[Land use and land cover charnge (LUCC) and landscape service: Evaluation, mapping and modeling].

PubMed

Song, Zhang-jian; Cao, Yu; Tan, Yong-zhong; Chen, Xiao-dong; Chen, Xian-peng

2015-05-01

Studies on ecosystem service from landscape scale aspect have received increasing attention from researchers all over the world. Compared with ecosystem scale, it should be more suitable to explore the influence of human activities on land use and land cover change (LUCC), and to interpret the mechanisms and processes of sustainable landscape dynamics on landscape scale. Based on comprehensive and systematic analysis of researches on landscape service, this paper firstly discussed basic concepts and classification of landscape service. Then, methods of evaluation, mapping and modeling of landscape service were analyzed and concluded. Finally, future trends for the research on landscape service were proposed. It was put forward that, exploring further connotation and classification system of landscape service, improving methods and quantitative indicators for evaluation, mapping and modelling of landscape service, carrying out long-term integrated researches on landscape pattern-process-service-scale relationships and enhancing the applications of theories and methods on landscape economics and landscape ecology are very important fields of the research on landscape service in future.

A modeling framework for the establishment and spread of invasive species in heterogeneous environments.

PubMed

Lustig, Audrey; Worner, Susan P; Pitt, Joel P W; Doscher, Crile; Stouffer, Daniel B; Senay, Senait D

2017-10-01

Natural and human-induced events are continuously altering the structure of our landscapes and as a result impacting the spatial relationships between individual landscape elements and the species living in the area. Yet, only recently has the influence of the surrounding landscape on invasive species spread started to be considered. The scientific community increasingly recognizes the need for broader modeling framework that focuses on cross-study comparisons at different spatiotemporal scales. Using two illustrative examples, we introduce a general modeling framework that allows for a systematic investigation of the effect of habitat change on invasive species establishment and spread. The essential parts of the framework are (i) a mechanistic spatially explicit model (a modular dispersal framework-MDIG) that allows population dynamics and dispersal to be modeled in a geographical information system (GIS), (ii) a landscape generator that allows replicated landscape patterns with partially controllable spatial properties to be generated, and (iii) landscape metrics that depict the essential aspects of landscape with which dispersal and demographic processes interact. The modeling framework provides functionality for a wide variety of applications ranging from predictions of the spatiotemporal spread of real species and comparison of potential management strategies, to theoretical investigation of the effect of habitat change on population dynamics. Such a framework allows to quantify how small-grain landscape characteristics, such as habitat size and habitat connectivity, interact with life-history traits to determine the dynamics of invasive species spread in fragmented landscape. As such, it will give deeper insights into species traits and landscape features that lead to establishment and spread success and may be key to preventing new incursions and the development of efficient monitoring, surveillance, control or eradication programs.

A methodology for creating greenways through multidisciplinary sustainable landscape planning.

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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 biogeochemical processes. This study not only helps us understand the coupled carbon-nitrogen cycle, but also serve as an instrument to develop practical approaches for reducing soil erosion and carbon loss when the landscape is affected by human activities.

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

PubMed

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

2012-05-01

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

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

NASA Technical Reports Server (NTRS)

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 landscape ecological processes.

Simulating forest management and its effect on landscape pattern

Treesearch

Eric J. Gustafson

2017-01-01

Landscapes are characterized by their structure (the spatial arrangement of landscape elements), their ecological function (how ecological processes operate within that structure), and the dynamics of change (disturbance and recovery). Thus, understanding the dynamic nature of landscapes and predicting their future dynamics are of particular emphasis. Landscape change...

Intermediate disturbance in experimental landscapes improves persistence of beetle metapopulations.

PubMed

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

2015-03-01

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

Dissecting Protein Configurational Entropy into Conformational and Vibrational Contributions.

PubMed

Chong, Song-Ho; Ham, Sihyun

2015-10-01

Quantifying how the rugged nature of the underlying free-energy landscape determines the entropic cost a protein must incur upon folding and ligand binding is a challenging problem. Here, we present a novel computational approach that dissects the protein configurational entropy on the basis of the classification of protein dynamics on the landscape into two separate components: short-term vibrational dynamics related to individual free-energy wells and long-term conformational dynamics associated with transitions between wells. We apply this method to separate the configurational entropy of the protein villin headpiece subdomain into its conformational and vibrational components. We find that the change in configurational entropy upon folding is dominated by the conformational entropy despite the fact that the magnitude of the vibrational entropy is the significantly larger component in each of the folded and unfolded states, which is in accord with the previous empirical estimations. The straightforward applicability of our method to unfolded proteins promises a wide range of applications, including those related to intrinsically disordered proteins.

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

PubMed

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

2011-01-01

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

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

USGS Publications Warehouse

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

2007-01-01

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

Dynamic Shade and Irradiance Simulation of Aquatic ...

EPA Pesticide Factsheets

Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulates across landscapes and is the main energy driver for increasing aquatic and landscape temperatures at both local and holistic scales. Landscape disturbances such as landuse change, clear cutting, and fire can cause significant variations in the resulting irradiance reaching particular locations. Penumbra can simulate solar angles and irradiance at definable temporal grains as low as one minute while simulating landscape shadowing up to an entire year. Landscapes can be represented at sub-meter resolutions with appropriate spatial data inputs, such as field data or elevation and surface object heights derived from light detection and ranging (LiDAR) data. This work describes Penumbra’s framework and methodology, external model integration capability, and appropriate model application for a variety of watershed restoration project types. First, an overview of Penumbra’s framework reveals what this model adds to the existing ecological modeling domain. Second, Penumbra’s stand-alone and integration modes are explained and demonstrated. Stand-alone modeling results are showcased within the 3-D visualization tool VISTAS (VISualizing Terrestrial-Aquatic Systems), which fluently summariz

[Application of spatially explicit landscape model in soil loss study in Huzhong area].

PubMed

Xu, Chonggang; Hu, Yuanman; Chang, Yu; Li, Xiuzhen; Bu, Renchang; He, Hongshi; Leng, Wenfang

2004-10-01

Universal Soil Loss Equation (USLE) has been widely used to estimate the average annual soil loss. In most of the previous work on soil loss evaluation on forestland, cover management factor was calculated from the static forest landscape. The advent of spatially explicit forest landscape model in the last decade, which explicitly simulates the forest succession dynamics under natural and anthropogenic disturbances (fire, wind, harvest and so on) on heterogeneous landscape, makes it possible to take into consideration the change of forest cover, and to dynamically simulate the soil loss in different year (e.g. 10 years and 20 years after current year). In this study, we linked a spatially explicit landscape model (LANDIS) with USLE to simulate the soil loss dynamics under two scenarios: fire and no harvest, fire and harvest. We also simulated the soil loss with no fire and no harvest as a control. The results showed that soil loss varied periodically with simulation year, and the amplitude of change was the lowest under the control scenario and the highest under the fire and no harvest scenario. The effect of harvest on soil loss could not be easily identified on the map; however, the cumulative effect of harvest on soil loss was larger than that of fire. Decreasing the harvest area and the percent of bare soil increased by harvest could significantly reduce soil loss, but had no significant effects on the dynamic of soil loss. Although harvest increased the annual soil loss, it tended to decrease the variability of soil loss between different simulation years.

Transcriptional atlas of cardiogenesis maps congenital heart disease interactome.

PubMed

Li, Xing; Martinez-Fernandez, Almudena; Hartjes, Katherine A; Kocher, Jean-Pierre A; Olson, Timothy M; Terzic, Andre; Nelson, Timothy J

2014-07-01

Mammalian heart development is built on highly conserved molecular mechanisms with polygenetic perturbations resulting in a spectrum of congenital heart diseases (CHD). However, knowledge of cardiogenic ontogeny that regulates proper cardiogenesis remains largely based on candidate-gene approaches. Mapping the dynamic transcriptional landscape of cardiogenesis from a genomic perspective is essential to integrate the knowledge of heart development into translational applications that accelerate disease discovery efforts toward mechanistic-based treatment strategies. Herein, we designed a time-course transcriptome analysis to investigate the genome-wide dynamic expression landscape of innate murine cardiogenesis ranging from embryonic stem cells to adult cardiac structures. This comprehensive analysis generated temporal and spatial expression profiles, revealed stage-specific gene functions, and mapped the dynamic transcriptome of cardiogenesis to curated pathways. Reconciling known genetic underpinnings of CHD, we deconstructed a disease-centric dynamic interactome encoded within this cardiogenic atlas to identify stage-specific developmental disturbances clustered on regulation of epithelial-to-mesenchymal transition (EMT), BMP signaling, NF-AT signaling, TGFb-dependent EMT, and Notch signaling. Collectively, this cardiogenic transcriptional landscape defines the time-dependent expression of cardiac ontogeny and prioritizes regulatory networks at the interface between health and disease. Copyright © 2014 the American Physiological Society.

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

Treesearch

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

2006-01-01

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

Evolving neural networks with genetic algorithms to study the string landscape

NASA Astrophysics Data System (ADS)

Ruehle, Fabian

2017-08-01

We study possible applications of artificial neural networks to examine the string landscape. Since the field of application is rather versatile, we propose to dynamically evolve these networks via genetic algorithms. This means that we start from basic building blocks and combine them such that the neural network performs best for the application we are interested in. We study three areas in which neural networks can be applied: to classify models according to a fixed set of (physically) appealing features, to find a concrete realization for a computation for which the precise algorithm is known in principle but very tedious to actually implement, and to predict or approximate the outcome of some involved mathematical computation which performs too inefficient to apply it, e.g. in model scans within the string landscape. We present simple examples that arise in string phenomenology for all three types of problems and discuss how they can be addressed by evolving neural networks from genetic algorithms.

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

NASA Technical Reports Server (NTRS)

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.

Bacterial predator–prey dynamics in microscale patchy landscapes

PubMed Central

Rotem, Or; Jurkevitch, Edouard; Dekker, Cees

2016-01-01

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

RCHILD - an R-package for flexible use of the landscape evolution model CHILD

NASA Astrophysics Data System (ADS)

Dietze, Michael

2014-05-01

Landscape evolution models provide powerful approaches to numerically assess earth surface processes, to quantify rates of landscape change, infer sediment transfer rates, estimate sediment budgets, investigate the consequences of changes in external drivers on a geomorphic system, to provide spatio-temporal interpolations between known landscape states or to test conceptual hypotheses. CHILD (Channel-Hillslope Integrated Landscape Development Model) is one of the most-used models of landscape change in the context of at least tectonic and geomorphologic process interactions. Running CHILD from command line and working with the model output can be a rather awkward task (static model control via text input file, only numeric output in text files). The package RCHILD is a collection of functions for the free statistical software R that help using CHILD in a flexible, dynamic and user-friendly way. The comprised functions allow creating maps, real-time scenes, animations and further thematic plots from model output. The model input files can be modified dynamically and, hence, (feedback-related) changes in external factors can be implemented iteratively. Output files can be written to common formats that can be readily imported to standard GIS software. This contribution presents the basic functionality of the model CHILD as visualised and modified by the package. A rough overview of the available functions is given. Application examples help to illustrate the great potential of numeric modelling of geomorphologic processes.

Integration of climatic water deficit and fine-scale physiography in process-based modeling of forest landscape resilience to large-scale tree mortality

NASA Astrophysics Data System (ADS)

Yang, J.; Weisberg, P.; Dilts, T.

2016-12-01

Climate warming can lead to large-scale drought-induced tree mortality events and greatly affect forest landscape resilience. Climatic water deficit (CWD) and its physiographic variations provide a key mechanism in driving landscape dynamics in response to climate change. Although CWD has been successfully applied in niche-based species distribution models, its application in process-based forest landscape models is still scarce. Here we present a framework incorporating fine-scale influence of terrain on ecohydrology in modeling forest landscape dynamics. We integrated CWD with a forest landscape succession and disturbance model (LANDIS-II) to evaluate how tree species distribution might shift in response to different climate-fire scenarios across an elevation-aspect gradient in a semi-arid montane landscape of northeastern Nevada, USA. Our simulations indicated that drought-intolerant tree species such as quaking aspen could experience greatly reduced distributions in the more arid portions of their existing ranges due to water stress limitations under future climate warming scenarios. However, even at the most xeric portions of its range, aspen is likely to persist in certain environmental settings due to unique and often fine-scale combinations of resource availability, species interactions and disturbance regime. The modeling approach presented here allowed identification of these refugia. In addition, this approach helped quantify how the direction and magnitude of fire influences on species distribution would vary across topoclimatic gradients, as well as furthers our understanding on the role of environmental conditions, fire, and inter-specific competition in shaping potential responses of landscape resilience to climate change.

BEEHAVE: a systems model of honeybee colony dynamics and foraging to explore multifactorial causes of colony failure

PubMed Central

Becher, Matthias A; Grimm, Volker; Thorbek, Pernille; Horn, Juliane; Kennedy, Peter J; Osborne, Juliet L

2014-01-01

A notable increase in failure of managed European honeybee Apis mellifera L. colonies has been reported in various regions in recent years. Although the underlying causes remain unclear, it is likely that a combination of stressors act together, particularly varroa mites and other pathogens, forage availability and potentially pesticides. It is experimentally challenging to address causality at the colony scale when multiple factors interact. In silico experiments offer a fast and cost-effective way to begin to address these challenges and inform experiments. However, none of the published bee models combine colony dynamics with foraging patterns and varroa dynamics. We have developed a honeybee model, BEEHAVE, which integrates colony dynamics, population dynamics of the varroa mite, epidemiology of varroa-transmitted viruses and allows foragers in an agent-based foraging model to collect food from a representation of a spatially explicit landscape. We describe the model, which is freely available online (www.beehave-model.net). Extensive sensitivity analyses and tests illustrate the model's robustness and realism. Simulation experiments with various combinations of stressors demonstrate, in simplified landscape settings, the model's potential: predicting colony dynamics and potential losses with and without varroa mites under different foraging conditions and under pesticide application. We also show how mitigation measures can be tested. Synthesis and applications. BEEHAVE offers a valuable tool for researchers to design and focus field experiments, for regulators to explore the relative importance of stressors to devise management and policy advice and for beekeepers to understand and predict varroa dynamics and effects of management interventions. We expect that scientists and stakeholders will find a variety of applications for BEEHAVE, stimulating further model development and the possible inclusion of other stressors of potential importance to honeybee colony dynamics. PMID:25598549

BEEHAVE: a systems model of honeybee colony dynamics and foraging to explore multifactorial causes of colony failure.

PubMed

Becher, Matthias A; Grimm, Volker; Thorbek, Pernille; Horn, Juliane; Kennedy, Peter J; Osborne, Juliet L

2014-04-01

A notable increase in failure of managed European honeybee Apis mellifera L. colonies has been reported in various regions in recent years. Although the underlying causes remain unclear, it is likely that a combination of stressors act together, particularly varroa mites and other pathogens, forage availability and potentially pesticides. It is experimentally challenging to address causality at the colony scale when multiple factors interact. In silico experiments offer a fast and cost-effective way to begin to address these challenges and inform experiments. However, none of the published bee models combine colony dynamics with foraging patterns and varroa dynamics.We have developed a honeybee model, BEEHAVE, which integrates colony dynamics, population dynamics of the varroa mite, epidemiology of varroa-transmitted viruses and allows foragers in an agent-based foraging model to collect food from a representation of a spatially explicit landscape.We describe the model, which is freely available online (www.beehave-model.net). Extensive sensitivity analyses and tests illustrate the model's robustness and realism. Simulation experiments with various combinations of stressors demonstrate, in simplified landscape settings, the model's potential: predicting colony dynamics and potential losses with and without varroa mites under different foraging conditions and under pesticide application. We also show how mitigation measures can be tested. Synthesis and applications . BEEHAVE offers a valuable tool for researchers to design and focus field experiments, for regulators to explore the relative importance of stressors to devise management and policy advice and for beekeepers to understand and predict varroa dynamics and effects of management interventions. We expect that scientists and stakeholders will find a variety of applications for BEEHAVE, stimulating further model development and the possible inclusion of other stressors of potential importance to honeybee colony dynamics.

The dynamics of adapting, unregulated populations and a modified fundamental theorem.

PubMed

O'Dwyer, James P

2013-01-06

A population in a novel environment will accumulate adaptive mutations over time, and the dynamics of this process depend on the underlying fitness landscape: the fitness of and mutational distance between possible genotypes in the population. Despite its fundamental importance for understanding the evolution of a population, inferring this landscape from empirical data has been problematic. We develop a theoretical framework to describe the adaptation of a stochastic, asexual, unregulated, polymorphic population undergoing beneficial, neutral and deleterious mutations on a correlated fitness landscape. We generate quantitative predictions for the change in the mean fitness and within-population variance in fitness over time, and find a simple, analytical relationship between the distribution of fitness effects arising from a single mutation, and the change in mean population fitness over time: a variant of Fisher's 'fundamental theorem' which explicitly depends on the form of the landscape. Our framework can therefore be thought of in three ways: (i) as a set of theoretical predictions for adaptation in an exponentially growing phase, with applications in pathogen populations, tumours or other unregulated populations; (ii) as an analytically tractable problem to potentially guide theoretical analysis of regulated populations; and (iii) as a basis for developing empirical methods to infer general features of a fitness landscape.

The potential energy landscape contribution to the dynamic heat capacity

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; McCoy, John D.

2011-05-01

The dynamic heat capacity of a simple polymeric, model glassformer was computed using molecular dynamics simulations by sinusoidally driving the temperature and recording the resultant energy. The underlying potential energy landscape of the system was probed by taking a time series of particle positions and quenching them. The resulting dynamic heat capacity demonstrates that the long time relaxation is the direct result of dynamics resulting from the potential energy landscape. Moreover, the equilibrium (low frequency) portion of the potential energy landscape contribution to the heat capacity is found to increase rapidly at low temperatures and at high packing fractions. This increase in the heat capacity is explained by a statistical mechanical model based on the distribution of minima in the potential energy landscape.

Solution landscapes in nematic microfluidics

NASA Astrophysics Data System (ADS)

Crespo, M.; Majumdar, A.; Ramos, A. M.; Griffiths, I. M.

2017-08-01

We study the static equilibria of a simplified Leslie-Ericksen model for a unidirectional uniaxial nematic flow in a prototype microfluidic channel, as a function of the pressure gradient G and inverse anchoring strength, B. We numerically find multiple static equilibria for admissible pairs (G , B) and classify them according to their winding numbers and stability. The case G = 0 is analytically tractable and we numerically study how the solution landscape is transformed as G increases. We study the one-dimensional dynamical model, the sensitivity of the dynamic solutions to initial conditions and the rate of change of G and B. We provide a physically interesting example of how the time delay between the applications of G and B can determine the selection of the final steady state.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Wei; Wang, Jin, E-mail: jin.wang.1@stonybrook.edu; State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022 Changchun, China and College of Physics, Jilin University, 130021 Changchun

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 andmore » 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.« less

Evaluation of Dynamic Coastal Response to Sea-level Rise Modifies Inundation Likelihood

NASA Technical Reports Server (NTRS)

Lentz, Erika E.; Thieler, E. Robert; Plant, Nathaniel G.; Stippa, Sawyer R.; Horton, Radley M.; Gesch, Dean B.

2016-01-01

Sea-level rise (SLR) poses a range of threats to natural and built environments, making assessments of SLR-induced hazards essential for informed decision making. We develop a probabilistic model that evaluates the likelihood that an area will inundate (flood) or dynamically respond (adapt) to SLR. The broad-area applicability of the approach is demonstrated by producing 30x30m resolution predictions for more than 38,000 sq km of diverse coastal landscape in the northeastern United States. Probabilistic SLR projections, coastal elevation and vertical land movement are used to estimate likely future inundation levels. Then, conditioned on future inundation levels and the current land-cover type, we evaluate the likelihood of dynamic response versus inundation. We find that nearly 70% of this coastal landscape has some capacity to respond dynamically to SLR, and we show that inundation models over-predict land likely to submerge. This approach is well suited to guiding coastal resource management decisions that weigh future SLR impacts and uncertainty against ecological targets and economic constraints.

AN INDICATOR OF FOREST DYNAMICS USING A SHIFTING LANDSCAPE MOSAIC

EPA Science Inventory

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

Recovery based on plot experiments is a poor predictor of landscape-level population impacts of agricultural pesticides.

PubMed

Topping, Christopher John; Kjaer, Lene Jung; Hommen, Udo; Høye, Toke Thomas; Preuss, Thomas G; Sibly, Richard M; van Vliet, Peter

2014-07-01

Current European Union regulatory risk assessment allows application of pesticides provided that recovery of nontarget arthropods in-crop occurs within a year. Despite the long-established theory of source-sink dynamics, risk assessment ignores depletion of surrounding populations and typical field trials are restricted to plot-scale experiments. In the present study, the authors used agent-based modeling of 2 contrasting invertebrates, a spider and a beetle, to assess how the area of pesticide application and environmental half-life affect the assessment of recovery at the plot scale and impact the population at the landscape scale. Small-scale plot experiments were simulated for pesticides with different application rates and environmental half-lives. The same pesticides were then evaluated at the landscape scale (10 km × 10 km) assuming continuous year-on-year usage. The authors' results show that recovery time estimated from plot experiments is a poor indicator of long-term population impact at the landscape level and that the spatial scale of pesticide application strongly determines population-level impact. This raises serious doubts as to the utility of plot-recovery experiments in pesticide regulatory risk assessment for population-level protection. Predictions from the model are supported by empirical evidence from a series of studies carried out in the decade starting in 1988. The issues raised then can now be addressed using simulation. Prediction of impacts at landscape scales should be more widely used in assessing the risks posed by environmental stressors. © 2014 SETAC.

Landscape dynamics of mountain pine beetles

Treesearch

John E. Lundquist; Robin M. Reich

2014-01-01

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

Free-energy landscapes from adaptively biased methods: Application to quantum systems

NASA Astrophysics Data System (ADS)

Calvo, F.

2010-10-01

Several parallel adaptive biasing methods are applied to the calculation of free-energy pathways along reaction coordinates, choosing as a difficult example the double-funnel landscape of the 38-atom Lennard-Jones cluster. In the case of classical statistics, the Wang-Landau and adaptively biased molecular-dynamics (ABMD) methods are both found efficient if multiple walkers and replication and deletion schemes are used. An extension of the ABMD technique to quantum systems, implemented through the path-integral MD framework, is presented and tested on Ne38 against the quantum superposition method.

Protocol for Landsat-Based Monitoring of Landscape Dynamics at North Coast and Cascades Network Parks

USGS Publications Warehouse

Kennedy, Robert E.; Cohen, Warren B.; Kirschbaum, Alan A.; Haunreiter, Erik

2007-01-01

Background and Objectives As part of the National Park Service's larger goal of developing long-term monitoring programs in response to the Natural Resource Challenge of 2000, the parks of the North Coast and Cascades Network (NCCN) have determined that monitoring of landscape dynamics is necessary to track ecosystem health (Weber and others, 2005). Landscape dynamics refer to a broad suite of ecological, geomorphological, and anthropogenic processes occurring across broad spatial scales. The NCCN has sought protocols that would leverage remote-sensing technologies to aid in monitoring landscape dynamics.

Local disturbance cycles and the maintenance of heterogeneity across scales in marine metapopulations.

PubMed

Gouhier, Tarik C; Guichard, Frédéric

2007-03-01

In marine systems, the occurrence and implications of disturbance-recovery cycles have been revealed at the landscape level, but only in demographically open or closed systems where landscape-level dynamics are assumed to have no feedback effect on regional dynamics. We present a mussel metapopulation model to elucidate the role of landscape-level disturbance cycles for regional response of mussel populations to onshore productivity and larval transport. Landscape dynamics are generated through spatially explicit rules, and each landscape is connected to its neighbor through unidirectional larval dispersal. The role of landscape disturbance cycles in the regional system behavior is elucidated (1) in demographically open vs. demographically coupled systems, in relation to (2) onshore reproductive output and (3) the temporal scale of landscape disturbance dynamics. By controlling for spatial structure at the landscape and metapopulation levels, we first demonstrate the interaction between landscape and oceanographic connectivity. The temporal scale of disturbance cycles, as controlled by mussel colonization rate, plays a critical role in the regional behavior of the system. Indeed, fast disturbance cycles are responsible for regional synchrony in relation to onshore reproductive output. Slow disturbance cycles, however, lead to increased robustness to changes in productivity and to demographic coupling. These testable predictions indicate that the occurrence and temporal scale of local disturbance-recovery dynamics can drive large-scale variability in demographically open systems, and the response of metapopulations to changes in nearshore productivity.

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

Treesearch

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

2017-01-01

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

Free Energy Computations by Minimization of Kullback-Leibler Divergence: An Efficient Adaptive Biasing Potential Method for Sparse Representations

DTIC Science & Technology

2011-10-14

landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells and...statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells and estimating the free energy...experimentally, to characterize global changes as well as investigate relative stabilities. In most applications, a brute- force computation based on

Dynamic effects of biochar concentration and particle size on hydraulic properties of sand

USDA-ARS?s Scientific Manuscript database

Large-scale application of biochar has been promoted as a strategy for reclaiming degraded soils and conserving natural landscapes because of biochar potentials to alter the soil biogeochemical and physical properties and improve soil quality. Several studies have reported that biochar amendment at ...

A Proposed Approach for Screening Level Assessment of Risk to Songbird Populations from Pesticide Application in Cotton Fields

EPA Science Inventory

Due to complex population dynamics and migration behaviors, the well-being of animal populations that host human diseases sometimes varies across landscapes in ways that cannot be deduced from geographic abundance patterns alone. In such cases, efficient management of ecologica...

Exploring the Decision Landscape using System Sketch: Integration and Display of Ecosystem Services & Indicators Using the DPSIR Framework and Dynamic Web Application

EPA Science Inventory

Stakeholders can use the tool to accomplish their sustainability goals by: Understanding interactions and feedback loops within human-environmental systems; Identifying areas of the system not previously considered and avoiding unintended consequences; Identifying metrics, indica...

Exploring the Decision Landscape: Integration of Human and Natural Systems Using the Driver-Pressure-State-Impact-Response Framework and Dynamic Web Application

EPA Science Inventory

Making decisions to increase community or regional sustainability requires a comprehensive understanding of the linkages between environmental, social, and economic systems. We present a visualization tool that can improve decision processes and improve interdisciplinary research...

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

Treesearch

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

2013-01-01

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

Towards integrated modelling of soil organic carbon cycling at landscape scale

NASA Astrophysics Data System (ADS)

Viaud, V.

2009-04-01

Soil organic carbon (SOC) is recognized as a key factor of the chemical, biological and physical quality of soil. Numerous models of soil organic matter turnover have been developed since the 1930ies, most of them dedicated to plot scale applications. More recently, they have been applied to national scales to establish the inventories of carbon stocks directed by the Kyoto protocol. However, only few studies consider the intermediate landscape scale, where the spatio-temporal pattern of land management practices, its interactions with the physical environment and its impacts on SOC dynamics can be investigated to provide guidelines for sustainable management of soils in agricultural areas. Modelling SOC cycling at this scale requires accessing accurate spatially explicit input data on soils (SOC content, bulk density, depth, texture) and land use (land cover, farm practices), and combining both data in a relevant integrated landscape representation. The purpose of this paper is to present a first approach to modelling SOC evolution in a small catchment. The impact of the way landscape is represented on SOC stocks in the catchment was more specifically addressed. This study was based on the field map, the soil survey, the crop rotations and land management practices of an actual 10-km² agricultural catchment located in Brittany (France). RothC model was used to drive soil organic matter dynamics. Landscape representation in the form of a systematic regular grid, where driving properties vary continuously in space, was compared to a representation where landscape is subdivided into a set of homogeneous geographical units. This preliminary work enabled to identify future needs to improve integrated soil-landscape modelling in agricultural areas.

Historical fire and vegetation dynamics in dry forests of the interior Pacific Northwest, USA, and relationships to northern spotted owl (Strix occidentalis caurina) habitat conservation

Treesearch

Rebecca S.H. Kennedy; Michael C. Wimberly

2009-01-01

Regional conservation planning frequently relies on general assumptions about historical disturbance regimes to inform decisions about landscape restoration, reserve allocations, and landscape management. Spatially explicit simulations of landscape dynamics provide quantitative estimates of landscape structure and allow for the testing of alternative scenarios. We used...

Experimental Beetle Metapopulations Respond Positively to Dynamic Landscapes and Reduced Connectivity

PubMed Central

Govindan, Byju N.; Swihart, Robert K.

2012-01-01

Interactive effects of multiple environmental factors on metapopulation dynamics have received scant attention. We designed a laboratory study to test hypotheses regarding interactive effects of factors affecting the metapopulation dynamics of red flour beetle, Tribolium castaneum. Within a four-patch landscape we modified resource level (constant and diminishing), patch connectivity (high and low) and patch configuration (static and dynamic) to conduct a 23 factorial experiment, consisting of 8 metapopulations, each with 3 replicates. For comparison, two control populations consisting of isolated and static subpopulations were provided with resources at constant or diminishing levels. Longitudinal data from 22 tri-weekly counts of beetle abundance were analyzed using Bayesian Poisson generalized linear mixed models to estimate additive and interactive effects of factors affecting abundance. Constant resource levels, low connectivity and dynamic patches yielded greater levels of adult beetle abundance. For a given resource level, frequency of colonization exceeded extinction in landscapes with dynamic patches when connectivity was low, thereby promoting greater patch occupancy. Negative density dependence of pupae on adults occurred and was stronger in landscapes with low connectivity and constant resources; these metapopulations also demonstrated greatest stability. Metapopulations in control landscapes went extinct quickly, denoting lower persistence than comparable landscapes with low connectivity. When landscape carrying capacity was constant, habitat destruction coupled with low connectivity created asynchronous local dynamics and refugia within which cannibalism of pupae was reduced. Increasing connectivity may be counter-productive and habitat destruction/recreation may be beneficial to species in some contexts. PMID:22509314

DYNAMIC LANDSCAPES, STABILITY AND ECOLOGICAL MODELING

EPA Science Inventory

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

State-and-transition simulation models: a framework for forecasting landscape change

USGS Publications Warehouse

Daniel, Colin; Frid, Leonardo; Sleeter, Benjamin M.; Fortin, Marie-Josée

2016-01-01

SummaryA wide range of spatially explicit simulation models have been developed to forecast landscape dynamics, including models for projecting changes in both vegetation and land use. While these models have generally been developed as separate applications, each with a separate purpose and audience, they share many common features.We present a general framework, called a state-and-transition simulation model (STSM), which captures a number of these common features, accompanied by a software product, called ST-Sim, to build and run such models. The STSM method divides a landscape into a set of discrete spatial units and simulates the discrete state of each cell forward as a discrete-time-inhomogeneous stochastic process. The method differs from a spatially interacting Markov chain in several important ways, including the ability to add discrete counters such as age and time-since-transition as state variables, to specify one-step transition rates as either probabilities or target areas, and to represent multiple types of transitions between pairs of states.We demonstrate the STSM method using a model of land-use/land-cover (LULC) change for the state of Hawai'i, USA. Processes represented in this example include expansion/contraction of agricultural lands, urbanization, wildfire, shrub encroachment into grassland and harvest of tree plantations; the model also projects shifts in moisture zones due to climate change. Key model output includes projections of the future spatial and temporal distribution of LULC classes and moisture zones across the landscape over the next 50 years.State-and-transition simulation models can be applied to a wide range of landscapes, including questions of both land-use change and vegetation dynamics. Because the method is inherently stochastic, it is well suited for characterizing uncertainty in model projections. When combined with the ST-Sim software, STSMs offer a simple yet powerful means for developing a wide range of models of landscape dynamics.

Carbonate landscapes evolution: Insights from 36Cl

NASA Astrophysics Data System (ADS)

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 transition toward a weathering-limited dynamics may prevent hillslope denudation from balancing the rate of base level fall imposed by the river network and could potentially explain the development of high local relief observed in many Mediterranean carbonate landscapes.

Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics.

PubMed

Hayes, Ryan L; Armacost, Kira A; Vilseck, Jonah Z; Brooks, Charles L

2017-04-20

Multisite λ dynamics (MSλD) is a powerful emerging method in free energy calculation that allows prediction of relative free energies for a large set of compounds from very few simulations. Calculating free energy differences between substituents that constitute large volume or flexibility jumps in chemical space is difficult for free energy methods in general, and for MSλD in particular, due to large free energy barriers in alchemical space. This study demonstrates that a simple biasing potential can flatten these barriers and introduces an algorithm that determines system specific biasing potential coefficients. Two sources of error, deep traps at the end points and solvent disruption by hard-core potentials, are identified. Both scale with the size of the perturbed substituent and are removed by sharp biasing potentials and a new soft-core implementation, respectively. MSλD with landscape flattening is demonstrated on two sets of molecules: derivatives of the heat shock protein 90 inhibitor geldanamycin and derivatives of benzoquinone. In the benzoquinone system, landscape flattening leads to 2 orders of magnitude improvement in transition rates between substituents and robust solvation free energies. Landscape flattening opens up new applications for MSλD by enabling larger chemical perturbations to be sampled with improved precision and accuracy.

A novel simulation methodology merging source-sink dynamics and landscape connectivity

EPA Science Inventory

Source-sink dynamics are an emergent property of complex species-landscape interactions. This study explores the patterns of source and sink behavior that become established across a large landscape, using a simulation model for the northern spotted owl (Strix occidentalis cauri...

Evaluation of dynamic coastal response to sea-level rise modifies inundation likelihood

USGS Publications Warehouse

Lentz, Erika E.; Thieler, E. Robert; Plant, Nathaniel G.; Stippa, Sawyer R.; Horton, Radley M.; Gesch, Dean B.

2016-01-01

Sea-level rise (SLR) poses a range of threats to natural and built environments1, 2, making assessments of SLR-induced hazards essential for informed decision making3. We develop a probabilistic model that evaluates the likelihood that an area will inundate (flood) or dynamically respond (adapt) to SLR. The broad-area applicability of the approach is demonstrated by producing 30 × 30 m resolution predictions for more than 38,000 km2 of diverse coastal landscape in the northeastern United States. Probabilistic SLR projections, coastal elevation and vertical land movement are used to estimate likely future inundation levels. Then, conditioned on future inundation levels and the current land-cover type, we evaluate the likelihood of dynamic response versus inundation. We find that nearly 70% of this coastal landscape has some capacity to respond dynamically to SLR, and we show that inundation models over-predict land likely to submerge. This approach is well suited to guiding coastal resource management decisions that weigh future SLR impacts and uncertainty against ecological targets and economic constraints.

An indicator of forest dynamics using a shifting landscape mosaic

Treesearch

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

2009-01-01

The composition of a landscape is a fundamental indicator in land-cover pattern assessments. The objective of this paper was to evaluate a landscape composition indicator called ‘landscape mosaic’ as a framework for interpreting land-cover dynamics over a 9-year period in a 360,000 km2 study area in the southern United States. The indicator...

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

Treesearch

Christopher A. Dicus; Kevin J. Osborne

2015-01-01

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

Brownian motion on random dynamical landscapes

NASA Astrophysics Data System (ADS)

Suñé Simon, Marc; Sancho, José María; Lindenberg, Katja

2016-03-01

We present a study of overdamped Brownian particles moving on a random landscape of dynamic and deformable obstacles (spatio-temporal disorder). The obstacles move randomly, assemble, and dissociate following their own dynamics. This landscape may account for a soft matter or liquid environment in which large obstacles, such as macromolecules and organelles in the cytoplasm of a living cell, or colloids or polymers in a liquid, move slowly leading to crowding effects. This representation also constitutes a novel approach to the macroscopic dynamics exhibited by active matter media. We present numerical results on the transport and diffusion properties of Brownian particles under this disorder biased by a constant external force. The landscape dynamics are characterized by a Gaussian spatio-temporal correlation, with fixed time and spatial scales, and controlled obstacle concentrations.

Exploring Curation as a Core Competency in Digital and Media Literacy Education

ERIC Educational Resources Information Center

Mihailidis, Paul; Cohen, James N.

2013-01-01

In today's hypermedia landscape, youth and young adults are increasingly using social media platforms, online aggregators and mobile applications for daily information use. Communication educators, armed with a host of free, easy-to-use online tools, have the ability to create dynamic approaches to teaching and learning about information and…

Exploring the Decision Landscape: Integration and Display of Ecosystem Services & Indicators Using the Driver-Pressure-State-Impact-Response Framework and Dynamic Web Application

EPA Science Inventory

Making decisions to increase community or regional sustainability requires a comprehensive understanding of the linkages between environmental, social, and economic systems. We present a visualization tool that can improve decision processes by enhancing understanding of system c...

Scale-dependent erosional patterns in steady-state and transient-state landscapes.

PubMed

Tejedor, Alejandro; Singh, Arvind; Zaliapin, Ilya; Densmore, Alexander L; Foufoula-Georgiou, Efi

2017-09-01

Landscape topography is the expression of the dynamic equilibrium between external forcings (for example, climate and tectonics) and the underlying lithology. The magnitude and spatial arrangement of erosional and depositional fluxes dictate the evolution of landforms during both statistical steady state (SS) and transient state (TS) of major landscape reorganization. For SS landscapes, the common expectation is that any point of the landscape has an equal chance to erode below or above the landscape median erosion rate. We show that this is not the case. Afforded by a unique experimental landscape that provided a detailed space-time recording of erosional fluxes and by defining the so-called E50-area curve, we reveal for the first time that there exists a hierarchical pattern of erosion. Specifically, hillslopes and fluvial channels erode more rapidly than the landscape median erosion rate, whereas intervening parts of the landscape in terms of upstream contributing areas (colluvial regime) erode more slowly. We explain this apparent paradox by documenting the dynamic nature of SS landscapes-landscape locations may transition from being a hillslope to being a valley and then to being a fluvial channel due to ridge migration, channel piracy, and small-scale landscape dynamics through time. Under TS conditions caused by increased precipitation, we show that the E50-area curve drastically changes shape during landscape reorganization. Scale-dependent erosional patterns, as observed in this study, suggest benchmarks in evaluating numerical models and interpreting the variability of sampled erosional rates in field landscapes.

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

PubMed

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.

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

PubMed Central

Olariu, Victor; Manesso, Erica

2017-01-01

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. PMID:28680655

Geographic applications of ERTS-A imagery to rural landscape change

NASA Technical Reports Server (NTRS)

Rehder, J. B. (Principal Investigator)

1972-01-01

There are no author-identified significant results in this report. The study area, centered on Knoxville, Tennessee, encompasses nearly 20,000 square miles. The Knoxville Test Site, an 11 x 21 mile area over the city of Knoxville and the western portion of Knox County, has been chosen for the analysis of landscape change detection associated with urban growth. The second area, the Cumberland Plateau Test Site, exhibits landscape change through forest alterations and landform disturbances associated with strip mining in the area and was so chosen for its sharp contrasts in physical and human phenomena as well as its change dynamics. Accomplishments since reception of ERTS-1 imagery include: (1) basic cataloging and classifying of the data into a filling system; (2) a densitometer analysis; (3) first look analysis; and (4) preparation of results from the project. Examples of all four bands of the MSS have been received and analyses reveal distinctive positive and negative reactions. Band 5 has been found to be best for landscape analysis of contrasts between urban and rural landscapes, and band 7 for topographic features and water surfaces. Preliminary results are summarized.

Landscape Pattern Dynamic Change Research of Harbin Songbei Based on GIS Technology

NASA Astrophysics Data System (ADS)

Chenyang, Ding; Kun, Wang; Kang, Li Kang

2018-05-01

With the rapid development of social economy in the Songhua River basin, there are big dynamic change of the landscape of the new area beside the river bank, which is represented by Harbin Songbei. This paper selects 13 representative indexes from landscape and patch level, analyzes the cause and process of the change of landscape pattern in Songbei during 2005-2015, and probes into the characteristics of the change based on the principle of landscape ecology, using remote sensing and GIS technology and Fragstats3.3 software data statistics.

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

PubMed

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.

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

Treesearch

Michael C. Wimberly; Rebecca S.H. Kennedy

2008-01-01

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

Scale-dependent erosional patterns in steady-state and transient-state landscapes

PubMed Central

Tejedor, Alejandro; Singh, Arvind; Zaliapin, Ilya; Densmore, Alexander L.; Foufoula-Georgiou, Efi

2017-01-01

Landscape topography is the expression of the dynamic equilibrium between external forcings (for example, climate and tectonics) and the underlying lithology. The magnitude and spatial arrangement of erosional and depositional fluxes dictate the evolution of landforms during both statistical steady state (SS) and transient state (TS) of major landscape reorganization. For SS landscapes, the common expectation is that any point of the landscape has an equal chance to erode below or above the landscape median erosion rate. We show that this is not the case. Afforded by a unique experimental landscape that provided a detailed space-time recording of erosional fluxes and by defining the so-called E50-area curve, we reveal for the first time that there exists a hierarchical pattern of erosion. Specifically, hillslopes and fluvial channels erode more rapidly than the landscape median erosion rate, whereas intervening parts of the landscape in terms of upstream contributing areas (colluvial regime) erode more slowly. We explain this apparent paradox by documenting the dynamic nature of SS landscapes—landscape locations may transition from being a hillslope to being a valley and then to being a fluvial channel due to ridge migration, channel piracy, and small-scale landscape dynamics through time. Under TS conditions caused by increased precipitation, we show that the E50-area curve drastically changes shape during landscape reorganization. Scale-dependent erosional patterns, as observed in this study, suggest benchmarks in evaluating numerical models and interpreting the variability of sampled erosional rates in field landscapes. PMID:28959728

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

USGS Publications Warehouse

Blandón, A.C.; Perelman, S.B.; Ramírez, M.; López, A.; Javier, O.; Robbins, Chandler S.

2016-01-01

Habitat loss and fragmentation are considered the main causes of species extinctions, particularly in tropical ecosystems. The objective of this work was to evaluate the temporal dynamics of tropical bird communities in landscapes with different levels of fragmentation in eastern Guatemala. We evaluated five bird community dynamic parameters for forest specialists and generalists: (1) species extinction, (2) species turnover, (3) number of colonizing species, (4) relative species richness, and (5) a homogeneity index. For each of 24 landscapes, community dynamic parameters were estimated from bird point count data, for the 1998–1999 and 2008–2009 periods, accounting for species’ detection probability. Forest specialists had higher extinction rates and a smaller number of colonizing species in landscapes with higher fragmentation, thus having lower species richness in both time periods. Alternatively, forest generalists elicited a completely different pattern, showing a curvilinear association to forest fragmentation for most parameters. Thus, greater community dynamism for forest generalists was shown in landscapes with intermediate levels of fragmentation. Our study supports general theory regarding the expected negative effects of habitat loss and fragmentation on the temporal dynamics of biotic communities, particularly for forest specialists, providing strong evidence from understudied tropical bird communities.

Increasing connectivity between metapopulation ecology and landscape ecology.

PubMed

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.

Aging, memory, and nonhierarchical energy landscape of spin jam

NASA Astrophysics Data System (ADS)

Samarakoon, Anjana; Sato, Taku J.; Chen, Tianran; Chern, Gai-Wei; Yang, Junjie; Klich, Israel; Sinclair, Ryan; Zhou, Haidong; Lee, Seung-Hun

2016-10-01

The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic alloys has been an exceptionally convenient laboratory frame for studying complex dynamics resulting from a hierarchical energy landscape with rugged funnels. Here, we show, by a bulk susceptibility and Monte Carlo simulation study, that densely populated frustrated magnets in a spin jam state exhibit much weaker memory effects than spin glasses, and the characteristic properties can be reproduced by a nonhierarchical landscape with a wide and nearly flat but rough bottom. Our results illustrate that the memory effects can be used to probe different slow dynamics of glassy materials, hence opening a window to explore their distinct energy landscapes.

Landscape matrix mediates occupancy dynamics of Neotropical avian insectivores

USGS Publications Warehouse

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

2011-01-01

In addition to patch-level attributes (i.e., area and isolation), the nature of land cover between habitat patches (the matrix) may drive colonization and extinction dynamics in fragmented landscapes. Despite a long-standing recognition of matrix effects in fragmented systems, an understanding of the relative impacts of different types of land cover on patterns and dynamics of species occurrence remains limited. We employed multi-season occupancy models to determine the relative influence of patch area, patch isolation, within-patch vegetation structure, and landscape matrix on occupancy dynamics of nine Neotropical nsectivorous birds in 99 forest patches embedded in four matrix types (agriculture, suburban evelopment, bauxite mining, and forest) in central Jamaica. We found that within-patch vegetation structure and the matrix type between patches were more important than patch area and patch isolation in determining local colonization and local extinction probabilities, and that the effects of patch area, isolation, and vegetation structure on occupancy dynamics tended to be matrix and species dependent. Across the avian community, the landscape matrix influenced local extinction more than local colonization, indicating that extinction processes, rather than movement, likely drive interspecific differences in occupancy dynamics. These findings lend crucial empirical support to the hypothesis that species occupancy dynamics in fragmented systems may depend greatly upon the landscape context.

Focusing ecological research for conservation.

PubMed

Cristescu, Bogdan; Boyce, Mark S

2013-11-01

Ecologists are increasingly actively involved in conservation. We identify five key topics from a broad sweep of ecology that merit research attention to meet conservation needs. We examine questions from landscape ecology, behavioral ecology, ecosystem dynamics, community ecology, and nutrient cycling related to key topics. Based on literature review and publication trend assessment, consultation with colleagues, and roundtable discussions at the 24th International Congress for Conservation Biology, focused research on the following topics could benefit conservation while advancing ecological understanding: 1. Carbon sequestration, requiring increased linkages to biodiversity conservation; 2. Ecological invasiveness, challenging our ability to find solutions to ecological aliens; 3. Individual variation, having applications in the conservation of rare species; 4. Movement of organisms, integrating ecological processes across landscapes and scales and addressing habitat fragmentation; and 5. Trophic-level interactions, driving ecological dynamics at the ecosystem-level. Addressing these will require cross-disciplinary research under the overarching framework of conservation ecology.

What you should know about land-cover data

USGS Publications Warehouse

Gallant, Alisa L.

2009-01-01

Wildlife biologists are using land-characteristics data sets for a variety of applications. Many kinds of landscape variables have been characterized and the resultant data sets or maps are readily accessible. Often, too little consideration is given to the accuracy or traits of these data sets, most likely because biologists do not know how such data are compiled and rendered, or the potential pitfalls that can be encountered when applying these data. To increase understanding of the nature of land-characteristics data sets, I introduce aspects of source information and data-handling methodology that include the following: ambiguity of land characteristics; temporal considerations and the dynamic nature of the landscape; type of source data versus landscape features of interest; data resolution, scale, and geographic extent; data entry and positional problems; rare landscape features; and interpreter variation. I also include guidance for determining the quality of land-characteristics data sets through metadata or published documentation, visual clues, and independent information. The quality or suitability of the data sets for wildlife applications may be improved with thematic or spatial generalization, avoidance of transitional areas on maps, and merging of multiple data sources. Knowledge of the underlying challenges in compiling such data sets will help wildlife biologists to better assess the strengths and limitations and determine how best to use these data.

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

NASA Astrophysics Data System (ADS)

Iqbal, J.; Garcia, C. V.

2009-04-01

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

Novel Kalman Filter Algorithm for Statistical Monitoring of Extensive Landscapes with Synoptic Sensor Data

PubMed Central

Czaplewski, Raymond L.

