Separating direct and indirect effects of global change: a population dynamic modeling approach using readily available field data.

PubMed

Farrer, Emily C; Ashton, Isabel W; Knape, Jonas; Suding, Katharine N

2014-04-01

Two sources of complexity make predicting plant community response to global change particularly challenging. First, realistic global change scenarios involve multiple drivers of environmental change that can interact with one another to produce non-additive effects. Second, in addition to these direct effects, global change drivers can indirectly affect plants by modifying species interactions. In order to tackle both of these challenges, we propose a novel population modeling approach, requiring only measurements of abundance and climate over time. To demonstrate the applicability of this approach, we model population dynamics of eight abundant plant species in a multifactorial global change experiment in alpine tundra where we manipulated nitrogen, precipitation, and temperature over 7 years. We test whether indirect and interactive effects are important to population dynamics and whether explicitly incorporating species interactions can change predictions when models are forecast under future climate change scenarios. For three of the eight species, population dynamics were best explained by direct effect models, for one species neither direct nor indirect effects were important, and for the other four species indirect effects mattered. Overall, global change had negative effects on species population growth, although species responded to different global change drivers, and single-factor effects were slightly more common than interactive direct effects. When the fitted population dynamic models were extrapolated under changing climatic conditions to the end of the century, forecasts of community dynamics and diversity loss were largely similar using direct effect models that do not explicitly incorporate species interactions or best-fit models; however, inclusion of species interactions was important in refining the predictions for two of the species. The modeling approach proposed here is a powerful way of analyzing readily available datasets which should be added to our toolbox to tease apart complex drivers of global change. © 2013 John Wiley & Sons Ltd.

Connecting micro dynamics and population distributions in system dynamics models

PubMed Central

Rahmandad, Hazhir; Chen, Hsin-Jen; Xue, Hong; Wang, Youfa

2014-01-01

Researchers use system dynamics models to capture the mean behavior of groups of indistinguishable population elements (e.g., people) aggregated in stock variables. Yet, many modeling problems require capturing the heterogeneity across elements with respect to some attribute(s) (e.g., body weight). This paper presents a new method to connect the micro-level dynamics associated with elements in a population with the macro-level population distribution along an attribute of interest without the need to explicitly model every element. We apply the proposed method to model the distribution of Body Mass Index and its changes over time in a sample population of American women obtained from the U.S. National Health and Nutrition Examination Survey. Comparing the results with those obtained from an individual-based model that captures the same phenomena shows that our proposed method delivers accurate results with less computation than the individual-based model. PMID:25620842

Temperature-driven regime shifts in the dynamics of size-structured populations.

PubMed

Ohlberger, Jan; Edeline, Eric; Vøllestad, Leif Asbjørn; Stenseth, Nils C; Claessen, David

2011-02-01

Global warming impacts virtually all biota and ecosystems. Many of these impacts are mediated through direct effects of temperature on individual vital rates. Yet how this translates from the individual to the population level is still poorly understood, hampering the assessment of global warming impacts on population structure and dynamics. Here, we study the effects of temperature on intraspecific competition and cannibalism and the population dynamical consequences in a size-structured fish population. We use a physiologically structured consumer-resource model in which we explicitly model the temperature dependencies of the consumer vital rates and the resource population growth rate. Our model predicts that increased temperature decreases resource density despite higher resource growth rates, reflecting stronger intraspecific competition among consumers. At a critical temperature, the consumer population dynamics destabilize and shift from a stable equilibrium to competition-driven generation cycles that are dominated by recruits. As a consequence, maximum age decreases and the proportion of younger and smaller-sized fish increases. These model predictions support the hypothesis of decreasing mean body sizes due to increased temperatures. We conclude that in size-structured fish populations, global warming may increase competition, favor smaller size classes, and induce regime shifts that destabilize population and community dynamics.

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations

PubMed Central

Henriksen, Niel M.; Roe, Daniel R.; Cheatham, Thomas E.

2013-01-01

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 microseconds of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations. PMID:23477537

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations.

PubMed

Henriksen, Niel M; Roe, Daniel R; Cheatham, Thomas E

2013-04-18

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example, by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 μs of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations.

IMPORTANCE OF MOVEMENT VARIES IN STATIC AND DYNAMIC LANDSCAPES

EPA Science Inventory

The relative sensitivity of spatially explicit population models (SEPMs) to movement parameters is a topic of ongoing debate among theoretical ecologists. In this study, we add additional realism to this debate by examining a SEPM's sensitivity to dispersal ability in static vs....

