmont, Patrick; Staley, Dennis M.; Simley, Jeffery; Arrowsmith, J. Ramon; Bode, Collin A.; Crosby, Christopher; DeLong, Stephen; Glenn, Nancy; Kelly, Sara; Lague, Dimitri; Sangireddy, Harish; Schaffrath, Keelin; Tarboton, David; Wasklewicz, Thad; Wheaton, Joseph

2015-01-01

The study of mass and energy transfer across landscapes has recently evolved to comprehensive considerations acknowledging the role of biota and humans as geomorphic agents, as well as the importance of small-scale landscape features. A contributing and supporting factor to this evolution is the emergence over the last two decades of technologies able to acquire high resolution topography (HRT) (meter and sub-meter resolution) data. Landscape features can now be captured at an appropriately fine spatial resolution at which surface processes operate; this has revolutionized the way we study Earth-surface processes. The wealth of information contained in HRT also presents considerable challenges. For example, selection of the most appropriate type of HRT data for a given application is not trivial. No definitive approach exists for identifying and filtering erroneous or unwanted data, yet inappropriate filtering can create artifacts or eliminate/distort critical features. Estimates of errors and uncertainty are often poorly defined and typically fail to represent the spatial heterogeneity of the dataset, which may introduce bias or error for many analyses. For ease of use, gridded products are typically preferred rather than the more information-rich point cloud representations. Thus many users take advantage of only a fraction of the available data, which has furthermore been subjected to a series of operations often not known or investigated by the user. Lastly, standard HRT analysis work-flows are yet to be established for many popular HRT operations, which has contributed to the limited use of point cloud data.In this review, we identify key research questions relevant to the Earth-surface processes community within the theme of mass and energy transfer across landscapes and offer guidance on how to identify the most appropriate topographic data type for the analysis of interest. We describe the operations commonly performed from raw data to raster products and

Dynamic Modelling with "MLE-Energy Dynamic" for Primary School

Science.gov (United States)

Giliberti, Enrico; Corni, Federico

During the recent years simulation and modelling are growing instances in science education. In primary school, however, the main use of software is the simulation, due to the lack of modelling software tools specially designed to fit/accomplish the needs of primary education. In particular primary school teachers need to use simulation in a framework that is both consistent and simple enough to be understandable by children [2]. One of the possible area to approach modelling is about the construction of the concept of energy, in particular for what concerns the relations among substance, potential, power [3]. Following the previous initial research results with this approach [2], and with the static version of the software MLE Energy [1], we suggest the design and the experimentation of a dynamic modelling software—MLE dynamic-capable to represent dynamically the relations occurring when two substance-like quantities exchange energy, modifying their potential. By means of this software the user can graphically choose the dependent and independent variables and leave the other parameters fixed. The software has been initially evaluated, during a course of science education with a group of primary school teachers-to-be, to test the ability of the software to improve teachers' way of thinking in terms of substance-like quantities and their effects (graphical representation of the extensive, intensive variables and their mutual relations); moreover, the software has been tested with a group of primary school teachers, asking their opinion about the software didactical relevance in the class work.

Fractal Landscape Algorithms for Environmental Simulations

Science.gov (United States)

Mao, H.; Moran, S.

2014-12-01

Natural science and geographical research are now able to take advantage of environmental simulations that more accurately test experimental hypotheses, resulting in deeper understanding. Experiments affected by the natural environment can benefit from 3D landscape simulations capable of simulating a variety of terrains and environmental phenomena. Such simulations can employ random terrain generation algorithms that dynamically simulate environments to test specific models against a variety of factors. Through the use of noise functions such as Perlin noise, Simplex noise, and diamond square algorithms, computers can generate simulations that model a variety of landscapes and ecosystems. This study shows how these algorithms work together to create realistic landscapes. By seeding values into the diamond square algorithm, one can control the shape of landscape. Perlin noise and Simplex noise are also used to simulate moisture and temperature. The smooth gradient created by coherent noise allows more realistic landscapes to be simulated. Terrain generation algorithms can be used in environmental studies and physics simulations. Potential studies that would benefit from simulations include the geophysical impact of flash floods or drought on a particular region and regional impacts on low lying area due to global warming and rising sea levels. Furthermore, terrain generation algorithms also serve as aesthetic tools to display landscapes (Google Earth), and simulate planetary landscapes. Hence, it can be used as a tool to assist science education. Algorithms used to generate these natural phenomena provide scientists a different approach in analyzing our world. The random algorithms used in terrain generation not only contribute to the generating the terrains themselves, but are also capable of simulating weather patterns.