2015-01-01

Wall-to-wall remotely sensed data are increasingly available to monitor landscape dynamics over large geographic areas. However, statistical monitoring programs that use post-stratification cannot fully utilize those sensor data. The Kalman filter (KF) is an alternative statistical estimator. I develop a new KF algorithm that is numerically robust with large numbers of study variables and auxiliary sensor variables. A National Forest Inventory (NFI) illustrates application within an official statistics program. Practical recommendations regarding remote sensing and statistical issues are offered. This algorithm has the potential to increase the value of synoptic sensor data for statistical monitoring of large geographic areas. PMID:26393588

Generalizing ecological site concepts of the Colorado Plateau for landscape-level applications

USGS Publications Warehouse

Duniway, Michael C.; Nauman, Travis; Johanson, Jamin K.; Green, Shane; Miller, Mark E.; Bestelmeyer, Brandon T.

2016-01-01

Numerous ecological site descriptions in the southern Utah portion of the Colorado Plateau can be difficult to navigate, so we held a workshop aimed at adding value and functionality to the current ecological site system.We created new groups of ecological sites and drafted state-and-transition models for these new groups.We were able to distill the current large number of ecological sites in the study area (ca. 150) into eight ecological site groups that capture important variability in ecosystem dynamics.Several inventory and monitoring programs and landscape scale planning actions will likely benefit from more generalized ecological site group concepts.

Landscape Pattern Determines Neighborhood Size and Structure within a Lizard Population

PubMed Central

Ryberg, Wade A.; Hill, Michael T.; Painter, Charles W.; Fitzgerald, Lee A.

2013-01-01

Although defining population structure according to discrete habitat patches is convenient for metapopulation theories, taking this approach may overlook structure within populations continuously distributed across landscapes. For example, landscape features within habitat patches direct the movement of organisms and define the density distribution of individuals, which can generate spatial structure and localized dynamics within populations as well as among them. Here, we use the neighborhood concept, which describes population structure relative to the scale of individual movements, to illustrate how localized dynamics within a population of lizards (Sceloporus arenicolus) arise in response to variation in landscape pattern within a continuous habitat patch. Our results emphasize links between individual movements at small scales and the emergence of spatial structure within populations which resembles metapopulation dynamics at larger scales. We conclude that population dynamics viewed in a landscape context must consider the explicit distribution and movement of individuals within continuous habitat as well as among habitat patches. PMID:23441217

A wave-mechanical model of incoherent quasielastic scattering in complex systems.

PubMed

Frauenfelder, Hans; Fenimore, Paul W; Young, Robert D

2014-09-02

Quasielastic incoherent neutron scattering (QENS) is an important tool for the exploration of the dynamics of complex systems such as biomolecules, liquids, and glasses. The dynamics is reflected in the energy spectra of the scattered neutrons. Conventionally these spectra are decomposed into a narrow elastic line and a broad quasielastic band. The band is interpreted as being caused by Doppler broadening due to spatial motion of the target molecules. We propose a quantum-mechanical model in which there is no separate elastic line. The quasielastic band is composed of sharp lines with twice the natural line width, shifted from the center by a random walk of the protein in the free-energy landscape of the target molecule. The walk is driven by vibrations and by external fluctuations. We first explore the model with the Mössbauer effect. In the subsequent application to QENS we treat the incoming neutron as a de Broglie wave packet. While the wave packet passes the protons in the protein and the hydration shell it exchanges energy with the protein during the passage time of about 100 ns. The energy exchange broadens the ensemble spectrum. Because the exchange involves the free-energy landscape of the protein, the QENS not only provides insight into the protein dynamics, but it may also illuminate the free-energy landscape of the protein-solvent system.

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

NASA Astrophysics Data System (ADS)

Zhou, Da; Qian, Hong

2011-09-01

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

The dynamics of human-induced land cover change in miombo ecosystems of southern Africa

NASA Astrophysics Data System (ADS)

Jaiteh, Malanding Sambou

Understanding human-induced land cover change in the miombo require the consistent, geographically-referenced, data on temporal land cover characteristics as well as biophysical and socioeconomic drivers of land use, the major cause of land cover change. The overall goal of this research to examine the applications of high-resolution satellite remote sensing data in studying the dynamics of human-induced land cover change in the miombo. Specific objectives are to: (1) evaluate the applications of computer-assisted classification of Landsat Thematic Mapper (TM) data for land cover mapping in the miombo and (2) analyze spatial and temporal patterns of landscape change locations in the miombo. Stepwise Thematic Classification, STC (a hybrid supervised-unsupervised classification) procedure for classifying Landsat TM data was developed and tested using Landsat TM data. Classification accuracy results were compared to those from supervised and unsupervised classification. The STC provided the highest classification accuracy i.e., 83.9% correspondence between classified and referenced data compared to 44.2% and 34.5% for unsupervised and supervised classification respectively. Improvements in the classification process can be attributed to thematic stratification of the image data into spectrally homogenous (thematic) groups and step-by-step classification of the groups using supervised or unsupervised classification techniques. Supervised classification failed to classify 18% of the scene evidence that training data used did not adequately represent all of the variability in the data. Application of the procedure in drier miombo produced overall classification accuracy of 63%. This is much lower than that of wetter miombo. The results clearly demonstrate that digital classification of Landsat TM can be successfully implemented in the miombo without intensive fieldwork. Spatial characteristics of land cover change in agricultural and forested landscapes in central Malawi were analyzed for the period 1984 to 1995 spatial pattern analysis methods. Shifting cultivation areas, Agriculture in forested landscape, experienced highest rate of woodland cover fragmentation with mean patch size of closed woodland cover decreasing from 20ha to 7.5ha. Permanent bare (cropland and settlement) in intensive agricultural matrix landscapes increased 52% largely through the conversion of fallow areas. Protected National Park area remained fairly unchanged although closed woodland area increased by 4%, mainly from regeneration of open woodland. This study provided evidence that changes in spatial characteristics in the miombo differ with landscape. Land use change (i.e. conversion to cropland) is the primary driving force behind changes in landscape spatial patterns. Also, results revealed that exclusion of intense human use (i.e. cultivation and woodcutting) through regulations and/or fencing increased both closed woodland area (through regeneration of open woodland) and overall connectivity in the landscape. Spatial characteristics of land cover change were analyzed at locations in Malawi (wetter miombo) and Zimbabwe (drier miombo). Results indicate land cover dynamics differ both between and within case study sites. In communal areas in the Kasungu scene, land cover change is dominated by woodland fragmentation to open vegetation. Change in private commercial lands was dominantly expansion of bare (settlement and cropland) areas primarily at the expense of open vegetation (fallow land).

Monitoring Freeze-Thaw States in the Pan-Arctic: Application of Microwave Remote Sensing to Monitoring Hydrologic and Ecological Processes

NASA Astrophysics Data System (ADS)

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

2004-12-01

The transition of the landscape between predominantly frozen and non-frozen conditions in seasonally frozen environments impacts climate, hydrological, ecological and biogeochemical processes profoundly. Satellite microwave remote sensing is uniquely capable of detecting and monitoring a range of related biophysical processes associated with the measurement of landscape freeze/thaw status. We present the development, physical basis, current techniques and selected hydrological applications of satellite-borne microwave remote sensing of landscape freeze/thaw states for the terrestrial cryosphere. Major landscape hydrological processes embracing the remotely-sensed freeze/thaw signal include timing and spatial dynamics of seasonal snowmelt and associated soil thaw, runoff generation and flooding, ice breakup in large rivers and lakes, and timing and length of vegetation growing seasons and associated productivity and trace gas exchange. Employing both active and passive microwave sensors, we apply a selection of temporal change classification algorithms to examine a variety of hydrologic processes. We investigate contemporaneous and retrospective applications of the QuikSCAT scatterometer, and the SSM/I and SMMR radiometers to this end. Results illustrate the strong correspondence between regional thawing, seasonal ice break up for rivers, and the springtime pulse in river flow. We present the physical principles of microwave sensitivity to landscape freeze/thaw state, recent progress in applying these principles toward satellite remote sensing of freeze/thaw processes over broad regions, and potential for future global monitoring of this significant phenomenon of the global cryosphere. This work was carried out at the Jet Propulsion Laboratory, California Institute of Technology, and at the University of Montana, Missoula, under contract to the National Aeronautics and Space Administration.

Aging, memory, and nonhierarchical energy landscape of spin jam

PubMed Central

Samarakoon, Anjana; Sato, Taku J.; Chen, Tianran; Chern, Gai-Wei; Yang, Junjie; Klich, Israel; Sinclair, Ryan; Zhou, Haidong; Lee, Seung-Hun

2016-01-01

The notion of complex energy landscape underpins the intriguing dynamical behaviors in many complex systems ranging from polymers, to brain activity, to social networks and glass transitions. The spin glass state found in dilute magnetic alloys has been an exceptionally convenient laboratory frame for studying complex dynamics resulting from a hierarchical energy landscape with rugged funnels. Here, we show, by a bulk susceptibility and Monte Carlo simulation study, that densely populated frustrated magnets in a spin jam state exhibit much weaker memory effects than spin glasses, and the characteristic properties can be reproduced by a nonhierarchical landscape with a wide and nearly flat but rough bottom. Our results illustrate that the memory effects can be used to probe different slow dynamics of glassy materials, hence opening a window to explore their distinct energy landscapes. PMID:27698141

Landscape dynamics analysis of the Yongding River watershed (Mentougou section) by multi-temporal Landsat imagery

NASA Astrophysics Data System (ADS)

Zhang, Yuhu; Yu, Changqing; Qi, Jiaguo; Zhang, Zili; Shi, Qinshan

2007-11-01

The problem of efficient use of multi-temporal remotely sensed data for land-cover and landscape pattern dynamics has already considerable attention in landscape ecology and some other disciplines. This research develops and tests a methodological approach to monitor and analysis landscape dynamics change of Yongding river watershed (Mentougou section) as study area from 1988 to 2005, The result shows that the OIF is the best method of optimal bands selection in Landsat TM remote sensing data, TM3, 4, 5 bands is optimal band combination ;the Mentougou Reach of Yongding river watershed landscape changed significantly in terms of its composition over the period 1988-2005, The total landscape patches of study area in 2005 are more those in 1988,2001, Mean patch size(MPS)decreased sharply, Number of patches(NP) increased sharply, The landscape pattern takes on the fragmentation trends under the effect on the human activity. The forest (woodland and shrubland)are the main landscape matrix. with a significant decrease in croplands and a increase in built-up (residential, urban land) and industrial minerals mining land(coal, open-pit)over the 17 years, And the underlying socio-economic and other drivers of landscape change in study area are discussed.

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

PubMed Central

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

2014-01-01

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

The organization and human use of terai riverine grasslands in the Royal Chitwan National Park, Nepal (Vol 2).

Treesearch

John F. Lehmkuhl

1999-01-01

I studied the landscape dynamics, organization, and productivity of a toll-grass and riverine forest mosaic in the eastern portion of Chitwan National Park, Nepal. Aerial photograph interpretation, releve sampling, experimental plots, models, and foraging studies were done. A model of landscape dynamics showed that fluvia1 action controlled landscape organization. Ten...

Variable flushing mechanisms and landscape structure control stream DOC export during snowmelt in a set of nested catchments

Treesearch

Vincent J. Pacific; Kelsey G. Jencso; Brian L. McGlynn

2010-01-01

Stream DOC dynamics during snowmelt have been the focus of much research, and numerous DOC mobilization and delivery mechanisms from riparian and upland areas have been proposed. However, landscape structure controls on DOC export from riparian and upland landscape elements remains poorly understood. We investigated stream and groundwater DOC dynamics across three...

Importance of ecotone type to landscape dynamics at biome transition zones

USDA-ARS?s Scientific Manuscript database

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

Global Langevin model of multidimensional biomolecular dynamics.

PubMed

Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard

2016-11-14

Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F(). To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F(), which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

Global Langevin model of multidimensional biomolecular dynamics

NASA Astrophysics Data System (ADS)

Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard

2016-11-01

Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F ( 𝒙 ) . To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F ( 𝒙 ) , which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

Dynamics of Soil Organic Carbon and Microbial Biomass Carbon in Relation to Water Erosion and Tillage Erosion

PubMed Central

Xiaojun, Nie; Jianhui, Zhang; Zhengan, Su

2013-01-01

Dynamics of soil organic carbon (SOC) are associated with soil erosion, yet there is a shortage of research concerning the relationship between soil erosion, SOC, and especially microbial biomass carbon (MBC). In this paper, we selected two typical slope landscapes including gentle and steep slopes from the Sichuan Basin, China, and used the 137Cs technique to determine the effects of water erosion and tillage erosion on the dynamics of SOC and MBC. Soil samples for the determination of 137Cs, SOC, MBC and soil particle-size fractions were collected on two types of contrasting hillslopes. 137Cs data revealed that soil loss occurred at upper slope positions of the two landscapes and soil accumulation at the lower slope positions. Soil erosion rates as well as distribution patterns of the <0.002-mm clay shows that water erosion is the major process of soil redistribution in the gentle slope landscape, while tillage erosion acts as the dominant process of soil redistribution in the steep slope landscape. In gentle slope landscapes, both SOC and MBC contents increased downslope and these distribution patterns were closely linked to soil redistribution rates. In steep slope landscapes, only SOC contents increased downslope, dependent on soil redistribution. It is noticeable that MBC/SOC ratios were significantly lower in gentle slope landscapes than in steep slope landscapes, implying that water erosion has a negative effect on the microbial biomass compared with tillage erosion. It is suggested that MBC dynamics are closely associated with soil redistribution by water erosion but independent of that by tillage erosion, while SOC dynamics are influenced by soil redistribution by both water erosion and tillage erosion. PMID:23717530

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

NASA Astrophysics Data System (ADS)

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 forces.

Accelerating atomistic simulations through self-learning bond-boost hyperdynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perez, Danny; Voter, Arthur F

2008-01-01

By altering the potential energy landscape on which molecular dynamics are carried out, the hyperdynamics method of Voter enables one to significantly accelerate the simulation state-to-state dynamics of physical systems. While very powerful, successful application of the method entails solving the subtle problem of the parametrization of the so-called bias potential. In this study, we first clarify the constraints that must be obeyed by the bias potential and demonstrate that fast sampling of the biased landscape is key to the obtention of proper kinetics. We then propose an approach by which the bond boost potential of Miron and Fichthorn canmore » be safely parametrized based on data acquired in the course of a molecular dynamics simulation. Finally, we introduce a procedure, the Self-Learning Bond Boost method, in which the parametrization is step efficiently carried out on-the-fly for each new state that is visited during the simulation by safely ramping up the strength of the bias potential up to its optimal value. The stability and accuracy of the method are demonstrated.« less

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

NASA Astrophysics Data System (ADS)

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 too severe, the buffering capacity of a heterogenous landscape could be overwhelmed. Incorporating spatial data will improve projections of future tree water stress and identification of potential resilient refugia.

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

NASA Astrophysics Data System (ADS)

Mansbach, Rachael A.; Ferguson, Andrew L.

2015-03-01

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.

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

PubMed

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.

Free-energy landscape of a hyperstable RNA tetraloop.

PubMed

Miner, Jacob C; Chen, Alan A; García, Angel E

2016-06-14

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

Beyond Standard Molecular Dynamics: Investigating the Molecular Mechanisms of G Protein-Coupled Receptors with Enhanced Molecular Dynamics Methods

PubMed Central

Johnston, Jennifer M.

2014-01-01

The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field. PMID:24158803

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

NASA Astrophysics Data System (ADS)

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

USDA-ARS?s Scientific Manuscript database

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

Spin glass model for dynamics of cell reprogramming

NASA Astrophysics Data System (ADS)

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

2015-03-01

Recent experiments show that differentiated cells can be reprogrammed to become pluripotent stem cells. The possible cell fates can be modeled as attractors in a dynamical system, the ``epigenetic landscape.'' Both cellular differentiation and reprogramming can be described in the landscape picture as motion from one attractor to another attractor. We perform Monte Carlo simulations in a simple model of the landscape. This model is based on spin glass theory and it can be used to construct a simulated epigenetic landscape starting from the experimental genomic data. We re-analyse data from several cell reprogramming experiments and compare with our simulation results. We find that the model can reproduce some of the main features of the dynamics of cell reprogramming.

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

PubMed Central

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-01-01

Within the framework of ‘Network Physiology’, we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain–heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain–heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems. PMID:27044991

Delay-correlation landscape reveals characteristic time delays of brain rhythms and heart interactions

NASA Astrophysics Data System (ADS)

Lin, Aijing; Liu, Kang K. L.; Bartsch, Ronny P.; Ivanov, Plamen Ch.

2016-05-01

Within the framework of `Network Physiology', we ask a fundamental question of how modulations in cardiac dynamics emerge from networked brain-heart interactions. We propose a generalized time-delay approach to identify and quantify dynamical interactions between physiologically relevant brain rhythms and the heart rate. We perform empirical analysis of synchronized continuous EEG and ECG recordings from 34 healthy subjects during night-time sleep. For each pair of brain rhythm and heart interaction, we construct a delay-correlation landscape (DCL) that characterizes how individual brain rhythms are coupled to the heart rate, and how modulations in brain and cardiac dynamics are coordinated in time. We uncover characteristic time delays and an ensemble of specific profiles for the probability distribution of time delays that underly brain-heart interactions. These profiles are consistently observed in all subjects, indicating a universal pattern. Tracking the evolution of DCL across different sleep stages, we find that the ensemble of time-delay profiles changes from one physiologic state to another, indicating a strong association with physiologic state and function. The reported observations provide new insights on neurophysiological regulation of cardiac dynamics, with potential for broad clinical applications. The presented approach allows one to simultaneously capture key elements of dynamic interactions, including characteristic time delays and their time evolution, and can be applied to a range of coupled dynamical systems.

Phase Transitions in Geomorphology

NASA Astrophysics Data System (ADS)

Ortiz, C. P.; Jerolmack, D. J.

2015-12-01

Landscapes are patterns in a dynamic steady-state, due to competing processes that smooth or sharpen features over large distances and times. Geomorphic transport laws have been developed to model the mass-flux due to different processes, but are unreasonably effective at recovering the scaling relations of landscape features. Using a continuum approximation to compare experimental landscapes and the observed landscapes of the earth, one finds they share similar morphodynamics despite a breakdown of classical dynamical similarity between the two. We propose the origin of this effectiveness is a different kind of dynamic similarity in the statistics of initiation and cessation of motion of groups of grains, which is common to disordered systems of grains under external driving. We will show how the existing data of sediment transport points to common signatures with dynamical phase transitions between "mobile" and "immobile" phases in other disordered systems, particularly granular materials, colloids, and foams. Viewing landscape evolution from the lens of non-equilibrium statistical physics of disordered systems leads to predictions that the transition of bulk measurements such as particle flux is continuous from one phase to another, that the collective nature of the particle dynamics leads to very slow aging of bulk properties, and that the dynamics are history-dependent. Recent results from sediment transport experiments support these predictions, suggesting that existing geomorphic transport laws may need to be replaced by a new generation of stochastic models with ingredients based on the physics of disordered phase transitions. We discuss possible strategies for extracting the necessary information to develop these models from measurements of geomorphic transport noise by connecting particle-scale collective dynamics and space-time fluctuations over landscape features.

[Application of hyperspectral remote sensing in research on ecological boundary in north farming-pasturing transition in China].

PubMed

Wang, Hong-Mei; Wang, Kun; Xie, Ying-Zhong

2009-06-01

Studies of ecological boundaries are important and have become a rapidly evolving part of contemporary ecology. The ecotones are dynamic and play several functional roles in ecosystem dynamics, and the changes in their locations can be used as an indicator of environment changes, and for these reasons, ecotones have recently become a focus of investigation of landscape ecology and global climate change. As the interest in ecotone increases, there is an increased need for formal techniques to detect it. Hence, to better study and understand the functional roles and dynamics of ecotones in ecosystem, we need quantitative methods to characterize them. In the semi-arid region of northern China, there exists a farming-pasturing transition resulting from grassland reclamation and deforestation. With the fragmentation of grassland landscape, the structure and function of the grassland ecosystem are changing. Given this perspective; new-image processing approaches are needed to focus on transition themselves. Hyperspectral remote sensing data, compared with wide-band remote sensing data, has the advantage of high spectral resolution. Hyperspectral remote sensing can be used to visualize transitional zones and to detect ecotone based on surface properties (e. g. vegetation, soil type, and soil moisture etc). In this paper, the methods of hyperspectral remote sensing information processing, spectral analysis and its application in detecting the vegetation classifications, vegetation growth state, estimating the canopy biochemical characteristics, soil moisture, soil organic matter etc are reviewed in detail. Finally the paper involves further application of hyperspectral remote sensing information in research on local climate in ecological boundary in north farming-pasturing transition in China.

Determining landscape extent for succession and disturbance simulation modeling

Treesearch

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...

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

Treesearch

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

2007-01-01

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

Hessian eigenvalue distribution in a random Gaussian landscape

NASA Astrophysics Data System (ADS)

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.

Coarse-grained simulations of protein-protein association: an energy landscape perspective.

PubMed

Ravikumar, Krishnakumar M; Huang, Wei; Yang, Sichun

2012-08-22

Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Coarse-Grained Simulations of Protein-Protein Association: An Energy Landscape Perspective

PubMed Central

Ravikumar, Krishnakumar M.; Huang, Wei; Yang, Sichun

2012-01-01

Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes. PMID:22947945

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

Manipulation of Superparamagnetic Beads on Patterned Exchange-Bias Layer Systems for Biosensing Applications.

PubMed

Ehresmann, Arno; Koch, Iris; Holzinger, Dennis

2015-11-13

A technology platform based on a remotely controlled and stepwise transport of an array arrangement of superparamagnetic beads (SPB) for efficient molecular uptake, delivery and accumulation in the context of highly specific and sensitive analyte molecule detection for the application in lab-on-a-chip devices is presented. The near-surface transport of SPBs is realized via the dynamic transformation of the SPBs' magnetic potential energy landscape above a magnetically stripe patterned Exchange-Bias (EB) thin film layer systems due to the application of sub-mT external magnetic field pulses. In this concept, the SPB velocity is dramatically influenced by the magnitude and gradient of the magnetic field landscape (MFL) above the magnetically stripe patterned EB substrate, the SPB to substrate distance, the magnetic properties of both the SPBs and the EB layer system, respectively, as well as by the properties of the external magnetic field pulses and the surrounding fluid. The focus of this review is laid on the specific MFL design in EB layer systems via light-ion bombardment induced magnetic patterning (IBMP). A numerical approach is introduced for the theoretical description of the MFL in comparison to experimental characterization via scanning Hall probe microscopy. The SPB transport mechanism will be outlined in terms of the dynamic interplay between the EB substrate's MFL and the pulse scheme of the external magnetic field.

Manipulation of Superparamagnetic Beads on Patterned Exchange-Bias Layer Systems for Biosensing Applications

PubMed Central

Ehresmann, Arno; Koch, Iris; Holzinger, Dennis

2015-01-01

A technology platform based on a remotely controlled and stepwise transport of an array arrangement of superparamagnetic beads (SPB) for efficient molecular uptake, delivery and accumulation in the context of highly specific and sensitive analyte molecule detection for the application in lab-on-a-chip devices is presented. The near-surface transport of SPBs is realized via the dynamic transformation of the SPBs’ magnetic potential energy landscape above a magnetically stripe patterned Exchange-Bias (EB) thin film layer systems due to the application of sub-mT external magnetic field pulses. In this concept, the SPB velocity is dramatically influenced by the magnitude and gradient of the magnetic field landscape (MFL) above the magnetically stripe patterned EB substrate, the SPB to substrate distance, the magnetic properties of both the SPBs and the EB layer system, respectively, as well as by the properties of the external magnetic field pulses and the surrounding fluid. The focus of this review is laid on the specific MFL design in EB layer systems via light-ion bombardment induced magnetic patterning (IBMP). A numerical approach is introduced for the theoretical description of the MFL in comparison to experimental characterization via scanning Hall probe microscopy. The SPB transport mechanism will be outlined in terms of the dynamic interplay between the EB substrate’s MFL and the pulse scheme of the external magnetic field. PMID:26580625

Modeling fluvial incision and transient landscape evolution: Influence of dynamic channel adjustment

NASA Astrophysics Data System (ADS)

Attal, M.; Tucker, G. E.; Whittaker, A. C.; Cowie, P. A.; Roberts, G. P.

2008-09-01

Channel geometry exerts a fundamental control on fluvial processes. Recent work has shown that bedrock channel width depends on a number of parameters, including channel slope, and is not solely a function of drainage area as is commonly assumed. The present work represents the first attempt to investigate the consequences of dynamic, gradient-sensitive channel adjustment for drainage-basin evolution. We use the Channel-Hillslope Integrated Landscape Development (CHILD) model to analyze the response of a catchment to a given tectonic perturbation, using, as a template, the topography of a well-documented catchment in the footwall of an active normal fault in the Apennines (Italy) that is known to be undergoing a transient response to tectonic forcing. We show that the observed transient response can be reproduced to first order with a simple detachment-limited fluvial incision law. Transient landscape is characterized by gentler gradients and a shorter response time when dynamic channel adjustment is allowed. The differences in predicted channel geometry between the static case (width dependent solely on upstream area) and dynamic case (width dependent on both drainage area and channel slope) lead to contrasting landscape morphologies when integrated at the scale of a whole catchment, particularly in presence of strong tilting and/or pronounced slip-rate acceleration. Our results emphasize the importance of channel width in controlling fluvial processes and landscape evolution. They stress the need for using a dynamic hydraulic scaling law when modeling landscape evolution, particularly when the relative uplift field is nonuniform.

Integrating Ecosystem Carbon Dynamics into State-and-Transition Simulation Models of Land Use/Land Cover Change

NASA Astrophysics Data System (ADS)

Sleeter, B. M.; Daniel, C.; Frid, L.; Fortin, M. J.

2016-12-01

State-and-transition simulation models (STSMs) provide a general approach for incorporating uncertainty into forecasts of landscape change. Using a Monte Carlo approach, STSMs generate spatially-explicit projections of the state of a landscape based upon probabilistic transitions defined between states. While STSMs are based on the basic principles of Markov chains, they have additional properties that make them applicable to a wide range of questions and types of landscapes. A current limitation of STSMs is that they are only able to track the fate of discrete state variables, such as land use/land cover (LULC) classes. There are some landscape modelling questions, however, for which continuous state variables - for example carbon biomass - are also required. Here we present a new approach for integrating continuous state variables into spatially-explicit STSMs. Specifically we allow any number of continuous state variables to be defined for each spatial cell in our simulations; the value of each continuous variable is then simulated forward in discrete time as a stochastic process based upon defined rates of change between variables. These rates can be defined as a function of the realized states and transitions of each cell in the STSM, thus providing a connection between the continuous variables and the dynamics of the landscape. We demonstrate this new approach by (1) developing a simple IPCC Tier 3 compliant model of ecosystem carbon biomass, where the continuous state variables are defined as terrestrial carbon biomass pools and the rates of change as carbon fluxes between pools, and (2) integrating this carbon model with an existing LULC change model for the state of Hawaii, USA.

Dynamic Shade and Irradiance Simulation of Aquatic Landscapes and Watersheds

EPA Science Inventory

Penumbra is a landscape shade and irradiance simulation model that simulates how solar energy spatially and temporally interacts within dynamic ecosystems such as riparian zones, forests, and other terrain that cast topological shadows. Direct and indirect solar energy accumulate...

Sampling of Protein Folding Transitions: Multicanonical Versus Replica Exchange Molecular Dynamics.

PubMed

Jiang, Ping; Yaşar, Fatih; Hansmann, Ulrich H E

2013-08-13

We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end β -sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel β -sheet formed by the two chain ends.

A Transient Landscape: Geospatial Analysis and Numerical Modeling of Coastal Geomorphology in the Outer Banks, North Carolina

NASA Astrophysics Data System (ADS)

Hardin, Eric Jon

Coastal landscapes can be relentlessly dynamic---owing to wave energy, tidal cycles, extreme weather events, and perpetual coastal winds. In these settings, the ever-changing landscape can threaten assets and infrastructure, necessitating costly measures to mitigate associated risks and to repair or maintain the changing landscape. Mapping and monitoring of terrain change, identification of areas susceptible to dramatic change, and understanding the processes that drive landscape change are critical for the development of responsible coastal management strategies and policies. Over the past two decades, LiDAR mapping has been conducted along the U.S. east coast (including the Outer Banks, North Carolina) on a near annual basis---generating a rich time series of topographic data with unprecedented accuracy, resolution, and extent. This time series has captured the response of the landscape to episodic storms, daily forcing of wind and waves, and anthropogenic activities. This work presents raster-based geospatial techniques developed to gain new insights into coastal geomorphology from the time series of available LiDAR. Per-cell statistical techniques derive information that is typically not obtained through the techniques traditionally employed by coastal scientists and engineers. Application of these techniques to study sites along the Outer Banks, NC, revealed substantial spatial and temporal variations in terrain change. Additionally, they identify the foredunes as being the most geomorphologically dynamic coastal features. In addition to per-cell statistical analysis, an approach is presented for the extraction of the dune ridge and dune toe (two features that are essential to standard vulnerability assessment). The approach employs a novel application of least cost path analysis and a physics-based model of an elastic sheet. The spatially distributed nature of the approach achieves a high level of automation and repeatability that semi-automated methods and manual digitization lack. Furthermore, the approach can be fully implemented with standard Geographic Information System (GIS) functionality, resulting in efficiency and ease of implementation. With this approach, a raster-based implementation of the U.S. Geological Survey (USGS) storm impact scale (designed to assess storm vulnerability of barrier islands) was developed. Vulnerability of 4km of the Outer Banks to Hurricane Isabel (2003) was assessed. The demonstrated approach produced vulnerability mapping at the high resolution of the input Digital Elevation Model (DEM)---providing results at the scale needed for local management, in contrast to the USGS approach, which is designed for continental scale vulnerability assessment. However, geospatial techniques cannot fully explain the observed geomorphology. Therefore, we present the Smoothed Particle Hydrodynamics (SPH) implementation of the Sauermann model for wind-driven sand transport. The SPH implementation enables the full nonlinearity of the model to be applied to complex scenarios that are typical of coastal landscapes. Through application of the SPH model and Computational Fluid Dynamics (CFD) modeling of the windborne surface shear stress (which drives sand transport), we present the sediment flux at two study sites along the Outer Banks. Scenarios were tested that involved steady-state surface shear stress as well as scenarios with intermittent variations in the surface shear stress. Results showed that intermittency in the surface shear stress has the potential to greatly influence the resulting flux. However, the degree to which intermittency does alter the flux is highly dependent on wind characteristics and wind direction relative to the orientation of salient topographic features.

Quantitative Connection Between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryo-EM and smFRET Investigations of the Ribosome

PubMed Central

Frank, Joachim; Gonzalez, Ruben L.

2015-01-01

At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describes transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy and single-molecule fluorescence resonance energy transfer studies of the bacterial ribosomal pretranslocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pretranslocation complex, which are observed in a cryogenic electron microscopy study, may not be observed in several single-molecule fluorescence resonance energy transfer studies. PMID:25785884

Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome.

PubMed

Thompson, Colin D Kinz; Sharma, Ajeet K; Frank, Joachim; Gonzalez, Ruben L; Chowdhury, Debashish

2015-08-27

At equilibrium, thermodynamic and kinetic information can be extracted from biomolecular energy landscapes by many techniques. However, while static, ensemble techniques yield thermodynamic data, often only dynamic, single-molecule techniques can yield the kinetic data that describe transition-state energy barriers. Here we present a generalized framework based upon dwell-time distributions that can be used to connect such static, ensemble techniques with dynamic, single-molecule techniques, and thus characterize energy landscapes to greater resolutions. We demonstrate the utility of this framework by applying it to cryogenic electron microscopy (cryo-EM) and single-molecule fluorescence resonance energy transfer (smFRET) studies of the bacterial ribosomal pre-translocation complex. Among other benefits, application of this framework to these data explains why two transient, intermediate conformations of the pre-translocation complex, which are observed in a cryo-EM study, may not be observed in several smFRET studies.

Place knowing of persons and populations: restoring the place work of nursing.

PubMed

Thomas, Elizabeth A

2013-12-01

Place emerges when space acquires definition in social constructions of meaning as landscape-languages, which reflect assumptions about physical and social realities. The place work of nursing, which resonated throughout Nightingale's work and the profession's evolution, focuses on human health and healing in the historical transitions and landscape-languages of populations. However, evidence-based practice dominated by empirical knowing inadequately addresses complex health and illness dynamics between place and populations. Translating evidence to the life course experiences of individuals and populations requires place knowing of human situated embodiment within discrete space. An exploration of the concept of place, its application to nursing, and the need for a place paradigm for practice is presented. A sense of salience and situated cognition has been identified as the essential element of the transformation needed in the education of nurses. Place knowing integrates other patterns of knowing (empirical, ethical, aesthetical, personal, unknowing, sociopolitical, and emancipatory) in a situated cognition. Place knowing, like other established patterns of knowing, is a significant epistemological foundation of nursing. Place knowing allows the nuanced intricately complex dynamics of embodied situated human health and illness to be examined, the salience of the particulars to be considered, and the whole of the landscape-languages to emerge.

Thermal Remote Sensing: A Powerful Tool in the Characterization of Landscapes on a Functional Basis

NASA Technical Reports Server (NTRS)

Jeffrey, Luvall C.; Kay, James; Fraser, Roydon

1999-01-01

Thermal remote sensing instruments can function as environmental measuring tools, with capabilities leading toward new directions in functional landscape ecology. Theoretical deduction and phenomenological observation leads us to believe that the second law of thermodynamics requires that all dynamically systems develop in a manner which dissipates gradients as rapidly as possible within the constraints of the system at hand. The ramification of this requirement is that dynamical systems will evolve dissipative structures which grow and complexify over time. This perspective has allowed us to develop a framework for discussing ecosystem development and integrity. In the context of this framework we have developed measures of development and integrity for ecosystems. One set of these measures is based on destruction of the exergy content of incoming solar energy. More developed ecosystems will be more effective at dissipating the solar gradient (destroying its exergy content). This can be measured by the effective surface temperature of the ecosystem on a landscape scale. These surface temperatures are measured using airborne thermal scanners such as the Thermal Infrared Multispectral Scanner (TIMS) and the Airborne Thermal/Visible Land Application Sensor(ATLAS) sensors. An analysis of agriculture and forest ecosystems will be used to illustrate the concept of ecological thermodynamics and the development of ecosystems.

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

Treesearch

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

2005-01-01

Dynamic zoning (systematic alteration in the spatial and temporal allocation of even-aged forest management practices) has been proposed as a means to change the spatial pattern of timber harvest across a landscape to maximize forest interior habitat while holding timber harvest levels constant. Simulation studies have established that dynamic zoning strategies...

Free-energy landscape of a hyperstable RNA tetraloop

PubMed Central

Miner, Jacob C.; Chen, Alan A.; García, Angel E.

2016-01-01

We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif. PMID:27233937

Impacts of road network expansion on landscape ecological risk in a megacity, China: A case study of Beijing.

PubMed

Mo, Wenbo; Wang, Yong; Zhang, Yingxue; Zhuang, Dafang

2017-01-01

Road networks affect the spatial structure of urban landscapes, and with continuous expansion, it will also exert more widespread influences on the regional ecological environment. With the support of geographic information system (GIS) technology, based on the application of various spatial analysis methods, this study analyzed the spatiotemporal changes of road networks and landscape ecological risk in the research area of Beijing to explore the impacts of road network expansion on ecological risk in the urban landscape. The results showed the following: 1) In the dynamic processes of change in the overall landscape pattern, the changing differences in landscape indices of various landscape types were obvious and were primarily related to land-use type. 2) For the changes in a time series, the expansion of the road kernel area was consistent with the extension of the sub-low-risk area in the urban center, but some differences were observed during different stages of development. 3) For the spatial position, the expanding changes in the road kernel area were consistent with the grade changes of the urban central ecological risk, primarily because both had a certain spatial correlation with the expressways. 4) The influence of road network expansion on the ecological risk in the study area had obvious spatial differences, which may be closely associated with the distribution of ecosystem types. Copyright © 2016 Office national des forêts. Published by Elsevier B.V. All rights reserved.

SEARCH: Spatially Explicit Animal Response to Composition of Habitat.

PubMed

Pauli, Benjamin P; McCann, Nicholas P; Zollner, Patrick A; Cummings, Robert; Gilbert, Jonathan H; Gustafson, Eric J

2013-01-01

Complex decisions dramatically affect animal dispersal and space use. Dispersing individuals respond to a combination of fine-scale environmental stimuli and internal attributes. Individual-based modeling offers a valuable approach for the investigation of such interactions because it combines the heterogeneity of animal behaviors with spatial detail. Most individual-based models (IBMs), however, vastly oversimplify animal behavior and such behavioral minimalism diminishes the value of these models. We present program SEARCH (Spatially Explicit Animal Response to Composition of Habitat), a spatially explicit, individual-based, population model of animal dispersal through realistic landscapes. SEARCH uses values in Geographic Information System (GIS) maps to apply rules that animals follow during dispersal, thus allowing virtual animals to respond to fine-scale features of the landscape and maintain a detailed memory of areas sensed during movement. SEARCH also incorporates temporally dynamic landscapes so that the environment to which virtual animals respond can change during the course of a simulation. Animals in SEARCH are behaviorally dynamic and able to respond to stimuli based upon their individual experiences. Therefore, SEARCH is able to model behavioral traits of dispersing animals at fine scales and with many dynamic aspects. Such added complexity allows investigation of unique ecological questions. To illustrate SEARCH's capabilities, we simulated case studies using three mammals. We examined the impact of seasonally variable food resources on the weight distribution of dispersing raccoons (Procyon lotor), the effect of temporally dynamic mortality pressure in combination with various levels of behavioral responsiveness in eastern chipmunks (Tamias striatus), and the impact of behavioral plasticity and home range selection on disperser mortality and weight change in virtual American martens (Martes americana). These simulations highlight the relevance of SEARCH for a variety of applications and illustrate benefits it can provide for conservation planning.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

SURFACE WATER FLOW IN LANDSCAPE MODELS: 1. EVERGLADES CASE STUDY. (R824766)

EPA Science Inventory

Many landscape models require extensive computational effort using a large array of grid cells that represent the landscape. The number of spatial cells may be in the thousands and millions, while the ecological component run in each of the cells to account for landscape dynamics...

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

NASA Astrophysics Data System (ADS)

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

2013-04-01

Soil organic carbon (SOC) sequestration is highly linked to soil use and farming practices, but also to soil redistributions, soil properties, and climate. In a global change context, landscape, farming practice and climate changes are expected; and they will most probably impact SOC dynamics. To assess their respective impacts, we modelled the SOC contents and stocks evolution at the scale of an agricultural landscape, by taking into account the soil redistribution by tillage and water processes. The simulations were conducted from 2010 to 2100 under different scenarios of landscape and climate. These scenarios combined different land uses associated to specific farming practices (mixed dairy with rotations of crops and grasslands, intensive cropping with only crops rotations or permanent grasslands), landscape managements (hedges planting or removal), and climates (business-as-usual climate and climate change, with temperature and precipitations increase). We used a spatially SOC dynamic model (adapted from RothC), coupled to a soil redistribution model (LandSoil). SOC dynamics were spatially modelled with a lateral resolution of 2-m and for soil organic layers up to 105 cm. Initial SOC stocks were described with a 2-m resolution map based on field data and produced with digital soil mapping methods. The major factor of change in SOC stocks was land use change, the second factor of importance was climate change, and finally landscape management: for the total SOC stocks (0-to-105 cm soil layer) the change of land use, climate and landscape management induced a respective mean absolute variation of 10 to 20 tC ha-1, 9 tC ha-1 and 0.4 tC ha-1. When considering the 0-to-105 cm soil layer, the different modelled landscapes showed the same sensitivity to climate change, with induced a mean decrease of 10 tC ha-1. However, the impact of climate change was found different according to the different modelled landscape when considering the 0-to-7.5 and 0-to-30 cm soil layers: the more sensitive landscapes were those of intensive cropping. This shows the importance of considering not only the plough layer, but also the vertical distribution of SOC stocks to assess the variation in SOC dynamics under land use, landscape management or climate change. Finally, rural hedgerow landscapes were proved to be quite well adapted for soil protection in a context of climate change, focusing on both carbon storage and soil erosion.

Canadian SAR remote sensing for the Terrestrial Wetland Global Change Research Network (TWGCRN)

USGS Publications Warehouse

Kaya, Shannon; Brisco, Brian; Cull, Andrew; Gallant, Alisa L.; Sadinski, Walter J.; Thompson, Dean

2010-01-01

The Canada Centre for Remote Sensing (CCRS) has more than 30 years of experience investigating the use of SAR remote sensing for many applications related to terrestrial water resources. Recently, CCRS scientists began contributing to the Terrestrial Wetland Global Change Research Network (TWGCRN), a bi-national research network dedicated to assessing impacts of global change on interconnected wetland-upland landscapes across a vital portion of North America. CCRS scientists are applying SAR remote sensing to characterize wetland components of these landscapes in three ways. First, they are using a comprehensive set of RADARSAT-2 SAR data collected during April to September 2009 to extract multi-temporal surface water information for key TWGCRN study landscapes in North America. Second, they are analyzing polarimetric RADARSAT-2 data to determine areas where double-bounce represents the primary scattering mechanism and is indicative of flooded vegetation in these landscapes. Third, they are testing advanced interferometric SAR techniques to estimate water levels with RADARSAT-2 Fine Quad polarimetric image pairs. The combined information from these three SAR analysis activities will provide TWGCRN scientists with an integrated view and monitoring capability for these dynamic wetland-upland landscapes. These data are being used in conjunction with other remote sensing and field data to study interactions between landscape and animal (birds and amphibians) responses to climate/global change.

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

PubMed

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

2012-09-01

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

Study on the oasis corridor landscape in the arid regions based on RS and GIS methods--application of Jinta Oasis, China.

PubMed

Ma, Ming-guo; Wang, Xue-mei; Cheng, Guo-dong

2003-03-01

The study on the oasis corridor landsape is a new hotspot in the ecological environment research in the arid regions. In oasis, main corridor landscape types include river, ditch, shelterbelt and road. This paper introduces the basic ecological effects of the corridor landscape on the transporting mass and energy and obstructing desert landscape expansion and incursion. Using Geographic Information System (GIS), we have researched the corridor distribution and its spatial relationship with other landscape types in the Jinta Oasis. Based on the dynamically monitoring on the landscape pattern change of the Jinta Oasis during the latter 10 years by using Remote Sensing (RS) and GIS, the driving functions of the corridors on this change have been analyzed in detail. The analysis results showed that all kinds of corridors' characteristics can be quantified by the indexes such as length and width, ratio of perimeter and area, density and non-heterogeneity. The total corridor length of Jinta Oasis is 1838.5 km and its density is 2.1 km/km2. The corridor density of the irrigation land, forest and resident area is maximal, which shows that affection degree of the oasis corridors on them is the most. The improvement of the corridors quality is one of the important driving factors on the irrigation land and so on. The organic combination of the RS and GIS technologies and landscape research methods would be an effective means for the corridor landscape research on arid region oasis.

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

PubMed

Hovick, Torre J; Allred, Brady W; Elmore, R Dwayne; Fuhlendorf, Samuel D; Hamilton, Robert G; Breland, Amber

2015-01-01

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 locations as static points, but rather as sites that shift around the landscape in response to shifting vegetation structure. Acknowledging shifting lek locations in these landscapes will help ensure conservation efforts are successful by targeting the appropriate areas for protection and management.

Evaluating Effects of Localized Habitat Manipulations on Landscape-level Dynamics of White-footed Mouse Populations

EPA Science Inventory

Due to complex population dynamics and migration behaviors, the well-being of animal populations that host human diseases sometimes varies across landscapes in ways that cannot be deduced from geographic abundance patterns alone. In such cases, efficient management of ecological...

MODELING THE DYNAMICS OF WILDLIFE HABITAT AND POPULATIONS AT THE LANDSCAPE SCALE

EPA Science Inventory

A forest dynamics model (FORCLIM) was linked to a spatial wildlife population model (PATCH) to assess the effects of habitat change in a landscape on selected wildlife species. The habitat changes included forest responses to harvesting, development, and climate change on a west...

Dynamics of coupled human-landscape systems

NASA Astrophysics Data System (ADS)

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

2007-11-01

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

Landscape analysis of methane flux across complex terrain

NASA Astrophysics Data System (ADS)

Kaiser, K. E.; McGlynn, B. L.; Dore, J. E.

2014-12-01

Greenhouse gas (GHG) fluxes into and out of the soil are influenced by environmental conditions resulting in landscape-mediated patterns of spatial heterogeneity. The temporal variability of inputs (e.g. precipitation) and internal redistribution (e.g. groundwater flow) and dynamics (e.g. microbial communities) make predicating these fluxes challenging. Complex terrain can provide a laboratory for improving understanding of the spatial patterns, temporal dynamics, and drivers of trace gas flux rates, requisite to constraining current GHG budgets and future scenarios. Our research builds on previous carbon cycle research at the USFS Tenderfoot Creek Experimental Forest, Little Belt Mountains, Montana that highlighted the relationships between landscape position and seasonal CO2 efflux, induced by the topographic redistribution of water. Spatial patterns and landscape scale mediation of CH4 fluxes in seasonally aerobic soils have not yet been elucidated. We measured soil methane concentrations and fluxes across a full range of landscape positions, leveraging topographic and seasonal gradients, to examine the relationships between environmental variables, hydrologic dynamics, and CH4 production and consumption. We determined that a threshold of ~30% VWC distinguished the direction of flux at individual time points, with the riparian area and uplands having distinct source/sink characteristics respectively. Riparian locations were either strong sources or fluctuated between sink and source behavior, resulting in near neutral seasonal flux. Upland sites however, exhibited significant relationships between sink strength and topographic/energy balance indices. Our results highlight spatial and temporal coherence to landscape scale heterogeneity of CH4 dynamics that can improve estimates of landscape scale CH4 balances and sensitivity to change.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor

The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimalmore » frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism.« less

Perfection and complexity in the lower Brazos River

NASA Astrophysics Data System (ADS)

Phillips, Jonathan D.

2007-11-01

The "perfect landscape" concept is based on the notion that any specific geomorphic system represents the combined, interacting effects of a set of generally applicable global laws and a set of geographically and historically contingent local controls. Because the joint probability of any specific combination of local and global controls is low, and the local controls are inherently idiosyncratic, the probability of existence of any given landscape is vanishingly small. A perfect landscape approach to geomorphic complexity views landscapes as circumstantial, contingent outcomes of deterministic laws operating in a specific environmental and historical context. Thus, explaining evolution of complex landscapes requires the integration of global and local approaches. Because perfection in this sense is the most important and pervasive form of complexity, the study of geomorphic complexity is not restricted to nonlinear dynamics, self-organization, or any other aspects of complexity theory. Beyond what can be achieved via complexity theory, the details of historical and geographic contexts must be addressed. One way to approach this is via synoptic analyses, where the relevant global laws are applied in specific situational contexts. A study of non-acute tributary junctions in the lower Brazos River, Texas illustrates this strategy. The application of generalizations about tributary junction angles, and of relevant theories, does not explain the unexpectedly high occurrence or the specific instances of barbed or straight junctions in the study area. At least five different causes for the development of straight or obtuse junction angles are evident in the lower Brazos. The dominant mechanism, however, is associated with river bank erosion and lateral channel migration which encroaches on upstream-oriented reaches of meandering tributaries. Because the tributaries are generally strongly incised in response to Holocene incision of the Brazos, the junctions are not readily reoriented to the expected acute angle. The findings are interpreted in the context of nonlinear divergent evolution, geographical and historical contingency, synoptic frameworks for generalizing results, and applicability of the dominant processes concept in geomorphology.