A bi-population based scheme for an explicit exploration/exploitation trade-off in dynamic environments

NASA Astrophysics Data System (ADS)

Ben-Romdhane, Hajer; Krichen, Saoussen; Alba, Enrique

2017-05-01

Optimisation in changing environments is a challenging research topic since many real-world problems are inherently dynamic. Inspired by the natural evolution process, evolutionary algorithms (EAs) are among the most successful and promising approaches that have addressed dynamic optimisation problems. However, managing the exploration/exploitation trade-off in EAs is still a prevalent issue, and this is due to the difficulties associated with the control and measurement of such a behaviour. The proposal of this paper is to achieve a balance between exploration and exploitation in an explicit manner. The idea is to use two equally sized populations: the first one performs exploration while the second one is responsible for exploitation. These tasks are alternated from one generation to the next one in a regular pattern, so as to obtain a balanced search engine. Besides, we reinforce the ability of our algorithm to quickly adapt after cnhanges by means of a memory of past solutions. Such a combination aims to restrain the premature convergence, to broaden the search area, and to speed up the optimisation. We show through computational experiments, and based on a series of dynamic problems and many performance measures, that our approach improves the performance of EAs and outperforms competing algorithms.

Influence of local demography on asymptotic and transient dynamics of a yellow-bellied marmot metapopulation.

PubMed

Ozgul, Arpat; Oli, Madan K; Armitage, Kenneth B; Blumstein, Daniel T; Van Vuren, Dirk H

2009-04-01

Despite recent advances in biodemography and metapopulation ecology, we still have limited understanding of how local demographic parameters influence short- and long-term metapopulation dynamics. We used long-term data from 17 local populations, along with the recently developed methods of matrix metapopulation modeling and transient sensitivity analysis, to investigate the influence of local demography on long-term (asymptotic) versus short-term (transient) dynamics of a yellow-bellied marmot metapopulation in Colorado. Both long- and short-term dynamics depended primarily on a few colony sites and were highly sensitive to changes in demography at these sites, particularly in survival of reproductive adult females. Interestingly, the relative importance of sites differed between long- and short-term dynamics; the spatial structure and local population sizes, while insignificant for asymptotic dynamics, were influential on transient dynamics. However, considering the spatial structure was uninformative about the relative influence of local demography on metapopulation dynamics. The vital rates that were the most influential on local dynamics were also the most influential on both long- and short-term metapopulation dynamics. Our results show that an explicit consideration of local demography is essential for a complete understanding of the dynamics and persistence of spatially structured populations.

The spatial dynamics of ecosystem engineers.

PubMed

Franco, Caroline; Fontanari, José F

2017-10-01

The changes on abiotic features of ecosystems have rarely been taken into account by population dynamics models, which typically focus on trophic and competitive interactions between species. However, understanding the population dynamics of organisms that must modify their habitats in order to survive, the so-called ecosystem engineers, requires the explicit incorporation of abiotic interactions in the models. Here we study a model of ecosystem engineers that is discrete both in space and time, and where the engineers and their habitats are arranged in patches fixed to the sites of regular lattices. The growth of the engineer population is modeled by Ricker equation with a density-dependent carrying capacity that is given by the number of modified habitats. A diffusive dispersal stage ensures that a fraction of the engineers move from their birth patches to neighboring patches. We find that dispersal influences the metapopulation dynamics only in the case that the local or single-patch dynamics exhibit chaotic behavior. In that case, it can suppress the chaotic behavior and avoid extinctions in the regime of large intrinsic growth rate of the population. Copyright © 2017 Elsevier Inc. All rights reserved.

CDMetaPOP: An individual-based, eco-evolutionary model for spatially explicit simulation of landscape demogenetics

USGS Publications Warehouse

Landguth, Erin L; Bearlin, Andrew; Day, Casey; Dunham, Jason B.

2016-01-01

1. Combining landscape demographic and genetics models offers powerful methods for addressing questions for eco-evolutionary applications.2. Using two illustrative examples, we present Cost–Distance Meta-POPulation, a program to simulate changes in neutral and/or selection-driven genotypes through time as a function of individual-based movement, complex spatial population dynamics, and multiple and changing landscape drivers.3. Cost–Distance Meta-POPulation provides a novel tool for questions in landscape genetics by incorporating population viability analysis, while linking directly to conservation applications.

Modelling hen harrier dynamics to inform human-wildlife conflict resolution: a spatially-realistic, individual-based approach.

PubMed

Heinonen, Johannes P M; Palmer, Stephen C F; Redpath, Steve M; Travis, Justin M J

2014-01-01

Individual-based models have gained popularity in ecology, and enable simultaneous incorporation of spatial explicitness and population dynamic processes to understand spatio-temporal patterns of populations. We introduce an individual-based model for understanding and predicting spatial hen harrier (Circus cyaneus) population dynamics in Great Britain. The model uses a landscape with habitat, prey and game management indices. The hen harrier population was initialised according to empirical census estimates for 1988/89 and simulated until 2030, and predictions for 1998, 2004 and 2010 were compared to empirical census estimates for respective years. The model produced a good qualitative match to overall trends between 1989 and 2010. Parameter explorations revealed relatively high elasticity in particular to demographic parameters such as juvenile male mortality. This highlights the need for robust parameter estimates from empirical research. There are clearly challenges for replication of real-world population trends, but this model provides a useful tool for increasing understanding of drivers of hen harrier dynamics and focusing research efforts in order to inform conflict management decisions.

Modelling Hen Harrier Dynamics to Inform Human-Wildlife Conflict Resolution: A Spatially-Realistic, Individual-Based Approach

PubMed Central

Heinonen, Johannes P. M.; Palmer, Stephen C. F.; Redpath, Steve M.; Travis, Justin M. J.