Analyzing landscape changes in the Bafa Lake Nature Park of Turkey using remote sensing and landscape structure metrics.

Science.gov (United States)

Esbah, Hayriye; Deniz, Bulent; Kara, Baris; Kesgin, Birsen

2010-06-01

Bafa Lake Nature Park is one of Turkey's most important legally protected areas. This study aimed at analyzing spatial change in the park environment by using object-based classification technique and landscape structure metrics. SPOT 2X (1994) and ASTER (2005) images are the primary research materials. Results show that artificial surfaces, low maqui, garrigue, and moderately high maqui covers have increased and coniferous forests, arable lands, permanent crop, and high maqui covers have decreased; coniferous forest, high maqui, grassland, and saline areas are in a disappearance stage of the land transformation; and the landscape pattern is more fragmented outside the park boundaries. The management actions should support ongoing vegetation regeneration, mitigate transformation of vegetation structure to less dense and discontinuous cover, control the dynamics at the agricultural-natural landscape interface, and concentrate on relatively low but steady increase of artificial surfaces.

The energy landscapes of repeat-containing proteins: topology, cooperativity, and the folding funnels of one-dimensional architectures.

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Diego U Ferreiro

2008-05-01

Full Text Available Repeat-proteins are made up of near repetitions of 20- to 40-amino acid stretches. These polypeptides usually fold up into non-globular, elongated architectures that are stabilized by the interactions within each repeat and those between adjacent repeats, but that lack contacts between residues distant in sequence. The inherent symmetries both in primary sequence and three-dimensional structure are reflected in a folding landscape that may be analyzed as a quasi-one-dimensional problem. We present a general description of repeat-protein energy landscapes based on a formal Ising-like treatment of the elementary interaction energetics in and between foldons, whose collective ensemble are treated as spin variables. The overall folding properties of a complete "domain" (the stability and cooperativity of the repeating array can be derived from this microscopic description. The one-dimensional nature of the model implies there are simple relations for the experimental observables: folding free-energy (DeltaG(water and the cooperativity of denaturation (m-value, which do not ordinarily apply for globular proteins. We show how the parameters for the "coarse-grained" description in terms of foldon spin variables can be extracted from more detailed folding simulations on perfectly funneled landscapes. To illustrate the ideas, we present a case-study of a family of tetratricopeptide (TPR repeat proteins and quantitatively relate the results to the experimentally observed folding transitions. Based on the dramatic effect that single point mutations exert on the experimentally observed folding behavior, we speculate that natural repeat proteins are "poised" at particular ratios of inter- and intra-element interaction energetics that allow them to readily undergo structural transitions in physiologically relevant conditions, which may be intrinsically related to their biological functions.

Relationship between dynamical entropy and energy dissipation far from thermodynamic equilibrium

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Green, Jason R.; Costa, Anthony B.; Grzybowski, Bartosz A.; Szleifer, Igal

2013-01-01

Connections between microscopic dynamical observables and macroscopic nonequilibrium (NE) properties have been pursued in statistical physics since Boltzmann, Gibbs, and Maxwell. The simulations we describe here establish a relationship between the Kolmogorov–Sinai entropy and the energy dissipated as heat from a NE system to its environment. First, we show that the Kolmogorov–Sinai or dynamical entropy can be separated into system and bath components and that the entropy of the system characterizes the dynamics of energy dissipation. Second, we find that the average change in the system dynamical entropy is linearly related to the average change in the energy dissipated to the bath. The constant energy and time scales of the bath fix the dynamical relationship between these two quantities. These results provide a link between microscopic dynamical variables and the macroscopic energetics of NE processes. PMID:24065832