Mapping landscape phenology preference of yellow-billed cuckoo with AVHRR data

Treesearch

Cynthia S. A. Wallace; Miguel Villarreal; Charles van Riper

2013-01-01

We mapped habitat for threatened Yellow-billed Cuckoo (Coccycus americanus occidentalis) in the State of Arizona using the temporal greenness dynamics of the landscape, or the landscape phenology. Landscape phenometrics were derived from Advanced Very High Resolution Radiometer (AVHRR) Normalized Difference Vegetation Index (NDVI) data for 1998 and 1999 by using...

The role of landscape-dependent disturbance and dispersal in metapopulation persistence.

PubMed

Elkin, Ché M; Possingham, Hugh

2008-10-01

The fundamental processes that influence metapopulation dynamics (extinction and recolonization) will often depend on landscape structure. Disturbances that increase patch extinction rates will frequently be landscape dependent such that they are spatially aggregated and have an increased likelihood of occurring in some areas. Similarly, landscape structure can influence organism movement, producing asymmetric dispersal between patches. Using a stochastic, spatially explicit model, we examine how landscape-dependent correlations between dispersal and disturbance rates influence metapopulation dynamics. Habitat patches that are situated in areas where the likelihood of disturbance is low will experience lower extinction rates and will function as partial refuges. We discovered that the presence of partial refuges increases metapopulation viability and that the value of partial refuges was contingent on whether dispersal was also landscape dependent. Somewhat counterintuitively, metapopulation viability was reduced when individuals had a preponderance to disperse away from refuges and was highest when there was biased dispersal toward refuges. Our work demonstrates that landscape structure needs to be incorporated into metapopulation models when there is either empirical data or ecological rationale for extinction and/or dispersal rates being landscape dependent.

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

PubMed

Aruhan; Yang, Chi

2007-11-01

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

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

EPA Science Inventory

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

Unfolding and melting of DNA (RNA) hairpins: the concept of structure-specific 2D dynamic landscapes.

PubMed

Lin, Milo M; Meinhold, Lars; Shorokhov, Dmitry; Zewail, Ahmed H

2008-08-07

A 2D free-energy landscape model is presented to describe the (un)folding transition of DNA/RNA hairpins, together with molecular dynamics simulations and experimental findings. The dependence of the (un)folding transition on the stem sequence and the loop length is shown in the enthalpic and entropic contributions to the free energy. Intermediate structures are well defined by the two coordinates of the landscape during (un)zipping. Both the free-energy landscape model and the extensive molecular dynamics simulations totaling over 10 mus predict the existence of temperature-dependent kinetic intermediate states during hairpin (un)zipping and provide the theoretical description of recent ultrafast temperature-jump studies which indicate that hairpin (un)zipping is, in general, not a two-state process. The model allows for lucid prediction of the collapsed state(s) in simple 2D space and we term it the kinetic intermediate structure (KIS) model.

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

NASA Technical Reports Server (NTRS)

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.

Engineering the entropy-driven free-energy landscape of a dynamic nanoporous protein assembly.

PubMed

Alberstein, Robert; Suzuki, Yuta; Paesani, Francesco; Tezcan, F Akif

2018-04-30

De novo design and construction of stimuli-responsive protein assemblies that predictably switch between discrete conformational states remains an essential but highly challenging goal in biomolecular design. We previously reported synthetic, two-dimensional protein lattices self-assembled via disulfide bonding interactions, which endows them with a unique capacity to undergo coherent conformational changes without losing crystalline order. Here, we carried out all-atom molecular dynamics simulations to map the free-energy landscape of these lattices, validated this landscape through extensive structural characterization by electron microscopy and established that it is predominantly governed by solvent reorganization entropy. Subsequent redesign of the protein surface with conditionally repulsive electrostatic interactions enabled us to predictably perturb the free-energy landscape and obtain a new protein lattice whose conformational dynamics can be chemically and mechanically toggled between three different states with varying porosities and molecular densities.

Introduction to special issue on carbon and landscape dynamics

USGS Publications Warehouse

Madej, Mary Ann; Wohl, Ellen E.

2016-01-01

In October, 2013, at the Geological Society of America annual meeting, a theme session focused on carbon and landscape dynamics.  That event led to interest in producing a special issue in ESPL compiling papers on this subject.  The 13 papers collected for this special issue reflect the diversity of recent geomorphic research, across a range of climatic and geomorphic settings, addressing some aspect of carbon dynamics.

Vacuum selection on axionic landscapes

DOE Office of Scientific and Technical Information (OSTI.GOV)

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

2016-04-01

We compute the distribution of minima that are reached dynamically on multi-field axionic landscapes, both numerically and analytically. Such landscapes are well suited for inflationary model building due to the presence of shift symmetries and possible alignment effects (the KNP mechanism). The resulting distribution of dynamically reached minima differs considerably from the naive expectation based on counting all vacua. These differences are more pronounced in the presence of many fields due to dynamical selection effects: while low lying minima are preferred as fields roll down the potential, trajectories are also more likely to get trapped by one of the manymore » 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.« less

Critical zone evolution and the origins of organised complexity in watersheds

NASA Astrophysics Data System (ADS)

Harman, C.; Troch, P. A.; Pelletier, J.; Rasmussen, C.; Chorover, J.

2012-04-01

The capacity of the landscape to store and transmit water is the result of a historical trajectory of landscape, soil and vegetation development, much of which is driven by hydrology itself. Progress in geomorphology and pedology has produced models of surface and sub-surface evolution in soil-mantled uplands. These dissected, denuding modeled landscapes are emblematic of the kinds of dissipative self-organized flow structures whose hydrologic organization may also be understood by low-dimensional hydrologic models. They offer an exciting starting-point for examining the mapping between the long-term controls on landscape evolution and the high-frequency hydrologic dynamics. Here we build on recent theoretical developments in geomorphology and pedology to try to understand how the relative rates of erosion, sediment transport and soil development in a landscape determine catchment storage capacity and the relative dominance of runoff process, flow pathways and storage-discharge relationships. We do so by using a combination of landscape evolution models, hydrologic process models and data from a variety of sources, including the University of Arizona Critical Zone Observatory. A challenge to linking the landscape evolution and hydrologic model representations is the vast differences in the timescales implicit in the process representations. Furthermore the vast array of processes involved makes parameterization of such models an enormous challenge. The best data-constrained geomorphic transport and soil development laws only represent hydrologic processes implicitly, through the transport and weathering rate parameters. In this work we propose to avoid this problem by identifying the relationship between the landscape and soil evolution parameters and macroscopic climate and geological controls. These macroscopic controls (such as the aridity index) have two roles: 1) they express the water and energy constraints on the long-term evolution of the landscape system, and 2) they bound the range of plausible short-term hydroclimatic regimes that may drive a particular landscape's hydrologic dynamics. To ensure that the hydrologic dynamics implicit in the evolutionary parameters are compatible with the dynamics observed in the hydrologic modeling, a set of consistency checks based on flow process dominance are developed.

Punctuated equilibrium and shock waves in molecular models of biological evolution.

PubMed

Saakian, David B; Ghazaryan, Makar H; Hu, Chin-Kun

2014-08-01

We consider the dynamics in infinite population evolution models with a general symmetric fitness landscape. We find shock waves, i.e., discontinuous transitions in the mean fitness, in evolution dynamics even with smooth fitness landscapes, which means that the search for the optimal evolution trajectory is more complicated. These shock waves appear in the case of positive epistasis and can be used to represent punctuated equilibria in biological evolution during long geological time scales. We find exact analytical solutions for discontinuous dynamics at the large-genome-length limit and derive optimal mutation rates for a fixed fitness landscape to send the population from the initial configuration to some final configuration in the fastest way.

Dynamic reorganization of river basins.

PubMed

Willett, Sean D; McCoy, Scott W; Perron, J Taylor; Goren, Liran; Chen, Chia-Yu

2014-03-07

River networks evolve as migrating drainage divides reshape river basins and change network topology by capture of river channels. We demonstrate that a characteristic metric of river network geometry gauges the horizontal motion of drainage divides. Assessing this metric throughout a landscape maps the dynamic states of entire river networks, revealing diverse conditions: Drainage divides in the Loess Plateau of China appear stationary; the young topography of Taiwan has migrating divides driving adjustment of major basins; and rivers draining the ancient landscape of the southeastern United States are reorganizing in response to escarpment retreat and coastal advance. The ability to measure the dynamic reorganization of river basins presents opportunities to examine landscape-scale interactions among tectonics, erosion, and ecology.

The potential and flux landscape theory of evolution.

PubMed

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

2012-08-14

We established the potential and flux landscape theory for evolution. We found explicitly the conventional Wright's gradient adaptive landscape based on the mean fitness is inadequate to describe the general evolutionary dynamics. We show the intrinsic potential as being Lyapunov function(monotonically decreasing in time) does exist and can define the adaptive landscape for general evolution dynamics for studying global stability. The driving force determining the dynamics can be decomposed into gradient of potential landscape and curl probability flux. Non-zero flux causes detailed balance breaking and measures how far the evolution from equilibrium state. The gradient of intrinsic potential and curl flux are perpendicular to each other in zero fluctuation limit resembling electric and magnetic forces on electrons. We quantified intrinsic energy, entropy and free energy of evolution and constructed non-equilibrium thermodynamics. The intrinsic non-equilibrium free energy is a Lyapunov function. Both intrinsic potential and free energy can be used to quantify the global stability and robustness of evolution. We investigated an example of three allele evolutionary dynamics with frequency dependent selection (detailed balance broken). We uncovered the underlying single, triple, and limit cycle attractor landscapes. We found quantitative criterions for stability through landscape topography. We also quantified evolution pathways and found paths do not follow potential gradient and are irreversible due to non-zero flux. We generalized the original Fisher's fundamental theorem to the general (i.e., frequency dependent selection) regime of evolution by linking the adaptive rate with not only genetic variance related to the potential but also the flux. We show there is an optimum potential where curl flux resulting from biotic interactions of individuals within a species or between species can sustain an endless evolution even if the physical environment is unchanged. We offer a theoretical basis for explaining the corresponding Red Queen hypothesis proposed by Van Valen. Our work provides a theoretical foundation for evolutionary dynamics.

NASA's Earth Science Use of Commercially Availiable Remote Sensing Datasets: Cover Image

NASA Technical Reports Server (NTRS)

Underwood, Lauren W.; Goward, Samuel N.; Fearon, Matthew G.; Fletcher, Rose; Garvin, Jim; Hurtt, George

2008-01-01

The cover image incorporates high resolution stereo pairs acquired from the DigitalGlobe(R) QuickBird sensor. It shows a digital elevation model of Meteor Crater, Arizona at approximately 1.3 meter point-spacing. Image analysts used the Leica Photogrammetry Suite to produce the DEM. The outside portion was computed from two QuickBird panchromatic scenes acquired October 2006, while an Optech laser scan dataset was used for the crater s interior elevations. The crater s terrain model and image drape were created in a NASA Constellation Program project focused on simulating lunar surface environments for prototyping and testing lunar surface mission analysis and planning tools. This work exemplifies NASA s Scientific Data Purchase legacy and commercial high resolution imagery applications, as scientists use commercial high resolution data to examine lunar analog Earth landscapes for advanced planning and trade studies for future lunar surface activities. Other applications include landscape dynamics related to volcanism, hydrologic events, climate change, and ice movement.

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

PubMed

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

2016-08-01

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

Synchrony in small mammal community dynamics across a forested landscape

Treesearch

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

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-07-01

Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.

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

PubMed

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

2015-07-01

Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields.

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

PubMed Central

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

2015-01-01

Fundamental understanding of domain dynamics in ferroic materials has been a longstanding issue because of its relevance to many systems and to the design of nanoscale domain-wall devices. Despite many theoretical and experimental studies, a full understanding of domain dynamics still remains incomplete, partly due to complex interactions between domain-walls and disorder. We report domain-shape-preserving deterministic domain-wall motion, which directly confirms microscopic return point memory, by observing domain-wall breathing motion in ferroelectric BiFeO3 thin film using stroboscopic piezoresponse force microscopy. Spatial energy landscape that provides new insights into domain dynamics is also mapped based on the breathing motion of domain walls. The evolution of complex domain structure can be understood by the process of occupying the lowest available energy states of polarization in the energy landscape which is determined by defect-induced internal fields. Our result highlights a pathway for the novel design of ferroelectric domain-wall devices through the engineering of energy landscape using defect-induced internal fields such as flexoelectric fields. PMID:26130159

Ecohydro-geomorphic implications of orographic precipitation on landform evolution using a landscape evolution model

NASA Astrophysics Data System (ADS)

Yetemen, O.; Saco, P. M.

2016-12-01

Orography induced precipitation and its implications on vegetation dynamics and landscape morphology have long been documented in the literature. However a numerical framework that integrates a range of ecohydrologic and geomorphic processes to explore the coupled ecohydro-geomorphic landscape response of catchments where pronounced orographic precipitation prevails has been missing. In this study, our aim is to realistically represent orographic-precipitation-driven ecohydrologic dynamics in a landscape evolution model (LEM). The model is used to investigate how ecohydro-geomorphic differences caused by differential precipitation patterns on the leeward and windward sides of low-relief landscapes lead to differences in the organization of modelled topography, soil moisture and plant biomass. We use the CHILD LEM equipped with a vegetation dynamics component that explicitly tracks above- and below-ground biomass, and a precipitation forcing component that simulates rainfall as a function of elevation and orientation. The preliminary results of the model show how the competition between an increased shear stress through runoff production and an enhanced resistance force due to denser canopy cover shape the landscape. Moreover, orographic precipitation leads to not only the migration of the divide between leeward and windward slopes but also a change in the concavity of streams. These results clearly demonstrate the strong coupling between landform evolution and climate processes.

Simulating forest landscape disturbances as coupled human and natural systems

USGS Publications Warehouse

Wimberly, Michael; Sohl, Terry L.; Liu, Zhihua; Lamsal, Aashis

2015-01-01

Anthropogenic disturbances resulting from human land use affect forest landscapes over a range of spatial and temporal scales, with diverse influences on vegetation patterns and dynamics. These processes fall within the scope of the coupled human and natural systems (CHANS) concept, which has emerged as an important framework for understanding the reciprocal interactions and feedbacks that connect human activities and ecosystem responses. Spatial simulation modeling of forest landscape change is an important technique for exploring the dynamics of CHANS over large areas and long time periods. Landscape models for simulating interactions between human activities and forest landscape dynamics can be grouped into two main categories. Forest landscape models (FLMs) focus on landscapes where forests are the dominant land cover and simulate succession and natural disturbances along with forest management activities. In contrast, land change models (LCMs) simulate mosaics of different land cover and land use classes that include forests in addition to other land uses such as developed areas and agricultural lands. There are also several examples of coupled models that combine elements of FLMs and LCMs. These integrated models are particularly useful for simulating human–natural interactions in landscapes where human settlement and agriculture are expanding into forested areas. Despite important differences in spatial scale and disciplinary scope, FLMs and LCMs have many commonalities in conceptual design and technical implementation that can facilitate continued integration. The ultimate goal will be to implement forest landscape disturbance modeling in a CHANS framework that recognizes the contextual effects of regional land use and other human activities on the forest ecosystem while capturing the reciprocal influences of forests and their disturbances on the broader land use mosaic.

Reversal time of jump-noise magnetization dynamics in nanomagnets via Monte Carlo simulations

NASA Astrophysics Data System (ADS)

Parthasarathy, Arun; Rakheja, Shaloo

2018-06-01

The jump-noise is a nonhomogeneous Poisson process which models thermal effects in magnetization dynamics, with special applications in low temperature escape rate phenomena. In this work, we develop improved numerical methods for Monte Carlo simulation of the jump-noise dynamics and validate the method by comparing the stationary distribution obtained empirically against the Boltzmann distribution. In accordance with the Néel-Brown theory, the jump-noise dynamics display an exponential relaxation toward equilibrium with a characteristic reversal time, which we extract for nanomagnets with uniaxial and cubic anisotropy. We relate the jump-noise dynamics to the equivalent Landau-Lifshitz dynamics up to second order correction for a general energy landscape and obtain the analogous Néel-Brown theory's solution of the reversal time. We find that the reversal time of jump-noise dynamics is characterized by Néel-Brown theory's solution at the energy saddle point for small noise. For large noise, the magnetization reversal due to jump-noise dynamics phenomenologically represents macroscopic tunneling of magnetization.

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

PubMed

Nabe-Nielsen, Jacob; Sibly, Richard M; Forchhammer, Mads C; Forbes, Valery E; Topping, Christopher J

2010-01-28

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. 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. 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 of landscapes, or landscape ecology, which accounts for landscape structure but has difficulty predicting the dynamics of populations living in them. Here we show how realistic and replicable individual-based models can bridge the gap between non-spatial population theory and non-dynamic landscape ecology. A major strength of the approach is its ability to identify population vulnerabilities not detected by standard population viability analyses.

[Dynamic evolution of wetland landscape spatial pattern in Nansi Lake, China].

PubMed

Chen, Zhi Cong; Xie, Xiao Ping; Bai, Mao Wei

2016-10-01

Based on Landsat images in 1987, 2002 and 2014 from Nansi Lake located in Shandong Province, landscape pattern index, dynamic index, landscape gradient and gridding model were used for analysis of the wetland distribution in the lake. The results showed that the landscape contagion index and aggregation index gradually decreased from 1987 to 2014, while the landscape diversity index and evenness index gradually increased. The distribution of landscape area was more uniform while its patterns trended to be fragmented. Human activities impacted Nansi wetland distribution and the disturbance presented an increasing trend. The total area of Nansi wetland gradually increased during the study period. The area of lake first decreased then increased, and the area reached the maximum in 2014. The area of the ponds along the riparian zone had increased gradually, but the increasing speed slowed down. The area of the rivers remained stable, while the area of the swamps decreased continually during the period. The change of landscape pattern of Nansi Lake wetland mainly resulted from agricultural activities, establishment of Nansi Lake Natural Reserve, and the South-to-North Water Diversion Project.

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

Treesearch

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...

Invasion complexity at large spatial scales is an emergent property of interactions among landscape characteristics and invader traits

PubMed Central

Jordan, Nicholas R.; Forester, James D.

2018-01-01

Invasion potential should be part of the evaluation of candidate species for any species introduction. However, estimating invasion risks remains a challenging problem, particularly in complex landscapes. Certain plant traits are generally considered to increase invasive potential and there is an understanding that landscapes influence invasions dynamics, but little research has been done to explore how those drivers of invasions interact. We evaluate the relative roles of, and potential interactions between, plant invasiveness traits and landscape characteristics on invasions with a case study using a model parameterized for the potentially invasive biomass crop, Miscanthus × giganteus. Using that model we simulate invasions on 1000 real landscapes to evaluate how landscape characteristics, including both composition and spatial structure, affect invasion outcomes. We conducted replicate simulations with differing strengths of plant invasiveness traits (dispersal ability, establishment ability, population growth rate, and the ability to utilize dispersal corridors) to evaluate how the importance of landscape characteristics for predicting invasion patterns changes depending on the invader details. Analysis of simulations showed that the presence of highly suitable habitat (e.g., grasslands) is generally the strongest determinant of invasion dynamics but that there are also more subtle interactions between landscapes and invader traits. These effects can also vary between different aspects of invasion dynamics (short vs. long time scales and population size vs. spatial extent). These results illustrate that invasions are complex emergent processes with multiple drivers and effective management needs to reflect the ecology of the species of interest and the particular goals or risks for which efforts need to be optimized. PMID:29771923

ENVIRONMENTAL QUALITY AND LANDSCAPE-RISK ASSESSMENT IN THE YANTRA RIVER BASIN

EPA Science Inventory

Landscape characteristics exert their impact on the processes occurring in river basins in many directions and may influence in a different way the environmental security and some related constraints like extreme natural events. The complex nature of landscape structure and dynam...

Recent developments in computer modeling add ecological realism to landscape genetics

EPA Science Inventory

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...

Dynamics in species composition of stream fish assemblages: environmental variability and nested subsets

Treesearch

Christopher M. Taylor; Melvin L. Warren

2001-01-01

Stream landscapes are highly variable in space and time and, like terrestrial landscapes, the resources they contain are patchily distributed. Organisms may disperse among patches to fulfill life-history requirements, but biotic and abiotic factors may limit patch or locality occupancy. Thus, the dynamics of immigration and extinction determine, in part, the local...

Dynamic landscape management

Treesearch

Valerie Rapp

2002-01-01

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

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

Treesearch

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

2016-01-01

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

Simulating dynamic and mixed-severity fire regimes: a process-based fire extension for LANDIS-II

Treesearch

Brian R. Sturtevant; Robert M. Scheller; Brian R. Miranda; Douglas Shinneman; Alexandra Syphard

2009-01-01

Fire regimes result from reciprocal interactions between vegetation and fire that may be further affected by other disturbances, including climate, landform, and terrain. In this paper, we describe fire and fuel extensions for the forest landscape simulation model, LANDIS-II, that allow dynamic interactions among fire, vegetation, climate, and landscape structure, and...

Dynamic landscape management.

Treesearch

Valerie Rapp

2003-01-01

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

Community Landscapes: An Integrative Approach to Determine Overlapping Network Module Hierarchy, Identify Key Nodes and Predict Network Dynamics

PubMed Central

Kovács, István A.; Palotai, Robin; Szalay, Máté S.; Csermely, Peter

2010-01-01

Background Network communities help the functional organization and evolution of complex networks. However, the development of a method, which is both fast and accurate, provides modular overlaps and partitions of a heterogeneous network, has proven to be rather difficult. Methodology/Principal Findings Here we introduce the novel concept of ModuLand, an integrative method family determining overlapping network modules as hills of an influence function-based, centrality-type community landscape, and including several widely used modularization methods as special cases. As various adaptations of the method family, we developed several algorithms, which provide an efficient analysis of weighted and directed networks, and (1) determine pervasively overlapping modules with high resolution; (2) uncover a detailed hierarchical network structure allowing an efficient, zoom-in analysis of large networks; (3) allow the determination of key network nodes and (4) help to predict network dynamics. Conclusions/Significance The concept opens a wide range of possibilities to develop new approaches and applications including network routing, classification, comparison and prediction. PMID:20824084

Enhanced sampling simulations to construct free-energy landscape of protein-partner substrate interaction.

PubMed

Ikebe, Jinzen; Umezawa, Koji; Higo, Junichi

2016-03-01

Molecular dynamics (MD) simulations using all-atom and explicit solvent models provide valuable information on the detailed behavior of protein-partner substrate binding at the atomic level. As the power of computational resources increase, MD simulations are being used more widely and easily. However, it is still difficult to investigate the thermodynamic properties of protein-partner substrate binding and protein folding with conventional MD simulations. Enhanced sampling methods have been developed to sample conformations that reflect equilibrium conditions in a more efficient manner than conventional MD simulations, thereby allowing the construction of accurate free-energy landscapes. In this review, we discuss these enhanced sampling methods using a series of case-by-case examples. In particular, we review enhanced sampling methods conforming to trivial trajectory parallelization, virtual-system coupled multicanonical MD, and adaptive lambda square dynamics. These methods have been recently developed based on the existing method of multicanonical MD simulation. Their applications are reviewed with an emphasis on describing their practical implementation. In our concluding remarks we explore extensions of the enhanced sampling methods that may allow for even more efficient sampling.

Dynamically incorporating late-successional forest in sustainable landscapes

Treesearch

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

1996-01-01

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

Exploring the fitness landscape of poliovirus

NASA Astrophysics Data System (ADS)

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.

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

PubMed

Jia, Ke-Li; Chang, Qing-Rui

2007-09-01

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

Multidecadal stability in tropical rain forest structure and dynamics across an old-growth landscape

PubMed Central

Clark, Deborah A.; Oberbauer, Steven F.; Kellner, James R.

2017-01-01

Have tropical rain forest landscapes changed directionally through recent decades? To answer this question requires tracking forest structure and dynamics through time and across within-forest environmental heterogeneity. While the impacts of major environmental gradients in soil nutrients, climate and topography on lowland tropical rain forest (TRF) structure and function have been extensively analyzed, the effects of the shorter environmental gradients typical of mesoscale TRF landscapes remain poorly understood. To evaluate multi-decadal performance of an old-growth TRF at the La Selva Biological Station, Costa Rica, we established 18 0.5-ha annually-censused forest inventory plots in a stratified-random design across major landscape edaphic gradients. Over the 17-year study period, there were moderate differences in stand dynamics and structure across these gradients but no detectable difference in woody productivity. We found large effects on forest structure and dynamics from the mega-Niño event at the outset of the study, with subdecadal recovery and subsequent stabilization. To extend the timeline to >40 years, we combined our findings with those from earlier studies at this site. While there were annual to multiannual variations in the structure and dynamics, particularly in relation to local disturbances and the mega-Niño event, at the longer temporal scale and broader spatial scale this landscape was remarkably stable. This stability contrasts notably with a current hypothesis of increasing biomass and dynamics of TRF, which we term the Bigger and Faster Hypothesis (B&FHo). We consider possible reasons for the contradiction and conclude that it is currently not possible to independently assess the vast majority of previously published B&FHo evidence due to restricted data access. PMID:28981502

Looking for the optimal rate of recombination for evolutionary dynamics

NASA Astrophysics Data System (ADS)

Saakian, David B.

2018-01-01

We consider many-site mutation-recombination models of evolution with selection. We are looking for situations where the recombination increases the mean fitness of the population, and there is an optimal recombination rate. We found two fitness landscapes supporting such nonmonotonic behavior of the mean fitness versus the recombination rate. The first case is related to the evolution near the error threshold on a neutral-network-like fitness landscape, for moderate genome lengths and large population. The more realistic case is the second one, in which we consider the evolutionary dynamics of a finite population on a rugged fitness landscape (the smooth fitness landscape plus some random contributions to the fitness). We also give the solution to the horizontal gene transfer model in the case of asymmetric mutations. To obtain nonmonotonic behavior for both mutation and recombination, we need a specially designed (ideal) fitness landscape.

Solvent viscosity and friction in protein folding dynamics.

PubMed

Hagen, Stephen J

2010-08-01

The famous Kramers rate theory for diffusion-controlled reactions has been extended in numerous ways and successfully applied to many types of reactions. Its application to protein folding reactions has been of particular interest in recent years, as many researchers have performed experiments and simulations to test whether folding reactions are diffusion-controlled, whether the solvent is the source of the reaction friction, and whether the friction-dependence of folding rates generally can provide insight into folding dynamics. These experiments involve many practical difficulties, however. They have also produced some unexpected results. Here we briefly review the Kramers theory for reactions in the presence of strong friction and summarize some of the subtle problems that arise in the application of the theory to protein folding. We discuss how the results of these experiments ultimately point to a significant role for internal friction in protein folding dynamics. Studies of friction in protein folding, far from revealing any weakness in Kramers theory, may actually lead to new approaches for probing diffusional dynamics and energy landscapes in protein folding.

From spatially variable streamflow to distributed hydrological models: Analysis of key modeling decisions

NASA Astrophysics Data System (ADS)

Fenicia, Fabrizio; Kavetski, Dmitri; Savenije, Hubert H. G.; Pfister, Laurent

2016-02-01

This paper explores the development and application of distributed hydrological models, focusing on the key decisions of how to discretize the landscape, which model structures to use in each landscape element, and how to link model parameters across multiple landscape elements. The case study considers the Attert catchment in Luxembourg—a 300 km2 mesoscale catchment with 10 nested subcatchments that exhibit clearly different streamflow dynamics. The research questions are investigated using conceptual models applied at hydrologic response unit (HRU) scales (1-4 HRUs) on 6 hourly time steps. Multiple model structures are hypothesized and implemented using the SUPERFLEX framework. Following calibration, space/time model transferability is tested using a split-sample approach, with evaluation criteria including streamflow prediction error metrics and hydrological signatures. Our results suggest that: (1) models using geology-based HRUs are more robust and capture the spatial variability of streamflow time series and signatures better than models using topography-based HRUs; this finding supports the hypothesis that, in the Attert, geology exerts a stronger control than topography on streamflow generation, (2) streamflow dynamics of different HRUs can be represented using distinct and remarkably simple model structures, which can be interpreted in terms of the perceived dominant hydrologic processes in each geology type, and (3) the same maximum root zone storage can be used across the three dominant geological units with no loss in model transferability; this finding suggests that the partitioning of water between streamflow and evaporation in the study area is largely independent of geology and can be used to improve model parsimony. The modeling methodology introduced in this study is general and can be used to advance our broader understanding and prediction of hydrological behavior, including the landscape characteristics that control hydrologic response, the dominant processes associated with different landscape types, and the spatial relations of catchment processes. This article was corrected on 14 MAR 2016. See the end of the full text for details.

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

PubMed

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.

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

PubMed

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

2015-10-01

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

Nitrogen dynamics in managed boreal forests: Recent advances and future research directions.

PubMed

Sponseller, Ryan A; Gundale, Michael J; Futter, Martyn; Ring, Eva; Nordin, Annika; Näsholm, Torgny; Laudon, Hjalmar

2016-02-01

Nitrogen (N) availability plays multiple roles in the boreal landscape, as a limiting nutrient to forest growth, determinant of terrestrial biodiversity, and agent of eutrophication in aquatic ecosystems. We review existing research on forest N dynamics in northern landscapes and address the effects of management and environmental change on internal cycling and export. Current research foci include resolving the nutritional importance of different N forms to trees and establishing how tree-mycorrhizal relationships influence N limitation. In addition, understanding how forest responses to external N inputs are mediated by above- and belowground ecosystem compartments remains an important challenge. Finally, forestry generates a mosaic of successional patches in managed forest landscapes, with differing levels of N input, biological demand, and hydrological loss. The balance among these processes influences the temporal patterns of stream water chemistry and the long-term viability of forest growth. Ultimately, managing forests to keep pace with increasing demands for biomass production, while minimizing environmental degradation, will require multi-scale and interdisciplinary perspectives on landscape N dynamics.

Folding energy landscape and network dynamics of small globular proteins

PubMed Central

Hori, Naoto; Chikenji, George; Berry, R. Stephen; Takada, Shoji

2009-01-01

The folding energy landscape of proteins has been suggested to be funnel-like with some degree of ruggedness on the slope. How complex the landscape, however, is still rather unclear. Many experiments for globular proteins suggested relative simplicity, whereas molecular simulations of shorter peptides implied more complexity. Here, by using complete conformational sampling of 2 globular proteins, protein G and src SH3 domain and 2 related random peptides, we investigated their energy landscapes, topological properties of folding networks, and folding dynamics. The projected energy surfaces of globular proteins were funneled in the vicinity of the native but also have other quite deep, accessible minima, whereas the randomized peptides have many local basins, including some leading to seriously misfolded forms. Dynamics in the denatured part of the network exhibited basin-hopping itinerancy among many conformations, whereas the protein reached relatively well-defined final stages that led to their native states. We also found that the folding network has the hierarchic nature characterized by the scale-free and the small-world properties. PMID:19114654

Folding energy landscape and network dynamics of small globular proteins.

PubMed

Hori, Naoto; Chikenji, George; Berry, R Stephen; Takada, Shoji

2009-01-06

The folding energy landscape of proteins has been suggested to be funnel-like with some degree of ruggedness on the slope. How complex the landscape, however, is still rather unclear. Many experiments for globular proteins suggested relative simplicity, whereas molecular simulations of shorter peptides implied more complexity. Here, by using complete conformational sampling of 2 globular proteins, protein G and src SH3 domain and 2 related random peptides, we investigated their energy landscapes, topological properties of folding networks, and folding dynamics. The projected energy surfaces of globular proteins were funneled in the vicinity of the native but also have other quite deep, accessible minima, whereas the randomized peptides have many local basins, including some leading to seriously misfolded forms. Dynamics in the denatured part of the network exhibited basin-hopping itinerancy among many conformations, whereas the protein reached relatively well-defined final stages that led to their native states. We also found that the folding network has the hierarchic nature characterized by the scale-free and the small-world properties.

Dihedral angle principal component analysis of molecular dynamics simulations.

PubMed

Altis, Alexandros; Nguyen, Phuong H; Hegger, Rainer; Stock, Gerhard

2007-06-28

It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {phi(n)} to the metric coordinate space {x(n)=cos phi(n),y(n)=sin phi(n)} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300 ns molecular dynamics simulation, a critical comparison of the various methods is given.

Dihedral angle principal component analysis of molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Altis, Alexandros; Nguyen, Phuong H.; Hegger, Rainer; Stock, Gerhard

2007-06-01

It has recently been suggested by Mu et al. [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {φn} to the metric coordinate space {xn=cosφn,yn=sinφn} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300ns molecular dynamics simulation, a critical comparison of the various methods is given.

Quantifying Grassland-to-Woodland Transitions and the Implications for Carbon and Nitrogen Dynamics in the Southwest United States

NASA Technical Reports Server (NTRS)

Wessman, Carol A.; Archer, Steven R.; Asner, Gregory P.; Bateson, C. Ann

2004-01-01

Replacement of grasslands and savannas by shrublands and woodlands has been widely reported in tropical, temperate and high-latitude rangelands worldwide (Archer 1994). These changes in vegetation structure may reflect historical shifts in climate and land use; and are likely to influence biodiversity, productivity, above- and below ground carbon and nitrogen sequestration and biophysical aspects of land surface-atmosphere interactions. The goal of our proposed research is to investigate how changes in the relative abundance of herbaceous and woody vegetation affect carbon and nitrogen dynamics across heterogeneous savannas and shrub/woodlands. By linking actual land-cover composition (derived through spectral mixture analysis of AVIRIS, TM, and AVHRR imagery) with a process-based ecosystem model, we will generate explicit predictions of the C and N storage in plants and soils resulting from changes in vegetation structure. Our specific objectives will be to (1) continue development and test applications of spectral mixture analysis across grassland-to-woodland transitions; (2) quantify temporal changes in plant and soil C and N storage and turnover for remote sensing and process model parameterization and verification; and (3) couple landscape fraction maps to an ecosystem simulation model to observe biogeochemical dynamics under changing landscape structure and climatological forcings.

Bedrock hillslopes to deltas: New insights into landscape mechanics

NASA Astrophysics Data System (ADS)

Lamb, M. P.

2012-12-01

A powerful record of environmental history on Earth and other planets is preserved in landscapes and sedimentary deposits formed by erosion, transport and deposition of sediment. To understand this record and predict future landscape change, we need mechanistic theories for transport processes and morphodynamics. Significant progress has been made to develop and test transport laws in some settings including soil-mantled landscapes and modest gradient alluvial channels where conventional hydraulic and sediment-transport theories apply. Fundamental opportunities exist, however, to explore the physical limits of existing theories and develop new theories at the frontier of our knowledge base. In this presentation, I will describe recent case studies from sediment-source areas to depositional sinks designed to test the limits of existing transport theories and identify transitions in dominant geomorphic processes by pushing to steeper slopes, greater discharges, and dynamic boundary conditions. First, field measurements, laboratory experiments and theory suggest that sediment transport on steep, rocky hillslopes is different than on soil mantled landscapes, and may be controlled by vegetation dams and sediment release following wildfire. Second, laboratory experiments show that grain stability is enhanced in steep mountain channels compared to moderate gradient channels due to the coincident change in the ratio of flow depth to grain size, until the threshold for mass failure is surpassed. Third, field observations and theory indicate that canyons can be cut by extreme floods at rates that exceed typical river-incision rates by many orders of magnitude due to the transition from abrasion to plucking and toppling of jointed rock, with implications for megafloods on Mars. Finally, numerical modeling, laboratory experiments, and field work show that coastal rivers are coupled to their offshore plumes, and that this coupling may determine the size of deltas. These case studies illustrate that relevant processes, from turbulence to tectonics, act over a wide range of spatial and temporal scales. A major future opportunity I see is to integrate topographic and geochronologic constraints on landscape kinematics with field and laboratory experiments on process dynamics to build mechanistic transport theories applicable across human and geomorphic timescales.

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

Treesearch

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

2001-01-01

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

Pathways for diffusion in the potential energy landscape of the network glass former SiO2

NASA Astrophysics Data System (ADS)

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

2017-10-01

We study the dynamical behaviour of a computer model for viscous silica, the archetypal strong glass former, and compare its diffusion mechanism with earlier studies of a fragile binary Lennard-Jones liquid. Three different methods of analysis are employed. First, the temperature and time scale dependence of the diffusion constant is analysed. Negative correlation of particle displacements influences transport properties in silica as well as in fragile liquids. We suggest that the difference between Arrhenius and super-Arrhenius diffusive behaviour results from competition between the correlation time scale and the caging time scale. Second, we analyse the dynamics using a geometrical definition of cage-breaking transitions that was proposed previously for fragile glass formers. We find that this definition accurately captures the bond rearrangement mechanisms that control transport in open network liquids, and reproduces the diffusion constants accurately at low temperatures. As the same method is applicable to both strong and fragile glass formers, we can compare correlation time scales in these two types of systems. We compare the time spent in chains of correlated cage breaks with the characteristic caging time and find that correlations in the fragile binary Lennard-Jones system persist for an order of magnitude longer than those in the strong silica system. We investigate the origin of the correlation behaviour by sampling the potential energy landscape for silica and comparing it with the binary Lennard-Jones model. We find no qualitative difference between the landscapes, but several metrics suggest that the landscape of the fragile liquid is rougher and more frustrated. Metabasins in silica are smaller than those in binary Lennard-Jones and contain fewer high-barrier processes. This difference probably leads to the observed separation of correlation and caging time scales.

Multi-scale characterization of the energy landscape of proteins with application to the C3D/Efb-C complex.

PubMed

Haspel, Nurit; Geisbrecht, Brian V; Lambris, John; Kavraki, Lydia

2010-03-01

We present a novel multi-level methodology to explore and characterize the low energy landscape and the thermodynamics of proteins. Traditional conformational search methods typically explore only a small portion of the conformational space of proteins and are hard to apply to large proteins due to the large amount of calculations required. In our multi-scale approach, we first provide an initial characterization of the equilibrium state ensemble of a protein using an efficient computational conformational sampling method. We then enrich the obtained ensemble by performing short Molecular Dynamics (MD) simulations on selected conformations from the ensembles as starting points. To facilitate the analysis of the results, we project the resulting conformations on a low-dimensional landscape to efficiently focus on important interactions and examine low energy regions. This methodology provides a more extensive sampling of the low energy landscape than an MD simulation starting from a single crystal structure as it explores multiple trajectories of the protein. This enables us to obtain a broader view of the dynamics of proteins and it can help in understanding complex binding, improving docking results and more. In this work, we apply the methodology to provide an extensive characterization of the bound complexes of the C3d fragment of human Complement component C3 and one of its powerful bacterial inhibitors, the inhibitory domain of Staphylococcus aureus extra-cellular fibrinogen-binding domain (Efb-C) and two of its mutants. We characterize several important interactions along the binding interface and define low free energy regions in the three complexes. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

A Model with Darwinian Dynamics on a Rugged Landscape

NASA Astrophysics Data System (ADS)

Brotto, Tommaso; Bunin, Guy; Kurchan, Jorge

2017-02-01

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

Integrating Dynamic Data and Sensors with Semantic 3D City Models in the Context of Smart Cities

NASA Astrophysics Data System (ADS)

Chaturvedi, K.; Kolbe, T. H.

2016-10-01

Smart cities provide effective integration of human, physical and digital systems operating in the built environment. The advancements in city and landscape models, sensor web technologies, and simulation methods play a significant role in city analyses and improving quality of life of citizens and governance of cities. Semantic 3D city models can provide substantial benefits and can become a central information backbone for smart city infrastructures. However, current generation semantic 3D city models are static in nature and do not support dynamic properties and sensor observations. In this paper, we propose a new concept called Dynamizer allowing to represent highly dynamic data and providing a method for injecting dynamic variations of city object properties into the static representation. The approach also provides direct capability to model complex patterns based on statistics and general rules and also, real-time sensor observations. The concept is implemented as an Application Domain Extension for the CityGML standard. However, it could also be applied to other GML-based application schemas including the European INSPIRE data themes and national standards for topography and cadasters like the British Ordnance Survey Mastermap or the German cadaster standard ALKIS.

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

Treesearch

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

2011-01-01

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

The effects of wind disturbance on temperate rain forest structure and dynamics of southeast Alaska.

Treesearch

Gregory J. Nowacki; Marc G. Kramer

1998-01-01

Wind disturbance plays a fundamental role in shaping forest dynamics in southeast Alaska. Recent studies have increased our appreciation for the effects of wind at both large and small scales. Current thinking is that wind disturbance characteristics change over a continuum dependent on landscape features (e.g., exposure, landscape position, topography). Data modeling...

Simulating ungulate herbivory across forest landscapes: A browsing extension for LANDIS-II

USGS Publications Warehouse

DeJager, Nathan R.; Drohan, Patrick J.; Miranda, Brian M.; Sturtevant, Brian R.; Stout, Susan L.; Royo, Alejandro; Gustafson, Eric J.; Romanski, Mark C.

2017-01-01

Browsing ungulates alter forest productivity and vegetation succession through selective foraging on species that often dominate early succession. However, the long-term and large-scale effects of browsing on forest succession are not possible to project without the use of simulation models. To explore the effects of ungulates on succession in a spatially explicit manner, we developed a Browse Extension that simulates the effects of browsing ungulates on the growth and survival of plant species cohorts within the LANDIS-II spatially dynamic forest landscape simulation model framework. We demonstrate the capabilities of the new extension and explore the spatial effects of ungulates on forest composition and dynamics using two case studies. The first case study examined the long-term effects of persistently high white-tailed deer browsing rates in the northern hardwood forests of the Allegheny National Forest, USA. In the second case study, we incorporated a dynamic ungulate population model to simulate interactions between the moose population and boreal forest landscape of Isle Royale National Park, USA. In both model applications, browsing reduced total aboveground live biomass and caused shifts in forest composition. Simulations that included effects of browsing resulted in successional patterns that were more similar to those observed in the study regions compared to simulations that did not incorporate browsing effects. Further, model estimates of moose population density and available forage biomass were similar to previously published field estimates at Isle Royale and in other moose-boreal forest systems. Our simulations suggest that neglecting effects of browsing when modeling forest succession in ecosystems known to be influenced by ungulates may result in flawed predictions of aboveground biomass and tree species composition.

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

NASA Astrophysics Data System (ADS)

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.

Detectability of landscape effects on recolonization increases with regional population density

PubMed Central

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

2015-01-01

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. PMID:26257881

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

PubMed

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.

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

PubMed

Gilpin, William; Feldman, Marcus W

2017-07-01

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

Using graph approach for managing connectivity in integrative landscape modelling

NASA Astrophysics Data System (ADS)

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). OpenFLUID-landr library has been developed in order i) to be used with no GIS expert skills needed (common gis formats can be read and simplified spatial management is provided), ii) to easily develop adapted rules of landscape discretization and graph creation to follow spatialized model requirements and iii) to allow model developers to manage dynamic and complex spatial topology. Graph management in OpenFLUID are shown with i) examples of hydrological modelizations on complex farmed landscapes and ii) the new implementation of Geo-MHYDAS tool based on the OpenFLUID-landr library, which allows to discretize a landscape and create graph structure for the MHYDAS model requirements.

Informational landscapes in art, science, and evolution.

PubMed

Cohen, Irun R

2006-07-01

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

Multiple successional pathways in human-modified tropical landscapes: new insights from forest succession, forest fragmentation and landscape ecology research.

PubMed

Arroyo-Rodríguez, Víctor; Melo, Felipe P L; Martínez-Ramos, Miguel; Bongers, Frans; Chazdon, Robin L; Meave, Jorge A; Norden, Natalia; Santos, Bráulio A; Leal, Inara R; Tabarelli, Marcelo

2017-02-01

Old-growth tropical forests are being extensively deforested and fragmented worldwide. Yet forest recovery through succession has led to an expansion of secondary forests in human-modified tropical landscapes (HMTLs). Secondary forests thus emerge as a potential repository for tropical biodiversity, and also as a source of essential ecosystem functions and services in HMTLs. Such critical roles are controversial, however, as they depend on successional, landscape and socio-economic dynamics, which can vary widely within and across landscapes and regions. Understanding the main drivers of successional pathways of disturbed tropical forests is critically needed for improving management, conservation, and restoration strategies. Here, we combine emerging knowledge from tropical forest succession, forest fragmentation and landscape ecology research to identify the main driving forces shaping successional pathways at different spatial scales. We also explore causal connections between land-use dynamics and the level of predictability of successional pathways, and examine potential implications of such connections to determine the importance of secondary forests for biodiversity conservation in HMTLs. We show that secondary succession (SS) in tropical landscapes is a multifactorial phenomenon affected by a myriad of forces operating at multiple spatio-temporal scales. SS is relatively fast and more predictable in recently modified landscapes and where well-preserved biodiversity-rich native forests are still present in the landscape. Yet the increasing variation in landscape spatial configuration and matrix heterogeneity in landscapes with intermediate levels of disturbance increases the uncertainty of successional pathways. In landscapes that have suffered extensive and intensive human disturbances, however, succession can be slow or arrested, with impoverished assemblages and reduced potential to deliver ecosystem functions and services. We conclude that: (i) succession must be examined using more comprehensive explanatory models, providing information about the forces affecting not only the presence but also the persistence of species and ecological groups, particularly of those taxa expected to be extirpated from HMTLs; (ii) SS research should integrate new aspects from forest fragmentation and landscape ecology research to address accurately the potential of secondary forests to serve as biodiversity repositories; and (iii) secondary forest stands, as a dynamic component of HMTLs, must be incorporated as key elements of conservation planning; i.e. secondary forest stands must be actively managed (e.g. using assisted forest restoration) according to conservation goals at broad spatial scales. © 2015 Cambridge Philosophical Society.

The Ancient Maya Landscape: Facing the Challenges and Embracing the Promise of Integrating Archaeology, Remote Sensing, Soil Science and Hydrologic Modeling for Coupled Natural and Human Systems.

NASA Astrophysics Data System (ADS)

Murtha, T., Jr.; Duffy, C.; Cook, B. D.; Schroder, W.; Webster, D.; French, K. D.; Alcover, O.; Golden, C.; Balzotti, C.; Shaffer, D.

2016-12-01

Relying on a niche inheritance perspective, this paper discusses the long-term spatial and temporal dynamics of land-use management, agricultural decision making and patterns of resource availability in the tropical lowlands of Central America. We introduce and describe ongoing research that addresses a series of long standing questions about coupled natural and human history dynamics in the Central Maya lowlands, emphasizing the role of landscape and region to address these questions. First, we summarize the results of a CNH pilot study focused on the evolution of the regional landscape of Tikal, Guatemala. Particular attention is centered on how we integrated landscape survey, traditional archaeology and soil studies to understand the spatial and temporal dynamics of agricultural land use and intensification over a two thousand period. Additionally, we discuss how these results were integrated into remote sensing, hydrological and erosion models to better understand how past changes in available water and productive land compare to what we know about settlement patterns in the Tikal Region over that same time period. We not only describe how the Maya transformed this landscape, but also how the region influenced changing patterns of settlement and land use. We finish this section with a discussion of some of the unique challenges integrating archaeological information to study CNH dynamics during this pilot study. Second, we introduce a new project designed to `scale up' the pilot study for a macro-regional analysis of the lowland Maya landscape. The new project leverages a uniquely sampled LIDAR data set designed to refine measurements of above ground carbon storage. Our new project quantitatively examines these data for evidence for past human activity. Preliminary results offer a promising path for tightly integrating archaeology, natural science, remote sensing and modeling for studying CNH dynamics in the deep and recent past.