2014-01-01

Individual-based models have gained popularity in ecology, and enable simultaneous incorporation of spatial explicitness and population dynamic processes to understand spatio-temporal patterns of populations. We introduce an individual-based model for understanding and predicting spatial hen harrier (Circus cyaneus) population dynamics in Great Britain. The model uses a landscape with habitat, prey and game management indices. The hen harrier population was initialised according to empirical census estimates for 1988/89 and simulated until 2030, and predictions for 1998, 2004 and 2010 were compared to empirical census estimates for respective years. The model produced a good qualitative match to overall trends between 1989 and 2010. Parameter explorations revealed relatively high elasticity in particular to demographic parameters such as juvenile male mortality. This highlights the need for robust parameter estimates from empirical research. There are clearly challenges for replication of real-world population trends, but this model provides a useful tool for increasing understanding of drivers of hen harrier dynamics and focusing research efforts in order to inform conflict management decisions. PMID:25405860

AN INDIVIDUAL-BASED SIMULATION MODEL FOR MOTTLED SCULPIN (COTTUS BAIRDI) IN A SOUTHERN APPALACHIAN STREAM

EPA Science Inventory

We describe and analyze a spatially explicit, individual-based model for the local population dynamics of mottled sculpin (Cottus bairdi). The model simulated daily growth, mortality, movement and spawning of individuals within a reach of stream. Juvenile and adult growth was bas...

Predicting extinction risks under climate change: coupling stochastic population models with dynamic bioclimatic habitat models.

PubMed

Keith, David A; Akçakaya, H Resit; Thuiller, Wilfried; Midgley, Guy F; Pearson, Richard G; Phillips, Steven J; Regan, Helen M; Araújo, Miguel B; Rebelo, Tony G

2008-10-23

Species responses to climate change may be influenced by changes in available habitat, as well as population processes, species interactions and interactions between demographic and landscape dynamics. Current methods for assessing these responses fail to provide an integrated view of these influences because they deal with habitat change or population dynamics, but rarely both. In this study, we linked a time series of habitat suitability models with spatially explicit stochastic population models to explore factors that influence the viability of plant species populations under stable and changing climate scenarios in South African fynbos, a global biodiversity hot spot. Results indicate that complex interactions between life history, disturbance regime and distribution pattern mediate species extinction risks under climate change. Our novel mechanistic approach allows more complete and direct appraisal of future biotic responses than do static bioclimatic habitat modelling approaches, and will ultimately support development of more effective conservation strategies to mitigate biodiversity losses due to climate change.

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

Kostova, T; Carlsen, T

We present a study, based on simulations with SERDYCA, a spatially-explicit individual based model of rodent dynamics, on the connection between population persistence and the presence of inhomogeneities in the habitat. We are specifically interested on the effect that inhomogeneities that do not fragment the environment, have on population persistence. Our results suggest that a certain percentage of inhomogeneities can increase the average time to extinction of the population. Inhomogeneities decrease the population density and can increase the ratio of juveniles in the population thus providing a better chance for the population to restore itself after a severe period withmore » critically low population density. We call this the ''inhomogeneity localization effect''.« less

Opinion Dynamics with Disagreement and Modulated Information

NASA Astrophysics Data System (ADS)

Sîrbu, Alina; Loreto, Vittorio; Servedio, Vito D. P.; Tria, Francesca

2013-04-01

Opinion dynamics concerns social processes through which populations or groups of individuals agree or disagree on specific issues. As such, modelling opinion dynamics represents an important research area that has been progressively acquiring relevance in many different domains. Existing approaches have mostly represented opinions through discrete binary or continuous variables by exploring a whole panoply of cases: e.g. independence, noise, external effects, multiple issues. In most of these cases the crucial ingredient is an attractive dynamics through which similar or similar enough agents get closer. Only rarely the possibility of explicit disagreement has been taken into account (i.e., the possibility for a repulsive interaction among individuals' opinions), and mostly for discrete or 1-dimensional opinions, through the introduction of additional model parameters. Here we introduce a new model of opinion formation, which focuses on the interplay between the possibility of explicit disagreement, modulated in a self-consistent way by the existing opinions' overlaps between the interacting individuals, and the effect of external information on the system. Opinions are modelled as a vector of continuous variables related to multiple possible choices for an issue. Information can be modulated to account for promoting multiple possible choices. Numerical results show that extreme information results in segregation and has a limited effect on the population, while milder messages have better success and a cohesion effect. Additionally, the initial condition plays an important role, with the population forming one or multiple clusters based on the initial average similarity between individuals, with a transition point depending on the number of opinion choices.

Isogeometric Collocation for Elastostatics and Explicit Dynamics

DTIC Science & Technology

2012-01-25

ICES REPORT 12-07 January 2012 Isogeometric collocation for elastostatics and explicit dynamics by F. Auricchio, L. Beirao da Veiga , T.J.R. Hughes, A...Auricchio, L. Beirao da Veiga , T.J.R. Hughes, A. Reali, G. Sangalli, Isogeometric collocation for elastostatics and explicit dynamics, ICES REPORT 12-07...Isogeometric collocation for elastostatics and explicit dynamics F. Auricchio a,c, L. Beirão da Veiga b,c, T.J.R. Hughes d, A. Reali a,c,∗, G

Improving predictions of large scale soil carbon dynamics: Integration of fine-scale hydrological and biogeochemical processes, scaling, and benchmarking

NASA Astrophysics Data System (ADS)

Riley, W. J.; Dwivedi, D.; Ghimire, B.; Hoffman, F. M.; Pau, G. S. H.; Randerson, J. T.; Shen, C.; Tang, J.; Zhu, Q.

2015-12-01

Numerical model representations of decadal- to centennial-scale soil-carbon dynamics are a dominant cause of uncertainty in climate change predictions. Recent attempts by some Earth System Model (ESM) teams to integrate previously unrepresented soil processes (e.g., explicit microbial processes, abiotic interactions with mineral surfaces, vertical transport), poor performance of many ESM land models against large-scale and experimental manipulation observations, and complexities associated with spatial heterogeneity highlight the nascent nature of our community's ability to accurately predict future soil carbon dynamics. I will present recent work from our group to develop a modeling framework to integrate pore-, column-, watershed-, and global-scale soil process representations into an ESM (ACME), and apply the International Land Model Benchmarking (ILAMB) package for evaluation. At the column scale and across a wide range of sites, observed depth-resolved carbon stocks and their 14C derived turnover times can be explained by a model with explicit representation of two microbial populations, a simple representation of mineralogy, and vertical transport. Integrating soil and plant dynamics requires a 'process-scaling' approach, since all aspects of the multi-nutrient system cannot be explicitly resolved at ESM scales. I will show that one approach, the Equilibrium Chemistry Approximation, improves predictions of forest nitrogen and phosphorus experimental manipulations and leads to very different global soil carbon predictions. Translating model representations from the site- to ESM-scale requires a spatial scaling approach that either explicitly resolves the relevant processes, or more practically, accounts for fine-resolution dynamics at coarser scales. To that end, I will present recent watershed-scale modeling work that applies reduced order model methods to accurately scale fine-resolution soil carbon dynamics to coarse-resolution simulations. Finally, we contend that creating believable soil carbon predictions requires a robust, transparent, and community-available benchmarking framework. I will present an ILAMB evaluation of several of the above-mentioned approaches in ACME, and attempt to motivate community adoption of this evaluation approach.

Explicit symplectic algorithms based on generating functions for charged particle dynamics.

PubMed

Zhang, Ruili; Qin, Hong; Tang, Yifa; Liu, Jian; He, Yang; Xiao, Jianyuan

2016-07-01

Dynamics of a charged particle in the canonical coordinates is a Hamiltonian system, and the well-known symplectic algorithm has been regarded as the de facto method for numerical integration of Hamiltonian systems due to its long-term accuracy and fidelity. For long-term simulations with high efficiency, explicit symplectic algorithms are desirable. However, it is generally believed that explicit symplectic algorithms are only available for sum-separable Hamiltonians, and this restriction limits the application of explicit symplectic algorithms to charged particle dynamics. To overcome this difficulty, we combine the familiar sum-split method and a generating function method to construct second- and third-order explicit symplectic algorithms for dynamics of charged particle. The generating function method is designed to generate explicit symplectic algorithms for product-separable Hamiltonian with form of H(x,p)=p_{i}f(x) or H(x,p)=x_{i}g(p). Applied to the simulations of charged particle dynamics, the explicit symplectic algorithms based on generating functions demonstrate superiorities in conservation and efficiency.

Explicit symplectic algorithms based on generating functions for charged particle dynamics

NASA Astrophysics Data System (ADS)

Zhang, Ruili; Qin, Hong; Tang, Yifa; Liu, Jian; He, Yang; Xiao, Jianyuan

2016-07-01

Dynamics of a charged particle in the canonical coordinates is a Hamiltonian system, and the well-known symplectic algorithm has been regarded as the de facto method for numerical integration of Hamiltonian systems due to its long-term accuracy and fidelity. For long-term simulations with high efficiency, explicit symplectic algorithms are desirable. However, it is generally believed that explicit symplectic algorithms are only available for sum-separable Hamiltonians, and this restriction limits the application of explicit symplectic algorithms to charged particle dynamics. To overcome this difficulty, we combine the familiar sum-split method and a generating function method to construct second- and third-order explicit symplectic algorithms for dynamics of charged particle. The generating function method is designed to generate explicit symplectic algorithms for product-separable Hamiltonian with form of H (x ,p ) =pif (x ) or H (x ,p ) =xig (p ) . Applied to the simulations of charged particle dynamics, the explicit symplectic algorithms based on generating functions demonstrate superiorities in conservation and efficiency.

Entrainment and Control of Bacterial Populations: An in Silico Study over a Spatially Extended Agent Based Model.