The Changing Landscape of Early Childhood Education: Implications for Policy and Practice

ERIC Educational Resources Information Center

Haslip, Michael J.; Gullo, Dominic F.

2018-01-01

Early childhood education is changing rapidly due to the dynamic nature of positive and negative trends affecting the profession. In this article, the changing landscape of early childhood education is discussed and analyzed. Both the positive and negative forces contributing to the changing landscape are examined. The focus of this discussion…

From soilscapes to landscapes: A landscape-oriented approach to simulate soil organic carbon dynamics in intensively managed landscapes

USDA-ARS?s Scientific Manuscript database

Most available biogeochemical models focus within a soil profile and cannot adequately resolve contributions of the lighter size fractions of organic rich soils for Enrichment Ratio (ER) estimates, thereby causing unintended errors in Soil Organic Carbon (SOC) storage predictions. These models set E...

Landscape epidemiology of emerging infectious diseases in natural and human-altered ecosystems

Treesearch

Ross K. Meentemeyer; Sarah E. Haas; Tomas Vaclavik

2012-01-01

A central challenge to studying emerging infectious diseases (EIDs) is a landscape dilemma: Our best empirical understanding of disease dynamics occurs at local scales, whereas pathogen invasions and management occur over broad spatial extents. The burgeoning field of landscape epidemiology integrates concepts and approaches from disease ecology with the...

Messy world: managing dynamic landscape.

Treesearch

Sally Duncan

1999-01-01

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

Geographic analysis and monitoring at the United States Geological Survey

USGS Publications Warehouse

Findley, J.

2003-01-01

The Geographic Analysis and Monitoring (GAM) Program of the U.S. Geological Survey assesses the Nation's land surface at a variety of spatial and temporal scales to understand the rates, causes, and consequences of natural and human-induced processes and their interactions that affect the landscape over time. The program plays an important role in developing National Map tools and application. The GAM is a science and synthesis program that not only assesses the rates of changes to the Earth's land surface, but also provides reports on the status and trends of the Nation's land resources on a periodic basis, produces a land-use and land- cover database for the periodically updated map and data set-the Geographic Face of the Nation, and conducts research leading to improved understanding and knowledge about geographic processes. Scientific investigations provide comprehensive information needed to understand the environmental, resource, and economic consequences of landscape change. These analyses responds to the needs of resource managers and offers the American public baseline information to help them understand the dynamic nature of our national landscape and to anticipate the opportunities and consequences of our actions.

Urban growth and landscape connectivity threats assessment at Saguaro National Park, Arizona, USA

USGS Publications Warehouse

Perkl, Ryan; Norman, Laura M.; Mitchell, David; Feller, Mark R.; Smith, Garrett; Wilson, Natalie R.

2018-01-01

Urban and exurban expansion results in habitat and biodiversity loss globally. We hypothesize that a coupled-model approach could connect urban planning for future cities with landscape ecology to consider wildland habitat connectivity. Our work combines urban growth simulations with models of wildlife corridors to examine how species will be impacted by development to test this hypothesis. We leverage a land use change model (SLEUTH) with structural and functional landscape-connectivity modeling techniques to ascertain the spatial extent and locations of connectivity related threats to a national park in southern Arizona, USA, and describe how protected areas might be impacted by urban expansion. Results of projected growth significantly altered structural connectivity (80%) when compared to current (baseline) corridor conditions. Moreover, projected growth impacted functional connectivity differently amongst species, indicating resilience of some species and near-complete displacement of others. We propose that implementing a geospatial-design-based model will allow for a better understanding of the impacts management decisions have on wildlife populations. The application provides the potential to understand both human and environmental impacts of land-system dynamics, critical for long-term sustainability.

Water: the bloodstream of the biosphere.

PubMed

Ripl, Wilhelm

2003-12-29

Water, the bloodstream of the biosphere, determines the sustainability of living systems. The essential role of water is expanded in a conceptual model of energy dissipation, based on the water balance of whole landscapes. In this model, the underlying role of water phase changes--and their energy-dissipative properties--in the function and the self-organized development of natural systems is explicitly recognized. The energy-dissipating processes regulate the ecological dynamics within the Earth's biosphere, in such a way that the development of natural systems is never allowed to proceed in an undirected or random way. A fundamental characteristic of self-organized development in natural systems is the increasing role of cyclic processes while loss processes are correspondingly reduced. This gives a coincidental increase in system efficiency, which is the basis of growing stability and sustainability. Growing sustainability can be seen as an increase of ecological efficiency, which is applicable at all levels up to whole landscapes. Criteria for necessary changes in society and for the design of the measures that are necessary to restore sustainable landscapes and waters are derived.

Water: the bloodstream of the biosphere.

PubMed Central

Ripl, Wilhelm

2003-01-01

Water, the bloodstream of the biosphere, determines the sustainability of living systems. The essential role of water is expanded in a conceptual model of energy dissipation, based on the water balance of whole landscapes. In this model, the underlying role of water phase changes--and their energy-dissipative properties--in the function and the self-organized development of natural systems is explicitly recognized. The energy-dissipating processes regulate the ecological dynamics within the Earth's biosphere, in such a way that the development of natural systems is never allowed to proceed in an undirected or random way. A fundamental characteristic of self-organized development in natural systems is the increasing role of cyclic processes while loss processes are correspondingly reduced. This gives a coincidental increase in system efficiency, which is the basis of growing stability and sustainability. Growing sustainability can be seen as an increase of ecological efficiency, which is applicable at all levels up to whole landscapes. Criteria for necessary changes in society and for the design of the measures that are necessary to restore sustainable landscapes and waters are derived. PMID:14728789

Research and Application of Remote Sensing Monitoring Method for Desertification Land Under Time and Space Constraints

NASA Astrophysics Data System (ADS)

Zhang, Nannnan; Wang, Rongbao; Zhang, Feng

2018-04-01

Serious land desertification and sandified threaten the urban ecological security and the sustainable economic and social development. In recent years, a large number of mobile sand dunes in Horqin sandy land flow into the northwest of Liaoning Province under the monsoon, make local agriculture suffer serious harm. According to the characteristics of desertification land in northwestern Liaoning, based on the First National Geographical Survey data, the Second National Land Survey data and the 1984-2014 Landsat satellite long time sequence data and other multi-source data, we constructed a remote sensing monitoring index system of desertification land in Northwest Liaoning. Through the analysis of space-time-spectral characteristics of desertification land, a method for multi-spectral remote sensing image recognition of desertification land under time-space constraints is proposed. This method was used to identify and extract the distribution and classification of desertification land of Chaoyang City (a typical citie of desertification in northwestern Liaoning) in 2008 and 2014, and monitored the changes and transfers of desertification land from 2008 to 2014. Sandification information was added to the analysis of traditional landscape changes, improved the analysis model of desertification land landscape index, and the characteristics and laws of landscape dynamics and landscape pattern change of desertification land from 2008 to 2014 were analyzed and revealed.

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

USGS Publications Warehouse

Yurek, Simeon; DeAngelis, Donald L.; 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 allowing enough time for them to regenerate. Testable, spatiotemporal predictions of the timing, location, duration, and magnitude of fish concentration pulses were produced by the model, and can be applied to restoration planning.

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

PubMed

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

2014-04-01

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

Exploring RNA structure and dynamics through enhanced sampling simulations.

PubMed

Mlýnský, Vojtěch; Bussi, Giovanni

2018-04-01

RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this timescale to be effectively extended in order to probe biologically relevant conformational changes and chemical reactions. Here, we review the role of enhanced sampling techniques in the study of RNA systems. We discuss the challenges and promises associated with the application of these methods to force-field validation, exploration of conformational landscapes and ion/ligand-RNA interactions, as well as catalytic pathways. Important technical aspects of these methods, such as the choice of the biased collective variables and the analysis of multi-replica simulations, are examined in detail. Finally, a perspective on the role of these methods in the characterization of RNA dynamics is provided. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed

Zhuravlev, Pavel I; Papoian, Garegin A

2010-08-01

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

Where Wolves Kill Moose: The Influence of Prey Life History Dynamics on the Landscape Ecology of Predation

PubMed Central

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

2014-01-01

The landscape ecology of predation is well studied and known to be influenced by habitat heterogeneity. Little attention has been given to how the influence of habitat heterogeneity on the landscape ecology of predation might be modulated by life history dynamics of prey in mammalian systems. We demonstrate how life history dynamics of moose (Alces alces) contribute to landscape patterns in predation by wolves (Canis lupus) in Isle Royale National Park, Lake Superior, USA. We use pattern analysis and kernel density estimates of moose kill sites to demonstrate that moose in senescent condition and moose in prime condition tend to be wolf-killed in different regions of Isle Royale in winter. Predation on senescent moose was clustered in one kill zone in the northeast portion of the island, whereas predation on prime moose was clustered in 13 separate kill zones distributed throughout the full extent of the island. Moreover, the probability of kill occurrence for senescent moose, in comparison to prime moose, increased in high elevation habitat with patches of dense coniferous trees. These differences can be attributed, at least in part, to senescent moose being more vulnerable to predation and making different risk-sensitive habitat decisions than prime moose. Landscape patterns emerging from prey life history dynamics and habitat heterogeneity have been observed in the predation ecology of fish and insects, but this is the first mammalian system for which such observations have been made. PMID:24622241

Present Day Biology seen in the Looking Glass of Physics of Complexity

NASA Astrophysics Data System (ADS)

Schuster, P.

Darwin's theory of variation and selection in its simplest form is directly applicable to RNA evolution in vitro as well as to virus evolution, and it allows for quantitative predictions. Understanding evolution at the molecular level is ultimately related to the central paradigm of structural biology: sequence⇒ structure ⇒ function. We elaborate on the state of the art in modeling and understanding evolution of RNA driven by reproduction and mutation. The focus will be laid on the landscape concept—originally introduced by Sewall Wright—and its application to problems in biology. The relation between genotypes and phenotypes is the result of two consecutive mappings from a space of genotypes called sequence space onto a space of phenotypes or structures, and fitness is the result of a mapping from phenotype space into non-negative real numbers. Realistic landscapes as derived from folding of RNA sequences into structures are characterized by two properties: (i) they are rugged in the sense that sequences lying nearby in sequence space may have very different fitness values and (ii) they are characterized by an appreciable degree of neutrality implying that a certain fraction of genotypes and/or phenotypes cannot be distinguished in the selection process. Evolutionary dynamics on realistic landscapes will be studied as a function of the mutation rate, and the role of neutrality in the selection process will be discussed.

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

PubMed

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.

Proceedings of the First Landscape State-and-Transition Simulation Modeling Conference, June 14–16, 2011, Portland, Oregon

Treesearch

Becky K. Kerns; Ayn J. Shlisky; Colin J. Daniel

2012-01-01

The first ever Landscape State-and-Transition Simulation Modeling Conference was held from June 14–16, 2011, in Portland Oregon. The conference brought together over 70 users of state-and-transition simulation modeling tools—the Vegetation Dynamics Development Tool (VDDT), the Tool for Exploratory Landscape Analysis (TELSA) and the Path Landscape Model. The goal of the...

Dynamic, spatial models of parasite transmission in wildlife: Their structure, applications and remaining challenges.

PubMed

White, Lauren A; Forester, James D; Craft, Meggan E

2018-05-01

Individual differences in contact rate can arise from host, group and landscape heterogeneity and can result in different patterns of spatial spread for diseases in wildlife populations with concomitant implications for disease control in wildlife of conservation concern, livestock and humans. While dynamic disease models can provide a better understanding of the drivers of spatial spread, the effects of landscape heterogeneity have only been modelled in a few well-studied wildlife systems such as rabies and bovine tuberculosis. Such spatial models tend to be either purely theoretical with intrinsic limiting assumptions or individual-based models that are often highly species- and system-specific, limiting the breadth of their utility. Our goal was to review studies that have utilized dynamic, spatial models to answer questions about pathogen transmission in wildlife and identify key gaps in the literature. We begin by providing an overview of the main types of dynamic, spatial models (e.g., metapopulation, network, lattice, cellular automata, individual-based and continuous-space) and their relation to each other. We investigate different types of ecological questions that these models have been used to explore: pathogen invasion dynamics and range expansion, spatial heterogeneity and pathogen persistence, the implications of management and intervention strategies and the role of evolution in host-pathogen dynamics. We reviewed 168 studies that consider pathogen transmission in free-ranging wildlife and classify them by the model type employed, the focal host-pathogen system, and their overall research themes and motivation. We observed a significant focus on mammalian hosts, a few well-studied or purely theoretical pathogen systems, and a lack of studies occurring at the wildlife-public health or wildlife-livestock interfaces. Finally, we discuss challenges and future directions in the context of unprecedented human-mediated environmental change. Spatial models may provide new insights into understanding, for example, how global warming and habitat disturbance contribute to disease maintenance and emergence. Moving forward, better integration of dynamic, spatial disease models with approaches from movement ecology, landscape genetics/genomics and ecoimmunology may provide new avenues for investigation and aid in the control of zoonotic and emerging infectious diseases. © 2017 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Evolution of complex dynamics

NASA Astrophysics Data System (ADS)

Wilds, Roy; Kauffman, Stuart A.; Glass, Leon

2008-09-01

We study the evolution of complex dynamics in a model of a genetic regulatory network. The fitness is associated with the topological entropy in a class of piecewise linear equations, and the mutations are associated with changes in the logical structure of the network. We compare hill climbing evolution, in which only mutations that increase the fitness are allowed, with neutral evolution, in which mutations that leave the fitness unchanged are allowed. The simple structure of the fitness landscape enables us to estimate analytically the rates of hill climbing and neutral evolution. In this model, allowing neutral mutations accelerates the rate of evolutionary advancement for low mutation frequencies. These results are applicable to evolution in natural and technological systems.

A new perspective on microbial landscapes within food production

PubMed Central

Bokulich, Nicholas A; Lewis, Zachery T; Boundy-Mills, Kyria; Mills, David A

2016-01-01

High-throughput, ‘next-generation’ sequencing tools offer many exciting new possibilities for food research. From investigating microbial dynamics within food fermentations to the ecosystem of the food-processing built environment, amplicon sequencing, metagenomics, and transcriptomics present novel applications for exploring microbial communities in, on, and around our foods. This review discusses the many uses of these tools for food-related and food facility-related research and highlights where they may yield nuanced insight into the microbial world of food production systems. PMID:26773388

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

PubMed

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

2012-04-10

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

Field migration rates of tidal meanders recapitulate fluvial morphodynamics

NASA Astrophysics Data System (ADS)

Finotello, Alvise; Lanzoni, Stefano; Ghinassi, Massimiliano; Marani, Marco; Rinaldo, Andrea; D'Alpaos, Andrea

2018-02-01

The majority of tidal channels display marked meandering features. Despite their importance in oil-reservoir formation and tidal landscape morphology, questions remain on whether tidal-meander dynamics could be understood in terms of fluvial processes and theory. Key differences suggest otherwise, like the periodic reversal of landscape-forming tidal flows and the widely accepted empirical notion that tidal meanders are stable landscape features, in stark contrast with their migrating fluvial counterparts. On the contrary, here we show that, once properly normalized, observed migration rates of tidal and fluvial meanders are remarkably similar. Key to normalization is the role of tidal channel width that responds to the strong spatial gradients of landscape-forming flow rates and tidal prisms. We find that migration dynamics of tidal meanders agree with nonlinear theories for river meander evolution. Our results challenge the conventional view of tidal channels as stable landscape features and suggest that meandering tidal channels recapitulate many fluvial counterparts owing to large gradients of tidal prisms across meander wavelengths.

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

PubMed

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

2010-12-01

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

Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method.

PubMed

Harada, Ryuhei; Kitao, Akio

2011-07-14

The folding process for a β-hairpin miniprotein, chignolin, was investigated by free energy landscape (FEL) calculations using the recently proposed multiscale free energy landscape calculation method (MSFEL). First, coarse-grained molecular dynamics simulations searched a broad conformational space, then multiple independent, all-atom molecular dynamics simulations with explicit solvent determined the detailed local FEL using massively distributed computing. The combination of the two models enabled efficient calculation of the free energy landscapes. The MSFEL analysis showed that chignolin has an intermediate state as well as a misfolded state. The folding process is initiated by the formation of a β-hairpin turn, followed by the formation of contacts in the hydrophobic core between Tyr2 and Trp9. Furthermore, mutation of Tyr2 shifts the population to the misfolded conformation. The results indicate that the hydrophobic core plays an important role in stabilizing the native state of chignolin. © 2011 American Chemical Society

Scale-dependent portfolio effects explain growth inflation and volatility reduction in landscape demography

PubMed Central

2017-01-01

Population demography is central to fundamental ecology and for predicting range shifts, decline of threatened species, and spread of invasive organisms. There is a mismatch between most demographic work, carried out on few populations and at local scales, and the need to predict dynamics at landscape and regional scales. Inspired by concepts from landscape ecology and Markowitz’s portfolio theory, we develop a landscape portfolio platform to quantify and predict the behavior of multiple populations, scaling up the expectation and variance of the dynamics of an ensemble of populations. We illustrate this framework using a 35-y time series on gypsy moth populations. We demonstrate the demography accumulation curve in which the collective growth of the ensemble depends on the number of local populations included, highlighting a minimum but adequate number of populations for both regional-scale persistence and cross-scale inference. The attainable set of landscape portfolios further suggests tools for regional population management for both threatened and invasive species. PMID:29109261

Calibrating a forest landscape model to simulate frequent fire in Mediterranean-type shrublands

USGS Publications Warehouse

Syphard, A.D.; Yang, J.; Franklin, J.; He, H.S.; Keeley, J.E.

2007-01-01

In Mediterranean-type ecosystems (MTEs), fire disturbance influences the distribution of most plant communities, and altered fire regimes may be more important than climate factors in shaping future MTE vegetation dynamics. Models that simulate the high-frequency fire and post-fire response strategies characteristic of these regions will be important tools for evaluating potential landscape change scenarios. However, few existing models have been designed to simulate these properties over long time frames and broad spatial scales. We refined a landscape disturbance and succession (LANDIS) model to operate on an annual time step and to simulate altered fire regimes in a southern California Mediterranean landscape. After developing a comprehensive set of spatial and non-spatial variables and parameters, we calibrated the model to simulate very high fire frequencies and evaluated the simulations under several parameter scenarios representing hypotheses about system dynamics. The goal was to ensure that observed model behavior would simulate the specified fire regime parameters, and that the predictions were reasonable based on current understanding of community dynamics in the region. After calibration, the two dominant plant functional types responded realistically to different fire regime scenarios. Therefore, this model offers a new alternative for simulating altered fire regimes in MTE landscapes. ?? 2007 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2009-03-01

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

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

USGS Publications Warehouse

Mueller, Thomas; Olson, K.A.; Dressler, G.; Leimgruber, Peter; Fuller, Todd K.; Nicholson, Craig; Novaro, A.J.; Bolgeri, M.J.; Wattles, 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  We show how broad-scale landscape unpredictability may lead to nomadism, an understudied type of long-distance movement. In contrast to classical migration where landscapes may vary at broad scales but in a predictable manner, long-distance movements of nomadic individuals are uncoordinated and independent from other such individuals. Landscapes with little broad-scale variability in vegetation productivity feature smaller-scale movements and allow for range residency. Nomadism requires distinct integrative conservation strategies that facilitate long-distance movements across the entire landscape and are not limited to certain migration corridors.

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

USGS Publications Warehouse

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

2011-01-01

Aim To demonstrate how the interrelations of individual movements form large-scale population-level movement patterns and how these patterns are associated with the underlying landscape dynamics by comparing ungulate movements across species. Locations Arctic tundra in Alaska and Canada, temperate forests in Massachusetts, Patagonian Steppes in Argentina, Eastern Steppes in Mongolia. Methods We used relocation data from four ungulate species (barren-ground caribou, Mongolian gazelle, guanaco and moose) to examine individual movements and the interrelation of movements among individuals. We applied and developed a suite of spatial metrics that measure variation in movement among individuals as population dispersion, movement coordination and realized mobility. Taken together, these metrics allowed us to quantify and distinguish among different large-scale population-level movement patterns such as migration, range residency and nomadism. We then related the population-level movement patterns to the underlying landscape vegetation dynamics via long-term remote sensing measurements of the temporal variability, spatial variability and unpredictability of vegetation productivity. Results Moose, which remained in sedentary home ranges, and guanacos, which were partially migratory, exhibited relatively short annual movements associated with landscapes having very little broad-scale variability in vegetation. Caribou and gazelle performed extreme long-distance movements that were associated with broad-scale variability in vegetation productivity during the peak of the growing season. Caribou exhibited regular seasonal migration in which individuals were clustered for most of the year and exhibited coordinated movements. In contrast, gazelle were nomadic, as individuals were independently distributed and moved in an uncoordinated manner that relates to the comparatively unpredictable (yet broad-scale) vegetation dynamics of their landscape. Main conclusions We show how broad-scale landscape unpredictability may lead to nomadism, an understudied type of long-distance movement. In contrast to classical migration where landscapes may vary at broad scales but in a predictable manner, long-distance movements of nomadic individuals are uncoordinated and independent from other such individuals. Landscapes with little broad-scale variability in vegetation productivity feature smaller-scale movements and allow for range residency. Nomadism requires distinct integrative conservation strategies that facilitate long-distance movements across the entire landscape and are not limited to certain migration corridors. ?? 2011 Blackwell Publishing Ltd.

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

Treesearch

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

1994-01-01

We examined the process of fragmentation in a managed forest landscape by comparing rates and patterns of disturbance (primarily clear-cutting) and regrowth between 1972 and 1988 using Landsat imagery. A 2589-km2 managed forest landscape in western Oregon was classified into two forest types, closed-canopy conifer forest (CF) (typically, > 60% conifer cover) and...

Landscape epidemiology of emerging infectious diseases in natural and human-altered ecosystems

Treesearch

Ross K. Meentemeyer; Sarah Haas; Tomáš Václavík

2013-01-01

A central challenge to studying emerging infectious diseases (EIDs) is a landscape dilemma: our best empirical understanding of disease dynamics occurs at local scales while pathogen invasions and management occur over broad spatial extents. The burgeoning field of landscape epidemiology integrates concepts and approaches from disease ecology with the macro-scale lens...

An object-oriented forest landscape model and its representation of tree species

Treesearch

Hong S. He; David J. Mladenoff; Joel Boeder

1999-01-01

LANDIS is a forest landscape model that simulates the interaction of large landscape processes and forest successional dynamics at tree species level. We discuss how object-oriented design (OOD) approaches such as modularity, abstraction and encapsulation are integrated into the design of LANDIS. We show that using OOD approaches, model decisions (olden as model...

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

Treesearch

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

2017-01-01

Context: Interactions among disturbances, climate, and vegetation influence landscape patterns and ecosystem processes. Climate changes, exotic invasions, beetle outbreaks, altered fire regimes, and human activities may interact to produce landscapes that appear and function beyond historical analogs. Objectives We used the mechanistic...

Automated Detection of Knickpoints and Knickzones Across Transient Landscapes

NASA Astrophysics Data System (ADS)

Gailleton, B.; Mudd, S. M.; Clubb, F. J.

2017-12-01

Mountainous regions are ubiquitously dissected by river channels, which transmit climate and tectonic signals to the rest of the landscape by adjusting their long profiles. Fluvial response to allogenic forcing is often expressed through the upstream propagation of steepened reaches, referred to as knickpoints or knickzones. The identification and analysis of these steepened reaches has numerous applications in geomorphology, such as modelling long-term landscape evolution, understanding controls on fluvial incision, and constraining tectonic uplift histories. Traditionally, the identification of knickpoints or knickzones from fluvial profiles requires manual selection or calibration. This process is both time-consuming and subjective, as different workers may select different steepened reaches within the profile. We propose an objective, statistically-based method to systematically pick knickpoints/knickzones on a landscape scale using an outlier-detection algorithm. Our method integrates river profiles normalised by drainage area (Chi, using the approach of Perron and Royden, 2013), then separates the chi-elevation plots into a series of transient segments using the method of Mudd et al. (2014). This method allows the systematic detection of knickpoints across a DEM, regardless of size, using a high-performance algorithm implemented in the open-source Edinburgh Land Surface Dynamics Topographic Tools (LSDTopoTools) software package. After initial knickpoint identification, outliers are selected using several sorting and binning methods based on the Median Absolute Deviation, to avoid the influence sample size. We test our method on a series of DEMs and grid resolutions, and show that our method consistently identifies accurate knickpoint locations across each landscape tested.

Higher temporal variability of forest breeding bird communities in fragmented landscapes

USGS Publications Warehouse

Boulinier, T.; Nichols, J.D.; Hines, J.E.; Sauer, J.R.; Flather, C.H.; Pollock, K.H.

1998-01-01

Understanding the relationship between animal community dynamics and landscape structure has become a priority for biodiversity conservation. In particular, predicting the effects of habitat destruction that confine species to networks of small patches is an important prerequisite to conservation plan development. Theoretical models that predict the occurrence of species in fragmented landscapes, and relationships between stability and diversity do exist. However, reliable empirical investigations of the dynamics of biodiversity have been prevented by differences in species detection probabilities among landscapes. Using long-term data sampled at a large spatial scale in conjunction with a capture-recapture approach, we developed estimates of parameters of community changes over a 22-year period for forest breeding birds in selected areas of the eastern United States. We show that forest fragmentation was associated not only with a reduced number of forest bird species, but also with increased temporal variability in the number of species. This higher temporal variability was associated with higher local extinction and turnover rates. These results have major conservation implications. Moreover, the approach used provides a practical tool for the study of the dynamics of biodiversity.

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

PubMed

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

2015-11-01

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

Towards a microscopic description of the free-energy landscape of water.

PubMed

Prada-Gracia, Diego; Shevchuk, Roman; Hamm, Peter; Rao, Francesco

2012-10-14

Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005 model is applied to investigate the free-energy landscape of water. The latter is built on top of a large set of water microstates describing the kinetic stability of local hydrogen-bond arrangements up to the second solvation shell. In temperature space, the landscape displays three different regimes. At around ambient conditions, the free-energy surface is characterized by many short-lived basins of attraction which are structurally well-defined (inhomogeneous regime). At lower temperatures instead, the liquid rapidly becomes homogeneous. In this regime, the free energy is funneled-like, with fully coordinated water arrangements at the bottom of the funnel. Finally, a third regime develops below the temperature of maximal compressibility (Widom line) where the funnel becomes steeper with few interconversions between microstates other than the fully coordinated ones. Our results present a way to manage the complexity of water structure and dynamics, connecting microscopic properties to its ensemble behavior.

Towards a systems approach for understanding honeybee decline: a stocktaking and synthesis of existing models

PubMed Central

Becher, Matthias A; Osborne, Juliet L; Thorbek, Pernille; Kennedy, Peter J; Grimm, Volker

2013-01-01

The health of managed and wild honeybee colonies appears to have declined substantially in Europe and the United States over the last decade. Sustainability of honeybee colonies is important not only for honey production, but also for pollination of crops and wild plants alongside other insect pollinators. A combination of causal factors, including parasites, pathogens, land use changes and pesticide usage, are cited as responsible for the increased colony mortality. However, despite detailed knowledge of the behaviour of honeybees and their colonies, there are no suitable tools to explore the resilience mechanisms of this complex system under stress. Empirically testing all combinations of stressors in a systematic fashion is not feasible. We therefore suggest a cross-level systems approach, based on mechanistic modelling, to investigate the impacts of (and interactions between) colony and land management. We review existing honeybee models that are relevant to examining the effects of different stressors on colony growth and survival. Most of these models describe honeybee colony dynamics, foraging behaviour or honeybee – varroa mite – virus interactions. We found that many, but not all, processes within honeybee colonies, epidemiology and foraging are well understood and described in the models, but there is no model that couples in-hive dynamics and pathology with foraging dynamics in realistic landscapes. Synthesis and applications. We describe how a new integrated model could be built to simulate multifactorial impacts on the honeybee colony system, using building blocks from the reviewed models. The development of such a tool would not only highlight empirical research priorities but also provide an important forecasting tool for policy makers and beekeepers, and we list examples of relevant applications to bee disease and landscape management decisions. PMID:24223431

A stand-alone tree demography and landscape structure module for Earth system models: integration with global forest data

NASA Astrophysics Data System (ADS)

Haverd, V.; Smith, B.; Nieradzik, L. P.; Briggs, P. R.

2014-02-01

Poorly constrained rates of biomass turnover are a key limitation of Earth system models (ESM). In light of this, we recently proposed a new approach encoded in a model called Populations-Order-Physiology (POP), for the simulation of woody ecosystem stand dynamics, demography and disturbance-mediated heterogeneity. POP is suitable for continental to global applications and designed for coupling to the terrestrial ecosystem component of any ESM. POP bridges the gap between first generation Dynamic Vegetation Models (DVMs) with simple large-area parameterisations of woody biomass (typically used in current ESMs) and complex second generation DVMs, that explicitly simulate demographic processes and landscape heterogeneity of forests. The key simplification in the POP approach, compared with second-generation DVMs, is to compute physiological processes such as assimilation at grid-scale (with CABLE or a similar land surface model), but to partition the grid-scale biomass increment among age classes defined at sub grid-scale, each subject to its own dynamics. POP was successfully demonstrated along a savanna transect in northern Australia, replicating the effects of strong rainfall and fire disturbance gradients on observed stand productivity and structure. Here, we extend the application of POP to a range of forest types around the globe, employing paired observations of stem biomass and density from forest inventory data to calibrate model parameters governing stand demography and biomass evolution. The calibrated POP model is then coupled to the CABLE land surface model and the combined model (CABLE-POP) is evaluated against leaf-stem allometry observations from forest stands ranging in age from 3 to 200 yr. Results indicate that simulated biomass pools conform well with observed allometry. We conclude that POP represents a preferable alternative to large-area parameterisations of woody biomass turnover, typically used in current ESMs.

Towards a systems approach for understanding honeybee decline: a stocktaking and synthesis of existing models.

PubMed

Becher, Matthias A; Osborne, Juliet L; Thorbek, Pernille; Kennedy, Peter J; Grimm, Volker

2013-08-01

The health of managed and wild honeybee colonies appears to have declined substantially in Europe and the United States over the last decade. Sustainability of honeybee colonies is important not only for honey production, but also for pollination of crops and wild plants alongside other insect pollinators. A combination of causal factors, including parasites, pathogens, land use changes and pesticide usage, are cited as responsible for the increased colony mortality.However, despite detailed knowledge of the behaviour of honeybees and their colonies, there are no suitable tools to explore the resilience mechanisms of this complex system under stress. Empirically testing all combinations of stressors in a systematic fashion is not feasible. We therefore suggest a cross-level systems approach, based on mechanistic modelling, to investigate the impacts of (and interactions between) colony and land management.We review existing honeybee models that are relevant to examining the effects of different stressors on colony growth and survival. Most of these models describe honeybee colony dynamics, foraging behaviour or honeybee - varroa mite - virus interactions.We found that many, but not all, processes within honeybee colonies, epidemiology and foraging are well understood and described in the models, but there is no model that couples in-hive dynamics and pathology with foraging dynamics in realistic landscapes. Synthesis and applications . We describe how a new integrated model could be built to simulate multifactorial impacts on the honeybee colony system, using building blocks from the reviewed models. The development of such a tool would not only highlight empirical research priorities but also provide an important forecasting tool for policy makers and beekeepers, and we list examples of relevant applications to bee disease and landscape management decisions.

Simulating the dynamics of the mechanochemical cycle of myosin-V

PubMed Central

Mukherjee, Shayantani; Alhadeff, Raphael; Warshel, Arieh

2017-01-01

The detailed dynamics of the cycle of myosin-V are explored by simulation approaches, examining the nature of the energy-driven motion. Our study started with Langevin dynamics (LD) simulations on a very coarse landscape with a single rate-limiting barrier and reproduced the stall force and the hand-over-hand dynamics. We then considered a more realistic landscape and used time-dependent Monte Carlo (MC) simulations that allowed trajectories long enough to reproduce the force/velocity characteristic sigmoidal correlation, while also reproducing the hand-over-hand motion. Overall, our study indicated that the notion of a downhill lever-up to lever-down process (popularly known as the powerstroke mechanism) is the result of the energetics of the complete myosin-V cycle and is not the source of directional motion or force generation on its own. The present work further emphasizes the need to use well-defined energy landscapes in studying molecular motors in general and myosin in particular. PMID:28193897

Soil conservation service landscape resource management

Treesearch

Sally Schauman; Carolyn Adams

1979-01-01

SCS Landscape Resource Management (LRM) is the application of landscape architecture to SCS conservation activities. LRM includes but is not limited to visual resource management. LRM can be summarized in three principles: (1) SCS landscape architecture considers the landscape as a composite of ecological, social and visual resources; (2) SCS landscapes exist in the...

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

Treesearch

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

2015-01-01

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

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

Treesearch

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...

Understanding the role of wildland fire, insects, and disease in predicting climate change effects on whitebark pine: Simulating vegetation, disturbance, and climate dynamics in a northern Rocky Mountain landscape

Treesearch

Robert Keane; Rachel Loehman

2010-01-01

Climate changes are projected to profoundly influence vegetation patterns and community compositions, either directly through increased species mortality and shifts in species distributions, or indirectly through disturbance dynamics such as increased wildfire activity and extent, shifting fire regimes, and pathogenesis. High-elevation landscapes have been shown to be...

Remotely-Sensed Urban Wet-Landscapes AN Indicator of Coupled Effects of Human Impact and Climate Change

NASA Astrophysics Data System (ADS)

Ji, Wei

2016-06-01

This study proposes the concept of urban wet-landscapes (loosely-defined wetlands) as against dry-landscapes (mainly impervious surfaces). The study is to examine whether the dynamics of urban wet-landscapes is a sensitive indicator of the coupled effects of the two major driving forces of urban landscape change - human built-up impact and climate (precipitation) variation. Using a series of satellite images, the study was conducted in the Kansas City metropolitan area of the United States. A rule-based classification algorithm was developed to identify fine-scale, hidden wetlands that could not be appropriately detected based on their spectral differentiability by a traditional image classification. The spatial analyses of wetland changes were implemented at the scales of metropolitan, watershed, and sub-watershed as well as based on the size of surface water bodies in order to reveal urban wetland change trends in relation to the driving forces. The study identified that wet-landscape dynamics varied in trend and magnitude from the metropolitan, watersheds, to sub-watersheds. The study also found that increased precipitation in the region in the past decades swelled larger wetlands in particular while smaller wetlands decreased mainly due to human development activities. These findings suggest that wet-landscapes, as against the dry-landscapes, can be a more effective indicator of the coupled effects of human impact and climate change.

The influence of landscape's dynamics on the Oriental Migratory Locust habitat change based on the time-series satellite data.

PubMed

Shi, Yue; Huang, Wenjiang; Dong, Yingying; Peng, Dailiang; Zheng, Qiong; Yang, Puyun

2018-07-15

Landscape structure and vegetation coverage are important habitat conditions for Oriental Migratory Locust infestation in East Asia. Characterizing the landscape's dynamics of locust habitat is meaningful for reducing the occupation of locusts and limiting potential risks. To better understand causes and consequences of landscape pattern and locust habitat, it is not enough to simply detect locust habitat of each year. Rather, landcover transitions causing the change of locust habitat area must also be explored. This paper proposes an integrated implement to quantify the influence of landscape's dynamics on locust habitat changes based on three tenets: 1) temporal context can provide insight into the land cover transitions, 2) the detection of locust habitat area is operated on patches rather than pixels with full consideration of landscape's ecology, 3) the modeling must be flexible and unsupervised. These ideas have not been previously explored in demonstrating the possible role of changes in landscape characteristics to drive locust habitat transitions. The case study focuses on the Dagang district, a hot spot of locust infestation of China, from 2000 to 2015. Firstly, the seasonal characteristics of typical landcovers in NDVI, TVI, and LST were extracted from fused Landsat-MODIS surface reflectance imagery. Subsequently, a landscape membership-based random forest (LMRF) algorithm was proposed to quantify the landscape structure and hydrological regimen of locust habitat at the patch level. Finally, we investigated the correlations between the specific landcover transitions and habitat changes. Within the 16 years observations, our findings suggest that the sparse reeds and weeds in the vicinity of beach land, riverbanks, and wetlands are the dominant landscape structure associated with locust habitat change (R 2  > 0.68), and the fluctuation in the water level is a key ecological factor to facilitate the locust habitat change (R 2  > 0.61). These results are instrumental for developing precision pesticide use to reduce environmental degradation, and providing positive perspectives for ecological management and transformation of locust habitats. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

PubMed

Dikou, Angela; Papapanagiotou, Evangelos; Troumbis, Andreas

2011-09-01

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

Ecohydrologic role of solar radiation on landscape evolution

NASA Astrophysics Data System (ADS)

Yetemen, Omer; Istanbulluoglu, Erkan; Flores-Cervantes, J. Homero; Vivoni, Enrique R.; Bras, Rafael L.

2015-02-01

Solar radiation has a clear signature on the spatial organization of ecohydrologic fluxes, vegetation patterns and dynamics, and landscape morphology in semiarid ecosystems. Existing landscape evolution models (LEMs) do not explicitly consider spatially explicit solar radiation as model forcing. Here, we improve an existing LEM to represent coupled processes of energy, water, and sediment balance for semiarid fluvial catchments. To ground model predictions, a study site is selected in central New Mexico where hillslope aspect has a marked influence on vegetation patterns and landscape morphology. Model predictions are corroborated using limited field observations in central NM and other locations with similar conditions. We design a set of comparative LEM simulations to investigate the role of spatially explicit solar radiation on landscape ecohydro-geomorphic development under different uplift scenarios. Aspect-control and network-control are identified as the two main drivers of soil moisture and vegetation organization on the landscape. Landscape-scale and long-term implications of these short-term ecohdrologic patterns emerged in modeled landscapes. As north facing slopes (NFS) get steeper by continuing uplift they support erosion-resistant denser vegetation cover which leads to further slope steepening until erosion and uplift attains a dynamic equilibrium. Conversely, on south facing slopes (SFS), as slopes grow with uplift, increased solar radiation exposure with slope supports sparser biomass and shallower slopes. At the landscape scale, these differential erosion processes lead to asymmetric development of catchment forms, consistent with regional observations. Understanding of ecohydrogeomorphic evolution will improve to assess the impacts of past and future climates on landscape response and morphology.

OpenFLUID: an open-source software environment for modelling fluxes in landscapes

NASA Astrophysics Data System (ADS)

Fabre, Jean-Christophe; Rabotin, Michaël; Crevoisier, David; Libres, Aline; Dagès, Cécile; Moussa, Roger; Lagacherie, Philippe; Raclot, Damien; Voltz, Marc

2013-04-01

Integrative landscape functioning has become a common concept in environmental management. Landscapes are complex systems where many processes interact in time and space. In agro-ecosystems, these processes are mainly physical processes, including hydrological-processes, biological processes and human activities. Modelling such systems requires an interdisciplinary approach, coupling models coming from different disciplines, developed by different teams. In order to support collaborative works, involving many models coupled in time and space for integrative simulations, an open software modelling platform is a relevant answer. OpenFLUID is an open source software platform for modelling landscape functioning, mainly focused on spatial fluxes. It provides an advanced object-oriented architecture allowing to i) couple models developed de novo or from existing source code, and which are dynamically plugged to the platform, ii) represent landscapes as hierarchical graphs, taking into account multi-scale, spatial heterogeneities and landscape objects connectivity, iii) run and explore simulations in many ways : using the OpenFLUID software interfaces for users (command line interface, graphical user interface), or using external applications such as GNU R through the provided ROpenFLUID package. OpenFLUID is developed in C++ and relies on open source libraries only (Boost, libXML2, GLib/GTK, OGR/GDAL, …). For modelers and developers, OpenFLUID provides a dedicated environment for model development, which is based on an open source toolchain, including the Eclipse editor, the GCC compiler and the CMake build system. OpenFLUID is distributed under the GPLv3 open source license, with a special exception allowing to plug existing models licensed under any license. It is clearly in the spirit of sharing knowledge and favouring collaboration in a community of modelers. OpenFLUID has been involved in many research applications, such as modelling of hydrological network transfer, diagnosis and prediction of water quality taking into account human activities, study of the effect of spatial organization on hydrological fluxes, modelling of surface-subsurface water exchanges, … At LISAH research unit, OpenFLUID is the supporting development platform of the MHYDAS model, which is a distributed model for agrosystems (Moussa et al., 2002, Hydrological Processes, 16, 393-412). OpenFLUID web site : http://www.openfluid-project.org

The Great Geologic Sponge: What Do Storage Dynamics Reveal About Runoff Generation In Young Volcanic Landscapes? (Invited)

NASA Astrophysics Data System (ADS)

Grant, G. E.; Jefferson, A. J.; Tague, C.; Lewis, S.

2010-12-01

In young volcanic landscapes, such as Hawaii or the Cascade Mountains of the U.S. Pacific Northwest, runoff generation is a hidden process. These landscapes are constructed by episodic volcanism, resulting in a layer-cake stratigraphy of multiple overlapping basaltic lava flows. Because of their cooling history, such lava flows are extremely porous, so that almost all precipitation infiltrates, and is stored as groundwater. Surficial channels are poorly defined or non-existent, and runoff is discharged at high-volume springs. These springs represent “windows” into the sub-surface, and the chemistry of the emerging water reveals important clues about the timescales, pathways, and storage volumes of water at the landscape scale. For example, water isotopes of Oregon High Cascades springs indicate transit times of years to decades, and can be used to identify recharge elevations and delineate cryptic flowpaths that do not necessarily obey topographic divides. Residence times can be used to infer aquifer thickness and overall landscape storage volumes, which are immense - on order of 20 -30 cubic kilometers. Moreover, inter-annual variability in discharge from springs can be used to interpret landscape memory and sensitivity to climate variation. These young volcanic landscapes are therefore perfect laboratories for exploring the role of storage dynamics in streamflow generation.

Variation in soil carbon dioxide efflux at two spatial scales in a topographically complex boreal forest

USGS Publications Warehouse

Kelsey, Katharine C.; Wickland, Kimberly P.; Striegl, Robert G.; Neff, Jason C.

2012-01-01

Carbon dynamics of high-latitude regions are an important and highly uncertain component of global carbon budgets, and efforts to constrain estimates of soil-atmosphere carbon exchange in these regions are contingent on accurate representations of spatial and temporal variability in carbon fluxes. This study explores spatial and temporal variability in soilatmosphere carbon dynamics at both fine and coarse spatial scales in a high-elevation, permafrost-dominated boreal black spruce forest. We evaluate the importance of landscape-level investigations of soil-atmosphere carbon dynamics by characterizing seasonal trends in soil-atmosphere carbon exchange, describing soil temperature-moisture-respiration relations, and quantifying temporal and spatial variability at two spatial scales: the plot scale (0–5 m) and the landscape scale (500–1000 m). Plot-scale spatial variability (average variation on a given measurement day) in soil CO2 efflux ranged from a coefficient of variation (CV) of 0.25 to 0.69, and plot-scale temporal variability (average variation of plots across measurement days) in efflux ranged from a CV of 0.19 to 0.36. Landscape-scale spatial and temporal variability in efflux was represented by a CV of 0.40 and 0.31, respectively, indicating that plot-scale spatial variability in soil respiration is as great as landscape-scale spatial variability at this site. While soil respiration was related to soil temperature at both the plot- and landscape scale, landscape-level descriptions of soil moisture were necessary to define soil respiration-moisture relations. Soil moisture variability was also integral to explaining temporal variability in soil respiration. Our results have important implications for research efforts in high-latitude regions where remote study sites make landscape-scale field campaigns challenging.

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

PubMed Central

2017-01-01

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. PMID:28678792

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

PubMed

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

2013-01-01

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

Lattice model simulation of interchain protein interactions and the folding dynamics and dimerization of the GCN4 Leucine zipper

NASA Astrophysics Data System (ADS)

Liu, Yanxin; Chapagain, Prem P.; Parra, Jose L.; Gerstman, Bernard S.

2008-01-01

The highest level in the hierarchy of protein structure and folding is the formation of protein complexes through protein-protein interactions. We have made modifications to a well established computer lattice model to expand its applicability to two-protein dimerization and aggregation. Based on Brownian dynamics, we implement translation and rotation moves of two peptide chains relative to each other, in addition to the intrachain motions already present in the model. We use this two-chain model to study the folding dynamics of the yeast transcription factor GCN4 leucine zipper. The calculated heat capacity curves agree well with experimental measurements. Free energy landscapes and median first passage times for the folding process are calculated and elucidate experimentally measured characteristics such as the multistate nature of the dimerization process.

Adaptation and Coevolution on an Emergent Global Competitive Landscape

NASA Astrophysics Data System (ADS)

Fellman, Philip Vos; Post, Jonathan Vos; Wright, Roxana; Dasari, Usha

Notions of Darwinian selection have been implicit in economic theory for at least sixty years. Richard Nelson and Sidney Winter have argued that while evolutionary thinking was prevalent in prewar economics, the postwar Neoclassical school became almost entirely preoccupied with equilibrium conditions and their mathematical conditions. One of the problems with the economic interpretation of firm selection through competition has been a weak grasp on an incomplete scientific paradigm. As I.F. Price notes: "The biological metaphor has long lurked in the background of management theory largely because the message of 'survival of the fittest' (usually wrongly attributed to Charles Darwin rather than Herbert Spencer) provides a seemingly natural model for market competition (e.g. Alchian 1950, Merrell 1984, Henderson 1989, Moore 1993), without seriously challenging the underlying paradigms of what an organisation is." [1] In this paper we examine the application of dynamic fitness landscape models to economic theory, particularly the theory of technology substitution, drawing on recent work by Kauffman, Arthur, McKelvey, Nelson and Winter, and Windrum and Birchenhall. In particular we use Professor Post's early work with John Holland on the genetic algorithm to explain some of the key differences between static and dynamic approaches to economic modeling.

The Hawaii Protocol for Scientific Monitoring of Coffee Berry Borer: a Model for Coffee Agroecosystems Worldwide

PubMed Central

Johnson, Melissa Anne; Hollingsworth, Robert; Fortna, Samuel; Aristizábal, Luis F.; Manoukis, Nicholas C.

2018-01-01

Coffee berry borer (CBB) is the most devastating insect pest for coffee crops worldwide. We developed a scientific monitoring protocol that is aimed at capturing and quantifying the dynamics and impact of this invasive insect pest as well as the development of its host plant across a heterogeneous landscape. The cornerstone of this comprehensive monitoring system is timely georeferenced data collection on CBB movement, coffee berry infestation, mortality by the fungus Beauveria bassiana, and coffee plant phenology via a mobile electronic data recording application. This electronic data collection system allows field records to be georeferenced through built-in global positioning systems, and is backed by a network of weather stations and records of farm management practices. Comprehensive monitoring of CBB and host plant dynamics is an essential part of an area-wide project in Hawaii to aggregate landscape-level data for research to improve management practices. Coffee agroecosystems in other parts of the world that experience highly variable environmental and socioeconomic factors will also benefit from implementing this protocol, in that it will drive the development of customized integrated pest management (IPM) to manage CBB populations. PMID:29608152

The Hawaii Protocol for Scientific Monitoring of Coffee Berry Borer: a Model for Coffee Agroecosystems Worldwide.