PubMed

Mina, Petros; Tsaneva-Atanasova, Krasimira; Bernardo, Mario di

2016-07-15

We extend a spatially explicit agent based model (ABM) developed previously to investigate entrainment and control of the emergent behavior of a population of synchronized oscillating cells in a microfluidic chamber. Unlike most of the work in models of control of cellular systems which focus on temporal changes, we model individual cells with spatial dependencies which may contribute to certain behavioral responses. We use the model to investigate the response of both open loop and closed loop strategies, such as proportional control (P-control), proportional-integral control (PI-control) and proportional-integral-derivative control (PID-control), to heterogeinities and growth in the cell population, variations of the control parameters and spatial effects such as diffusion in the spatially explicit setting of a microfluidic chamber setup. We show that, as expected from the theory of phase locking in dynamical systems, open loop control can only entrain the cell population in a subset of forcing periods, with a wide variety of dynamical behaviors obtained outside these regions of entrainment. Closed-loop control is shown instead to guarantee entrainment in a much wider region of control parameter space although presenting limitations when the population size increases over a certain threshold. In silico tracking experiments are also performed to validate the ability of classical control approaches to achieve other reference behaviors such as a desired constant output or a linearly varying one. All simulations are carried out in BSim, an advanced agent-based simulator of microbial population which is here extended ad hoc to include the effects of control strategies acting onto the population.

Human population dynamics in Europe over the Last Glacial Maximum.

PubMed

Tallavaara, Miikka; Luoto, Miska; Korhonen, Natalia; Järvinen, Heikki; Seppä, Heikki

2015-07-07

The severe cooling and the expansion of the ice sheets during the Last Glacial Maximum (LGM), 27,000-19,000 y ago (27-19 ky ago) had a major impact on plant and animal populations, including humans. Changes in human population size and range have affected our genetic evolution, and recent modeling efforts have reaffirmed the importance of population dynamics in cultural and linguistic evolution, as well. However, in the absence of historical records, estimating past population levels has remained difficult. Here we show that it is possible to model spatially explicit human population dynamics from the pre-LGM at 30 ky ago through the LGM to the Late Glacial in Europe by using climate envelope modeling tools and modern ethnographic datasets to construct a population calibration model. The simulated range and size of the human population correspond significantly with spatiotemporal patterns in the archaeological data, suggesting that climate was a major driver of population dynamics 30-13 ky ago. The simulated population size declined from about 330,000 people at 30 ky ago to a minimum of 130,000 people at 23 ky ago. The Late Glacial population growth was fastest during Greenland interstadial 1, and by 13 ky ago, there were almost 410,000 people in Europe. Even during the coldest part of the LGM, the climatically suitable area for human habitation remained unfragmented and covered 36% of Europe.

Human population dynamics in Europe over the Last Glacial Maximum

PubMed Central

Tallavaara, Miikka; Luoto, Miska; Korhonen, Natalia; Järvinen, Heikki; Seppä, Heikki

2015-01-01

The severe cooling and the expansion of the ice sheets during the Last Glacial Maximum (LGM), 27,000–19,000 y ago (27–19 ky ago) had a major impact on plant and animal populations, including humans. Changes in human population size and range have affected our genetic evolution, and recent modeling efforts have reaffirmed the importance of population dynamics in cultural and linguistic evolution, as well. However, in the absence of historical records, estimating past population levels has remained difficult. Here we show that it is possible to model spatially explicit human population dynamics from the pre-LGM at 30 ky ago through the LGM to the Late Glacial in Europe by using climate envelope modeling tools and modern ethnographic datasets to construct a population calibration model. The simulated range and size of the human population correspond significantly with spatiotemporal patterns in the archaeological data, suggesting that climate was a major driver of population dynamics 30–13 ky ago. The simulated population size declined from about 330,000 people at 30 ky ago to a minimum of 130,000 people at 23 ky ago. The Late Glacial population growth was fastest during Greenland interstadial 1, and by 13 ky ago, there were almost 410,000 people in Europe. Even during the coldest part of the LGM, the climatically suitable area for human habitation remained unfragmented and covered 36% of Europe. PMID:26100880

Outbreak and Extinction Dynamics in a Stochastic Ebola Model

NASA Astrophysics Data System (ADS)

Nieddu, Garrett; Bianco, Simone; Billings, Lora; Forgoston, Eric; Kaufman, James

A zoonotic disease is a disease that can be passed between animals and humans. In many cases zoonotic diseases can persist in the animal population even if there are no infections in the human population. In this case we call the infected animal population the reservoir for the disease. Ebola virus disease (EVD) and SARS are both notable examples of such diseases. There is little work devoted to understanding stochastic disease extinction and reintroduction in the presence of a reservoir. Here we build a stochastic model for EVD and explicitly consider the presence of an animal reservoir. Using a master equation approach and a WKB ansatz, we determine the associated Hamiltonian of the system. Hamilton's equations are then used to numerically compute the 12-dimensional optimal path to extinction, which is then used to estimate mean extinction times. We also numerically investigate the behavior of the model for dynamic population size. Our results provide an improved understanding of outbreak and extinction dynamics in diseases like EVD.

Social Organization, Population, and Land Use*

PubMed Central

Axinn, William G.; Ghimire, Dirgha J.