PubMed

Johnson, Melissa Anne; Hollingsworth, Robert; Fortna, Samuel; Aristizábal, Luis F; Manoukis, Nicholas C

2018-03-19

Coffee berry borer (CBB) is the most devastating insect pest for coffee crops worldwide. We developed a scientific monitoring protocol that is aimed at capturing and quantifying the dynamics and impact of this invasive insect pest as well as the development of its host plant across a heterogeneous landscape. The cornerstone of this comprehensive monitoring system is timely georeferenced data collection on CBB movement, coffee berry infestation, mortality by the fungus Beauveria bassiana, and coffee plant phenology via a mobile electronic data recording application. This electronic data collection system allows field records to be georeferenced through built-in global positioning systems, and is backed by a network of weather stations and records of farm management practices. Comprehensive monitoring of CBB and host plant dynamics is an essential part of an area-wide project in Hawaii to aggregate landscape-level data for research to improve management practices. Coffee agroecosystems in other parts of the world that experience highly variable environmental and socioeconomic factors will also benefit from implementing this protocol, in that it will drive the development of customized integrated pest management (IPM) to manage CBB populations.

Applications of landscape genetics to connectivity research in terrestrial animals [Chapter 12

Treesearch

Lisette P. Waits; Samuel A. Cushman; Steve F. Spear

2016-01-01

Landscape genetic studies have focused on terrestrial animals more than any other taxonomic group. This chapter focuses on applications of landscape genetics for understanding connectivity of terrestrial animal populations. It starts with a general introduction covering unique characteristics and challenges of the terrestrial study system. This is followed by...

Landscape dynamics in the wildland-urban interface

Treesearch

Wayne C. Zipperer

2012-01-01

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

Extinction risk in successional landscapes subject to catastrophic disturbances.

Treesearch

David Boughton; Urmila Malvadkar

2002-01-01

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...

Predicting the spread of sudden oak death in California (2010-2030): epidemic outcomes under no control

Treesearch

Ross K. Meentemeyer; Nik Cunniffe; Alex Cook; David M. Rizzo; Chris A. Gilligan

2010-01-01

Landscape- to regional-scale models of plant epidemics are direly needed to predict largescale impacts of disease and assess practicable options for control. While landscape heterogeneity is recognized as a major driver of disease dynamics, epidemiological models are rarely applied to realistic landscape conditions due to computational and data limitations. Here we...

Strategies for control of sudden oak death in Humboldt County-informed guidance based on a parameterized epidemiological model

Treesearch

João A. N. Filipe; Richard C. Cobb; David M. Rizzo; Ross K. Meentemeyer; Christopher A. Gilligan

2010-01-01

Landscape- to regional-scale models of plant epidemics are direly needed to predict largescale impacts of disease and assess practicable options for control. While landscape heterogeneity is recognized as a major driver of disease dynamics, epidemiological models are rarely applied to realistic landscape conditions due to computational and data limitations. Here we...

Dynamics of a temperate deciduous forest under landscape-scale management: Implications for adaptability to climate change

Treesearch

Matthew G. Olson; Benjamin O. Knapp; John M. Kabrick

2017-01-01

Landscape forest management is an approach to meeting diverse objectives that collectively span multiple spatial scales. It is critical that we understand the long-term effects of landscape management on the structure and composition of forest tree communities to ensure that these practices are sustainable. Furthermore, it is increasingly important to also consider...

A gradient analysis on urban sprawl and urban landscape pattern between 1985 and 2000 in the Pearl River Delta, China

NASA Astrophysics Data System (ADS)

Dai, Erfu; Wu, Zhuo; Du, Xiaodian

2017-04-01

Urbanization is an irreversible trend worldwide, especially in rapidly developing China. Accelerated urbanization has resulted in rapid urban sprawl and urban landscape pattern changes. Quantifying the spatiotemporal dynamics of urban land use and landscape pattern not only can reveal the characteristics of social transfer and economic development, but also can provide insights into the driving mechanisms of land use changes. In this study, we integrated remote sensing (RS), geographic information system (GIS), landscape metrics, and gradient analysis to quantitatively compare the spatiotemporal dynamics of land use, urban sprawl, and landscape pattern for nine cities in the Pearl River Delta from 1985‒2000. For the whole study region, urbanization was obvious. The results show an increase in urban buildup land and shrinkage of cropland in the Pearl River Delta. However, the nine cities differed greatly in terms of the process and magnitude of urban sprawl for both the spatial and temporal dimensions. This was most evident for the cities of Guangzhou and Shenzhen. Gradient analysis on urban landscape changes could deepen understanding of the stages of urban development and provide a scientific foundation for future urban planning and land management strategies in China.

Exploring the Free Energy Landscape: From Dynamics to Networks and Back

PubMed Central

Prada-Gracia, Diego; Gómez-Gardeñes, Jesús; Echenique, Pablo; Falo, Fernando

2009-01-01

Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers there are, what the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times and rate constants, or hierarchical relationships among basins, completes the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides. PMID:19557191

Exploring the free energy landscape: from dynamics to networks and back.

PubMed

Prada-Gracia, Diego; Gómez-Gardeñes, Jesús; Echenique, Pablo; Falo, Fernando

2009-06-01

Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers there are, what the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times and rate constants, or hierarchical relationships among basins, completes the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.

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

PubMed

Wu, Wei; Wang, Jin

2013-09-28

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

Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein

PubMed Central

Wang, Yong; Tang, Chun; Wang, Erkang; Wang, Jin

2012-01-01

An increasing number of biological machines have been revealed to have more than two macroscopic states. Quantifying the underlying multiple-basin functional landscape is essential for understanding their functions. However, the present models seem to be insufficient to describe such multiple-state systems. To meet this challenge, we have developed a coarse grained triple-basin structure-based model with implicit ligand. Based on our model, the constructed functional landscape is sufficiently sampled by the brute-force molecular dynamics simulation. We explored maltose-binding protein (MBP) which undergoes large-scale domain motion between open, apo-closed (partially closed) and holo-closed (fully closed) states responding to ligand binding. We revealed an underlying mechanism whereby major induced fit and minor population shift pathways co-exist by quantitative flux analysis. We found that the hinge regions play an important role in the functional dynamics as well as that increases in its flexibility promote population shifts. This finding provides a theoretical explanation of the mechanistic discrepancies in PBP protein family. We also found a functional “backtracking” behavior that favors conformational change. We further explored the underlying folding landscape in response to ligand binding. Consistent with earlier experimental findings, the presence of ligand increases the cooperativity and stability of MBP. This work provides the first study to explore the folding dynamics and functional dynamics under the same theoretical framework using our triple-basin functional model. PMID:22532792

Linking river management to species conservation using dynamic landscape scale models

USGS Publications Warehouse

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

2013-01-01

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

Simulation Based Exploration of Critical Zone Dynamics in Intensively Managed Landscapes

NASA Astrophysics Data System (ADS)

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.

Towards a landscape scale management of pesticides: ERA using changes in modelled occupancy and abundance to assess long-term population impacts of pesticides.

PubMed

Topping, Chris J; Craig, Peter S; de Jong, Frank; Klein, Michael; Laskowski, Ryszard; Manachini, Barbara; Pieper, Silvia; Smith, Rob; Sousa, José Paulo; Streissl, Franz; Swarowsky, Klaus; Tiktak, Aaldrik; van der Linden, Ton

2015-12-15

Pesticides are regulated in Europe and this process includes an environmental risk assessment (ERA) for non-target arthropods (NTA). Traditionally a non-spatial or field trial assessment is used. In this study we exemplify the introduction of a spatial context to the ERA as well as suggest a way in which the results of complex models, necessary for proper inclusion of spatial aspects in the ERA, can be presented and evaluated easily using abundance and occupancy ratios (AOR). We used an agent-based simulation system and an existing model for a widespread carabid beetle (Bembidion lampros), to evaluate the impact of a fictitious highly-toxic pesticide on population density and the distribution of beetles in time and space. Landscape structure and field margin management were evaluated by comparing scenario-based ERAs for the beetle. Source-sink dynamics led to an off-crop impact even when no pesticide was present off-crop. In addition, the impacts increased with multi-year application of the pesticide whereas current ERA considers only maximally one year. These results further indicated a complex interaction between landscape structure and pesticide effect in time, both in-crop and off-crop, indicating the need for NTA ERA to be conducted at landscape- and multi-season temporal-scales. Use of AOR indices to compare ERA outputs facilitated easy comparison of scenarios, allowing simultaneous evaluation of impacts and planning of mitigation measures. The landscape and population ERA approach also demonstrates that there is a potential to change from regulation of a pesticide in isolation, towards the consideration of pesticide management at landscape scales and provision of biodiversity benefits via inclusion and testing of mitigation measures in authorisation procedures. Copyright © 2015 Elsevier B.V. All rights reserved.

Predictors of breeding site occupancy by amphibians in montane landscapes

USGS Publications Warehouse

Groff, Luke A.; Loftin, Cynthia S.; Calhoun, Aram J.K.

2017-01-01

Ecological relationships and processes vary across species’ geographic distributions, life stages and spatial, and temporal scales. Montane landscapes are characterized by low wetland densities, rugged topographies, and cold climates. Consequently, aquatic-dependent and low-vagility ectothermic species (e.g., pool-breeding amphibians) may exhibit unique ecological associations in montane landscapes. We evaluated the relative importance of breeding- and landscape-scale features associated with spotted salamander (Ambystoma maculatum) and wood frog (Lithobates sylvaticus) wetland occupancy in Maine's Upper Montane-Alpine Zone ecoregion, and we determined whether models performed better when the inclusive landscape-scale covariates were estimated with topography-weighted or circular buffers. We surveyed 135 potential breeding sites during May 2013–June 2014 and evaluated environmental relationships with multi-season implicit dynamics occupancy models. Breeding site occupancy by both species was influenced solely by breeding-scale habitat features. Spotted salamander occupancy probabilities increased with previous or current beaver (Castor canadensis) presence, and models generally were better supported when the inclusive landscape-scale covariates were estimated with topography-weighted rather than circular buffers. Wood frog occupancy probabilities increased with site area and percent shallows, but neither buffer type was better supported than the other. Model rank order and support varied between buffer types, but model inferences did not. Our results suggest pool-breeding amphibian conservation in montane Maine include measures to maintain beaver populations and large wetlands with proportionally large areas of shallows ≤1-m deep. Inconsistencies between our study and previous studies substantiate the value of region-specific research for augmenting species’ conservation management plans and suggest the application of out-of-region inferences may promote ineffective conservation. 

Environmental condition assessment of US military installations using GIS based spatial multi-criteria decision analysis.

PubMed

Singer, Steve; Wang, Guangxing; Howard, Heidi; Anderson, Alan

2012-08-01

Environment functions in various aspects including soil and water conservation, biodiversity and habitats, and landscape aesthetics. Comprehensive assessment of environmental condition is thus a great challenge. The issues include how to assess individual environmental components such as landscape aesthetics and integrate them into an indicator that can comprehensively quantify environmental condition. In this study, a geographic information systems based spatial multi-criteria decision analysis was used to integrate environmental variables and create the indicator. This approach was applied to Fort Riley Military installation in which land condition and its dynamics due to military training activities were assessed. The indicator was derived by integrating soil erosion, water quality, landscape fragmentation, landscape aesthetics, and noise based on the weights from the experts by assessing and ranking the environmental variables in terms of their importance. The results showed that landscape level indicator well quantified the overall environmental condition and its dynamics, while the indicator at level of patch that is defined as a homogeneous area that is different from its surroundings detailed the spatiotemporal variability of environmental condition. The environmental condition was mostly determined by soil erosion, then landscape fragmentation, water quality, landscape aesthetics, and noise. Overall, environmental condition at both landscape and patch levels greatly varied depending on the degree of ground and canopy disturbance and their spatial patterns due to military training activities and being related to slope. It was also determined the environment itself could be recovered quickly once military training was halt or reduced. Thus, this study provided an effective tool for the army land managers to monitor environmental dynamics and plan military training activities. Its limitation lies at that the obtained values of the indicator vary and are subjective to the experts' knowledge and experience. Thus, further advancing this approach is needed by developing a scientific method to derive the weights of environmental variables.

Quantization of parameters and the string landscape problem

NASA Astrophysics Data System (ADS)

Bouhmadi-López, Mariam; Vargas Moniz, Paulo

2007-05-01

We broaden the domain of application of Brustein and de Alwis's recent paper, where they introduce a (dynamical) selection principle on the landscape of string solutions using FRW quantum cosmology. More precisely, we (i) explain how their analysis is based in choosing a restrictive range of parameters, thereby affecting the validity of the predictions extracted and (ii) subsequently provide a wider and cohesive description, regarding the probability distribution induced by quantum cosmological transition amplitudes. In addition, employing DeWitt's argument for an initial condition on the wavefunction of the Universe, we found that the string and gravitational parameters become related through interesting expressions involving an integer n, suggesting a quantization relation for some of the involved parameters. This research work was supported by the grants POCI/FP/63916/2005, FEDER-POCI/P/FIS/57547/2004 and Acções Integradas (CRUP-CSIC) Luso-Espanholas E-138/04.

Vortices in high-performance high-temperature superconductors

DOE PAGES

Kwok, Wai-Kwong; Welp, Ulrich; Glatz, Andreas; ...

2016-09-21

The behavior of vortex matter in high-temperature superconductors (HTS) controls the entire electromagnetic response of the material, including its current carrying capacity. In this paper, we review the basic concepts of vortex pinning and its application to a complex mixed pinning landscape to enhance the critical current and to reduce its anisotropy. We focus on recent scientific advances that have resulted in large enhancements of the in-field critical current in state-of-the-art second generation (2G) YBCO coated conductors and on the prospect of an isotropic, high-critical current superconductor in the iron-based superconductors. Finally, we discuss an emerging new paradigm of criticalmore » current by design—a drive to achieve a quantitative correlation between the observed critical current density and mesoscale mixed pinning landscapes by using realistic input parameters in an innovative and powerful large-scale time dependent Ginzburg–Landau approach to simulating vortex dynamics.« less

Characterization of biosurfactant produced by petrofilic bacteria isolated from hydrocarbon impacted soil and its potential application in bioremediation

NASA Astrophysics Data System (ADS)

Arsyah, D. M.; Kardena, E.; Helmy, Q.

2018-01-01

The study adopts a multi-level perspective in technology transition to analyse how the transition process in the development of geothermal energy in Indonesia is able to compete against the incumbent fossil-fuelled energy sources. Three levels of multi-level perspective are socio-technical landscape (ST-landscape), socio-technical regime (ST-regime) and niche innovations in Indonesia geothermal development. The identification, mapping and analysis of the dynamic relationship between each level are the important pillars of the multi-level perspective framework. The analysis considers the set of rules, actors and controversies that may arise in the technological transition process. The identified geothermal resource risks are the basis of the emerging geothermal technological innovations in Indonesian geothermal. The analysis of this study reveals the transition pathway, which yields a forecast for the Indonesian geothermal technology transition in the form of scenarios and probable impacts.

Dynamics of sea level rise and coastal flooding on a changing landscape

NASA Astrophysics Data System (ADS)

Bilskie, M. V.; Hagen, S. C.; Medeiros, S. C.; Passeri, D. L.

2014-02-01

Standard approaches to determining the impacts of sea level rise (SLR) on storm surge flooding employ numerical models reflecting present conditions with modified sea states for a given SLR scenario. In this study, we advance this paradigm by adjusting the model framework so that it reflects not only a change in sea state but also variations to the landscape (morphologic changes and urbanization of coastal cities). We utilize a numerical model of the Mississippi and Alabama coast to simulate the response of hurricane storm surge to changes in sea level, land use/land cover, and land surface elevation for past (1960), present (2005), and future (2050) conditions. The results show that the storm surge response to SLR is dynamic and sensitive to changes in the landscape. We introduce a new modeling framework that includes modification of the landscape when producing storm surge models for future conditions.

Landscape community genomics: understanding eco-evolutionary processes in complex environments

USGS Publications Warehouse

Hand, Brian K.; Lowe, Winsor H.; Kovach, Ryan P.; Muhlfeld, Clint C.; Luikart, Gordon

2015-01-01

Extrinsic factors influencing evolutionary processes are often categorically lumped into interactions that are environmentally (e.g., climate, landscape) or community-driven, with little consideration of the overlap or influence of one on the other. However, genomic variation is strongly influenced by complex and dynamic interactions between environmental and community effects. Failure to consider both effects on evolutionary dynamics simultaneously can lead to incomplete, spurious, or erroneous conclusions about the mechanisms driving genomic variation. We highlight the need for a landscape community genomics (LCG) framework to help to motivate and challenge scientists in diverse fields to consider a more holistic, interdisciplinary perspective on the genomic evolution of multi-species communities in complex environments.

Modeling the effect of pathogenic mutations on the conformational landscape of protein kinases.

PubMed

Saladino, Giorgio; Gervasio, Francesco Luigi

2016-04-01

Most proteins assume different conformations to perform their cellular functions. This conformational dynamics is physiologically regulated by binding events and post-translational modifications, but can also be affected by pathogenic mutations. Atomistic molecular dynamics simulations complemented by enhanced sampling approaches are increasingly used to probe the effect of mutations on the conformational dynamics and on the underlying conformational free energy landscape of proteins. In this short review we discuss recent successful examples of simulations used to understand the molecular mechanism underlying the deregulation of physiological conformational dynamics due to non-synonymous single point mutations. Our examples are mostly drawn from the protein kinase family. Copyright © 2016 Elsevier Ltd. All rights reserved.

Anthropogenic Halo Disturbances Alter Landscape and Plant Richness: A Ripple Effect

PubMed Central

Liu, Bingliang; Su, Jinbao; Chen, Jianwei; Cui, Guofa; Ma, Jianzhang

2013-01-01

Although anthropogenic landscape fragmentation is often considered as the primary threat to biodiversity, other factors such as immediate human disturbances may also simultaneously threaten species persistence in various ways. In this paper, we introduce a conceptual framework applied to recreation landscapes (RLs), with an aim to provide insight into the composite influences of landscape alteration accompanying immediate human disturbances on plant richness dynamics. These impacts largely occur at patch-edges. They can not only alter patch-edge structure and environment, but also permeate into surrounding natural matrices/patches affecting species persistence–here we term these “Halo disturbance effects” (HDEs). We categorized species into groups based on seed or pollen dispersal mode (animal- vs. wind-dispersed) as they can be associated with species richness dynamics. We evaluated the richness of the two groups and total species in our experimental landscapes by considering the distance from patch-edge, the size of RLs and the intensity of human use over a six-year period. Our results show that animal-dispersed species decreased considerably, whereas wind-dispersed species increased while their richness presented diverse dynamics at different distances from patch-edges. Our findings clearly demonstrate that anthropogenic HDEs produce ripple effects on plant, providing an experimental interpretation for the diverse responses of species to anthropogenic disturbances. This study highlights the importance of incorporating these composite threats into conservation and management strategies. PMID:23424648

Extracting temporal and spatial information from remotely sensed data for mapping wildlife habitat: Tucson

USGS Publications Warehouse

Wallace, Cynthia S.A.; Advised by Marsh, Stuart E.

2002-01-01

The research accomplished in this dissertation used both mathematical and statistical techniques to extract and evaluate measures of landscape temporal dynamics and spatial structure from remotely sensed data for the purpose of mapping wildlife habitat. By coupling the landscape measures gleaned from the remotely sensed data with various sets of animal sightings and population data, effective models of habitat preference were created.Measures of temporal dynamics of vegetation greenness as measured by National Oceanographic and Atmospheric Administration’s Advanced Very High Resolution Radiometer (AVHRR) satellite were used to effectively characterize and map season specific habitat of the Sonoran pronghorn antelope, as well as produce preliminary models of potential yellow-billed cuckoo habitat in Arizona. Various measures that capture different aspects of the temporal dynamics of the landscape were derived from AVHRR Normalized Difference Vegetation Index composite data using three main classes of calculations: basic statistics, standardized principal components analysis, and Fourier analysis. Pronghorn habitat models based on the AVHRR measures correspond visually and statistically to GIS-based models produced using data that represent detailed knowledge of ground-condition.Measures of temporal dynamics also revealed statistically significant correlations with annual estimates of elk population in selected Arizona Game Management Units, suggesting elk respond to regional environmental changes that can be measured using satellite data. Such relationships, once verified and established, can be used to help indirectly monitor the population.Measures of landscape spatial structure derived from IKONOS high spatial resolution (1-m) satellite data using geostatistics effectively map details of Sonoran pronghorn antelope habitat. Local estimates of the nugget, sill, and range variogram parameters calculated within 25 x 25-meter image windows describe the spatial autocorrelation of the image, permitting classification of all pixels into coherent units whose signature graphs exhibit a classic variogram shape. The variogram parameters captured in these signatures have been shown in previous studies to discriminate between different species-specific vegetation associations.The synoptic view of the landscape provided by satellite data can inform resource management efforts. The ability to characterize the spatial structure and temporal dynamics of habitat using repeatable remote sensing data allows closer monitoring of the relationship between a species and its landscape.

Early Holocene to present landscape dynamics of the tectonic lakes of west-central Mexico

NASA Astrophysics Data System (ADS)

Castillo, Miguel; Muñoz-Salinas, Esperanza; Arce, José Luis; Roy, Priyadarsi

2017-12-01

Paleoclimatic reconstructions from lake sediments of central Mexico indicate that the environmental conditions in the Holocene have oscillated from cool-dry to warm-wet, thus, landscape erosion rates have been modified accordingly. The Cenozoic tectonics and volcanic activity of west-central Mexico have produced a set of lakes in warmer and drier conditions compared to lakes of central Mexico. Nevertheless, the Holocene landscape dynamics for this area remains understudied. Using age-depth models, OSL and multi-element chemistry analysis of sediments in the lakes of San Marcos and Sayula we explore the landscape dynamics from early Holocene present of west-central Mexico. Our results indicate that the sedimentation rates in San Marcos Lake notably increased from 240 yr BP to the present. Since AD 1950 the sedimentation rate in Sayula Lake rose fourfold the rates of the last 2000 years. Analysis of OSL and chemistry of major elements of sediments indicates that IRSL/BLSL strongly correlates with Ti/Al (R2 = 0.93) and with the mean monthly rainfall (R2 = 0.70). We propose that the IRSL/BLSL can be used as a proxy to infer past changes in landscape dynamics. Analysis of climatic data from the 1950s to present indicates that rainfall, and consequently water runoff, is enhanced in summers free of ENSO conditions. Extreme one-day rainfall can, however, exceed mean seasonal rainfall and occur in all phases of ENSO. Droughts are particularly severe in the phase of La Niña. Our results indicate that the erosion rate in San Marcos Lake was high from ∼8000 to ∼7000 yr BP in a period coinciding with the advance and recession of glaciers in Central Mexico, however, the erosion rates in the last 165 years have surpassed the rates of the early to mid-Holocene. By constraining the age of sediment and using environmental proxies such as the Ti/Al and IRSL/BLSL from lake sediments of Sayula and San Marcos we present the first model of landscape dynamics of this part of Mexico from the Early Holocene to present times.

Trends of Forest Dynamics in Tiger Landscapes Across Asia

NASA Astrophysics Data System (ADS)

Mondal, Pinki; Nagendra, Harini

2011-10-01

Protected areas (PAs) are cornerstones of biodiversity conservation, but small parks alone cannot support wide-ranging species, such as the tiger. Hence, forest dynamics in the surrounding landscapes of PAs are also important to tiger conservation. Tiger landscapes often support considerable human population in proximity of the PA, sometimes within the core itself, and thus are subject to various land use activities (such as agricultural expansion and road development) driving habitat loss and fragmentation. We synthesize information from 27 journal articles in 24 tiger landscapes to assess forest-cover dynamics in tiger-range countries. Although 29% of the PAs considered in this study have negligible change in overall forest cover, approximately 71% are undergoing deforestation and fragmentation. Approximately 58% of the total case studies have human settlements within the core area. Most changes—including agricultural expansion, plantation, and farming (52%), fuelwood and fodder collection (43%), logging (38%), grazing (38%), and tourism and development (10%)—can be attributed to human impacts largely linked to the nature of the management regime. This study highlights the need for incorporating new perspectives, ideas, and lessons learned locally and across borders into management plans to ensure tiger conservation in landscapes dominated by human activities. Given the increasing isolation of most parks due to agricultural, infrastructural, and commercial developments at the periphery, it is imperative to conduct planning and evaluation at the landscape level, as well as incorporate multiple actors and institutions in planning, instead of focusing solely on conservation within the PAs as is currently the case in most tiger parks.

Trends of forest dynamics in tiger landscapes across Asia.

PubMed

Mondal, Pinki; Nagendra, Harini

2011-10-01

Protected areas (PAs) are cornerstones of biodiversity conservation, but small parks alone cannot support wide-ranging species, such as the tiger. Hence, forest dynamics in the surrounding landscapes of PAs are also important to tiger conservation. Tiger landscapes often support considerable human population in proximity of the PA, sometimes within the core itself, and thus are subject to various land use activities (such as agricultural expansion and road development) driving habitat loss and fragmentation. We synthesize information from 27 journal articles in 24 tiger landscapes to assess forest-cover dynamics in tiger-range countries. Although 29% of the PAs considered in this study have negligible change in overall forest cover, approximately 71% are undergoing deforestation and fragmentation. Approximately 58% of the total case studies have human settlements within the core area. Most changes-including agricultural expansion, plantation, and farming (52%), fuelwood and fodder collection (43%), logging (38%), grazing (38%), and tourism and development (10%)-can be attributed to human impacts largely linked to the nature of the management regime. This study highlights the need for incorporating new perspectives, ideas, and lessons learned locally and across borders into management plans to ensure tiger conservation in landscapes dominated by human activities. Given the increasing isolation of most parks due to agricultural, infrastructural, and commercial developments at the periphery, it is imperative to conduct planning and evaluation at the landscape level, as well as incorporate multiple actors and institutions in planning, instead of focusing solely on conservation within the PAs as is currently the case in most tiger parks.

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

PubMed Central

2012-01-01

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

Time-Lag in Responses of Birds to Atlantic Forest Fragmentation: Restoration Opportunity and Urgency.

PubMed

Uezu, Alexandre; Metzger, Jean Paul

2016-01-01

There are few opportunities to evaluate the relative importance of landscape structure and dynamics upon biodiversity, especially in highly fragmented tropical landscapes. Conservation strategies and species risk evaluations often rely exclusively on current aspects of landscape structure, although such limited assumptions are known to be misleading when time-lag responses occur. By relating bird functional-group richness to forest patch size and isolation in ten-year intervals (1956, 1965, 1978, 1984, 1993 and 2003), we revealed that birds with different sensitivity to fragmentation display contrasting responses to landscape dynamics in the Brazilian Atlantic Forest. For non-sensitive groups, there was no time-lag in response: the recent degree of isolation best explains their variation in richness, which likely relates to these species' flexibility to adapt to changes in landscape structure. However, for sensitive bird groups, the 1978 patch area was the best explanatory variable, providing evidence for a 25-year time-lag in response to habitat reduction. Time-lag was more likely in landscapes that encompass large patches, which can support temporarily the presence of some sensitive species, even when habitat cover is relatively low. These landscapes potentially support the most threatened populations and should be priorities for restoration efforts to avoid further species loss. Although time-lags provide an opportunity to counteract the negative consequences of fragmentation, it also reinforces the urgency of restoration actions. Fragmented landscapes will be depleted of biodiversity if landscape structure is only maintained, and not improved. The urgency of restoration action may be even higher in landscapes where habitat loss and fragmentation history is older and where no large fragment remained to act temporarily as a refuge.

Dynamical analysis of cellular ageing by modeling of gene regulatory network based attractor landscape.

PubMed

Chong, Ket Hing; Zhang, Xiaomeng; Zheng, Jie

2018-01-01

Ageing is a natural phenomenon that is inherently complex and remains a mystery. Conceptual model of cellular ageing landscape was proposed for computational studies of ageing. However, there is a lack of quantitative model of cellular ageing landscape. This study aims to investigate the mechanism of cellular ageing in a theoretical model using the framework of Waddington's epigenetic landscape. We construct an ageing gene regulatory network (GRN) consisting of the core cell cycle regulatory genes (including p53). A model parameter (activation rate) is used as a measure of the accumulation of DNA damage. Using the bifurcation diagrams to estimate the parameter values that lead to multi-stability, we obtained a conceptual model for capturing three distinct stable steady states (or attractors) corresponding to homeostasis, cell cycle arrest, and senescence or apoptosis. In addition, we applied a Monte Carlo computational method to quantify the potential landscape, which displays: I) one homeostasis attractor for low accumulation of DNA damage; II) two attractors for cell cycle arrest and senescence (or apoptosis) in response to high accumulation of DNA damage. Using the Waddington's epigenetic landscape framework, the process of ageing can be characterized by state transitions from landscape I to II. By in silico perturbations, we identified the potential landscape of a perturbed network (inactivation of p53), and thereby demonstrated the emergence of a cancer attractor. The simulated dynamics of the perturbed network displays a landscape with four basins of attraction: homeostasis, cell cycle arrest, senescence (or apoptosis) and cancer. Our analysis also showed that for the same perturbed network with low DNA damage, the landscape displays only the homeostasis attractor. The mechanistic model offers theoretical insights that can facilitate discovery of potential strategies for network medicine of ageing-related diseases such as cancer.

Landscape genetics of high mountain frog metapopulations

USGS Publications Warehouse

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

2010-01-01

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

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

PubMed

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.

41 CFR 102-76.20 - What issues must Federal agencies consider in providing site planning and landscape design services?

Code of Federal Regulations, 2010 CFR

2010-07-01

... Public Contracts and Property Management Federal Property Management Regulations System (Continued... an expansion need is identified to exist; (e) Create a landscape design that is a pleasant, dynamic...

Do rising temperatures always increase forest productivity? Interacting effects of temperature, precipitation, cloudiness and soil texture on tree species growth and competition

Treesearch

Eric J. Gustafson; Brian R. Miranda; Arjan M.G. De Bruijn; Brian R. Sturtevant; Mark E. Kubiske

2017-01-01

Forest landscape models (FLM) are increasingly used to project the effects of climate change on forested landscapes, yet most use phenomenological approaches with untested assumptions about future forest dynamics. We used a FLM that relies on first principles to mechanistically simulate growth (LANDIS-II with PnET-Succession) to systematically explore how landscapes...

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

Treesearch

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

2011-01-01

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

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

Treesearch

Oswald J. Schmitz; Anne M. Trainor

2014-01-01

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

Landscape-and regional-scale shifts in forest composition under climate change in the Central Hardwood Region of the United States

Treesearch

Wen J. Wang; Hong S. He; Frank R. Thompson; Jacob S. Fraser; William D. Dijak

2016-01-01

Tree species distribution and abundance are affected by forces operating at multiple scales. Niche and biophysical process models have been commonly used to predict climate change effects at regional scales, however, these models have limited capability to include site-scale population dynamics and landscape- scale disturbance and dispersal. We applied a landscape...

Simulated cavity tree dynamics under alternative timber harvest regimes

Treesearch

Zhaofei Fan; Stephen R Shifley; Frank R Thompson; David R Larsen

2004-01-01

We modeled cavity tree abundance on a landscape as a function of forest stand age classes and as a function of aggregate stand size classes.We explored the impact of five timber harvest regimes on cavity tree abundance on a 3261 ha landscape in southeast Missouri, USA, by linking the stand level cavity tree distribution model to the landscape age structure simulated by...

Deriving principal channel metrics from bank and long-profile geometry with the R package cmgo

NASA Astrophysics Data System (ADS)

Golly, Antonius; Turowski, Jens M.

2017-09-01

Landscape patterns result from landscape forming processes. This link can be exploited in geomorphological research by reversely analyzing the geometrical content of landscapes to develop or confirm theories of the underlying processes. Since rivers represent a dominant control on landscape formation, there is a particular interest in examining channel metrics in a quantitative and objective manner. For example, river cross-section geometry is required to model local flow hydraulics, which in turn determine erosion and thus channel dynamics. Similarly, channel geometry is crucial for engineering purposes, water resource management, and ecological restoration efforts. These applications require a framework to capture and derive the data. In this paper we present an open-source software tool that performs the calculation of several channel metrics (length, slope, width, bank retreat, knickpoints, etc.) in an objective and reproducible way based on principal bank geometry that can be measured in the field or in a GIS. Furthermore, the software provides a framework to integrate spatial features, for example the abundance of species or the occurrence of knickpoints. The program is available at https://github.com/AntoniusGolly/cmgo and is free to use, modify, and redistribute under the terms of the GNU General Public License version 3 as published by the Free Software Foundation.

Contrasting watershed-scale trends in runoff and sediment yield complicate rangeland water resources planning

NASA Astrophysics Data System (ADS)

Berg, Matthew D.; Marcantonio, Franco; Allison, Mead A.; McAlister, Jason; Wilcox, Bradford P.; Fox, William E.

2016-06-01

Rangelands cover a large portion of the earth's land surface and are undergoing dramatic landscape changes. At the same time, these ecosystems face increasing expectations to meet growing water supply needs. To address major gaps in our understanding of rangeland hydrologic function, we investigated historical watershed-scale runoff and sediment yield in a dynamic landscape in central Texas, USA. We quantified the relationship between precipitation and runoff and analyzed reservoir sediment cores dated using cesium-137 and lead-210 radioisotopes. Local rainfall and streamflow showed no directional trend over a period of 85 years, resulting in a rainfall-runoff ratio that has been resilient to watershed changes. Reservoir sedimentation rates generally were higher before 1963, but have been much lower and very stable since that time. Our findings suggest that (1) rangeland water yields may be stable over long periods despite dramatic landscape changes while (2) these same landscape changes influence sediment yields that impact downstream reservoir storage. Relying on rangelands to meet water needs demands an understanding of how these dynamic landscapes function and a quantification of the physical processes at work.

Landscape genomics: A brief perspective [Chapter 9

Treesearch

Michael K. Schwartz; Gordon Luikart; Kevin S. McKelvey; Samuel A. Cushman

2010-01-01

Landscape genetics is the amalgamation of population genetics and landscape ecology (see Manel et al. 2003; Storfer et al. 2007). In Chapter 17, we discuss landscape genetics and provide two examples of applications in the area of modeling population connectivity and inferring fragmentation. These examples, like virtually all extant landscape genetic analyses, were...

On modeling the organization of landscapes and vegetation patterns controlled by solar radiation

NASA Astrophysics Data System (ADS)

Istanbulluoglu, E.; Yetemen, O.

2014-12-01

Solar radiation is a critical driver of ecohydrologic processes and vegetation dynamics. Patterns of runoff generation and vegetation dictate landscape geomorphic response. Distinct patterns in the organization of soil moisture, vegetation type, and landscape morphology have been documented in close relation to aspect in a range of climates. Within catchments, from north to south facing slopes, studies have shown ecotone shifts from forest to shrub species, and steep diffusion-dominated landforms to fluvial landforms. Over the long term differential evolution of ecohydrology and geomorphology leads to observed asymmetric structure in the planform of channel network and valley morphology. In this talk we present examples of coupled modeling of ecohydrology and geomorphology driven by solar radiation. In a cellular automata model of vegetation dynamics we will first show how plants organize in north and south facing slopes and how biodiversity changes with elevation. When vegetation-erosion feedbacks are coupled emergent properties of the coupled system are observed in the modeled elevation and vegetation fields. Integrating processes at a range of temporal and spatial scales, coupled models of ecohydrologic and geomorphic dynamics enable examination of global change impacts on landscapes and ecosystems.

Forest fragmentation and bird community dynamics: inference at regional scales

USGS Publications Warehouse

Boulinier, T.; Nichols, J.D.; Hines, J.E.; Sauer, J.R.; Flather, C.H.; Pollock, K.H.

2001-01-01

With increasing fragmentation of natural areas and a dramatic reduction of forest cover in several parts of the world, quantifying the impact of such changes on species richness and community dynamics has been a subject of much concern. Here, we tested whether in more fragmented landscapes there was a lower number of area-sensitive species and higher local extinction and turnover rates, which could explain higher temporal variability in species richness. To investigate such potential landscape effects at a regional scale, we merged two independent, large-scale monitoring efforts: the North American Breeding Bird Survey (BBS) and the Land Use and Land Cover Classification data from the U.S. Geological Survey. We used methods that accounted for heterogeneity in the probability of detecting species to estimate species richness and temporal changes in the bird communities for BBS routes in three mid-Atlantic U.S. states. Forest breeding bird species were grouped prior to the analyses into area-sensitive and non-area-sensitive species according to previous studies. We tested predictions relating measures of forest structure at one point in time (1974) to species richness at that time and to parameters of forest bird community change over the following 22-yr-period (1975-1996). We used the mean size of forest patches to characterize landscape structure, as high correlations among landscape variables did not allow us to disentangle the relative roles of habitat fragmentation per se and habitat loss. As predicted, together with lower species richness for area-sensitive species on routes surrounded by landscapes with lower mean forest-patch size, we found higher mean year-to-year rates of local extinction. Moreover, the mean year-to-year rates of local turnover (proportion of locally new species) for area-sensitive species were also higher in landscapes with lower mean forest-patch size. These associations were not observed for the non-area-sensitive species group. These results suggest that landscape structure may influence forest bird communities at regional scales through its effects on the total number of species but also on the temporal rates of change in community composition. Evidence for higher rates of local extinction and turnover in more fragmented landscapes suggests that bird communities function as metapopulations at a regional scale, and points out the importance of colonizations and recolonizations from surrounding landscapes to local community dynamics. Further, our results illustrate that the methods used to estimate the community parameters can be a powerful statistical tool in addressing questions relative to the dynamics of communities.

Derivation of two well-behaved theoretical contagion indices and their sampling properties and application for assessing forest landscape diversity

Treesearch

Bernard R. Parresol

2011-01-01

Studies of spatial patterns of landscapes are useful to quantify human impact, predict wildlife effects, or describe variability of landscape features. A common approach to identify and quantify landscape structure is with a landscape scale model known as a contagion index. A contagion index quantifies two distinct components of landscape diversity: composition and...

Integrating the landscape epidemiology and genetics of RNA viruses: rabies in domestic dogs as a model.

PubMed

Brunker, K; Hampson, K; Horton, D L; Biek, R

2012-12-01

Landscape epidemiology and landscape genetics combine advances in molecular techniques, spatial analyses and epidemiological models to generate a more real-world understanding of infectious disease dynamics and provide powerful new tools for the study of RNA viruses. Using dog rabies as a model we have identified how key questions regarding viral spread and persistence can be addressed using a combination of these techniques. In contrast to wildlife rabies, investigations into the landscape epidemiology of domestic dog rabies requires more detailed assessment of the role of humans in disease spread, including the incorporation of anthropogenic landscape features, human movements and socio-cultural factors into spatial models. In particular, identifying and quantifying the influence of anthropogenic features on pathogen spread and measuring the permeability of dispersal barriers are important considerations for planning control strategies, and may differ according to cultural, social and geographical variation across countries or continents. Challenges for dog rabies research include the development of metapopulation models and transmission networks using genetic information to uncover potential source/sink dynamics and identify the main routes of viral dissemination. Information generated from a landscape genetics approach will facilitate spatially strategic control programmes that accommodate for heterogeneities in the landscape and therefore utilise resources in the most cost-effective way. This can include the efficient placement of vaccine barriers, surveillance points and adaptive management for large-scale control programmes.

SedInConnect: a stand-alone, free and open source tool for the assessment of sediment connectivity

NASA Astrophysics Data System (ADS)

Crema, Stefano; Cavalli, Marco

2018-02-01

There is a growing call, within the scientific community, for solid theoretic frameworks and usable indices/models to assess sediment connectivity. Connectivity plays a significant role in characterizing structural properties of the landscape and, when considered in combination with forcing processes (e.g., rainfall-runoff modelling), can represent a valuable analysis for an improved landscape management. In this work, the authors present the development and application of SedInConnect: a free, open source and stand-alone application for the computation of the Index of Connectivity (IC), as expressed in Cavalli et al. (2013) with the addition of specific innovative features. The tool is intended to have a wide variety of users, both from the scientific community and from the authorities involved in the environmental planning. Thanks to its open source nature, the tool can be adapted and/or integrated according to the users' requirements. Furthermore, presenting an easy-to-use interface and being a stand-alone application, the tool can help management experts in the quantitative assessment of sediment connectivity in the context of hazard and risk assessment. An application to a sample dataset and an overview on up-to-date applications of the approach and of the tool shows the development potential of such analyses. The modelled connectivity, in fact, appears suitable not only to characterize sediment dynamics at the catchment scale but also to integrate prediction models and as a tool for helping geomorphological interpretation.

Interactions of forest disturbance-recovery dynamics with a changing climate

NASA Astrophysics Data System (ADS)

Anderson-Teixeira, K. J.; Miller, A. D.; Tepley, A. J.; Bennett, A. C.; Wang, M.

2015-12-01

As the climate changes, altered disturbance-recovery dynamics in forests worldwide are likely to result in significant biogeochemical and biophysical feedbacks to the climate system. Climate shapes forest disturbance events including tree mortality and fire, with consequent climate feedbacks. For instance, in forests globally, drought increases tree mortality rates, having a stronger impact on larger trees and resulting in greater feedbacks to climate change than would occur if drought sensitivities were equal across tree size classes. Forest regeneration and associated biogeochemical and biophysical feedbacks are also shaped by climate: across the tropics the rate of biomass accumulation is faster in everwet than in seasonally dry climates, and in the Klamath region (N California / S Oregon), post-fire vegetation dynamics and microclimate are shaped by aridity. Forest recovery dynamics will be affected by elevated CO2 and climate change; for instance, models predict that forest regeneration rate, successional dynamics, and climate feedbacks will all be altered under elevated CO2. In combination, climatic impacts on disturbance and recovery can result in dramatic shifts in forest cover on the landscape level. For instance, in fire-prone forested landscapes, forest cover decreases with increasing frequency of high-severity fire and decreasing forest recovery rate, both of which could be altered by climate change, producing rapid loss of forest on the landscape level. Such effects may be amplified by the existence of alternative stable states, which can cause systems to experience non-reversible changes in cover type. Critical transitions in landscape-level forest cover would have significant biogeochemical and biophysical feedbacks. Thus, altered disturbance-recovery dynamics under a changing climate may have sudden and dramatic impacts on forest-climate interactions.

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

NASA Astrophysics Data System (ADS)

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.

scEpath: Energy landscape-based inference of transition probabilities and cellular trajectories from single-cell transcriptomic data.

PubMed

Jin, Suoqin; MacLean, Adam L; Peng, Tao; Nie, Qing

2018-02-05

Single-cell RNA-sequencing (scRNA-seq) offers unprecedented resolution for studying cellular decision-making processes. Robust inference of cell state transition paths and probabilities is an important yet challenging step in the analysis of these data. Here we present scEpath, an algorithm that calculates energy landscapes and probabilistic directed graphs in order to reconstruct developmental trajectories. We quantify the energy landscape using "single-cell energy" and distance-based measures, and find that the combination of these enables robust inference of the transition probabilities and lineage relationships between cell states. We also identify marker genes and gene expression patterns associated with cell state transitions. Our approach produces pseudotemporal orderings that are - in combination - more robust and accurate than current methods, and offers higher resolution dynamics of the cell state transitions, leading to new insight into key transition events during differentiation and development. Moreover, scEpath is robust to variation in the size of the input gene set, and is broadly unsupervised, requiring few parameters to be set by the user. Applications of scEpath led to the identification of a cell-cell communication network implicated in early human embryo development, and novel transcription factors important for myoblast differentiation. scEpath allows us to identify common and specific temporal dynamics and transcriptional factor programs along branched lineages, as well as the transition probabilities that control cell fates. A MATLAB package of scEpath is available at https://github.com/sqjin/scEpath. qnie@uci.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2018. Published by Oxford University Press.

Transport and selective chaining of bidisperse particles in a travelling wave potential.

PubMed

Tierno, Pietro; Straube, Arthur V

2016-05-01

We combine experiments, theory and numerical simulation to investigate the dynamics of a binary suspension of paramagnetic colloidal particles dispersed in water and transported above a stripe-patterned magnetic garnet film. The substrate generates a one-dimensional periodic energy landscape above its surface. The application of an elliptically polarized rotating magnetic field causes the landscape to translate, inducing direct transport of paramagnetic particles placed above the film. The ellipticity of the applied field can be used to control and tune the interparticle interactions, from net repulsive to net attractive. When considering particles of two distinct sizes, we find that, depending on their elevation above the surface of the magnetic substrate, the particles feel effectively different potentials, resulting in different mobilities. We exploit this feature to induce selective chaining for certain values of the applied field parameters. In particular, when driving two types of particles, we force only one type to condense into travelling parallel chains. These chains confine the movement of the other non-chaining particles within narrow colloidal channels. This phenomenon is explained by considering the balance of pairwise magnetic forces between the particles and their individual coupling with the travelling landscape.

Anticipating forest and range land development in central Oregon (USA) for landscape analysis, with an example application involving mule deer

Treesearch

Jeffrey D. Kline; Alissa Moses; Theresa Burcsu

2010-01-01

Forest policymakers, public lands managers, and scientists in the Pacific Northwest (USA) seek ways to evaluate the landscape-level effects of policies and management through the multidisciplinary development and application of spatially explicit methods and models. The Interagency Mapping and Analysis Project (IMAP) is an ongoing effort to generate landscape-wide...

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

PubMed

Krivov, Sergei V

2011-07-01

Dimensionality reduction is ubiquitous in the analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide a complete and accurate description of the dynamics. Here I describe how to perform dimensionality reduction while preserving the essential properties of the dynamics. The approach is illustrated by analyzing the chess game--the archetype of complex dynamics. A variable that provides complete and accurate description of chess dynamics is constructed. The winning probability is predicted by describing the game as a random walk on the free-energy landscape associated with the variable. The approach suggests a possible way of obtaining a simple yet accurate description of many important complex phenomena. The analysis of the chess game shows that the approach can quantitatively describe the dynamics of processes where human decision-making plays a central role, e.g., financial and social dynamics.

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

NASA Astrophysics Data System (ADS)

Krivov, Sergei V.

2011-07-01

Dimensionality reduction is ubiquitous in the analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide a complete and accurate description of the dynamics. Here I describe how to perform dimensionality reduction while preserving the essential properties of the dynamics. The approach is illustrated by analyzing the chess game—the archetype of complex dynamics. A variable that provides complete and accurate description of chess dynamics is constructed. The winning probability is predicted by describing the game as a random walk on the free-energy landscape associated with the variable. The approach suggests a possible way of obtaining a simple yet accurate description of many important complex phenomena. The analysis of the chess game shows that the approach can quantitatively describe the dynamics of processes where human decision-making plays a central role, e.g., financial and social dynamics.

A new perspective on microbial landscapes within food production.

PubMed

Bokulich, Nicholas A; Lewis, Zachery T; Boundy-Mills, Kyria; Mills, David A

2016-02-01

High-throughput, 'next-generation' sequencing tools offer many exciting new possibilities for food research. From investigating microbial dynamics within food fermentations to the ecosystem of the food-processing built environment, amplicon sequencing, metagenomics, and transcriptomics present novel applications for exploring microbial communities in, on, and around our foods. This review discusses the many uses of these tools for food-related and food facility-related research and highlights where they may yield nuanced insight into the microbial world of food production systems. Copyright © 2016. Published by Elsevier Ltd.

Functionality limit of classical simulated annealing

NASA Astrophysics Data System (ADS)

Hasegawa, M.

2015-09-01

By analyzing the system dynamics in the landscape paradigm, optimization function of classical simulated annealing is reviewed on the random traveling salesman problems. The properly functioning region of the algorithm is experimentally determined in the size-time plane and the influence of its boundary on the scalability test is examined in the standard framework of this method. From both results, an empirical choice of temperature length is plausibly explained as a minimum requirement that the algorithm maintains its scalability within its functionality limit. The study exemplifies the applicability of computational physics analysis to the optimization algorithm research.

Travelling in the eastern Mediterranean with landscape character assessment

NASA Astrophysics Data System (ADS)

Abu Jaber, N.; Abunnasr, Y.; Abu Yahya, A.; Boulad, N.; Christou, O.; Dimitropoulos, G.; Dimopoulos, T.; Gkoltsiou, K.; Khreis, N.; Manolaki, P.; Michael, K.; Odeh, T.; Papatheodoulou, A.; Sorotou, A.; Sinno, S.; Suliman, O.; Symons, N.; Terkenli, T.; Trigkas, Vassilis; Trovato, M. G.; Victora, M.; Zomeni, M.; Vogiatzakis, I. N.

2015-06-01

Following its application in Northern Europe, Landscape Character Assessment has also been implemented in Euro-Mediterranean countries as a tool for classifying, describing and assessing landscapes. Many landscape classifications employed in the Euro-Mediterranean area are similar in philosophy and application to the ones developed in Northern Europe. However, many aspects of landform, climate, land-use and ecology, as well as socio-economic context are distinctive of Mediterranean landscapes. The paper discusses the conceptual and methodological issues faced during landscape mapping and characterisation in four East-Mediterranean countries (within the MEDSCAPES project): Cyprus, Greece, Jordan and Lebanon. The major hurdles to overcome during the first phase of methodology development include variation in availability, quality, scale and coverage of spatial datasets between countries and also terminology semantics around landscapes. For example, the concept of landscape - a well-defined term in Greek and English - did not exist in Arabic. Another issue is the use of relative terms like 'high mountains,' `uplands' `lowlands' or ' hills'. Such terms, which are regularly used in landscape description, were perceived slightly differently in the four participating countries. In addition differences exist in nomenclature and classification systems used by each country for the dominant landscape-forming factors i.e. geology, soils and land use- but also in the cultural processes shaping the landscapes - compared both to each other and to the Northern-European norms. This paper argues for the development of consistent, regionally adapted, relevant and standardised methodologies if the results and application of LCA in the eastern Mediterranean region are to be transferable and comparable between countries.

Consequences of Energetic Frustration on the Ligand-Coupled Folding/Dimerization Dynamics of Allosteric Protein S100A12.

PubMed

Ren, Weitong; Li, Wenfei; Wang, Jun; Zhang, Jian; Wang, Wei

2017-10-26

Allosteric proteins are featured by energetic degeneracy of two (or more) functionally relevant conformations, therefore their energy landscapes are often locally frustrated. How such frustration affects the protein folding/binding dynamics is not well understood. Here, by using molecular simulations we study the consequences of local frustration in the dimerization dynamics of allosteric proteins based on a homodimer protein S100A12. Despite of the structural symmetry of the two EF-hand motifs in the three-dimensional structures, the S100A12 homodimer shows allosteric behaviors and local frustration only in half of its structural elements, i.e., the C-terminal EF-hand. We showed that such spatially asymmetric location of frustration leads to asymmetric dimerization pathways, in which the dimerization is dominantly initiated by the interchain binding of the minimally frustrated N-terminal EF-hands, achieving optimal balance between the requirements of rapid conformational switching and interchain assembling to the energy landscapes. We also showed that the local frustration, as represented by the double-basin topography of the energy landscape, gives rise to multiple cross-linked dimerization pathways, in which the dimerization is coupled with the allosteric motions of the C-terminal EF-hands. Binding of metal ions tends to reshape the energy landscape and modulate the dimerization pathways. In addition, by employing the frustratometer method, we showed that the highly frustrated residue-pairs in the C-terminal EF-hand are partially unfolded during the conformational transitions of the native homodimer, leading to lowing of free energy barrier. Our results revealed tight interplay between the local frustration of the energy landscape and the dimerization dynamics for allosteric proteins.

Reconstructing ancient river dynamics from the stratigraphic record: can lessons from the past inform our future?

NASA Astrophysics Data System (ADS)

Hajek, E. A.; Chamberlin, E.; Baisden, T.

2014-12-01

The richness of the deep-time record and its potential for revealing important characteristics of ancient fluvial landscapes has been demonstrated time and again, including compelling examples of rivers altering their behavior in response to changes in vegetation patterns or abrupt shifts in water and sediment discharge. At present, reconstructions of ancient river and floodplain dynamics are commonly qualitative, and when quantitative metrics are used, it is often for comparison among ancient deposits. Without being able to reconstruct, more comprehensively, important aspects of ancient river and floodplains dynamics, this information has only anecdotal relevance for evaluating and managing present-day landscapes. While methods for reconstructing hydrodynamic and morphodynamic aspects of ancient rivers and floodplains are useful, uncertainties associated with these snapshots complicate the ability to translate observations from geologic to engineering scales, thereby limiting the utility of insight from Earth's past in decision-making and development of sustainable landscape-management practices for modern fluvial landscapes. Here, we explore the degree to which paleomorphodynamic reconstructions from ancient channel and floodplain deposits can be used to make specific, quantitative inferences about ancient river dynamics. We compare a suite of paleoenvironmental measurements from a variety of ancient fluvial deposits (including reconstructions of paleoflow depth, paleoslope, paleo-channel mobility, the caliber of paleo-sediment load, and paleo-floodplain heterogeneity) in an effort to evaluate sampling and empirical uncertainties associated with these methods and identify promising avenues for developing more detailed landscape reconstructions. This work is aimed at helping to develop strategies for extracting practicable information from the stratigraphic record that is relevant for sustainably managing and predicting changes in today's environments.

Multidimensional spatial characterization of plant invasions in 'El Pinacate y Gran Desierto de Altar' Biosphere Reserve

NASA Astrophysics Data System (ADS)

Sanchez Flores, Erick

Invasive species are considered an agent of ecological change with more significant effects than global warming. Exotic plant invasions threaten biodiversity and ecosystem viability worldwide. Their effects in the Sonoran Desert ecosystems are a growing concern among ecologists and land managers. We hypothesized that highly dynamic desert environments are unstable, therefore more vulnerable to invasion by exotic plant species. To test this hypothesis we used a multidimensional approach to assess the spatial distribution of two exotic species: Brassica tournefortii (Saharan mustard) and Schismus arabicus (Arabian grass), in a portion of 'El Pinacate y Gran Desierto de Altar' Biosphere Reserve (PBR) in northwestern Sonora, Mexico. This approach combined genetic algorithms, geographic information systems, field methods, statistical analysis, and remote sensing modeling at multiple spatial and temporal scales to predict and test the current and potential distribution of the invasives over dynamic landscapes. Predicted probability of invasion was influenced strongly by human factors: Road networks were the strongest predictors of presence, revealing the potential importance of humans as vectors of invasiveness. Dynamic landscapes, associated mostly with vegetation losses, were detected spectrally in the eastern portion of the study area, very likely associated with past agricultural and current grazing activity. Combined models of high probability for invasion by B. tournefortii and S. arabicus over dynamic landscapes were tested against confirmed locations of the invasives and land cover types associated with invasion. Results confirmed the hypothesis of the study and suggest that more dynamic landscapes are more prone to invasion by these two exotic plants in the PBR. B. tournefortii was found associated mostly with landscapes occupied by microphyllous desert scrub and grassland, as well as sarcocaulescent desert scrub. S. arabicus was found more abundantly in the flat low lands occupied by microphyllous and crassicaulescent desert scrub. These relationships cannot, however, be conclusive and require further investigation due to the complex ecology of these invasives.

Gentlest ascent dynamics for calculating first excited state and exploring energy landscape of Kohn-Sham density functionals.

PubMed

Li, Chen; Lu, Jianfeng; Yang, Weitao

2015-12-14

We develop the gentlest ascent dynamics for Kohn-Sham density functional theory to search for the index-1 saddle points on the energy landscape of the Kohn-Sham density functionals. These stationary solutions correspond to excited states in the ground state functionals. As shown by various examples, the first excited states of many chemical systems are given by these index-1 saddle points. Our novel approach provides an alternative, more robust way to obtain these excited states, compared with the widely used ΔSCF approach. The method can be easily generalized to target higher index saddle points. Our results also reveal the physical interest and relevance of studying the Kohn-Sham energy landscape.

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

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

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

PubMed

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

2009-03-30

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

Molecular dynamics coupled with a virtual system for effective conformational sampling.

PubMed

Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

2018-07-15

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

PubMed

Fujisaki, Hiroshi; Moritsugu, Kei; Matsunaga, Yasuhiro; Morishita, Tetsuya; Maragliano, Luca

2015-01-01

Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.

Impact of natural climate change and historical land use on vegetation cover and geomorphological process dynamics in the Serra dos Órgãos mountain range in Rio de Janeiro State, Brazil

NASA Astrophysics Data System (ADS)

Nehren, U.; Sattler, D.; Heinrich, J.

2010-03-01

The Serra dos Órgãos mountain range in the hinterland of Rio de Janeiro contains extensive remnants of the Atlantic Forest (Mata Atlântica) biome, which once covered about 1.5 million km² from Northeast to South Brazil and further inland to Paraguay and Argentina. As a result of historical deforestation and recent land use intensification processes today only 5 to 8% of the original Atlantic Forest remains. Despite the dramatic habitat loss and a high degree of forest fragmentation, the remnants are among the Earth’s most diverse habitats in terms of species richness. Furthermore, they are characterized by a high level of endemism. Therefore, the biome is considered a "hotspot of biodiversity". In the last years many efforts have been taken to investigate the Mata Atlântica biome in different spatial and time scales and from different scientific perspectives. We are working in the Atlantic Forest of Rio de Janeiro since 2004 and focus in our research particularly on Quaternary landscape evolution and landscape history. By means of landscape and soil archives we reconstruct changes in the landscape system, which are mainly the result of Quaternary climate variability, young tectonic uplift and human impact. The findings throw light on paleoecological conditions in the Late Quaternary and the impact of pre-colonial and colonial land use practices on these landscapes. In this context, a main focus is set on climate and human-driven changes of the vegetation cover and its consequences for the geomorphological process dynamics, in particular erosion and sedimentation processes. Research methods include geomorphological field studies, interpretation of satellite images, physical and chemical sediment and soil analyses as well as relative and absolute dating (Feo/Fed ratio and 14C dating). For the Late Quaternary landscape evolution, the findings are compared with results from paleoclimatic and paloecological investigations in Southeast and South Brazil using other dating techniques, such as pollen analysis. The impact of early civilizations on deforestation, forest fragmentation and geomorphological process dynamics is estimated on the basis of archaeological and anthropological findings. Furthermore, historical sources, such as written documents, maps, paintings and photographs, were collected and analysed to get a more detailed picture of the younger landscape history. As a result we present a landscape genetic model for the Late Quaternary in the Serra dos Órgãos mountain range and the Guanabara Basin. Based on a functional analysis of the natural process dynamics we reconstruct the human impact on the vegetation cover and related erosion and sedimentation processes in different time periods. According to this, the polycyclic climate fluctuations in the Pleistocene emerge as periods of stability and instability in the landscape system. During dry and cool periods of the Ice Ages forests drew back and erosion processes increased, causing higher erosion and deposition rates on slopes and stronger incision of river beds, accompanied by a deposition of gravels. The colluvial soils presently found in the mountain region were mainly deposited during the last instability period in the Late Pleistocene (Wisconsin) and Early Holocene. With the return of rainforests from their retreats under wetter climate conditions in the mid Holocene, slopes were stabilized under a dense vegetation cover. In the Late Holocene erosion conditions changed again with human deforestation and land use, which led to high erosion rates in the mountainous landscape. Concerning the human impact on rainforests and geomorphological process dynamics we give an overview of the pre-historical (Sambaqui, Tupi) and historical (colonial exploitation cycles) landscape transformation and degradation processes for different landscape units within the Serra dos Órgãos and its floodplains. The results not only give a detailed picture of historical land use patterns and landscape degradation processes, but also contribute to the understanding of recent changes in the landscape system. Thus, landscape genetic and historical analysis is essential for assessing the present landscape status with respect to degradation, stability, resilience and land use potentials, and moreover it is a reference for the development of future scenarios.

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

NASA Astrophysics Data System (ADS)

Plowes, Robert Merrick

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

Landscape composition and configuration in the central highlands of Ethiopia.

PubMed

Tolessa, Terefe; Senbeta, Feyera; Kidane, Moges

2016-10-01

Landscape dynamics are common phenomenon in the human-dominated environments whereby it can be observed that the composition and configuration between landscape elements change over time. This dynamism brings about habitat loss and fragmentation that can greatly alter ecosystem services at patch, class, and landscape levels. We conducted a study to examine composition and configuration of forested landscape in the central highlands of Ethiopia using satellite images of over a period of four decades, and FRAGSTAT raster dataset was used to analyze fragmentation. Our result showed five land use/land cover (LULC) types in the study area. Cultivated land and settlement land increased at the expense of forestland, shrubland, and grassland. Fragmentation analysis showed the number of patches increased for all LULC types, indicating the level of fragmentation and interspersion. Juxtaposition increased for shrubland, grassland, and cultivated lands and decreased for settlement and forestland resulting in the fragmentation and isolation of patches. The study of LULC along with fragmentation at the landscape level can help improve our understanding of the pace at which conversion of landscape elements is happening and the impacts on ecosystem services as studies of LULC are courser in nature and would not show how each land use is reducing in size, proximity and shape among other things that determine ecosystem services. Such type of studies in rural landscapes are very vital to consider appropriate land management policies for the landscape level by taking into account the interaction between each element for sustainable development. We recommend land managers, conservationists, and land owners for observing the roles of each patch in the matrix to maximize the benefits than focusing on a single element.

Modeling Fluvial Incision and Transient Landscape Evolution: Influence of Dynamic Channel Adjustment

NASA Astrophysics Data System (ADS)

Attal, M.; Tucker, G. E.; Cowie, P. A.; Whittaker, A. C.; Roberts, G. P.

2007-12-01

Channel geometry exerts a fundamental control on fluvial processes. Recent work has shown that bedrock channel width (W) depends on a number of parameters, including channel slope, and is not only a function of drainage area (A) as is commonly assumed. The present work represents the first attempt to investigate the consequences, for landscape evolution, of using a static expression of channel width (W ~ A0.5) versus a relationship that allows channels to dynamically adjust to changes in slope. We consider different models for the evolution of the channel geometry, including constant width-to-depth ratio (after Finnegan et al., Geology, v. 33, no. 3, 2005), and width-to-depth ratio varying as a function of slope (after Whittaker et al., Geology, v. 35, no. 2, 2007). We use the Channel-Hillslope Integrated Landscape Development (CHILD) model to analyze the response of a catchment to a given tectonic disturbance. The topography of a catchment in the footwall of an active normal fault in the Apennines (Italy) is used as a template for the study. We show that, for this catchment, the transient response can be fairly well reproduced using a simple detachment-limited fluvial incision law. We also show that, depending on the relationship used to express channel width, initial steady-state topographies differ, as do transient channel width, slope, and the response time of the fluvial system. These differences lead to contrasting landscape morphologies when integrated at the scale of a whole catchment. Our results emphasize the importance of channel width in controlling fluvial processes and landscape evolution. They stress the need for using a dynamic hydraulic scaling law when modeling landscape evolution, particularly when the uplift field is non-uniform.

Application of portfolio theory to risk-based allocation of surveillance resources in animal populations.

PubMed

Prattley, D J; Morris, R S; Stevenson, M A; Thornton, R

2007-09-14

Distribution of finite levels of resources between multiple competing tasks can be a challenging problem. Resources need to be distributed across time periods and geographic locations to increase the probability of detection of a disease incursion or significant change in disease pattern. Efforts should focus primarily on areas and populations where risk factors for a given disease reach relatively high levels. In order to target resources into these areas, the overall risk level can be evaluated periodically across locations to create a dynamic national risk landscape. Methods are described to integrate the levels of various risk factors into an overall risk score for each area, to account for the certainty or variability around those measures and then to allocate surveillance resources across this risk landscape. In addition to targeting resources into high risk areas, surveillance continues in lower risk areas where there is a small yet positive chance of disease occurrence. In this paper we describe the application of portfolio theory concepts, routinely used in finance, to design surveillance portfolios for a series of examples. The appropriate level of resource investment is chosen for each disease or geographical area and time period given the degree of disease risk and uncertainty present.

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

To meet the challenge of predicting landscape-scale changes in Earth system behavior, the University of Arizona has designed and constructed a new large-scale and community-oriented scientific facility - the Landscape Evolution Observatory (LEO). The primary scientific objectives are to quantify interactions among hydrologic partitioning, geochemical weathering, ecology, microbiology, atmospheric processes, and geomorphic change associated with incipient hillslope development. LEO consists of three identical, sloping, 333 m2 convergent landscapes inside a 5,000 m2 environmentally controlled facility. These engineered landscapes contain 1 meter of basaltic tephra ground to homogenous loamy sand and contains a spatially dense sensor and sampler network capable of resolving meter-scale lateral heterogeneity and sub-meter scale vertical heterogeneity in moisture, energy and carbon states and fluxes. Each ~1000 metric ton landscape has load cells embedded into the structure to measure changes in total system mass with 0.05% full-scale repeatability (equivalent to less than 1 cm of precipitation), to facilitate better quantification of evapotraspiration. Each landscape has an engineered rain system that allows application of precipitation at rates between3 and 45 mm/hr. These landscapes are being studied in replicate as "bare soil" for an initial period of several years. After this initial phase, heat- and drought-tolerant vascular plant communities will be introduced. Introduction of vascular plants is expected to change how water, carbon, and energy cycle through the landscapes, with potentially dramatic effects on co-evolution of the physical and biological systems. LEO also provides a physical comparison to computer models that are designed to predict interactions among hydrological, geochemical, atmospheric, ecological and geomorphic processes in changing climates. These computer models will be improved by comparing their predictions to physical measurements made in LEO. The main focus of our iterative modeling and measurement discovery cycle is to use rapid data assimilation to facilitate validation of newly coupled open-source Earth systems models. LEO will be a community resource for Earth system science research, education, and outreach. The LEO project operational philosophy includes 1) open and real-time availability of sensor network data, 2) a framework for community collaboration and facility access that includes integration of new or comparative measurement capabilities into existing facility cyberinfrastructure, 3) community-guided science planning and 4) development of novel education and outreach programs.Artistic rendering of the University of Arizona Landscape Evolution Observatory

Three decades of landscape change in Alaska documented using spatiotemporal analyses of remote sensing imagery

NASA Astrophysics Data System (ADS)

Pastick, N. J.; Jorgenson, T.; Swanson, D. K.; Jorgenson, J. C.; Goetz, S. J.; Jones, B. M.; Wylie, B. K.; Knight, J. F.; Minsley, B. J.; Helene, G.

2017-12-01

Contemporary climate change in Alaska has resulted in amplified rates of press and pulse disturbances that have significant consequences for socio-environmental systems. With the heightened susceptibility of arctic and boreal landscapes to change, the characterization of landscape dynamics and the identification of environmental drivers of change across northern high latitudes is critical. Here, we characterize the historical sensitivity of Alaska's ecosystems to natural and anthropogenic disturbances using expert knowledge, remote sensing data, spatiotemporal analyses, and modeling. Time-series analysis of moderate- and high-resolution imagery was used to characterize landscape dynamics across Alaska and along randomly sampled change-detection grids (n=312). Expert interpretations of ecological and geomorphological changes were made at each grid using historical air photos and high-resolution satellite imagery (1980s, 2000s, 2010s), and corroborate land surface greening, browning, and wetness/moisture trends derived from peak-growing season (July 1st - August 31st) Landsat imagery acquired from 1984 to 2015. Spectral change metrics, climatic data, maps of biophysical characteristics, and interpretations of change were incorporated into a modeling framework for mapping and understanding change across Alaska. At the landscape scale, substantial increases in remotely sensed vegetation productivity were most pronounced in western and northern foothills of Alaska, which is associated with recent warming-induced shrub expansion and vegetation growth. Significant browning trends in interior Alaska were largely the­­­­ result of recent wildland fires, but browning trends are also driven by increases in evaporative demand and surface water gains that have predominately occurred over warming permafrost landscapes. Increased rates of photosynthetic activity were also associated with stabilization and recovery processes following wildfire, timber harvesting, insect damage, thermokarst, and glacial retreat, as well as lake infilling and drainage events. This study documents historical landscape dynamics and drivers of change, which is important for understanding potential future trajectories of change and for identifying areas most likely vulnerable to change.

Graph-based analysis of kinetics on multidimensional potential-energy surfaces.

PubMed

Okushima, T; Niiyama, T; Ikeda, K S; Shimizu, Y

2009-09-01

The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters.

The molecular and mathematical basis of Waddington's epigenetic landscape: a framework for post-Darwinian biology?

PubMed

Huang, Sui

2012-02-01

The Neo-Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo-Darwinism. It needs to incorporate the non-linear, stochastic dynamics of gene networks. A first step is to consider the mathematical correspondence between gene regulatory networks and Waddington's metaphoric 'epigenetic landscape', which actually represents the quasi-potential function of global network dynamics. It explains the coexistence of multiple stable phenotypes within one genotype. The landscape's topography with its attractors is shaped by evolution through mutational re-wiring of regulatory interactions - offering a link between genetic mutation and sudden, broad evolutionary changes. Copyright © 2012 WILEY Periodicals, Inc.

Applications of landscape genetics in conservation biology: concepts and challenges

Treesearch

Gernot Segelbacher; Samuel A. Cushman; Bryan K. Epperson; Marie-Josee Fortin; Olivier Francois; Olivier J. Hardy; Rolf Holderegger; Stephanie Manel

2010-01-01

Landscape genetics plays an increasingly important role in the management and conservation of species. Here, we highlight some of the opportunities and challenges in using landscape genetic approaches in conservation biology. We first discuss challenges related to sampling design and introduce several recent methodological developments in landscape genetics (analyses...

Forward and backward evolution of the Calhoun CZO: the effect of natural and anthropogenic disturbances

NASA Astrophysics Data System (ADS)

Bonetti, S.; Porporato, A. M.

2017-12-01

The time evolution of a landscape topography through erosional and depositional mechanisms is modified by both human and natural disturbances. This is particularly evident in the Calhoun Critical Zone Observatory, where decades of land-use resulted in a distinct topography with gullies, interfluves, hillslopes and significantly eroded areas. Understanding the role of different geomorphological processes that led to these conditions is crucial to reconstruct sediment and soil carbon fluxes, predict critical conditions of landscape degradation, and implement strategies of land recovery. To model these dynamics, an analytical theory of the drainage area (which represents a surrogate for water surface runoff responsible for fluvial incision) is used to evolve ridge and valley lines. Furthermore, the coupled dynamics of surface water runoff and landscape evolution is analyzed theoretically and numerically to detect thresholds leading to either stable landscape configurations or critical conditions of land erosion. Observed erosional cycles due to vegetation disturbances are explored and used to predict future evolutions under various levels of anthropogenic disturbance.

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

PubMed

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

2017-11-01

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.

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

PubMed

Leong, Misha; Ponisio, Lauren C; Kremen, Claire; Thorp, Robbin W; Roderick, George K

2016-03-01

Urbanization and agricultural intensification of landscapes are important drivers of global change, which in turn have direct impacts on local ecological communities leading to shifts in species distributions and interactions. Here, we illustrate how human-altered landscapes, with novel ornamental and crop plant communities, result not only in changes to local community diversity of floral-dependent species, but also in shifts in seasonal abundance of bee pollinators. Three years of data on the spatio-temporal distributions of 91 bee species show that seasonal patterns of abundance and species richness in human-altered landscapes varied significantly less compared to natural habitats in which floral resources are relatively scarce in the dry summer months. These findings demonstrate that anthropogenic environmental changes in urban and agricultural systems, here mediated through changes in plant resources and water inputs, can alter the temporal dynamics of pollinators that depend on them. Changes in phenology of interactions can be an important, though frequently overlooked, mechanism of global change. © 2015 John Wiley & Sons Ltd.

Studying Wildlife at Local and Landscape Scales: Bachman's Sparrow at the Savannah River Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunning, J.B.; Danielson, B.J.; Watts, B.D.

2000-10-01

Mutual interests between land managers at SRS and scientists resulted in a landscape ecology study of Bachman's sparrow. The species is declining throughout it's range. The distribution of suitable habitats across the landscape may provide an explanation. The species occupies early successional and late successional savanna habitat. Modeling was closely linked to field observations to demonstrate how the species demographics change with the distribution and dynamics of habitats.

Assessing knowledge ambiguity in the creation of a model based on expert knowledge and comparison with the results of a landscape succession model in central Labrador. Chapter 10.

Treesearch

Frederik Doyon; Brian Sturtevant; Michael J. Papaik; Andrew Fall; Brian Miranda; Daniel D. Kneeshaw; Christian Messier; Marie-Josee Fortin; Patrick M.A. James

2012-01-01

Sustainable forest management (SFM) recognizes that the spatial and temporal patterns generated at different scales by natural landscape and stand dynamics processes should serve as a guide for managing the forest within its range of natural variability. Landscape simulation modeling is a powerful tool that can help encompass such complexity and support SFM planning....

Tensor modes on the string theory landscape

NASA Astrophysics Data System (ADS)

Westphal, Alexander

2013-04-01

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.

[Quantitative analysis of landscape patterns at the juncture of Shaanxi, Shanxi and Inner Mongolia, based on remote sensing data--taking Yulin sheet TM image as an example].

PubMed

Li, Tuansheng

2004-03-01

Based on the TM image of Yulin sheet and with the help of ERDAS, ARC/INFO and ARC/VIEW software, the landscape of Yulin sheet was classified. Using the spatial pattern analysis software FRAGSTATS of the vector version, a set of landscape indices were calculated at three scale levels of patches, classes and landscape. The results showed that landscape pattern indices could be successfully used in characterizing the spatial pattern of the studied area. However, this study should be further extended to the landscape of the same area in other period to analyze its dynamic change. FRAGSTATS was a good software, but should be improved by adding some indices such as PD2 developed by us.

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

PubMed

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.

Nonequilibrium landscape theory of neural networks.

PubMed

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

2013-11-05

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

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

The van Hove distribution function for Brownian hard spheres: Dynamical test particle theory and computer simulations for bulk dynamics

NASA Astrophysics Data System (ADS)

Hopkins, Paul; Fortini, Andrea; Archer, Andrew J.; Schmidt, Matthias

2010-12-01

We describe a test particle approach based on dynamical density functional theory (DDFT) for studying the correlated time evolution of the particles that constitute a fluid. Our theory provides a means of calculating the van Hove distribution function by treating its self and distinct parts as the two components of a binary fluid mixture, with the "self " component having only one particle, the "distinct" component consisting of all the other particles, and using DDFT to calculate the time evolution of the density profiles for the two components. We apply this approach to a bulk fluid of Brownian hard spheres and compare to results for the van Hove function and the intermediate scattering function from Brownian dynamics computer simulations. We find good agreement at low and intermediate densities using the very simple Ramakrishnan-Yussouff [Phys. Rev. B 19, 2775 (1979)] approximation for the excess free energy functional. Since the DDFT is based on the equilibrium Helmholtz free energy functional, we can probe a free energy landscape that underlies the dynamics. Within the mean-field approximation we find that as the particle density increases, this landscape develops a minimum, while an exact treatment of a model confined situation shows that for an ergodic fluid this landscape should be monotonic. We discuss possible implications for slow, glassy, and arrested dynamics at high densities.

Cumulative effects of wildfires on forest dynamics in the eastern Cascade Mountains, USA.

PubMed

Reilly, Matthew J; Elia, Mario; Spies, Thomas A; Gregory, Matthew J; Sanesi, Giovanni; Lafortezza, Raffaele

2018-03-01

Wildfires pose a unique challenge to conservation in fire-prone regions, yet few studies quantify the cumulative effects of wildfires on forest dynamics (i.e., changes in structural conditions) across landscape and regional scales. We assessed the contribution of wildfire to forest dynamics in the eastern Cascade Mountains, USA from 1985 to 2010 using imputed maps of forest structure (i.e., tree size and canopy cover) and remotely sensed burn severity maps. We addressed three questions: (1) How do dynamics differ between the region as a whole and the unburned portion of the region? (2) How do dynamics vary among vegetation zones differing in biophysical setting and historical fire frequency? (3) How have forest structural conditions changed in a network of late successional reserves (LSRs)? Wildfires affected 10% of forests in the region, but the cumulative effects at this scale were primarily slight losses of closed-canopy conditions and slight gains in open-canopy conditions. In the unburned portion of the region (the remaining 90%), closed-canopy conditions primarily increased despite other concurrent disturbances (e.g., harvest, insects). Although the effects of fire were largely dampened at the regional scale, landscape scale dynamics were far more variable. The warm ponderosa pine and cool mixed conifer zones experienced less fire than the region as a whole despite experiencing the most frequent fire historically. Open-canopy conditions increased slightly in the mixed conifer zone, but declined across the ponderosa pine zone even with wildfires. Wildfires burned 30% of the cold subalpine zone, which experienced the greatest increase in open-canopy conditions and losses of closed-canopy conditions. LSRs were more prone to wildfire than the region as a whole, and experienced slight declines in late seral conditions. Despite losses of late seral conditions, wildfires contributed to some conservation objectives by creating open habitats (e.g., sparse early seral and woodland conditions) that otherwise generally decreased in unburned landscapes despite management efforts to increase landscape diversity. This study demonstrates the potential for wildfires to contribute to regional scale conservation objectives, but implications for management and biodiversity at landscape scales vary geographically among biophysical settings, and are contingent upon historical dynamics and individual species habitat preferences. © 2017 by the Ecological Society of America.

Historical Delineation of Landscape Units Using Physical Geographic Characteristics and Land Use/Cover Change

NASA Astrophysics Data System (ADS)

Campos-Campos, Oswaldo; Cruz-Cárdenas, Gustavo; Aquino, Roque Juan Carrasco; Moncayo-Estrada, Rodrigo; Machuca, Martha Alicia Velázquez; Meléndez, Luis Arturo Ávila

2018-03-01

Landscape units are conceived as a part of the territory that share similar physical and geographic characteristics. Their delineation can contribute to identify the physical and social dynamics that emerge in the spatial environment and to propose strategies of planning and management of the territory. The main objective was to make a historical delineation of landscape units in the Duero river basin that demonstrate the dynamics of changes in the territory, the description of the actors involved, and the affectations in the natural and social environment. We analyzed the vegetation change and urban growth from 1983 to 2014, incorporating climatic, edaphic, and topographic variables. A Principal Component Analysis was performed with the information and results were used in Maximum Likelihood procedure to define different clusters based on environmental characteristics. We defined five categories from the Landsat images. Results showed landscape units with homogeneous environmental characteristics and some differences in the units' delineation were mainly influenced by political and socioeconomic factors. Temporally there was an increased tendency of landscape units, three in 1983, nine in 1990, 1995, 2000 and 2011, and eight in 2014. This increase resulted from territory fragmentation because of berries and avocado cultivars expansion over wooded area.

Modulation of a protein free-energy landscape by circular permutation.

PubMed

Radou, Gaël; Enciso, Marta; Krivov, Sergei; Paci, Emanuele

2013-11-07

Circular permutations usually retain the native structure and function of a protein while inevitably perturbing its folding dynamics. By using simulations with a structure-based model and a rigorous methodology to determine free-energy surfaces from trajectories, we evaluate the effect of a circular permutation on the free-energy landscape of the protein T4 lysozyme. We observe changes which, although subtle, largely affect the cooperativity between the two subdomains. Such a change in cooperativity has been previously experimentally observed and recently also characterized using single molecule optical tweezers and the Crooks relation. The free-energy landscapes show that both the wild type and circular permutant have an on-pathway intermediate, previously experimentally characterized, in which one of the subdomains is completely formed. The landscapes, however, differ in the position of the rate-limiting step for folding, which occurs before the intermediate in the wild type and after in the circular permutant. This shift of transition state explains the observed change in the cooperativity. The underlying free-energy landscape thus provides a microscopic description of the folding dynamics and the connection between circular permutation and the loss of cooperativity experimentally observed.

Conformational Sub-states and Populations in Enzyme Catalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agarwal, Pratul K; Doucet, Nicholas; Chennubholta, C

reactants in the active site, chemical turnover, and release of products. In addition to formation of crucial structural interactions between enzyme and substrate(s), coordinated motions within the enzyme substrate complex allow reaction to proceed at a much faster rate, compared to the reaction in solution and in the absence of enzyme. An increasing number of enzyme systems show the presence of conserved protein motions that are important for function. A wide variety of motions are naturally sampled (over femtosecond to millisecond time-scales) as the enzyme complex moves along the energetic landscape, driven by temperature and dynamical events from the surroundingmore » environment. Areas of low energy along the landscape form conformational sub-states, which show higher conformational populations than surrounding areas. A small number of these protein conformational sub-states contain functionally important structural and dynamical features, which assist the enzyme mechanism along the catalytic cycle. Identification and characterization of these higher-energy (also called excited) sub-states and the associated populations are challenging, as these sub-states are very short-lived and therefore rarely populated. Specialized techniques based on computer simulations, theoretical modeling, and nuclear magnetic resonance have been developed for quantitative characterization of these sub-states and populations. This chapter discusses these techniques and provides examples of their applications to enzyme systems.« less

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

USGS Publications Warehouse

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

2000-01-01

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

Exploring an Ecologically Sustainable Scheme for Landscape Restoration of Abandoned Mine Land: Scenario-Based Simulation Integrated Linear Programming and CLUE-S Model

PubMed Central

Zhang, Liping; Zhang, Shiwen; Huang, Yajie; Cao, Meng; Huang, Yuanfang; Zhang, Hongyan

2016-01-01

Understanding abandoned mine land (AML) changes during land reclamation is crucial for reusing damaged land resources and formulating sound ecological restoration policies. This study combines the linear programming (LP) model and the CLUE-S model to simulate land-use dynamics in the Mentougou District (Beijing, China) from 2007 to 2020 under three reclamation scenarios, that is, the planning scenario based on the general land-use plan in study area (scenario 1), maximal comprehensive benefits (scenario 2), and maximal ecosystem service value (scenario 3). Nine landscape-scale graph metrics were then selected to describe the landscape characteristics. The results show that the coupled model presented can simulate the dynamics of AML effectively and the spatially explicit transformations of AML were different. New cultivated land dominates in scenario 1, while construction land and forest land account for major percentages in scenarios 2 and 3, respectively. Scenario 3 has an advantage in most of the selected indices as the patches combined most closely. To conclude, reclaiming AML by transformation into more forest can reduce the variability and maintain the stability of the landscape ecological system in study area. These findings contribute to better mapping AML dynamics and providing policy support for the management of AML. PMID:27023575

Exploring an Ecologically Sustainable Scheme for Landscape Restoration of Abandoned Mine Land: Scenario-Based Simulation Integrated Linear Programming and CLUE-S Model.

PubMed

Zhang, Liping; Zhang, Shiwen; Huang, Yajie; Cao, Meng; Huang, Yuanfang; Zhang, Hongyan

2016-03-24

Understanding abandoned mine land (AML) changes during land reclamation is crucial for reusing damaged land resources and formulating sound ecological restoration policies. This study combines the linear programming (LP) model and the CLUE-S model to simulate land-use dynamics in the Mentougou District (Beijing, China) from 2007 to 2020 under three reclamation scenarios, that is, the planning scenario based on the general land-use plan in study area (scenario 1), maximal comprehensive benefits (scenario 2), and maximal ecosystem service value (scenario 3). Nine landscape-scale graph metrics were then selected to describe the landscape characteristics. The results show that the coupled model presented can simulate the dynamics of AML effectively and the spatially explicit transformations of AML were different. New cultivated land dominates in scenario 1, while construction land and forest land account for major percentages in scenarios 2 and 3, respectively. Scenario 3 has an advantage in most of the selected indices as the patches combined most closely. To conclude, reclaiming AML by transformation into more forest can reduce the variability and maintain the stability of the landscape ecological system in study area. These findings contribute to better mapping AML dynamics and providing policy support for the management of AML.

Spatially Distributed Assimilation of Remotely Sensed Leaf Area Index and Potential Evapotranspiration for Hydrologic Modeling in Wetland Landscapes

EPA Science Inventory

Evapotranspiration (ET), a highly dynamic flux in wetland landscapes, regulates the accuracy of surface/sub-surface runoff simulation in a hydrologic model. However, considerable uncertainty in simulating ET-related processes remains, including our limited ability to incorporate ...

Dynamic Tracking: The Study of Changes in Landscape.

ERIC Educational Resources Information Center

Strang, Carl A.

1996-01-01

States that tracking, or the study of changes in landscapes, offers clues that give us a direct experiential connection to the past and consequently enriches our appreciation of how the present came to be. Discusses tracking animals and footprints, tree tracking, and geomorphology or landforms. (AIM)

A heuristic for landscape management

Treesearch

Martín Alfonso B. Mendoza; Jesús S. Zepeta; Juan José A. Fajardo

2006-01-01

The development of landscape ecology has stressed out the importance of spatial and sequential relationships as explanations to forest stand dynamics, and for other natural ambiences. This presentation offers a specific design that introduces spatial considerations into forest planning with the idea of regulating fragmentation and connectivity in commercial forest...

Free energy landscape theory of glass transition

NASA Astrophysics Data System (ADS)

Odagaki, Takashi

2010-03-01

I first present a free energy landscape (FEL) description of statistical mechanics, which is an exact reformulation of statistical mechanics and can be applied to non-equilibrium systems. Then, I discuss thermodynamic and dynamic properties of the vitrification process on the basis of the FEL formalism. I show that thermodynamic and dynamic anomalies at the glass transition, including the cooling rate dependence, can be understood in a unified manner which has not been achieved by any other theories of the glass transition. Namely, I show that the vitrification is a transition from annealed to quenched averages in the FEL and that the fast beta, the JG and the slow alpha relaxations are attributed to stochastic dynamics within a basin of FEL, jumping motion among locally connected basins and diffusive dynamics over barriers of the FEL.

Application of cellular automata approach for cloud simulation and rendering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christopher Immanuel, W.; Paul Mary Deborrah, S.; Samuel Selvaraj, R.

Current techniques for creating clouds in games and other real time applications produce static, homogenous clouds. These clouds, while viable for real time applications, do not exhibit an organic feel that clouds in nature exhibit. These clouds, when viewed over a time period, were able to deform their initial shape and move in a more organic and dynamic way. With cloud shape technology we should be able in the future to extend to create even more cloud shapes in real time with more forces. Clouds are an essential part of any computer model of a landscape or an animation ofmore » an outdoor scene. A realistic animation of clouds is also important for creating scenes for flight simulators, movies, games, and other. Our goal was to create a realistic animation of clouds.« less

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

PubMed

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

2015-01-01

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

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

PubMed Central

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

2015-01-01

Sustainable forest management is based on functional relationships between management actions, landscape conditions, and forest values. Changes in management practices make it fundamentally more difficult to study these relationships because the impacts of current practices are difficult to disentangle from the persistent influences of past practices. Within the Atlantic Northern Forest of Maine, U.S.A., forest policy and management practices changed abruptly in the early 1990s. During the 1970s-1980s, a severe insect outbreak stimulated salvage clearcutting of large contiguous tracts of spruce-fir forest. Following clearcut regulation in 1991, management practices shifted abruptly to near complete dependence on partial harvesting. Using a time series of Landsat satellite imagery (1973-2010) we assessed cumulative landscape change caused by these very different management regimes. We modeled predominant temporal patterns of harvesting and segmented a large study area into groups of landscape units with similar harvest histories. Time series of landscape composition and configuration metrics averaged within groups revealed differences in landscape dynamics caused by differences in management history. In some groups (24% of landscape units), salvage caused rapid loss and subdivision of intact mature forest. Persistent landscape change was created by large salvage clearcuts (often averaging > 100 ha) and conversion of spruce-fir to deciduous and mixed forest. In groups that were little affected by salvage (56% of landscape units), contemporary partial harvesting caused loss and subdivision of intact mature forest at even greater rates. Patch shape complexity and edge density reached high levels even where cumulative harvest area was relatively low. Contemporary practices introduced more numerous and much smaller patches of stand-replacing disturbance (typically averaging <15 ha) and a correspondingly large amount of edge. Management regimes impacted different areas to different degrees, producing different trajectories of landscape change that should be recognized when studying the impact of policy and management practices on forest ecology. PMID:26106893

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

PubMed

Luo, Xiaosheng; Xu, Liufang; Han, Bo; Wang, Jin

2017-09-01

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 strategy of cancer.

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

PubMed Central

2017-01-01

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 strategy of cancer. PMID:28892489

Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland

PubMed Central

Spotswood, Erica N.; Bartolome, James W.; Allen-Diaz, Barbara

2015-01-01

Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species), temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery. PMID:26222069

Hotspots of Community Change: Temporal Dynamics Are Spatially Variable in Understory Plant Composition of a California Oak Woodland.

PubMed

Spotswood, Erica N; Bartolome, James W; Allen-Diaz, Barbara

2015-01-01

Community response to external drivers such climate and disturbance can lead to fluctuations in community composition, or to directional change. Temporal dynamics can be influenced by a combination of drivers operating at multiple spatial scales, including external landscape scale drivers, local abiotic conditions, and local species pools. We hypothesized that spatial variation in these factors can create heterogeneity in temporal dynamics within landscapes. We used understory plant species composition from an 11 year dataset from a California oak woodland to compare plots where disturbance was experimentally manipulated with the removal of livestock grazing and a prescribed burn. We quantified three properties of temporal variation: compositional change (reflecting the appearance and disappearance of species), temporal fluctuation, and directional change. Directional change was related most strongly to disturbance type, and was highest at plots where grazing was removed during the study. Temporal fluctuations, compositional change, and directional change were all related to intrinsic abiotic factors, suggesting that some locations are more responsive to external drivers than others. Temporal fluctuations and compositional change were linked to local functional composition, indicating that environmental filters can create subsets of the local species pool that do not respond in the same way to external drivers. Temporal dynamics are often assumed to be relatively static at the landscape scale, provided disturbance and climate are continuous. This study shows that local and landscape scale factors jointly influence temporal dynamics creating hotspots that are particularly responsive to climate and disturbance. Thus, adequate predictions of response to disturbance or to changing climate will only be achieved by considering how factors at multiple spatial scales influence community resilience and recovery.

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

PubMed Central

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

2016-01-01

Habitat destruction, a key determinant of species loss, can be characterized by two components, patch loss and patch fragmentation, where the former refers to the reduction in patch availability, and the latter to the division of the remaining patches. Classical metacommunity models have recently explored how food web dynamics respond to patch loss, but the effects of patch fragmentation have largely been overlooked. Here we develop an extended patch-dynamic model that tracks the patch occupancy of the various trophic links subject to colonization-extinction-predation dynamics by incorporating species dispersal with patch connectivity. We found that, in a simple food chain, species at higher trophic level become extinct sooner with increasing patch loss and fragmentation due to the constraint in resource availability, confirming the trophic rank hypothesis. Yet, effects of fragmentation on species occupancy are largely determined by patch loss, with maximal fragmentation effects occurring at intermediate patch loss. Compared to the spatially explicit simulations that we also performed, the current model with pair approximation generates similar community patterns especially in spatially clustered landscapes. Overall, our extended framework can be applied to model more complex food webs in fragmented landscapes, broadening the scope of existing metacommunity theory. PMID:27608823

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

PubMed

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.

Principal component analysis on a torus: Theory and application to protein dynamics.

PubMed

Sittel, Florian; Filk, Thomas; Stock, Gerhard

2017-12-28

A dimensionality reduction method for high-dimensional circular data is developed, which is based on a principal component analysis (PCA) of data points on a torus. Adopting a geometrical view of PCA, various distance measures on a torus are introduced and the associated problem of projecting data onto the principal subspaces is discussed. The main idea is that the (periodicity-induced) projection error can be minimized by transforming the data such that the maximal gap of the sampling is shifted to the periodic boundary. In a second step, the covariance matrix and its eigendecomposition can be computed in a standard manner. Adopting molecular dynamics simulations of two well-established biomolecular systems (Aib 9 and villin headpiece), the potential of the method to analyze the dynamics of backbone dihedral angles is demonstrated. The new approach allows for a robust and well-defined construction of metastable states and provides low-dimensional reaction coordinates that accurately describe the free energy landscape. Moreover, it offers a direct interpretation of covariances and principal components in terms of the angular variables. Apart from its application to PCA, the method of maximal gap shifting is general and can be applied to any other dimensionality reduction method for circular data.

Principal component analysis on a torus: Theory and application to protein dynamics

NASA Astrophysics Data System (ADS)

Sittel, Florian; Filk, Thomas; Stock, Gerhard

2017-12-01

A dimensionality reduction method for high-dimensional circular data is developed, which is based on a principal component analysis (PCA) of data points on a torus. Adopting a geometrical view of PCA, various distance measures on a torus are introduced and the associated problem of projecting data onto the principal subspaces is discussed. The main idea is that the (periodicity-induced) projection error can be minimized by transforming the data such that the maximal gap of the sampling is shifted to the periodic boundary. In a second step, the covariance matrix and its eigendecomposition can be computed in a standard manner. Adopting molecular dynamics simulations of two well-established biomolecular systems (Aib9 and villin headpiece), the potential of the method to analyze the dynamics of backbone dihedral angles is demonstrated. The new approach allows for a robust and well-defined construction of metastable states and provides low-dimensional reaction coordinates that accurately describe the free energy landscape. Moreover, it offers a direct interpretation of covariances and principal components in terms of the angular variables. Apart from its application to PCA, the method of maximal gap shifting is general and can be applied to any other dimensionality reduction method for circular data.

Southern California landslides-an overview

USGS Publications Warehouse

,

2005-01-01

Southern California lies astride a major tectonic plate boundary defined by the San Andreas Fault and numerous related faults that are spread across a broad region. This dynamic tectonic environment has created a spectacular landscape of rugged mountains and steep-walled valleys that compose much of the region’s scenic beauty. Unfortunately, this extraordinary landscape also presents serious geologic hazards. Just as tectonic forces are steadily pushing the landscape upward, gravity is relentlessly tugging it downward. When gravity prevails, landslides can occur.