2011-01-01

We present a new approach to the investigation of human influences on environmental change that explicitly adds consideration of social organization. This approach identifies social organization as an influence on the environment that is independent of population size, affluence, and technology. The framework we present also identifies population events, such as births, that are likely to influence environmental outcomes beyond the consequences of population size. The theoretical framework we construct explains that explicit attention to social organization is necessary for micro-level investigation of the population-environment relationship because social organization influences both. We use newly available longitudinal, multilevel, mixed-method measures of local land use changes, local population dynamics, and social organization from the Nepalese Himalayas to provide empirical tests of this new framework. These tests reveal that measures of change in social organization are strongly associated with measures of change in land use, and that the association is independent of common measures of population size, affluence, and technology. Also, local birth events shape local land use changes and key proximate determinants of land use change. Together the empirical results demonstrate key new scientific opportunities arising from the approach we present. PMID:21876607

Extinction rates in tumour public goods games.

PubMed

Gerlee, Philip; Altrock, Philipp M

2017-09-01

Cancer evolution and progression are shaped by cellular interactions and Darwinian selection. Evolutionary game theory incorporates both of these principles, and has been proposed as a framework to understand tumour cell population dynamics. A cornerstone of evolutionary dynamics is the replicator equation, which describes changes in the relative abundance of different cell types, and is able to predict evolutionary equilibria. Typically, the replicator equation focuses on differences in relative fitness. We here show that this framework might not be sufficient under all circumstances, as it neglects important aspects of population growth. Standard replicator dynamics might miss critical differences in the time it takes to reach an equilibrium, as this time also depends on cellular turnover in growing but bounded populations. As the system reaches a stable manifold, the time to reach equilibrium depends on cellular death and birth rates. These rates shape the time scales, in particular, in coevolutionary dynamics of growth factor producers and free-riders. Replicator dynamics might be an appropriate framework only when birth and death rates are of similar magnitude. Otherwise, population growth effects cannot be neglected when predicting the time to reach an equilibrium, and cell-type-specific rates have to be accounted for explicitly. © 2017 The Authors.

Using stylized agent-based models for population-environment research: A case study from the Galápagos Islands

PubMed Central

Miller, Brian W.; Breckheimer, Ian; McCleary, Amy L.; Guzmán-Ramirez, Liza; Caplow, Susan C.; Jones-Smith, Jessica C.; Walsh, Stephen J.

2010-01-01

Agent Based Models (ABMs) are powerful tools for population-environment research but are subject to trade-offs between model complexity and abstraction. This study strikes a compromise between abstract and highly specified ABMs by designing a spatially explicit, stylized ABM and using it to explore policy scenarios in a setting that is facing substantial conservation and development challenges. Specifically, we present an ABM that reflects key Land Use / Land Cover (LULC) dynamics and livelihood decisions on Isabela Island in the Galápagos Archipelago of Ecuador. We implement the model using the NetLogo software platform, a free program that requires relatively little programming experience. The landscape is composed of a satellite-derived distribution of a problematic invasive species (common guava) and a stylized representation of the Galápagos National Park, the community of Puerto Villamil, the agricultural zone, and the marine area. The agent module is based on publicly available data and household interviews, and represents the primary livelihoods of the population in the Galápagos Islands – tourism, fisheries, and agriculture. We use the model to enact hypothetical agricultural subsidy scenarios aimed at controlling invasive guava and assess the resulting population and land cover dynamics. Findings suggest that spatially explicit, stylized ABMs have considerable utility, particularly during preliminary stages of research, as platforms for (1) sharpening conceptualizations of population-environment systems, (2) testing alternative scenarios, and (3) uncovering critical data gaps. PMID:20539752

Individual-Based Spatially-Explicit Model of an Herbivore and Its Resource: The Effect of Habitat Reduction and Fragmentation

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

Kostova, T; Carlsen, T; Kercher, J

2002-06-17

We present an individual-based, spatially-explicit model of the dynamics of a small mammal and its resource. The life histories of each individual animal are modeled separately. The individuals can have the status of residents or wanderers and belong to behaviorally differing groups of juveniles or adults and males or females. Their territory defending and monogamous behavior is taken into consideration. The resource, green vegetation, grows depending on seasonal climatic characteristics and is diminished due to the herbivore's grazing. Other specifics such as a varying personal energetic level due to feeding and starvation of the individuals, mating preferences, avoidance of competitors,more » dispersal of juveniles, as a result of site overgrazing, etc. are included in the model. We determined model parameters from real data for the species Microtus ochrogaster (prairie vole). The simulations are done for a case of an enclosed habitat without predators or other species competitors. The goal of the study is to find the relation between size of habitat and population persistence. The experiments with the model show the populations go extinct due to severe overgrazing, but that the length of population persistence depends on the area of the habitat as well as on the presence of fragmentation. Additionally, the total population size of the vole population obtained during the simulations exhibits yearly fluctuations as well as multi-yearly peaks of fluctuations. This dynamics is similar to the one observed in prairie vole field studies.« less

Using stylized agent-based models for population-environment research: A case study from the Galápagos Islands.