Deformation of Attractor Landscape via Cholinergic Presynaptic Modulations: A Computational Study Using a Phase Neuron Model

PubMed Central

Kanamaru, Takashi; Fujii, Hiroshi; Aihara, Kazuyuki

2013-01-01

Corticopetal acetylcholine (ACh) is released transiently from the nucleus basalis of Meynert (NBM) into the cortical layers and is associated with top-down attention. Recent experimental data suggest that this release of ACh disinhibits layer 2/3 pyramidal neurons (PYRs) via muscarinic presynaptic effects on inhibitory synapses. Together with other possible presynaptic cholinergic effects on excitatory synapses, this may result in dynamic and temporal modifications of synapses associated with top-down attention. However, the system-level consequences and cognitive relevance of such disinhibitions are poorly understood. Herein, we propose a theoretical possibility that such transient modifications of connectivity associated with ACh release, in addition to top-down glutamatergic input, may provide a neural mechanism for the temporal reactivation of attractors as neural correlates of memories. With baseline levels of ACh, the brain returns to quasi-attractor states, exhibiting transitive dynamics between several intrinsic internal states. This suggests that top-down attention may cause the attention-induced deformations between two types of attractor landscapes: the quasi-attractor landscape (Q-landscape, present under low-ACh, non-attentional conditions) and the attractor landscape (A-landscape, present under high-ACh, top-down attentional conditions). We present a conceptual computational model based on experimental knowledge of the structure of PYRs and interneurons (INs) in cortical layers 1 and 2/3 and discuss the possible physiological implications of our results. PMID:23326520

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

NASA Astrophysics Data System (ADS)

Beylich, Achim A.

2017-04-01

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

A web based spatial decision supporting system for land management and soil conservation

NASA Astrophysics Data System (ADS)

Terribile, F.; Agrillo, A.; Bonfante, A.; Buscemi, G.; Colandrea, M.; D'Antonio, A.; De Mascellis, R.; De Michele, C.; Langella, G.; Manna, P.; Marotta, L.; Mileti, F. A.; Minieri, L.; Orefice, N.; Valentini, S.; Vingiani, S.; Basile, A.

2015-02-01

Today it is evident that there are many contrasting demands on our landscape (e.g. food security, more sustainable agriculture, higher income in rural areas, etc.) but also many land degradation problems. It has been proved that providing operational answers to these demands and problems is extremely difficult. Here we aim to demonstrate that a Spatial Decision Support System based on geospatial cyber-infrastructure (GCI) can embody all of the above, so producing a smart system for supporting decision making for agriculture, forestry and urban planning with respect to the landscape. In this paper, we discuss methods and results of a special kind of GCI architecture, one that is highly focused on soil and land conservation (SOILCONSWEB-LIFE+ project). The system allows us to obtain dynamic, multidisciplinary, multiscale, and multifunctional answers to agriculture, forestry and urban planning issues through the web. The system has been applied to and tested in an area of about 20 000 ha in the South of Italy, within the framework of a European LIFE+ project. The paper reports - as a case study - results from two different applications dealing with agriculture (olive growth tool) and environmental protection (soil capability to protect groundwater). Developed with the help of end users, the system is starting to be adopted by local communities. The system indirectly explores a change of paradigm for soil and landscape scientists. Indeed, the potential benefit is shown of overcoming current disciplinary fragmentation over landscape issues by offering - through a smart web based system - truly integrated geospatial knowledge that may be directly and freely used by any end user (http://www.landconsultingweb.eu). This may help bridge the last much important divide between scientists working on the landscape and end users.

No Future in the Past? The role of initial topography on landform evolution model predictions

NASA Astrophysics Data System (ADS)

Hancock, G. R.; Coulthard, T. J.; Lowry, J.

2014-12-01

Our understanding of earth surface processes is based on long-term empirical understandings, short-term field measurements as well as numerical models. In particular, numerical landscape evolution models (LEMs) have been developed which have the capability to capture a range of both surface (erosion and deposition), tectonics, as well as near surface or critical zone processes (i.e. pedogenesis). These models have a range of applications for understanding both surface and whole of landscape dynamics through to more applied situations such as degraded site rehabilitation. LEMs are now at the stage of development where if calibrated, can provide some level of reliability. However, these models are largely calibrated based on parameters determined from present surface conditions which are the product of much longer-term geology-soil-climate-vegetation interactions. Here, we assess the effect of the initial landscape dimensions and associated error as well as parameterisation for a potential post-mining landform design. The results demonstrate that subtle surface changes in the initial DEM as well as parameterisation can have a large impact on landscape behaviour, erosion depth and sediment discharge. For example, the predicted sediment output from LEM's is shown to be highly variable even with very subtle changes in initial surface conditions. This has two important implications in that decadal time scale field data is needed to (a) better parameterise models and (b) evaluate their predictions. We question how a LEM using parameters derived from field plots can firstly be employed to examine long-term landscape evolution. Secondly, the potential range of outcomes is examined based on estimated temporal parameter change and thirdly, the need for more detailed and rigorous field data for calibration and validation of these models is discussed.

A Web-based spatial decision supporting system for land management and soil conservation

NASA Astrophysics Data System (ADS)

Terribile, F.; Agrillo, A.; Bonfante, A.; Buscemi, G.; Colandrea, M.; D'Antonio, A.; De Mascellis, R.; De Michele, C.; Langella, G.; Manna, P.; Marotta, L.; Mileti, F. A.; Minieri, L.; Orefice, N.; Valentini, S.; Vingiani, S.; Basile, A.

2015-07-01

Today it is evident that there are many contrasting demands on our landscape (e.g. food security, more sustainable agriculture, higher income in rural areas, etc.) as well as many land degradation problems. It has been proved that providing operational answers to these demands and problems is extremely difficult. Here we aim to demonstrate that a spatial decision support system based on geospatial cyberinfrastructure (GCI) can address all of the above, so producing a smart system for supporting decision making for agriculture, forestry, and urban planning with respect to the landscape. In this paper, we discuss methods and results of a special kind of GCI architecture, one that is highly focused on land management and soil conservation. The system allows us to obtain dynamic, multidisciplinary, multiscale, and multifunctional answers to agriculture, forestry, and urban planning issues through the Web. The system has been applied to and tested in an area of about 20 000 ha in the south of Italy, within the framework of a European LIFE+ project (SOILCONSWEB). The paper reports - as a case study - results from two different applications dealing with agriculture (olive growth tool) and environmental protection (soil capability to protect groundwater). Developed with the help of end users, the system is starting to be adopted by local communities. The system indirectly explores a change of paradigm for soil and landscape scientists. Indeed, the potential benefit is shown of overcoming current disciplinary fragmentation over landscape issues by offering - through a smart Web-based system - truly integrated geospatial knowledge that may be directly and freely used by any end user (www.landconsultingweb.eu). This may help bridge the last very important divide between scientists working on the landscape and end users.

Landscape determinants of fine-scale genetic structure of a small rodent in a heterogeneous landscape (Hluhluwe-iMfolozi Park, South Africa)

PubMed Central

Russo, Isa-Rita M.; Sole, Catherine L.; Barbato, Mario; von Bramann, Ullrich; Bruford, Michael W.

2016-01-01

Small mammals provide ecosystem services, acting, for example, as pollinators and seed dispersers. In addition, they are also disease reservoirs that can be detrimental to human health and they can also act as crop pests. Knowledge of their dispersal preferences is therefore useful for population management and landscape planning. Genetic data were used alongside landscape data to examine the influence of the landscape on the demographic connectedness of the Natal multimammate mouse (Mastomys natalensis) and to identify landscape characteristics that influence the genetic structure of this species across a spatially and temporally varying environment. The most significant landscape features shaping gene flow were aspect, vegetation cover, topographic complexity (TC) and rivers, with western facing slopes, topographic complexity and rivers restricting gene flow. In general, thicket vegetation was correlated with increased gene flow. Identifying features of the landscape that facilitate movement/dispersal in M. natalensis potentially has application for other small mammals in similar ecosystems. As the primary reservoir host of the zoonotic Lassa virus, a landscape genetics approach may have applications in determining areas of high disease risk to humans. Identifying these landscape features may also be important in crop management due to damage by rodent pests. PMID:27406468

Landscape determinants of fine-scale genetic structure of a small rodent in a heterogeneous landscape (Hluhluwe-iMfolozi Park, South Africa).

PubMed

Russo, Isa-Rita M; Sole, Catherine L; Barbato, Mario; von Bramann, Ullrich; Bruford, Michael W

2016-07-13

Small mammals provide ecosystem services, acting, for example, as pollinators and seed dispersers. In addition, they are also disease reservoirs that can be detrimental to human health and they can also act as crop pests. Knowledge of their dispersal preferences is therefore useful for population management and landscape planning. Genetic data were used alongside landscape data to examine the influence of the landscape on the demographic connectedness of the Natal multimammate mouse (Mastomys natalensis) and to identify landscape characteristics that influence the genetic structure of this species across a spatially and temporally varying environment. The most significant landscape features shaping gene flow were aspect, vegetation cover, topographic complexity (TC) and rivers, with western facing slopes, topographic complexity and rivers restricting gene flow. In general, thicket vegetation was correlated with increased gene flow. Identifying features of the landscape that facilitate movement/dispersal in M. natalensis potentially has application for other small mammals in similar ecosystems. As the primary reservoir host of the zoonotic Lassa virus, a landscape genetics approach may have applications in determining areas of high disease risk to humans. Identifying these landscape features may also be important in crop management due to damage by rodent pests.

Chapter 7 - Mapping potential vegetation type for the LANDFIRE Prototype Project

Treesearch

Tracey S. Frescino; Matthew G. Rollins

2006-01-01

Mapped potential vegetation functioned as a key component in the Landscape Fire and Resource Management Planning Tools Prototype Project (LANDFIRE Prototype Project). Disturbance regimes, vegetation response and succession, and wildland fuel dynamics across landscapes are controlled by patterns of the environmental factors (biophysical settings) that entrain the...

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

USDA-ARS?s Scientific Manuscript database

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

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

USDA-ARS?s Scientific Manuscript database

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

Using LANDIS II to study the effects of global change in Siberia

Treesearch

Eric J. Gustafson; Brian R. Sturtevant; Anatoly Z. Shvidenko; Robert M. Scheller

2010-01-01

Landscape dynamics are characterized by complex interactions among multiple disturbance regimes, anthropogenic use and management, and the mosaic of diverse ecological conditions. LANDIS-IT is a landscape forest succession and disturbance model that independently simulates multiple ecological and disturbance processes, accounting for complex interactions to predict...

Estimating density of a territorial species in a dynamic landscape

Treesearch

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

2017-01-01

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

LanDPro: Landscape Dynamics Program

DTIC Science & Technology

2012-09-18

of Major Accomplishments............................................................... 7 1. Landscape history and response to land use change and...site potential using geologic, geomorphic, and geophysical techniques, U.S. Marine Corps Base Camp Pendleton, CA...safe, realistic military training environments while maximizing use for active training, DoD spends upwards of $100 million annually on land management

A Coupled SD and CLUE-S Model for Exploring the Impact of Land Use Change on Ecosystem Service Value: A Case Study in Baoshan District, Shanghai, China

NASA Astrophysics Data System (ADS)

Wu, Meng; Ren, Xiangyu; Che, Yue; Yang, Kai

2015-08-01

Most of the cities in developing countries are experiencing rapid urbanization. Land use change driven by urban sprawl, population growth, and intensified socio-economic activities have led to a steep decline of ecosystem service value (ESV) in rapid urbanization areas, and decision-makers often ignore some valuable ecosystem service functions and values in land use planning. In this paper, we attempt to build a modeling framework which integrated System Dynamics model with Conversion of Land Use and its Effects at Small Extent model to simulate the dynamics of ESV of landscape and explore the potential impacts of land use change on ESV. We take Baoshan district of Shanghai as an example which is a fast urbanization area of metropolitan in China. The results of the study indicate that: (1) The integrated methodology can improve the characterization and presentation of the dynamics of ESV, which may give insight into understanding the possible impacts of land use change on ESV and provide information for land use planning. (2) Land use polices can affect the magnitude and location of ESV both directly and indirectly. Land use changes tend to weaken and simplify ecosystem service functions and values of landscape at urban rural fringe where land use change is more intensive. (3) The application of the methodology has proved that the integration of currently existing models within a single modeling framework could be a beneficial exploration, and should be encouraged and enhanced in the future research on the changing dynamics of ESV due to the complexity of ecosystem services and land use system.

A Coupled SD and CLUE-S Model for Exploring the Impact of Land Use Change on Ecosystem Service Value: A Case Study in Baoshan District, Shanghai, China.

PubMed

Wu, Meng; Ren, Xiangyu; Che, Yue; Yang, Kai

2015-08-01

Most of the cities in developing countries are experiencing rapid urbanization. Land use change driven by urban sprawl, population growth, and intensified socio-economic activities have led to a steep decline of ecosystem service value (ESV) in rapid urbanization areas, and decision-makers often ignore some valuable ecosystem service functions and values in land use planning. In this paper, we attempt to build a modeling framework which integrated System Dynamics model with Conversion of Land Use and its Effects at Small Extent model to simulate the dynamics of ESV of landscape and explore the potential impacts of land use change on ESV. We take Baoshan district of Shanghai as an example which is a fast urbanization area of metropolitan in China. The results of the study indicate that: (1) The integrated methodology can improve the characterization and presentation of the dynamics of ESV, which may give insight into understanding the possible impacts of land use change on ESV and provide information for land use planning. (2) Land use polices can affect the magnitude and location of ESV both directly and indirectly. Land use changes tend to weaken and simplify ecosystem service functions and values of landscape at urban rural fringe where land use change is more intensive. (3) The application of the methodology has proved that the integration of currently existing models within a single modeling framework could be a beneficial exploration, and should be encouraged and enhanced in the future research on the changing dynamics of ESV due to the complexity of ecosystem services and land use system.

SPATIAL SCALE OF AUTOCORRELATION IN WISCONSIN FROG AND TOAD SURVEY DATA

EPA Science Inventory

The degree to which local population dynamics are correlated with nearby sites has important implications for metapopulation dynamics and landscape management. Spatially extensive monitoring data can be used to evaluate large-scale population dynamic processes. Our goals in this ...

Rapid evolution accelerates plant population spread in fragmented experimental landscapes.

PubMed

Williams, Jennifer L; Kendall, Bruce E; Levine, Jonathan M

2016-07-29

Predicting the speed of biological invasions and native species migrations requires an understanding of the ecological and evolutionary dynamics of spreading populations. Theory predicts that evolution can accelerate species' spread velocity, but how landscape patchiness--an important control over traits under selection--influences this process is unknown. We manipulated the response to selection in populations of a model plant species spreading through replicated experimental landscapes of varying patchiness. After six generations of change, evolving populations spread 11% farther than nonevolving populations in continuously favorable landscapes and 200% farther in the most fragmented landscapes. The greater effect of evolution on spread in patchier landscapes was consistent with the evolution of dispersal and competitive ability. Accounting for evolutionary change may be critical when predicting the velocity of range expansions. Copyright © 2016, American Association for the Advancement of Science.

Forest dynamics in the U.S. indicate disproportionate attrition in western forests, rural areas and public lands

PubMed Central

2017-01-01

Forests are experiencing significant changes; studying geographic patterns in forests is critical in understanding the impact of forest dynamics to biodiversity, soil erosion, water chemistry and climate. Few studies have examined forest geographic pattern changes other than fragmentation; however, other spatial processes of forest dynamics are of equal importance. Here, we study forest attrition, the complete removal of forest patches, that can result in complete habitat loss, severe decline of population sizes and species richness, and shifts of local and regional environmental conditions. We aim to develop a simple yet insightful proximity-based spatial indicator capturing forest attrition that is independent of spatial scale and boundaries with worldwide application potential. Using this proximity indicator, we evaluate forest attrition across ecoregions, land ownership and urbanization stratifications across continental United States of America. Nationally, the total forest cover loss was approximately 90,400 km2, roughly the size of the state of Maine, constituting a decline of 2.96%. Examining the spatial arrangement of this change the average FAD was 3674m in 1992 and increased by 514m or 14.0% in 2001. Simulations of forest cover loss indicate only a 10m FAD increase suggesting that the observed FAD increase was more than an order of magnitude higher than expected. Furthermore, forest attrition is considerably higher in the western United States, in rural areas and in public lands. Our mathematical model (R2 = 0.93) supports estimation of attrition for a given forest cover. The FAD metric quantifies forest attrition across spatial scales and geographic boundaries and assesses unambiguously changes over time. The metric is applicable to any landscape and offers a new complementary insight on forest landscape patterns from local to global scales, improving future exploration of drivers and repercussions of forest cover changes and supporting more informative management of forest carbon, changing climate and species biodiversity. PMID:28225787

A stand-alone tree demography and landscape structure module for Earth system models: integration with inventory data from temperate and boreal forests

NASA Astrophysics Data System (ADS)

Haverd, V.; Smith, B.; Nieradzik, L. P.; Briggs, P. R.

2014-08-01

Poorly constrained rates of biomass turnover are a key limitation of Earth system models (ESMs). In light of this, we recently proposed a new approach encoded in a model called Populations-Order-Physiology (POP), for the simulation of woody ecosystem stand dynamics, demography and disturbance-mediated heterogeneity. POP is suitable for continental to global applications and designed for coupling to the terrestrial ecosystem component of any ESM. POP bridges the gap between first-generation dynamic vegetation models (DVMs) with simple large-area parameterisations of woody biomass (typically used in current ESMs) and complex second-generation DVMs that explicitly simulate demographic processes and landscape heterogeneity of forests. The key simplification in the POP approach, compared with second-generation DVMs, is to compute physiological processes such as assimilation at grid-scale (with CABLE (Community Atmosphere Biosphere Land Exchange) or a similar land surface model), but to partition the grid-scale biomass increment among age classes defined at sub-grid-scale, each subject to its own dynamics. POP was successfully demonstrated along a savanna transect in northern Australia, replicating the effects of strong rainfall and fire disturbance gradients on observed stand productivity and structure. Here, we extend the application of POP to wide-ranging temporal and boreal forests, employing paired observations of stem biomass and density from forest inventory data to calibrate model parameters governing stand demography and biomass evolution. The calibrated POP model is then coupled to the CABLE land surface model, and the combined model (CABLE-POP) is evaluated against leaf-stem allometry observations from forest stands ranging in age from 3 to 200 year. Results indicate that simulated biomass pools conform well with observed allometry. We conclude that POP represents an ecologically plausible and efficient alternative to large-area parameterisations of woody biomass turnover, typically used in current ESMs.

Forest dynamics in the U.S. indicate disproportionate attrition in western forests, rural areas and public lands.

PubMed

Yang, Sheng; Mountrakis, Giorgos

2017-01-01

Forests are experiencing significant changes; studying geographic patterns in forests is critical in understanding the impact of forest dynamics to biodiversity, soil erosion, water chemistry and climate. Few studies have examined forest geographic pattern changes other than fragmentation; however, other spatial processes of forest dynamics are of equal importance. Here, we study forest attrition, the complete removal of forest patches, that can result in complete habitat loss, severe decline of population sizes and species richness, and shifts of local and regional environmental conditions. We aim to develop a simple yet insightful proximity-based spatial indicator capturing forest attrition that is independent of spatial scale and boundaries with worldwide application potential. Using this proximity indicator, we evaluate forest attrition across ecoregions, land ownership and urbanization stratifications across continental United States of America. Nationally, the total forest cover loss was approximately 90,400 km2, roughly the size of the state of Maine, constituting a decline of 2.96%. Examining the spatial arrangement of this change the average FAD was 3674m in 1992 and increased by 514m or 14.0% in 2001. Simulations of forest cover loss indicate only a 10m FAD increase suggesting that the observed FAD increase was more than an order of magnitude higher than expected. Furthermore, forest attrition is considerably higher in the western United States, in rural areas and in public lands. Our mathematical model (R2 = 0.93) supports estimation of attrition for a given forest cover. The FAD metric quantifies forest attrition across spatial scales and geographic boundaries and assesses unambiguously changes over time. The metric is applicable to any landscape and offers a new complementary insight on forest landscape patterns from local to global scales, improving future exploration of drivers and repercussions of forest cover changes and supporting more informative management of forest carbon, changing climate and species biodiversity.

Monte Carlo Sampling in Fractal Landscapes

NASA Astrophysics Data System (ADS)

Leitão, Jorge C.; Lopes, J. M. Viana Parente; Altmann, Eduardo G.

2013-05-01

We design a random walk to explore fractal landscapes such as those describing chaotic transients in dynamical systems. We show that the random walk moves efficiently only when its step length depends on the height of the landscape via the largest Lyapunov exponent of the chaotic system. We propose a generalization of the Wang-Landau algorithm which constructs not only the density of states (transient time distribution) but also the correct step length. As a result, we obtain a flat-histogram Monte Carlo method which samples fractal landscapes in polynomial time, a dramatic improvement over the exponential scaling of traditional uniform-sampling methods. Our results are not limited by the dimensionality of the landscape and are confirmed numerically in chaotic systems with up to 30 dimensions.

SDE decomposition and A-type stochastic interpretation in nonequilibrium processes

NASA Astrophysics Data System (ADS)

Yuan, Ruoshi; Tang, Ying; Ao, Ping

2017-12-01

An innovative theoretical framework for stochastic dynamics based on the decomposition of a stochastic differential equation (SDE) into a dissipative component, a detailed-balance-breaking component, and a dual-role potential landscape has been developed, which has fruitful applications in physics, engineering, chemistry, and biology. It introduces the A-type stochastic interpretation of the SDE beyond the traditional Ito or Stratonovich interpretation or even the α-type interpretation for multidimensional systems. The potential landscape serves as a Hamiltonian-like function in nonequilibrium processes without detailed balance, which extends this important concept from equilibrium statistical physics to the nonequilibrium region. A question on the uniqueness of the SDE decomposition was recently raised. Our review of both the mathematical and physical aspects shows that uniqueness is guaranteed. The demonstration leads to a better understanding of the robustness of the novel framework. In addition, we discuss related issues including the limitations of an approach to obtaining the potential function from a steady-state distribution.

3D and 4D Simulations for Landscape Reconstruction and Damage Scenarios: GIS Pilot Applications

ERIC Educational Resources Information Center

Pesaresi, Cristano; Van Der Schee, Joop; Pavia, Davide

2017-01-01

The project "3D and 4D Simulations for Landscape Reconstruction and Damage Scenarios: GIS Pilot Applications" has been devised with the intention to deal with the demand for research, innovation and applicative methodology on the part of the international programme, requiring concrete results to increase the capacity to know, anticipate…

Towards a virtual hub approach for landscape assessment and multimedia ecomuseum using multitemporal-maps

NASA Astrophysics Data System (ADS)

Brumana, R.; Santana Quintero, M.; Barazzetti, L.; Previtali, M.; Banfi, F.; Oreni, D.; Roels, D.; Roncoroni, F.

2015-08-01

Landscapes are dynamic entities, stretching and transforming across space and time, and need to be safeguarded as living places for the future, with interaction of human, social and economic dimensions. To have a comprehensive landscape evaluation several open data are needed, each one characterized by its own protocol, service interface, limiting or impeding this way interoperability and their integration. Indeed, nowadays the development of websites targeted to landscape assessment and touristic purposes requires many resources in terms of time, cost and IT skills to be implemented at different scales. For this reason these applications are limited to few cases mainly focusing on worldwide known touristic sites. The capability to spread the development of web-based multimedia virtual museum based on geospatial data relies for the future being on the possibility to discover the needed geo-spatial data through a single point of access in an homogenous way. In this paper the proposed innovative approach may facilitate the access to open data in a homogeneous way by means of specific components (the brokers) performing interoperability actions required to interconnect heterogeneous data sources. In the specific case study here analysed it has been implemented an interface to migrate a geo-swat chart based on local and regional geographic information into an user friendly Google Earth©-based infrastructure, integrating ancient cadastres and modern cartography, accessible by professionals and tourists via web and also via portable devices like tables and smartphones. The general aim of this work on the case study on the Lake of Como (Tremezzina municipality), is to boost the integration of assessment methodologies with digital geo-based technologies of map correlation for the multimedia ecomuseum system accessible via web. The developed WebGIS system integrates multi-scale and multi-temporal maps with different information (cultural, historical, landscape levels) represented by thematic icons allowing to transfer the richness of the landscape value to both tourists and professionals.

Ligand-induced dynamical change of G-protein-coupled receptor revealed by neutron scattering

NASA Astrophysics Data System (ADS)

Shrestha, Utsab R.; Bhowmik, Debsindhu; Mamontov, Eugene; Chu, Xiang-Qiang

Light activation of the visual G-protein-coupled receptor rhodopsin leads to the significant change in protein conformation and structural fluctuations, which further activates the cognate G-protein (transducin) and initiates the biological signaling. In this work, we studied the rhodopsin activation dynamics using state-of-the-art neutron scattering technique. Our quasi-elastic neutron scattering (QENS) results revealed a broadly distributed relaxation rate of the hydrogen atom in rhodopsin on the picosecond to nanosecond timescale (beta-relaxation region), which is crucial for the protein function. Furthermore, the application of mode-coupling theory to the QENS analysis uncovers the subtle changes in rhodopsin dynamics due to the retinal cofactor. Comparing the dynamics of the ligand-free apoprotein, opsin versus the dark-state rhodopsin, removal of the retinal cofactor increases the relaxation time in the beta-relaxation region, which is due to the possible open conformation. Moreover, we utilized the concept of free-energy landscape to explain our results for the dark-state rhodopsin and opsin dynamics, which can be further applied to other GPCR systems to interpret various dynamic behaviors in ligand-bound and ligand-free protein.

Observations and assessment of forest carbon dynamics following disturbance in North America

Treesearch

S. J. Goetz; B. Bond-Lamberty; B. E. Law; J. A. Hicke; C. Huang; R. A. Houghton; S. McNulty; T. O’Halloran; M. Harmon; A. J. H. Meddens; E. M. Pfeifer; D. Mildrexler; E. S. Kasischke

2012-01-01

Disturbance processes of various types substantially modify ecosystem carbon dynamics both temporally and spatially, and constitute a fundamental part of larger landscape-level dynamics. Forests typically lose carbon for several years to several decades following severe disturbance, but our understanding of the duration and dynamics of post-disturbance forest carbon...

Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations.

PubMed

Harpole, Tyler J; Delemotte, Lucie

2018-04-01

The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscapes of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulations allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors. We focus on the various enhanced sampling techniques used to study these questions, how the conclusions come together to build a coherent picture, and the relationship between simulation outcomes and experimental observables. Copyright © 2017 Elsevier B.V. All rights reserved.

Glassy dynamics of landscape evolution

PubMed Central

Ortiz, Carlos P.; Jerolmack, Douglas J.

2018-01-01

Soil creeps imperceptibly downhill, but also fails catastrophically to create landslides. Despite the importance of these processes as hazards and in sculpting landscapes, there is no agreed-upon model that captures the full range of behavior. Here we examine the granular origins of hillslope soil transport by discrete element method simulations and reanalysis of measurements in natural landscapes. We find creep for slopes below a critical gradient, where average particle velocity (sediment flux) increases exponentially with friction coefficient (gradient). At critical gradient there is a continuous transition to a dense-granular flow rheology. Slow earthflows and landslides thus exhibit glassy dynamics characteristic of a wide range of disordered materials; they are described by a two-phase flux equation that emerges from grain-scale friction alone. This glassy model reproduces topographic profiles of natural hillslopes, showing its promise for predicting hillslope evolution over geologic timescales. PMID:29686102

Spatial and temporal dimensions of landscape fragmentation across the Brazilian Amazon.

PubMed

Rosa, Isabel M D; Gabriel, Cristina; Carreiras, Joāo M B

2017-01-01

The Brazilian Amazon in the past decades has been suffering severe landscape alteration, mainly due to anthropogenic activities, such as road building and land clearing for agriculture. Using a high-resolution time series of land cover maps (classified as mature forest, non-forest, secondary forest) spanning from 1984 through 2011, and four uncorrelated fragmentation metrics (edge density, clumpiness index, area-weighted mean patch size and shape index), we examined the temporal and spatial dynamics of forest fragmentation in three study areas across the Brazilian Amazon (Manaus, Santarém and Machadinho d'Oeste), inside and outside conservation units. Moreover, we compared the impacts on the landscape of: (1) different land uses (e.g. cattle ranching, crop production), (2) occupation processes (spontaneous vs. planned settlements) and (3) implementation of conservation units. By 2010/2011, municipalities located along the Arc of Deforestation had more than 55% of the remaining mature forest strictly confined to conservation units. Further, the planned settlement showed a higher rate of forest loss, a more persistent increase in deforested areas and a higher relative incidence of deforestation inside conservation units. Distinct agricultural activities did not lead to significantly different landscape structures; the accessibility of the municipality showed greater influence in the degree of degradation of the landscapes. Even with a high proportion of the landscapes covered by conservation units, which showed a strong inhibitory effect on forest fragmentation, we show that dynamic agriculturally driven economic activities, in municipalities with extensive road development, led to more regularly shaped, heavily fragmented landscapes, with higher densities of forest edge.

Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

PubMed Central

Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

2013-01-01

Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431

Modeling the influence of long term human-induced land use conversion on sediment fluxes and carbon dynamics at the catchment scale

NASA Astrophysics Data System (ADS)

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

2014-05-01

Over the past 20 years, there has been increasing evidence of the strong impact of human activities on the landscape, specifically on soil erosion due to the removal of natural vegetation cover for agricultural and urban purposes. The results question the widespread hypothesis of a steady state landscape since it appears that the balance between soil production and erosion may be broken altering the interactions between chemical, physical and biological processes in both soil and landscape system. Yet, the relationship between this accelerated erosion and the carbon dynamics at the landscape scale remains an important area of investigation. Recent attempts to combine geomorphic models, soil redistribution and carbon dynamic has proved themselves valuable in term of supporting the importance of lateral fluxes as a crucial control of carbon dynamic at the landscape scale. We use the SPEROS LT model, a modified version of SPEROS-C which includes dynamic land use and soil physical properties, to assess the impact of historical land use conversion on sediment and carbon fluxes in the Dijle catchment. This particular location has experienced a significant human impact since the Roman period, undergoing heavy deforestation and expansion of agricultural lands followed by a period of abandonment. The last 400 to 500 years saw a dramatic increase in the intensity of land use conversion associated to population growth leading to forest cleaning and urbanization. Our main objective is to validate the combined geomorphic and soil carbon turnover process descriptions of the model. Historical land use proportions are based on existing literature estimations and spatial assignation of the land conversion relies on simple allocation rules based on criteria such as slope or soil texture. Land use scenarios are constructed for the last 2000 years. We confront the model results with observations and perform a sensitivity analysis. The results indicate that the general trends in sediment production and deposition, as well as soil carbon storage are well predicted by the model. We discuss the key-parameters of the model and the implications of past erosion-deposition for the future C budget of the Dijle catchment.

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

EPA Science Inventory

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

Anomalous dynamics of interstitial dopants in soft crystals

PubMed Central

Tauber, Justin; Higler, Ruben; Sprakel, Joris

2016-01-01

The dynamics of interstitial dopants govern the properties of a wide variety of doped crystalline materials. To describe the hopping dynamics of such interstitial impurities, classical approaches often assume that dopant particles do not interact and travel through a static potential energy landscape. Here we show, using computer simulations, how these assumptions and the resulting predictions from classical Eyring-type theories break down in entropically stabilized body-centered cubic (BCC) crystals due to the thermal excitations of the crystalline matrix. Deviations are particularly severe close to melting where the lattice becomes weak and dopant dynamics exhibit strongly localized and heterogeneous dynamics. We attribute these anomalies to the failure of both assumptions underlying the classical description: (i) The instantaneous potential field experienced by dopants becomes largely disordered due to thermal fluctuations and (ii) elastic interactions cause strong dopant–dopant interactions even at low doping fractions. These results illustrate how describing nonclassical dopant dynamics requires taking the effective disordered potential energy landscape of strongly excited crystals and dopant–dopant interactions into account. PMID:27856751

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

NASA Astrophysics Data System (ADS)

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

2015-07-01

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

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

NASA Astrophysics Data System (ADS)

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.

Repeat Photography of Alaskan Glaciers and Landscapes as Both Art and as a Means of Communicating Climat Change

NASA Astrophysics Data System (ADS)

Molnia, B. F.

2013-12-01

For nearly 15 years, I have used repeat photography of Alaskan glaciers and landscapes to communicate to fellow scientists, policymakers, the media, and society that Alaskan glaciers and landscapes have been experiencing significant change in response to post-Little Ice Age climate change. I began this pursuit after being contacted by a U.S. Department of the Interior senior official who requested unequivocal and unambiguous documentation that climate change was real and underway. After considering several options as to how best respond to this challenge, I decided that if a picture is worth a thousand words, then a pair of photographs, both with the same field of view, spanning a century or more, and showing dramatic differences, would speak volumes to documenting that dynamic climate change is occurring over a very broad region of Alaska. To me, understating the obvious with photographic pairs was the best mechanism to present irrefutable, unambiguous, nonjudgmental, as well as unequivocal visual documentation that climate change was both underway and real. To date, more than 150 pairs that meet these criteria have been produced. What has surprised me most is that the many of the photographs contained in the pairs present beautiful images of stark, remote landscapes that convey the majestic nature of this dynamic region with its unique topography and landscapes. Typically, over periods of just several decades, the photographed landscapes change from black and white to blue and green. White ice becomes blue water and dark rock becomes lush vegetation. Repeat photography is a technique in which a historical photograph and a modern photograph, both having the same field of view, are compared and contrasted to quantitatively and qualitatively determine their similarities and differences. I have used this technique from both ground-based photo stations and airborne platforms at Alaskan locations in Kenai Fjords National Park, Glacier Bay National Park and Preserve, Wrangell-St. Elias National Park and Preserve, Denali National Park and Preserve, the northern and northwestern Prince William Sound area of the Chugach National Forest, and the Mendenhall Glacier area of the Tongass National Forest to document and determine the extent of changing glaciers and landscapes. The use of repeat photography to document temporal change is not new. It originated as a glacier-monitoring technique in the European Alps more than 150 years ago. What is unique in this Alaskan application of repeat photography is the systematic approach being used to obtain photographic documentation of glacier and landscape change for every glacier-hosting fiord in western southcentral Alaska, as well as at many Alaskan valley glacier sites. What is also unique is the development of an annotated website which presents many pairs of these photographs as well as ancillary materials to help convey the basics of Alaskan glaciers and climate change. The website, titled 'Glacier and Landscape Change in Response to Changing Climate', (http://www.usgs.gov/climate_landuse/glaciers/) was awarded the 2010 USGS Shoemaker External Communications Award.

Role of conformational dynamics in the evolution of novel enzyme function.

PubMed

Maria-Solano, Miguel A; Serrano-Hervás, Eila; Romero-Rivera, Adrian; Iglesias-Fernández, Javier; Osuna, Sílvia

2018-05-21

The free energy landscape concept that describes enzymes as an ensemble of differently populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme activity, enantioselectivity, and specificity. Mutations introduced in the enzyme sequence can alter the populations of the pre-existing conformational states, thus strongly modifying the enzyme ability to accommodate alternative substrates, revert its enantiopreferences, and even increase the activity for some residual promiscuous reactions. In this feature article, we present an overview of the current experimental and computational strategies to explore the conformational free energy landscape of enzymes. We provide a series of recent publications that highlight the key role of conformational dynamics for the enzyme evolution towards new functions and substrates, and provide some perspectives on how conformational dynamism should be considered in future computational enzyme design protocols.

Metapopulation modelling of riparian tree species persistence in river networks under climate change.

PubMed

Van Looy, Kris; Piffady, Jérémy

2017-11-01

Floodplain landscapes are highly fragmented by river regulation resulting in habitat degradation and flood regime perturbation, posing risks to population persistence. Climate change is expected to pose supplementary risks in this context of fragmented landscapes, and especially for river systems adaptation management programs are developed. The association of habitat quality and quantity with the landscape dynamics and resilience to human-induced disturbances is still poorly understood in the context of species survival and colonization processes, but essential to prioritize conservation and restoration actions. We present a modelling approach that elucidates network connectivity and landscape dynamics in spatial and temporal context to identify vital corridors and conservation priorities in the Loire river and its tributaries. Alteration of flooding and flow regimes is believed to be critical to population dynamics in river ecosystems. Still, little is known of critical levels of alteration both spatially and temporally. We applied metapopulation modelling approaches for a dispersal-limited tree species, white elm; and a recruitment-limited tree species, black poplar. In different model steps the connectivity and natural dynamics of the river landscape are confronted with physical alterations (dams/dykes) to species survival and then future scenarios for climatic changes and potential adaptation measures are entered in the model and translated in population persistence over the river basin. For the two tree species we highlighted crucial network zones in relation to habitat quality and connectivity. Where the human impact model already shows currently restricted metapopulation development, climate change is projected to aggravate this persistence perspective substantially. For both species a significant drawback to the basin population is observed, with 1/3 for elm and ¼ for poplar after 25 years already. But proposed adaptation measures prove effective to even bring metapopulation strength and persistence up to a level above the current level. Copyright © 2016 Elsevier Ltd. All rights reserved.

A method to efficiently apply a biogeochemical model to a landscape.

Treesearch

Robert E. Kennedy; David P. Turner; Warren B. Cohen; Michael Guzy

2006-01-01

Biogeochemical models offer an important means of understanding carbon dynamics, but the computational complexity of many models means that modeling all grid cells on a large landscape is computationally burdensome. Because most biogeochemical models ignore adjacency effects between cells, however, a more efficient approach is possible. Recognizing that spatial...

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

ERIC Educational Resources Information Center

Eanes, Francis R.

2016-01-01

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

A landscape analysis plan

Treesearch

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...

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

Treesearch

Colin J. Daniel; Leonardo Frid

2012-01-01

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

Restoring fire-prone Inland Pacific landscapes: seven core principles

Treesearch

Paul F. Hessburg; Derek J. Churchill; Andrew J. Larson; Ryan D. Haugo; Carol Miller; Thomas A. Spies; Malcolm P. North; Nicholas A. Povak; R. Travis Belote; Peter H. Singleton; William L. Gaines; Robert E. Keane; Gregory H. Aplet; Scott L. Stephens; Penelope Morgan; Peter A. Bisson; Bruce E. Rieman; R. Brion Salter; Gordon H. Reeves

2015-01-01

Context More than a century of forest and fire management of Inland Pacific landscapes has transformed their successional and disturbance dynamics. Regional connectivity of many terrestrial and aquatic habitats is fragmented, flows of some ecological and physical processes have been altered in space and time, and the frequency, size and intensity of many disturbances...

Disturbance regimes and the historical range and variation in terrestrial ecosystems

Treesearch

Robert Keane

2017-01-01

Disturbances are major drivers of ecological dynamics and it is the cumulative effects of disturbances across space and time that define a disturbance regime and dictate biodiversity by influencing the ranges of vegetation structures, compositions, and processes on landscapes. This range and variation of landscape characteristics under historical disturbance regimes...

Toward Gleasonian landscape ecology: From communities to species, from patches to pixels

Treesearch

Samuel A. Cushman; Jeffrey S. Evans; Kevin McGarigal; Joseph M. Kiesecker

2010-01-01

The fusion of individualistic community ecology with the Hutchinsonian niche concept enabled a broad integration of ecological theory, spanning all the way from the niche characteristics of individual species, to the composition, structure, and dynamics of ecological communities. Landscape ecology has been variously described as the study of the structure, function,...

Landscape-scale carbon sampling strategy-lessons learned. Chapter 17

Treesearch

John B. Bradford; Peter Weishampel; Marie-Louise Smith; Randall Kolka; David Y. Hollinger; Richard A. Birdsey; Scott Ollinger; Michael Ryan

2008-01-01

Previous chapters examined individual processes relevant to forest carbon cycling, and characterized measurement approaches for understanding those processes at landscape scales. In this final chapter, we address our overall approach to understanding forest carbon dynamics over large areas. Our objective is to identify any lessons that we learned in the course of...

Landscape-scale prediction of hemlock woolly adelgid, Adelges tsugae (Homoptera: Adelgidae), infestation in the Southern Appalachian Mountains

Treesearch

F.H. Koch; H.M. Cheshire; H.A. Devine

2006-01-01

After causing substantial mortality in the northeastern and mid-Atlantic United States, the hemlock woolly adelgid, Adelges tsugae Annand (Homoptera: Adelgidae), has recently invaded the southern Appalachian region. Although general estimates of regional spread exist, the landscape level dynamics of A. tsugae invasion are poorly...

Bioversity in Multi-Ownership Landscapes

Treesearch

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...

Public acceptance of disturbance-based forest management: factors influencing support

Treesearch

Christine S. Olsen; Angela L. Mallon; Bruce A. Shindler

2012-01-01

Growing emphasis on ecosystem and landscape-level forest management across North America has spurred an examination of alternative management strategies which focus on emulating dynamic natural disturbance processes, particularly those associated with forest fire regimes. This topic is the cornerstone of research in the Blue River Landscape Study (BRLS) on the...

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

USDA-ARS?s Scientific Manuscript database

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

Geographical patterns of onchocerciasis in southern Venezuela: relationships between environment and infection prevalence.

PubMed

Botto, C; Escalona, E; Vivas-Martinez, S; Behm, V; Delgado, L; Coronel, P

2005-03-01

Onchocerciasis is a chronic filarial infection transmitted by Simulium flies that has a focal geographical distribution in Latin America. The southern Venezuelan focus has a gradient of endemicity that includes the largest number of hyperendemic communities in the continent, many of them in remote forest and mountainous areas, where it is an important public health problem among the Yanomami indigenous population. The recent introduction of Geographical Information Systems (GIS) tools and a landscape epidemiology approach for study of vector borne diseases is helping to understand relationships between environment and transmission dynamics of onchocerciasis. Striking differences in the transmission dynamics of onchocerciasis between different river courses were detected. A significant relationship between onchocerciasis and temperature was also demonstrated. The geologic substrate, kind of landscape and vegetation seemed also to influence the transmission of onchocerciasis. In the Venezuelan Amazon, different kinds of landscapes associated with distinctive vector species, show different intensities of transmission of onchocerciasis. In this sense, landscape analysis aided by GIS, may prove to be a useful tool for better identification of the spatial distribution of onchocerciasis risk in the Orinoco basin.

Mapping landscape phenology preference of yellow-billed cuckoo with AVHRR data

USGS Publications Warehouse

Wallace, Cynthia S.A.; Villarreal, Miguel; van Riper, Charles

2013-01-01

We mapped habitat for threatened Yellow-billed Cuckoo (Coccycus americanus occidentalis) in the State of Arizona using the temporal greenness dynamics of the landscape, or the landscape phenology. Landscape phenometrics were derived from Advanced Very High Resolution Radiometer (AVHRR) Normalized Difference Vegetation Index (NDVI) data for 1998 and 1999 by using Fourier harmonic analysis to analyze the waveform of the annual NDVI profile at each pixel. We modeled the spatial distribution of Yellow-billed Cuckoo habitat by coupling the field data of Cuckoo presence or absence and point-based samples of riparian and cottonwood-willow vegetation types with satellite phenometrics for 1998. Models were validated using field and satellite data collected in 1999. The results indicate that Yellow-billed Cuckoo occupy locations within their preferred habitat that exhibit peak greenness after the start of the summer monsoon and are greener and more dynamic than “average” habitat. Identification of preferred phenotypes within recognized habitat areas can be used to refine habitat models, inform predictions of habitat response to climate change, and suggest adaptation strategies.

Controlling for Landform Age When Determining the Settlement History of the Kuril Islands

PubMed Central

MacInnes, Breanyn; Fitzhugh, Ben; Holman, Darryl

2014-01-01

Archaeological investigations of settlement patterns in dynamic landscapes can be strongly biased by the evolution of the Earth’s surface. The Kuril Island volcanic arc exemplifies such a dynamic landscape, where landscape-modifying geological forces were active during settlement, including sea-level changes, tectonic emergence, volcanic eruptive processes, coastal aggradation, and dune formation. With all these ongoing processes, in this paper we seek to understand how new landscape formation in the Holocene might bias archaeological interpretations of human settlement in the Kurils. Resolving this issue is fundamental to any interpretation of human settlement history derived from the distribution and age of archaeological sites from the region. On the basis of a comparison of landform ages and earliest archaeological occupation ages on those landforms, we conclude that landform creation did not significantly bias our aggregate archaeological evidence for earliest settlement. Some sections of the archipelago have larger proportions of landform creation dates closer to archaeological evidence of settlement and undoubtedly some archaeological sites have been lost to geomorphic processes. However, comparisons between regions reveal comparable archaeological establishment patterns irrespective of geomorphic antiquity. PMID:25684855

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

PubMed

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

2008-12-09

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

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

PubMed

Jacobson, Daniel; Stratt, Richard M

2014-05-07

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

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

NASA Astrophysics Data System (ADS)

Jacobson, Daniel; Stratt, Richard M.

2014-05-01

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

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

NASA Astrophysics Data System (ADS)

Larsen, L.; Watts, D.; Khurana, A.; Anderson, J. L.; Xu, C.; Merritts, D. J.

2015-12-01

The classic signal of self-organization in nature is pattern formation. However, the interactions and feedbacks that organize depositional landscapes do not always result in regular or fractal patterns. How might we detect their existence and effects in these "irregular" landscapes? Emergent landscapes such as newly forming deltaic marshes or some restoration sites provide opportunities to study the autogenic processes that organize landscapes and their physical signatures. Here we describe a quest to understand autogenic vs. allogenic controls on landscape evolution in Big Spring Run, PA, a landscape undergoing restoration from bare-soil conditions to a target wet meadow landscape. The contemporary motivation for asking questions about autogenic vs. allogenic controls is to evaluate how important initial conditions or environmental controls may be for the attainment of management objectives. However, these questions can also inform interpretation of the sedimentary record by enabling researchers to separate signals that may have arisen through self-organization processes from those resulting from environmental perturbations. Over three years at Big Spring Run, we mapped the dynamic evolution of floodplain vegetation communities and distributions of abiotic variables and topography. We used principal component analysis and transition probability analysis to detect associative interactions between vegetation and geomorphic variables and convergent cross-mapping on lidar data to detect causal interactions between biomass and topography. Exploratory statistics revealed that plant communities with distinct morphologies exerted control on landscape evolution through stress divergence (i.e., channel initiation) and promoting the accumulation of fine sediment in channels. Together, these communities participated in a negative feedback that maintains low energy and multiple channels. Because of the spatially explicit nature of this feedback, causal interactions could not be uncovered from convergent cross-mapping with this limited dataset, serving as a reminder that spatially explicit approaches for revealing causality are needed to reconstruct self-organizing mechanisms from data.

Landscape-scale forest disturbance regimes in southern Peruvian Amazonia.

PubMed

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.

Uncovering the mechanisms of Caenorhabditis elegans ageing from global quantification of the underlying landscape.

PubMed

Zhao, Lei; Wang, Jin

2016-11-01

Recent studies on Caenorhabditis elegans reveal that gene manipulations can extend its lifespan several fold. However, how the genes work together to determine longevity is still an open question. Here we construct a gene regulatory network for worm ageing and quantify its underlying potential and flux landscape. We found ageing and rejuvenation states can emerge as basins of attraction at certain gene expression levels. The system state can switch from one attractor to another driven by the intrinsic or external perturbations through genetics or the environment. Furthermore, we simulated gene silencing experiments and found that the silencing of longevity-promoting or lifespan-limiting genes leads to ageing or rejuvenation domination, respectively. This indicates that the difference in depths between ageing and the rejuvenation attractor is highly correlated with worm longevity. We further uncovered some key genes and regulations which have a strong influence on landscape basin stability. A dynamic landscape model is proposed to describe the whole process of ageing: the ageing attractor dominates when senescence progresses. We also uncovered the oscillation dynamics, and a similar behaviour was observed in the long-lived creature Turritopsis dohrnii Our landscape theory provides a global and physical approach to explore the underlying mechanisms of ageing. © 2016 The Author(s).

Colonizing Dynamic Alluvial and Coastal Landscapes in the Holocene

NASA Astrophysics Data System (ADS)

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.

[Application of land economic ecological niche in landscape pattern analysis at county level: A case study of Jinghe County in Xinjiang, China].

PubMed

Yu, Hai-yang; Zhang, Fei; Wang, Juan; Zhou, Mei

2015-12-01

The theory of land economic ecological niche was used to analyze the regional landscape pattern in this article, with an aim to provide a new method for the characterization and representation of landscape pattern. The Jinghe County region, which is ecologically fragile, was selected as an example for the study, and the Landsat images of 1990, 1998, 2011 and 2013 were selected as remote sensing data. The land economic ecological niche of land use types calculated by ecostate-ecorole theory, combined with landscape ecology theory, was discussed in application of land economic ecological niche in county landscape pattern analysis. The results showed that, during the study period, the correlations between land economic ecological niche of farmland, construction land, and grassland with the parameters, including landscape patch number (NP), aggregated index (AI), fragmented index (FN) and fractal dimension (FD), were significant. Regional landscape was driven by the changes of land economic ecological niche, and the trend of economic development could be represented by land economic ecological niche change in Jinghe County. Land economic ecological niche was closely related with the land use types which could yield direct economic benefits, which could well explain the landscape pattern characteristics in Jinghe County when combined with the landscape indices.

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

PubMed

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

2006-05-22

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

Artificial neural network in cosmic landscape

NASA Astrophysics Data System (ADS)

Liu, Junyu

2017-12-01

In this paper we propose that artificial neural network, the basis of machine learning, is useful to generate the inflationary landscape from a cosmological point of view. Traditional numerical simulations of a global cosmic landscape typically need an exponential complexity when the number of fields is large. However, a basic application of artificial neural network could solve the problem based on the universal approximation theorem of the multilayer perceptron. A toy model in inflation with multiple light fields is investigated numerically as an example of such an application.

Simulating forest fuel and fire risk dynamics across landscapes--LANDIS fuel module design

Treesearch

Hong S. He; Bo Z. Shang; Thomas R. Crow; Eric J. Gustafson; Stephen R. Shifley

2004-01-01

Understanding fuel dynamics over large spatial (103-106 ha) and temporal scales (101-103 years) is important in comprehensive wildfire management. We present a modeling approach to simulate fuel and fire risk dynamics as well as impacts of alternative fuel treatments. The...

Detecting trends in landscape pattern metrics over a 20-year period using a sampling-based monitoring programme

USGS Publications Warehouse

Griffith, J.A.; Stehman, S.V.; Sohl, Terry L.; Loveland, Thomas R.

2003-01-01

Temporal trends in landscape pattern metrics describing texture, patch shape and patch size were evaluated in the US Middle Atlantic Coastal Plain Ecoregion. The landscape pattern metrics were calculated for a sample of land use/cover data obtained for four points in time from 1973-1992. The multiple sampling dates permit evaluation of trend, whereas availability of only two sampling dates allows only evaluation of change. Observed statistically significant trends in the landscape pattern metrics demonstrated that the sampling-based monitoring protocol was able to detect a trend toward a more fine-grained landscape in this ecoregion. This sampling and analysis protocol is being extended spatially to the remaining 83 ecoregions in the US and temporally to the year 2000 to provide a national and regional synthesis of the temporal and spatial dynamics of landscape pattern covering the period 1973-2000.

Bioprecipitation: a feedback cycle linking earth history, ecosystem dynamics and land use through biological ice nucleators in the atmosphere.

PubMed

Morris, Cindy E; Conen, Franz; Alex Huffman, J; Phillips, Vaughan; Pöschl, Ulrich; Sands, David C

2014-02-01

Landscapes influence precipitation via the water vapor and energy fluxes they generate. Biologically active landscapes also generate aerosols containing microorganisms, some being capable of catalyzing ice formation and crystal growth in clouds at temperatures near 0 °C. The resulting precipitation is beneficial for the growth of plants and microorganisms. Mounting evidence from observations and numerical simulations support the plausibility of a bioprecipitation feedback cycle involving vegetated landscapes and the microorganisms they host. Furthermore, the evolutionary history of ice nucleation-active bacteria such as Pseudomonas syringae supports that they have been part of this process on geological time scales since the emergence of land plants. Elucidation of bioprecipitation feedbacks involving landscapes and their microflora could contribute to appraising the impact that modified landscapes have on regional weather and biodiversity, and to avoiding inadvertent, negative consequences of landscape management. © 2013 John Wiley & Sons Ltd.

How cells explore shape space: a quantitative statistical perspective of cellular morphogenesis.

PubMed

Yin, Zheng; Sailem, Heba; Sero, Julia; Ardy, Rico; Wong, Stephen T C; Bakal, Chris

2014-12-01

Through statistical analysis of datasets describing single cell shape following systematic gene depletion, we have found that the morphological landscapes explored by cells are composed of a small number of attractor states. We propose that the topology of these landscapes is in large part determined by cell-intrinsic factors, such as biophysical constraints on cytoskeletal organization, and reflects different stable signaling and/or transcriptional states. Cell-extrinsic factors act to determine how cells explore these landscapes, and the topology of the landscapes themselves. Informational stimuli primarily drive transitions between stable states by engaging signaling networks, while mechanical stimuli tune, or even radically alter, the topology of these landscapes. As environments fluctuate, the topology of morphological landscapes explored by cells dynamically adapts to these fluctuations. Finally we hypothesize how complex cellular and tissue morphologies can be generated from a limited number of simple cell shapes. © 2014 WILEY Periodicals, Inc.

Landscape scale prediction of earthquake-induced landsliding based on seismological and geomorphological parameters.

NASA Astrophysics Data System (ADS)

Marc, O.; Hovius, N.; Meunier, P.; Rault, C.

2017-12-01

In tectonically active areas, earthquakes are an important trigger of landslides with significant impact on hillslopes and river evolutions. However, detailed prediction of landslides locations and properties for a given earthquakes remain difficult.In contrast we propose, landscape scale, analytical prediction of bulk coseismic landsliding, that is total landslide area and volume (Marc et al., 2016a) as well as the regional area within which most landslide must distribute (Marc et al., 2017). The prediction is based on a limited number of seismological (seismic moment, source depth) and geomorphological (landscape steepness, threshold acceleration) parameters, and therefore could be implemented in landscape evolution model aiming at engaging with erosion dynamics at the scale of the seismic cycle. To assess the model we have compiled and normalized estimates of total landslide volume, total landslide area and regional area affected by landslides for 40, 17 and 83 earthquakes, respectively. We have found that low landscape steepness systematically leads to overprediction of the total area and volume of landslides. When this effect is accounted for, the model is able to predict within a factor of 2 the landslide areas and associated volumes for about 70% of the cases in our databases. The prediction of regional area affected do not require a calibration for the landscape steepness and gives a prediction within a factor of 2 for 60% of the database. For 7 out of 10 comprehensive inventories we show that our prediction compares well with the smallest region around the fault containing 95% of the total landslide area. This is a significant improvement on a previously published empirical expression based only on earthquake moment.Some of the outliers seems related to exceptional rock mass strength in the epicentral area or shaking duration and other seismic source complexities ignored by the model. Applications include prediction on the mass balance of earthquakes and this model predicts that only earthquakes generated on a narrow range of fault sizes may cause more erosion than uplift (Marc et al., 2016b), while very large earthquakes are expected to always build topography. The model could also be used to physically calibrate hillslope erosion or perturbations to river network within landscape evolution model.

Fluxes of carbon dioxide and methane from diverse aquatic environments in an agricultural landscape

NASA Astrophysics Data System (ADS)

Stanley, E. H.; Crawford, J. T.; Loken, L. C.; Casson, N. J.; Gubbins, N. J.; Oliver, S. K.

2014-12-01

The contribution of aquatic environments to landscape carbon cycling is particularly apparent in carbon- and water-rich regions. Such areas arguably represent an end member in terms of the relative significance of aquatic carbon cycling, while dry, carbon-poor zones are the likely opposing end member. Not surprisingly, most limnological attention has focused on these former regions, leaving open questions as to how aquatic systems in other locales influence larger-scale carbon dynamics. This includes human-dominated landscapes where agricultural and urban land uses can fundamentally alter carbon dynamics. Surveys of streams, ponds, and lakes in a southern Wisconsin landscape highlight three findings relevant to understanding the role of these aquatic systems in larger-scale carbon dynamics. First, streams and ponds had unexpectedly high summertime concentrations in and fluxes of CO2 and CH4. These values were approximately an order of magnitude greater than for less disturbed, forest and wetland-dominated landscapes in northern Wisconsin. Second, while mean C gas concentrations in lakes were lower than in streams and ponds, detailed spatial measurements demonstrate variability in surface water CO2 (43-1090 ppm pCO2) and CH4 (6-839 ppm pCH4) within a lake on a single day is similar to that observed among 25 streams included in our survey (260-6000 ppm pCO2; 50-600 ppm pCH4). This small-scale heterogeneity highlights a basic challenge for upscaling site-specific data collected at one or a few points to the whole lake and across lakes. Third, while agricultural and urban ecosystems are not necessarily carbon-rich environments, area-specific carbon storage in streams and ponds is substantial (up to 3000-5000 g C per m2). Further, carbon storage was strongly related to CH4 concentrations in streams, as C-rich sediments provided both an environment and substrate to fuel methanogenesis. The picture that emerges of C processing in aquatic environments throughout this human-dominated landscape is one of large C pools and fluxes and high spatial variability, suggesting that these land uses may be accelerating rates of aquatic C cycling and amplifying the role of these ecosystems in anthropogenic landscapes.

Quantifying the Energy Landscape Statistics in Proteins - a Relaxation Mode Analysis

NASA Astrophysics Data System (ADS)

Cai, Zhikun; Zhang, Yang

Energy landscape, the hypersurface in the configurational space, has been a useful concept in describing complex processes that occur over a very long time scale, such as the multistep slow relaxations of supercooled liquids and folding of polypeptide chains into structured proteins. Despite extensive simulation studies, its experimental characterization still remains a challenge. To address this challenge, we developed a relaxation mode analysis (RMA) for liquids under a framework analogous to the normal mode analysis for solids. Using RMA, important statistics of the activation barriers of the energy landscape becomes accessible from experimentally measurable two-point correlation functions, e.g. using quasi-elastic and inelastic scattering experiments. We observed a prominent coarsening effect of the energy landscape. The results were further confirmed by direct sampling of the energy landscape using a metadynamics-like adaptive autonomous basin climbing computation. We first demonstrate RMA in a supercooled liquid when dynamical cooperativity emerges in the landscape-influenced regime. Then we show this framework reveals encouraging energy landscape statistics when applied to proteins.

Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

NASA Astrophysics Data System (ADS)

VandeVondele, Joost; Rothlisberger, Ursula

2000-09-01

We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

Process-Driven Ecological Modeling for Landscape Change Analysis

NASA Astrophysics Data System (ADS)

Altman, S.; Reif, M. K.; Swannack, T. M.

2013-12-01

Landscape pattern is an important driver in ecosystem dynamics and can control system-level functions such as nutrient cycling, connectivity, biodiversity and carbon sequestration. However, the links between process, pattern and function remain ambiguous. Understanding the quantitative relationship between ecological processes and landscape pattern across temporal and spatial scales is vital for successful management and implementation of ecosystem-level projects. We used remote sensing imagery to develop critical landscape metrics to understand the factors influencing landscape change. Our study area, a coastal area in southwest Florida, is highly dynamic with critically eroding beaches and a range of natural and developed land cover types. Hurricanes in 2004 and 2005 caused a breach along the coast of North Captiva Island that filled in by 2010. We used a time series of light detection and ranging (lidar) elevation data and hyperspectral imagery from 2006 and 2010 to determine land cover changes. Landscape level metrics used included: Largest Patch Index, Class Area, Area-weighted mean area, Clumpiness, Area-weighted Contiguity Index, Number of Patches, Percent of landcover, Area-weighted Shape. Our results showed 1) 27% increase in sand/soil class as the channel repaired itself and shoreline was reestablished, 2) 40% decrease in the mudflat class area due to conversion to sand/soil and water, 3) 30% increase in non-wetland vegetation class as a result of new vegetation around the repaired channel, and 4) the water class only slightly increased though there was a marked increase in the patch size area. Thus, the smaller channels disappeared with the infilling of the channel, leaving much larger, less complex patches behind the breach. Our analysis demonstrated that quantification of landscape pattern is critical to linking patterns to ecological processes and understanding how both affect landscape change. Our proof of concept indicated that ecological processes can correlate to landscape pattern and that ecosystem function changes significantly as pattern changes. However, the number of links between landscape metrics and ecological processes are highly variable. Extensively studied processes such as biodiversity can be linked to numerous landscape metrics. In contrast, correlations between sediment cycling and landscape pattern have only been evaluated for a limited number of metrics. We are incorporating these data into a relational database linking landscape and ecological patterns, processes and metrics. The database will be used to parameterize site-specific landscape evolution models projecting how landscape pattern will change as a result of future ecosystem restoration projects. The model is a spatially-explicit, grid-based model that projects changes in community composition based on changes in soil elevations. To capture scalar differences in landscape change, local and regional landscape metrics are analyzed at each time step and correlated with ecological processes to determine how ecosystem function changes with scale over time.

The Potential and Flux Landscape Theory of Ecology

PubMed Central

Zhang, Kun; Wang, Erkang; Wang, Jin

2014-01-01

The species in ecosystems are mutually interacting and self sustainable stable for a certain period. Stability and dynamics are crucial for understanding the structure and the function of ecosystems. We developed a potential and flux landscape theory of ecosystems to address these issues. We show that the driving force of the ecological dynamics can be decomposed to the gradient of the potential landscape and the curl probability flux measuring the degree of the breaking down of the detailed balance (due to in or out flow of the energy to the ecosystems). We found that the underlying intrinsic potential landscape is a global Lyapunov function monotonically going down in time and the topology of the landscape provides a quantitative measure for the global stability of the ecosystems. We also quantified the intrinsic energy, the entropy, the free energy and constructed the non-equilibrium thermodynamics for the ecosystems. We studied several typical and important ecological systems: the predation, competition, mutualism and a realistic lynx-snowshoe hare model. Single attractor, multiple attractors and limit cycle attractors emerge from these studies. We studied the stability and robustness of the ecosystems against the perturbations in parameters and the environmental fluctuations. We also found that the kinetic paths between the multiple attractors do not follow the gradient paths of the underlying landscape and are irreversible because of the non-zero flux. This theory provides a novel way for exploring the global stability, function and the robustness of ecosystems. PMID:24497975

Nonequilibrium landscape theory of neural networks

PubMed Central

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

Measurement of energy landscape roughness of folded and unfolded proteins

PubMed Central

Milanesi, Lilia; Waltho, Jonathan P.; Hunter, Christopher A.; Shaw, Daniel J.; Beddard, Godfrey S.; Reid, Gavin D.; Dev, Sagarika; Volk, Martin

2012-01-01

The dynamics of protein conformational changes, from protein folding to smaller changes, such as those involved in ligand binding, are governed by the properties of the conformational energy landscape. Different techniques have been used to follow the motion of a protein over this landscape and thus quantify its properties. However, these techniques often are limited to short timescales and low-energy conformations. Here, we describe a general approach that overcomes these limitations. Starting from a nonnative conformation held by an aromatic disulfide bond, we use time-resolved spectroscopy to observe nonequilibrium backbone dynamics over nine orders of magnitude in time, from picoseconds to milliseconds, after photolysis of the disulfide bond. We find that the reencounter probability of residues that initially are in close contact decreases with time following an unusual power law that persists over the full time range and is independent of the primary sequence. Model simulations show that this power law arises from subdiffusional motion, indicating a wide distribution of trapping times in local minima of the energy landscape, and enable us to quantify the roughness of the energy landscape (4–5 kBT). Surprisingly, even under denaturing conditions, the energy landscape remains highly rugged with deep traps (>20 kBT) that result from multiple nonnative interactions and are sufficient for trapping on the millisecond timescale. Finally, we suggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of proteins with low contact order by enhancing contact formation between nearby residues. PMID:23150572

Land cover and landscape changes in Shaanxi Province during China's Grain for Green Program (2000-2010).

PubMed

Chen, Hai; Marter-Kenyon, Jessica; López-Carr, David; Liang, Xiao-ying

2015-10-01

This study examines landscape changes in the context of China's national Grain for Green (GFG) policy, one of the world's largest "payment for environmental/ecosystem services" (PES) programs. We explored landscape structures and dynamics between 2000 and 2010 in Shaanxi Province, the Chinese province with the greatest amount of cropland conversion and reforestation in recent decades. We used Landsat Thematic Mapper (TM)-derived data and landscape metrics for six land cover classes to determine (1) the major land cover changes during enforcement of the policy, (2) the spatial and temporal variations in these changes, and (3) the effects of land cover changes on landscape structure and dynamics. The results suggested that provincial-level land cover changes modestly reflected the goals of the GFG. Over the 10-year study period, the forest and grassland coverages expanded from 95,737.9 to 97,017.4 km(2) and from 37,235.9 to 40,613.1 km(2), respectively, while the cropland coverage decreased from 59,222.8 to 54,007.6 km(2). The conversion direction differed regionally: the targeted croplands in Shanbei, namely, types III and IV, were mainly transformed into grassland while those in Shannan were mainly transformed into forestland. Reforestation was associated with increased inter-landscape aggregation and connection. Despite this large-scale reforestation trend, we found notable and significant differences in the land cover changes at the subprovincial level.

[Applicability of traditional landscape metrics in evaluating urban heat island effect].

PubMed

Chen, Ai-Lian; Sun, Ran-Hao; Chen, Li-Ding

2012-08-01

By using 24 landscape metrics, this paper evaluated the urban heat island effect in parts of Beijing downtown area. QuickBird (QB) images were used to extract the landscape type information, and the thermal bands from Landsat Enhanced Thematic Mapper Plus (ETM+) images were used to extract the land surface temperature (LST) in four seasons of the same year. The 24 landscape pattern metrics were calculated at landscape and class levels in a fixed window with 120 mx 120 m in size, with the applicability of these traditional landscape metrics in evaluating the urban heat island effect examined. Among the 24 landscape metrics, only the percentage composition of landscape (PLAND), patch density (PD), largest patch index (LPI), coefficient of Euclidean nearest-neighbor distance variance (ENN_CV), and landscape division index (DIVISION) at landscape level were significantly correlated with the LST in March, May, and November, and the PLAND, LPI, DIVISION, percentage of like adjacencies, and interspersion and juxtaposition index at class level showed significant correlations with the LST in March, May, July, and December, especially in July. Some metrics such as PD, edge density, clumpiness index, patch cohesion index, effective mesh size, splitting index, aggregation index, and normalized landscape shape index showed varying correlations with the LST at different class levels. The traditional landscape metrics could not be appropriate in evaluating the effects of river on LST, while some of the metrics could be useful in characterizing urban LST and analyzing the urban heat island effect, but screening and examining should be made on the metrics.

Integrating landscape system and meta-ecosystem frameworks to advance the understanding of ecosystem function in heterogeneous landscapes: An analysis on the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan.

PubMed

Yang, Haile; Chen, Jiakuan

2018-01-01

The successful integration of ecosystem ecology with landscape ecology would be conducive to understanding how landscapes function. There have been several attempts at this, with two main approaches: (1) an ecosystem-based approach, such as the meta-ecosystem framework and (2) a landscape-based approach, such as the landscape system framework. These two frameworks are currently disconnected. To integrate these two frameworks, we introduce a protocol, and then demonstrate application of the protocol using a case study. The protocol includes four steps: 1) delineating landscape systems; 2) classifying landscape systems; 3) adjusting landscape systems to meta-ecosystems and 4) integrating landscape system and meta-ecosystem frameworks through meta-ecosystems. The case study is the analyzing of the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan using this protocol. The application of this protocol revealed that one could follow this protocol to construct a meta-ecosystem and analyze it using the integrative framework of landscape system and meta-ecosystem frameworks. That is, one could (1) appropriately describe and analyze the spatial heterogeneity of the meta-ecosystem; (2) understand the emergent properties arising from spatial coupling of local ecosystems in the meta-ecosystem. In conclusion, this protocol is a useful approach for integrating the meta-ecosystem framework and the landscape system framework, which advances the describing and analyzing of the spatial heterogeneity and ecosystem function of interconnected ecosystems.

Integrating landscape system and meta-ecosystem frameworks to advance the understanding of ecosystem function in heterogeneous landscapes: An analysis on the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan

PubMed Central

Chen, Jiakuan

2018-01-01

The successful integration of ecosystem ecology with landscape ecology would be conducive to understanding how landscapes function. There have been several attempts at this, with two main approaches: (1) an ecosystem-based approach, such as the meta-ecosystem framework and (2) a landscape-based approach, such as the landscape system framework. These two frameworks are currently disconnected. To integrate these two frameworks, we introduce a protocol, and then demonstrate application of the protocol using a case study. The protocol includes four steps: 1) delineating landscape systems; 2) classifying landscape systems; 3) adjusting landscape systems to meta-ecosystems and 4) integrating landscape system and meta-ecosystem frameworks through meta-ecosystems. The case study is the analyzing of the carbon fluxes in the Northern Highlands Lake District (NHLD) of Wisconsin and Michigan using this protocol. The application of this protocol revealed that one could follow this protocol to construct a meta-ecosystem and analyze it using the integrative framework of landscape system and meta-ecosystem frameworks. That is, one could (1) appropriately describe and analyze the spatial heterogeneity of the meta-ecosystem; (2) understand the emergent properties arising from spatial coupling of local ecosystems in the meta-ecosystem. In conclusion, this protocol is a useful approach for integrating the meta-ecosystem framework and the landscape system framework, which advances the describing and analyzing of the spatial heterogeneity and ecosystem function of interconnected ecosystems. PMID:29415066

How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics?

NASA Astrophysics Data System (ADS)

Maisuradze, Gia G.; Liwo, Adam; Scheraga, Harold A.

2009-06-01

The molecular dynamics trajectories of protein folding or unfolding, generated with the coarse-grained united-residue force field for the B domain of staphylococcal protein A, were analyzed by principal component analysis (PCA). The folding or unfolding process was examined by using free-energy landscapes (FELs) in PC space. By introducing a novel multidimensional FEL, it was shown that the low-dimensional FELs are not always sufficient for the description of folding or unfolding processes. Similarities between the topographies of FELs along low- and high-indexed principal components were observed.

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

PubMed

Wardrop, Richard M; Berkowitz, Lee R

2017-02-01

The promotion of change and growth within medical education is oftentimes the result of a complex mix of societal, cultural and economic forces. Graduate medical education in internal medicine is not immune to these forces. Several entities and organizations can be identified as having a major influence on internal medicine training and graduate medical education as a whole. We have reviewed how this is effectively accomplished through these entities and organizations. The result is a constantly changing and dynamic landscape for internal medicine training. Copyright © 2017 Southern Society for Clinical Investigation. Published by Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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.

Navigating the patent landscapes for nanotechnology: English gardens or tangled grounds?

PubMed

Sylvester, Douglas J; Bowman, Diana M

2011-01-01

The patent landscape, like a garden, can tell you much about its designers and users: their motivations, biases, and general interests. While both patent landscapes and gardens may appear to the casual observer as refined and ordered, an in-depth exploration of the terrain is likely to reveal unforeseen challenges including, for example, alien species, thickets, and trolls. As this chapter illustrates, patent landscapes are dynamic and have been forced to continually evolve in response to technological innovation. While emerging technologies such as biotechnology and information communication technology have challenged the traditional patent landscape, the overarching framework and design have largely remained intact. But will this always be the case? The aim of this chapter is to highlight how nanotechnology is challenging the existing structures and underlying foundation of the patent landscape and the implications thereof for the technology, industry, and public more generally. The chapter concludes by asking the question whether the current patent landscape will be able to withstand the ubiquitous nature of the technology, or whether nanotechnology will be a catalyst for governments and policy makers for overhauling the current landscape design.

INTRODUCTION TO THE LANDSCAPE ANALYSIS TOOLS ARCVIEW EXTENSION

EPA Science Inventory

Geographic Information Systems (GIS) have become a powerful tool in the field of landscape ecology. A common application of GIS is the generation of landscape indicators, which are quantitative measurements of the status or potential health of an area (e.g. watershed or county). ...

ANALYTICAL TOOLS INTERFACE FOR LANDSCAPE ASSESSMENTS (ATTILA) ARCVIEW EXTENTION

EPA Science Inventory

Geographic Information Systems (GIS) have become a powerful tool in the field of landscape ecology. A common application of GIS is the generation of landscape metrics, which are quantitative measurements of the status or potential health of an area (e.g. ecological region, waters...

AnnAGNPS Model Application for the Future Midwest Landscape Study

EPA Science Inventory

The Future Midwest Landscape (FML) project is part of the US Environmental Protection Agency (EPA)’s new Ecosystem Services Research Program, undertaken to examine the variety of ways in which landscapes that include crop lands, conservation areas, wetlands, lakes, and streams af...

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

PubMed

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

2007-03-20

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

Screening variability and change of soil moisture under wide-ranging climate conditions: Snow dynamics effects.

PubMed

Verrot, Lucile; Destouni, Georgia

2015-01-01

Soil moisture influences and is influenced by water, climate, and ecosystem conditions, affecting associated ecosystem services in the landscape. This paper couples snow storage-melting dynamics with an analytical modeling approach to screening basin-scale, long-term soil moisture variability and change in a changing climate. This coupling enables assessment of both spatial differences and temporal changes across a wide range of hydro-climatic conditions. Model application is exemplified for two major Swedish hydrological basins, Norrström and Piteälven. These are located along a steep temperature gradient and have experienced different hydro-climatic changes over the time period of study, 1950-2009. Spatially, average intra-annual variability of soil moisture differs considerably between the basins due to their temperature-related differences in snow dynamics. With regard to temporal change, the long-term average state and intra-annual variability of soil moisture have not changed much, while inter-annual variability has changed considerably in response to hydro-climatic changes experienced so far in each basin.

On the theory of drainage area for regular and non-regular points.

PubMed

Bonetti, S; Bragg, A D; Porporato, A

2018-03-01

The drainage area is an important, non-local property of a landscape, which controls surface and subsurface hydrological fluxes. Its role in numerous ecohydrological and geomorphological applications has given rise to several numerical methods for its computation. However, its theoretical analysis has lagged behind. Only recently, an analytical definition for the specific catchment area was proposed (Gallant & Hutchinson. 2011 Water Resour. Res. 47 , W05535. (doi:10.1029/2009WR008540)), with the derivation of a differential equation whose validity is limited to regular points of the watershed. Here, we show that such a differential equation can be derived from a continuity equation (Chen et al. 2014 Geomorphology 219 , 68-86. (doi:10.1016/j.geomorph.2014.04.037)) and extend the theory to critical and singular points both by applying Gauss's theorem and by means of a dynamical systems approach to define basins of attraction of local surface minima. Simple analytical examples as well as applications to more complex topographic surfaces are examined. The theoretical description of topographic features and properties, such as the drainage area, channel lines and watershed divides, can be broadly adopted to develop and test the numerical algorithms currently used in digital terrain analysis for the computation of the drainage area, as well as for the theoretical analysis of landscape evolution and stability.

On the theory of drainage area for regular and non-regular points

NASA Astrophysics Data System (ADS)

Bonetti, S.; Bragg, A. D.; Porporato, A.

2018-03-01

The drainage area is an important, non-local property of a landscape, which controls surface and subsurface hydrological fluxes. Its role in numerous ecohydrological and geomorphological applications has given rise to several numerical methods for its computation. However, its theoretical analysis has lagged behind. Only recently, an analytical definition for the specific catchment area was proposed (Gallant & Hutchinson. 2011 Water Resour. Res. 47, W05535. (doi:10.1029/2009WR008540)), with the derivation of a differential equation whose validity is limited to regular points of the watershed. Here, we show that such a differential equation can be derived from a continuity equation (Chen et al. 2014 Geomorphology 219, 68-86. (doi:10.1016/j.geomorph.2014.04.037)) and extend the theory to critical and singular points both by applying Gauss's theorem and by means of a dynamical systems approach to define basins of attraction of local surface minima. Simple analytical examples as well as applications to more complex topographic surfaces are examined. The theoretical description of topographic features and properties, such as the drainage area, channel lines and watershed divides, can be broadly adopted to develop and test the numerical algorithms currently used in digital terrain analysis for the computation of the drainage area, as well as for the theoretical analysis of landscape evolution and stability.

Spatial Correlation Of Streamflows: An Analytical Approach

NASA Astrophysics Data System (ADS)

Betterle, A.; Schirmer, M.; Botter, G.

2016-12-01

The interwoven space and time variability of climate and landscape properties results in complex and non-linear hydrological response of streamflow dynamics. Understanding how meteorologic and morphological characteristics of catchments affect similarity/dissimilarity of streamflow timeseries at their outlets represents a scientific challenge with application in water resources management, ecological studies and regionalization approaches aimed to predict streamflows in ungauged areas. In this study, we establish an analytical approach to estimate the spatial correlation of daily streamflows in two arbitrary locations within a given hydrologic district or river basin at seasonal and annual time scales. The method is based on a stochastic description of the coupled streamflow dynamics at the outlet of two catchments. The framework aims to express the correlation of daily streamflows at two locations along a river network as a function of a limited number of physical parameters characterizing the main underlying hydrological drivers, that include climate conditions, precipitation regime and catchment drainage rates. The proposed method portrays how heterogeneity of climate and landscape features affect the spatial variability of flow regimes along river systems. In particular, we show that frequency and intensity of synchronous effective rainfall events in the relevant contributing catchments are the main driver of the spatial correlation of daily discharge, whereas only pronounced differences in the drainage rate of the two basins bear a significant effect on the streamflow correlation. The topological arrangement of the two outlets also influences the underlying streamflow correlation, as we show that nested catchments tend to maximize the spatial correlation of flow regimes. The application of the method to a set of catchments in the South-Eastern US suggests the potential of the proposed tool for the characterization of spatial connections of flow regimes in the absence of discharge measurements.

Geographic information analysis: An ecological approach for the management of wildlife on the forest landscape

NASA Technical Reports Server (NTRS)

Ripple, William J.

1995-01-01

This document is a summary of the project funded by NAGw-1460 as part of the Earth Observation Commericalization/Applications Program (EOCAP) directed by NASA's Earth Science and Applications Division. The goal was to work with several agencies to focus on forest structure and landscape characterizations for wildlife habitat applications. New analysis techniques were used in remote sensing and landscape ecology with geographic information systems (GIS). The development of GIS and the emergence of the discipline of landscape ecology provided us with an opportunity to study forest and wildlife habitat resources from a new perspective. New techniques were developed to measure forest structure across scales from the canopy to the regional level. This paper describes the project team, technical advances, and technology adoption process that was used. Reprints of related refereed journal articles are in the Appendix.

An individual-based process model to simulate landscape-scale forest ecosystem dynamics

Treesearch

Rupert Seidl; Werner Rammer; Robert M. Scheller; Thomas Spies

2012-01-01

Forest ecosystem dynamics emerges from nonlinear interactions between adaptive biotic agents (i.e., individual trees) and their relationship with a spatially and temporally heterogeneous abiotic environment. Understanding and predicting the dynamics resulting from these complex interactions is crucial for the sustainable stewardship of ecosystems, particularly in the...

Comprehensive Representation of Hydrologic and Geomorphic Process Coupling in Numerical Models: Internal Dynamics and Basin Evolution

NASA Astrophysics Data System (ADS)

Istanbulluoglu, E.; Vivoni, E. R.; Ivanov, V. Y.; Bras, R. L.

2005-12-01

Landscape morphology has an important control on the spatial and temporal organization of basin hydrologic response to climate forcing, affecting soil moisture redistribution as well as vegetation function. On the other hand, erosion, driven by hydrology and modulated by vegetation, produces landforms over geologic time scales that reflect characteristic signatures of the dominant land forming process. Responding to extreme climate events or anthropogenic disturbances of the land surface, infrequent but rapid forms of erosion (e.g., arroyo development, landsliding) can modify topography such that basin hydrology is significantly influenced. Despite significant advances in both hydrologic and geomorphic modeling over the past two decades, the dynamic interactions between basin hydrology, geomorphology and terrestrial ecology are not adequately captured in current model frameworks. In order to investigate hydrologic-geomorphic-ecologic interactions at the basin scale we present initial efforts in integrating the CHILD landscape evolution model (Tucker et al. 2001) with the tRIBS hydrology model (Ivanov et al. 2004), both developed in a common software environment. In this talk, we present preliminary results of the numerical modeling of the coupled evolution of basin hydro-geomorphic response and resulting landscape morphology in two sets of examples. First, we discuss the long-term evolution of both the hydrologic response and the resulting basin morphology from an initially uplifted plateau. In the second set of modeling experiments, we implement changes in climate and land-use to an existing topography and compare basin hydrologic response to the model results when landscape form is fixed (e.g. no coupling between hydrology and geomorphology). Model results stress the importance of internal basin dynamics, including runoff generation mechanisms and hydrologic states, in shaping hydrologic response as well as the importance of employing comprehensive conceptualizations of hydrology in modeling landscape evolution.

Testing Lithospheric versus Deep-Mantle Dynamics on Post-100 Ma Evolution of Western U.S. using Landscape Evolution Modeling

NASA Astrophysics Data System (ADS)

Chang, C.; Liu, L.

2017-12-01

Driving mechanisms of the topographic evolution of central-western North America from the Cretaceous Western Interior Seaway (WIS) to its present-day high elevation remain ellusive. Quantifying the effects of lithospheric deformation versus deep-mantle induced topography on the landscape evolution of the region is a key to better constraining the history of North American tectonics and mantle dynamics. One way to tackle this problem is through running landscape evolution simulation coupled with uplift histories characteristic to these tectonic processes. We then use available surface observations, e.g., sedimentation records, land erosion, and drainage evolution, to infer the likely lithospheric and mantle processes that formed the WIS, the subsequent Laramide orogeny, and the present-day high topography of central-western North America. In practice, we use BadLands to simulate the evolution of surface process. To validate a given uplift history, we quantitatively compare model predictions with onshore and offshore stratigraphy data from the literature. Furthermore, critical forcings of landscape evolution, such as climate, lithology and sea level, will also be examined to better attest the effects of different uplift scenarios. Preliminary results demonstrate that only with geographically migratory subsidence, as predicted by an inverse mantle convection model, can we re-produce large scale tilted strata and shifting sediment deposition observed in the WIS basins. Ongoing work will also look into styles of Cenozoic uplift events that ended the WIS and produced the landscape features today. Eventually, we hope to place new constraints on the evolution and properties of lithospheric and deep-mantle dynamics of North American and to locate the best-fit scenario of its coresponding surface evolution since 100 Ma.

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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

2010-11-28

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

Glassy dynamics of landscape evolution.

PubMed

Ferdowsi, Behrooz; Ortiz, Carlos P; Jerolmack, Douglas J

2018-05-08

Soil creeps imperceptibly downhill, but also fails catastrophically to create landslides. Despite the importance of these processes as hazards and in sculpting landscapes, there is no agreed-upon model that captures the full range of behavior. Here we examine the granular origins of hillslope soil transport by discrete element method simulations and reanalysis of measurements in natural landscapes. We find creep for slopes below a critical gradient, where average particle velocity (sediment flux) increases exponentially with friction coefficient (gradient). At critical gradient there is a continuous transition to a dense-granular flow rheology. Slow earthflows and landslides thus exhibit glassy dynamics characteristic of a wide range of disordered materials; they are described by a two-phase flux equation that emerges from grain-scale friction alone. This glassy model reproduces topographic profiles of natural hillslopes, showing its promise for predicting hillslope evolution over geologic timescales. Copyright © 2018 the Author(s). Published by PNAS.

Role of small oligomers on the amyloidogenic aggregation free-energy landscape.

PubMed

He, Xianglan; Giurleo, Jason T; Talaga, David S

2010-01-08

We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of beta-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.

How main-chains of proteins explore the free-energy landscape in native states.

PubMed

Senet, Patrick; Maisuradze, Gia G; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A

2008-12-16

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an alpha/beta protein (crambin) and a beta-sheet polypeptide (BS2) in their "native" states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive C(alpha) atoms, increases as a power law of time, t(alpha), with an exponent alpha between 0.08 and 0.39 (alpha = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles.

How main-chains of proteins explore the free-energy landscape in native states

PubMed Central

Senet, Patrick; Maisuradze, Gia G.; Foulie, Colette; Delarue, Patrice; Scheraga, Harold A.

2008-01-01

Understanding how a single native protein diffuses on its free-energy landscape is essential to understand protein kinetics and function. The dynamics of a protein is complex, with multiple relaxation times reflecting a hierarchical free-energy landscape. Using all-atom molecular dynamics simulations of an α/β protein (crambin) and a β-sheet polypeptide (BS2) in their “native” states, we demonstrate that the mean-square displacement of dihedral angles, defined by 4 successive Cα atoms, increases as a power law of time, tα, with an exponent α between 0.08 and 0.39 (α = 1 corresponds to Brownian diffusion), at 300 K. Residues with low exponents are located mainly in well-defined secondary elements and adopt 1 conformational substate. Residues with high exponents are found in loops/turns and chain ends and exist in multiple conformational substates, i.e., they move on multiple-minima free-energy profiles. PMID:19073932

Inflation with a graceful exit in a random landscape

NASA Astrophysics Data System (ADS)

Pedro, F. G.; Westphal, A.

2017-03-01

We develop a stochastic description of small-field inflationary histories with a graceful exit in a random potential whose Hessian is a Gaussian random matrix as a model of the unstructured part of the string landscape. The dynamical evolution in such a random potential from a small-field inflation region towards a viable late-time de Sitter (dS) minimum maps to the dynamics of Dyson Brownian motion describing the relaxation of non-equilibrium eigenvalue spectra in random matrix theory. We analytically compute the relaxation probability in a saddle point approximation of the partition function of the eigenvalue distribution of the Wigner ensemble describing the mass matrices of the critical points. When applied to small-field inflation in the landscape, this leads to an exponentially strong bias against small-field ranges and an upper bound N ≪ 10 on the number of light fields N participating during inflation from the non-observation of negative spatial curvature.

Postfire encroachment of Fabiana imbricata is real? Assessing changes of shrubland occupation during 40 years in NW Patagonia steppe

NASA Astrophysics Data System (ADS)

Lasaponara, Rosa; Oddi, Facundo; Ghermandi, Luciana

2014-05-01

Landscapes are dynamic in space and time, being spatio-temporal processes of particular interest for landscape ecology. In particular, grasslands can change their structure through the expansion of shrubs in the landscape matrix. Shrub encroachment affect biodiversity as well as forage availability that is the key component of the productive use of rangelands. However, despite its recognition as a global problem, knowledge on the rates, dynamics and encroachment patterns is even scarce. For example, although it is generally accepted that fire control shrub encroachment, certain shrubby species could be favored by the occurrence of fire. In northwestern Patagonian steppe, Fabiana imbricata form large monospecific shrublands that are part of the landscape mosaic and its dynamics of regeneration is strongly related to fire. This long-lived shrub (≡ 150 years) is a typical seeder that is killed by fire and recruits seedlings almost exclusively in post-fire, establishing even-age patches. Our objective was to determine whether F. imbricata shrublands have expanded during the last 40 years in a landscape fire prone. The study area corresponds to San Ramon ranch (22,000 ha) located in northwestern Patagonia steppe, Argentina (latitude -41° 04'; longitude -70° 51'). Two distribution maps of the species were made that corresponds to the study area in 1968 and 2011. The 1968 map was elaborated from the digitalization of aerial photographs (1:45000) while the 2011 map was produced with very high resolution satellite images, current aerial photographs and GPS field data. Both maps were loaded into a GIS environment, in which landscape metrics at patch and class level were determined and then compared. From remote sensing and dendroecological techniques, we know that the study area was almost entirely affected by fires during the study period. Therefore, the comparison of both maps allows us to know post-fire changes in the shrublands spatial configuration at the landscape scale and to infer the fire effect on these changes. Our results show that during the studied period F. imbricata shrublands has expanded over the grassland. Nowadays, the species occupies 20% more area than in 1968 and this area, is divided into a smaller number of patches that are closer to each other. The observed change in the shrublands spatial pattern is evidence of a post-fire shrub encroachment. These results contribute to the understanding of the role of fire in vegetation dynamics in fire prone ecosystems

The Landlab v1.0 OverlandFlow component: a Python tool for computing shallow-water flow across watersheds

NASA Astrophysics Data System (ADS)

Adams, Jordan M.; Gasparini, Nicole M.; Hobley, Daniel E. J.; Tucker, Gregory E.; Hutton, Eric W. H.; Nudurupati, Sai S.; Istanbulluoglu, Erkan

2017-04-01

Representation of flowing water in landscape evolution models (LEMs) is often simplified compared to hydrodynamic models, as LEMs make assumptions reducing physical complexity in favor of computational efficiency. The Landlab modeling framework can be used to bridge the divide between complex runoff models and more traditional LEMs, creating a new type of framework not commonly used in the geomorphology or hydrology communities. Landlab is a Python-language library that includes tools and process components that can be used to create models of Earth-surface dynamics over a range of temporal and spatial scales. The Landlab OverlandFlow component is based on a simplified inertial approximation of the shallow water equations, following the solution of de Almeida et al.(2012). This explicit two-dimensional hydrodynamic algorithm simulates a flood wave across a model domain, where water discharge and flow depth are calculated at all locations within a structured (raster) grid. Here, we illustrate how the OverlandFlow component contained within Landlab can be applied as a simplified event-based runoff model and how to couple the runoff model with an incision model operating on decadal timescales. Examples of flow routing on both real and synthetic landscapes are shown. Hydrographs from a single storm at multiple locations in the Spring Creek watershed, Colorado, USA, are illustrated, along with a map of shear stress applied on the land surface by flowing water. The OverlandFlow component can also be coupled with the Landlab DetachmentLtdErosion component to illustrate how the non-steady flow routing regime impacts incision across a watershed. The hydrograph and incision results are compared to simulations driven by steady-state runoff. Results from the coupled runoff and incision model indicate that runoff dynamics can impact landscape relief and channel concavity, suggesting that, on landscape evolution timescales, the OverlandFlow model may lead to differences in simulated topography in comparison with traditional methods. The exploratory test cases described within demonstrate how the OverlandFlow component can be used in both hydrologic and geomorphic applications.

Revegetation for aesthetics

Treesearch

Bernard M. Slick

1980-01-01

Surface mining is changing the landscape character of forests in the East. Aesthetic visual aspects of the landscape are considered in the analysis, planning, and design of revegetation strategies. Application of landscape architectural design techniques in the revegetation of surface-mined lands, as well as knowledge of biological characteristics, will enhance the...

Application of Partial Least Square (PLS) Regression to Determine Landscape-Scale Aquatic Resources Vulnerability in the Ozark Mountains

EPA Science Inventory

Partial least squares (PLS) analysis offers a number of advantages over the more traditionally used regression analyses applied in landscape ecology, particularly for determining the associations among multiple constituents of surface water and landscape configuration. Common dat...

Integrating ecophysiology and forest landscape models to improve projections of drought effects under climate change

Treesearch

Eric J. Gustafson; Arjan M.G. De Bruijn; Robert E. Pangle; Jean-Marc Limousin; Nate G. McDowell; William T. Pockman; Brian R. Sturtevant; Jordan D. Muss; Mark E. Kubiske

2015-01-01

Fundamental drivers of ecosystem processes such as temperature and precipitation are rapidly changing and creating novel environmental conditions. Forest landscape models (FLM) are used by managers and policy-makers to make projections of future ecosystem dynamics under alternative management or policy options, but the links between the fundamental drivers and...

Land Breeze and Thermals: A Scale Threshold to Distinguish Their Effects

Treesearch

Yongqiang Liu

2005-01-01

Land breeze is a type of mesoscale circulation developed due to thermal forcing over a heterogeneous landscape. It can contribute to atmospheric dynamic and hydrologic processes through affecting heat and water fluxes on the land-atmosphere interface and generating shallow convective precipitation. If the scale of the landscape heterogeneity is smaller than a certain...

Landslides through the fish-eye lens.

Treesearch

Sally Duncan

1998-01-01

This issue examines research the Station has been conducting on how catastrophic disturbances affect fish habitat. Whereas our February issue discussed the physical dynamics of a flood on a landscape, here we expand to major disturbances in general while narrowing in a fish habitat still at a landscape scale.Our work in this area is unfolding new knowledge...

Modeling landscape net ecosystem productivity (LandNEP) under alternative management regimes

Treesearch

Eugenie S. Euskirchen; Jiquan Chen; Harbin Li; Eric J. Gustafson; Thomas R. Crow

2002-01-01

Forests have been considered as a major carbon sink within the global carbon budget. However, a fragmented forest landscape varies significantly in its composition and age structure, and the amount of carbon sequestered at this level remains generally unknown to the scientific community. More precisely, the temporal dynamics and spatial distribution of net ecosystem...

Chapter 6 - Developing the LANDFIRE Vegetation and Biophysical Settings Map Unit Classifications for the LANDFIRE Prototype Project

Treesearch

Jennifer L. Long; Melanie Miller; James P. Menakis; Robert E. Keane

2006-01-01

The Landscape Fire and Resource Management Planning Tools Prototype Project, or LANDFIRE Prototype Project, required a system for classifying vegetation composition, biophysical settings, and vegetation structure to facilitate the mapping of vegetation and wildland fuel characteristics and the simulation of vegetation dynamics using landscape modeling. We developed...

Influence of climate and environment on post-fire recovery of mountain big sagebrush

Treesearch

Zachary J. Nelson; Peter J. Weisberg; Stanley G. Kitchen

2014-01-01

In arid and semi-arid landscapes around the world, wildfire plays a key role in maintaining species diversity. Dominant plant associations may depend upon particular fire regime characteristics for their persistence. Mountain shrub communities in high-elevation landscapes of the Intermountain West, USA, are strongly influenced by the post-fire recovery dynamics of the...

Approaches to incorporating climate change effects in state and transition simulation models of vegetation

Treesearch

Becky K. Kerns; Miles A. Hemstrom; David Conklin; Gabriel I. Yospin; Bart Johnson; Dominique Bachelet; Scott Bridgham

2012-01-01

Understanding landscape vegetation dynamics often involves the use of scientifically-based modeling tools that are capable of testing alternative management scenarios given complex ecological, management, and social conditions. State-and-transition simulation model (STSM) frameworks and software such as PATH and VDDT are commonly used tools that simulate how landscapes...

Landscape host abundance and configuration regulate periodic outbreak behavior in spruce budworm Choristoneura fumiferana

Treesearch

Louis-Etienne Robert; Brian R. Sturtevant; Barry J. Cooke; Patrick M. A. James; Marie-Josée Fortin; Philip A. Townsend; Peter T. Wolter; Daniel Kneeshaw

2018-01-01

Landscape-level forest management has long been hypothesized to affect forest insect outbreak dynamics, but empirical evidence remains elusive. We hypothesized that the combination of increased hardwood relative to host tree species, prevalence of younger forests, and fragmentation of those forests due to forest harvesting legacies would reduce outbreak intensity,...