PubMed

Miller, Brian W; Breckheimer, Ian; McCleary, Amy L; Guzmán-Ramirez, Liza; Caplow, Susan C; Jones-Smith, Jessica C; Walsh, Stephen J

2010-05-01

Agent Based Models (ABMs) are powerful tools for population-environment research but are subject to trade-offs between model complexity and abstraction. This study strikes a compromise between abstract and highly specified ABMs by designing a spatially explicit, stylized ABM and using it to explore policy scenarios in a setting that is facing substantial conservation and development challenges. Specifically, we present an ABM that reflects key Land Use / Land Cover (LULC) dynamics and livelihood decisions on Isabela Island in the Galápagos Archipelago of Ecuador. We implement the model using the NetLogo software platform, a free program that requires relatively little programming experience. The landscape is composed of a satellite-derived distribution of a problematic invasive species (common guava) and a stylized representation of the Galápagos National Park, the community of Puerto Villamil, the agricultural zone, and the marine area. The agent module is based on publicly available data and household interviews, and represents the primary livelihoods of the population in the Galápagos Islands - tourism, fisheries, and agriculture. We use the model to enact hypothetical agricultural subsidy scenarios aimed at controlling invasive guava and assess the resulting population and land cover dynamics. Findings suggest that spatially explicit, stylized ABMs have considerable utility, particularly during preliminary stages of research, as platforms for (1) sharpening conceptualizations of population-environment systems, (2) testing alternative scenarios, and (3) uncovering critical data gaps.

Informations in Models of Evolutionary Dynamics

NASA Astrophysics Data System (ADS)

Rivoire, Olivier

2016-03-01

Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of evolutionary dynamics and show how explicit results are obtained for a solvable subclass of these models. In several limits, the results coincide with those obtained in studies of information processing for communication, gambling or thermodynamics. In the most general case, however, information processing by biological populations shows unique features that motivate the analysis of specific models.

Electron-phonon thermalization in a scalable method for real-time quantum dynamics

NASA Astrophysics Data System (ADS)

Rizzi, Valerio; Todorov, Tchavdar N.; Kohanoff, Jorge J.; Correa, Alfredo A.

2016-01-01

We present a quantum simulation method that follows the dynamics of out-of-equilibrium many-body systems of electrons and oscillators in real time. Its cost is linear in the number of oscillators and it can probe time scales from attoseconds to hundreds of picoseconds. Contrary to Ehrenfest dynamics, it can thermalize starting from a variety of initial conditions, including electronic population inversion. While an electronic temperature can be defined in terms of a nonequilibrium entropy, a Fermi-Dirac distribution in general emerges only after thermalization. These results can be used to construct a kinetic model of electron-phonon equilibration based on the explicit quantum dynamics.

An individual-based simulation model for mottled sculpin (Cottus bairdi) in a southern Appalachian stream

Treesearch

Brenda Rashleigh; Gary D. Grossman

2005-01-01

We describe and analyze a spatially explicit, individual-based model for the local population dynamics of mottled sculpin (Cottus bairdi). The model simulated daily growth, mortality, movement and spawning of individuals within a reach of stream. Juvenile and adult growth was based on consumption bioenergetics of benthic macroinvertebrate prey;...

The role of density-dependent individual growth in the persistence of freshwater salmonid populations.

PubMed

Vincenzi, Simone; Crivelli, Alain J; Jesensek, Dusan; De Leo, Giulio A

2008-06-01

Theoretical and empirical models of populations dynamics have paid little attention to the implications of density-dependent individual growth on the persistence and regulation of small freshwater salmonid populations. We have therefore designed a study aimed at testing our hypothesis that density-dependent individual growth is a process that enhances population recovery and reduces extinction risk in salmonid populations in a variable environment subject to disturbance events. This hypothesis was tested in two newly introduced marble trout (Salmo marmoratus) populations living in Slovenian streams (Zakojska and Gorska) subject to severe autumn floods. We developed a discrete-time stochastic individual-based model of population dynamics for each population with demographic parameters and compensatory responses tightly calibrated on data from individually tagged marble trout. The occurrence of severe flood events causing population collapses was explicitly accounted for in the model. We used the model in a population viability analysis setting to estimate the quasi-extinction risk and demographic indexes of the two marble trout populations when individual growth was density-dependent. We ran a set of simulations in which the effect of floods on population abundance was explicitly accounted for and another set of simulations in which flood events were not included in the model. These simulation results were compared with those of scenarios in which individual growth was modelled with density-independent Von Bertalanffy growth curves. Our results show how density-dependent individual growth may confer remarkable resilience to marble trout populations in case of major flood events. The resilience to flood events shown by the simulation results can be explained by the increase in size-dependent fecundity as a consequence of the drop in population size after a severe flood, which allows the population to quickly recover to the pre-event conditions. Our results suggest that density-dependent individual growth plays a potentially powerful role in the persistence of freshwater salmonids living in streams subject to recurrent yet unpredictable flood events.

Hydration dynamics promote bacterial coexistence on rough surfaces

PubMed Central

Wang, Gang; Or, Dani

2013-01-01

Identification of mechanisms that promote and maintain the immense microbial diversity found in soil is a central challenge for contemporary microbial ecology. Quantitative tools for systematic integration of complex biophysical and trophic processes at spatial scales, relevant for individual cell interactions, are essential for making progress. We report a modeling study of competing bacterial populations cohabiting soil surfaces subjected to highly dynamic hydration conditions. The model explicitly tracks growth, motion and life histories of individual bacterial cells on surfaces spanning dynamic aqueous networks that shape heterogeneous nutrient fields. The range of hydration conditions that confer physical advantages for rapidly growing species and support competitive exclusion is surprisingly narrow. The rapid fragmentation of soil aqueous phase under most natural conditions suppresses bacterial growth and cell dispersion, thereby balancing conditions experienced by competing populations with diverse physiological traits. In addition, hydration fluctuations intensify localized interactions that promote coexistence through disproportional effects within densely populated regions during dry periods. Consequently, bacterial population dynamics is affected well beyond responses predicted from equivalent and uniform hydration conditions. New insights on hydration dynamics could be considered in future designs of soil bioremediation activities, affect longevity of dry food products, and advance basic understanding of bacterial diversity dynamics and its role in global biogeochemical cycles. PMID:23051694

Predator-prey-subsidy population dynamics on stepping-stone domains.

PubMed

Shen, Lulan; Van Gorder, Robert A

2017-05-07

Predator-prey-subsidy dynamics on stepping-stone domains are examined using a variety of network configurations. Our problem is motivated by the interactions between arctic foxes (predator) and lemmings (prey) in the presence of seal carrion (subsidy) provided by polar bears. We use the n-Patch Model, which considers space explicitly as a "Stepping Stone" system. We consider the role that the carrying capacity, predator migration rate, input subsidy rate, predator mortality rate, and proportion of predators surviving migration play in the predator-prey-subsidy population dynamics. We find that for certain types of networks, added mobility will help predator populations, allowing them to survive or coexist when they would otherwise go extinct if confined to one location, while in other situations (such as when sparsely distributed nodes in the network have few resources available) the added mobility will hurt the predator population. We also find that a combination of favourable conditions for the prey and subsidy can lead to the formation of limit cycles (boom and bust dynamic) from stable equilibrium states. These modifications to the dynamics vary depending on the specific network structure employed, highlighting the fact that network structure can strongly influence the predator-prey-subsidy dynamics in stepping-stone domains. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evolutionary behaviour, trade-offs and cyclic and chaotic population dynamics.

PubMed

Hoyle, Andy; Bowers, Roger G; White, Andy

2011-05-01

Many studies of the evolution of life-history traits assume that the underlying population dynamical attractor is stable point equilibrium. However, evolutionary outcomes can change significantly in different circumstances. We present an analysis based on adaptive dynamics of a discrete-time demographic model involving a trade-off whose shape is also an important determinant of evolutionary behaviour. We derive an explicit expression for the fitness in the cyclic region and consequently present an adaptive dynamic analysis which is algebraic. We do this fully in the region of 2-cycles and (using a symbolic package) almost fully for 4-cycles. Simulations illustrate and verify our results. With equilibrium population dynamics, trade-offs with accelerating costs produce a continuously stable strategy (CSS) whereas trade-offs with decelerating costs produce a non-ES repellor. The transition to 2-cycles produces a discontinuous change: the appearance of an intermediate region in which branching points occur. The size of this region decreases as we move through the region of 2-cycles. There is a further discontinuous fall in the size of the branching region during the transition to 4-cycles. We extend our results numerically and with simulations to higher-period cycles and chaos. Simulations show that chaotic population dynamics can evolve from equilibrium and vice-versa.

Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda

PubMed Central

Tournebize, Rémi; Manel, Stéphanie; Vigouroux, Yves; Munoz, François; de Kochko, Alexandre

2017-01-01

Past climate fluctuations shaped the population dynamics of organisms in space and time, and have impacted their present intra-specific genetic structure. Demo-genetic modelling allows inferring the way past demographic and migration dynamics have determined this structure. Amborella trichopoda is an emblematic relict plant endemic to New Caledonia, widely distributed in the understory of non-ultramafic rainforests. We assessed the influence of the last glacial climates on the demographic history and the paleo-distribution of 12 Amborella populations covering the whole current distribution. We performed coalescent genetic modelling of these dynamics, based on both whole-genome resequencing and microsatellite genotyping data. We found that the two main genetic groups of Amborella were shaped by the divergence of two ancestral populations during the last glacial maximum. From 12,800 years BP, the South ancestral population has expanded 6.3-fold while the size of the North population has remained stable. Recent asymmetric gene flow between the groups further contributed to the phylogeographical pattern. Spatially explicit coalescent modelling allowed us to estimate the location of ancestral populations with good accuracy (< 22 km) and provided indications regarding the mid-elevation pathways that facilitated post-glacial expansion. PMID:28820899

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.

Social and spatial effects on genetic variation between foraging flocks in a wild bird population.

PubMed

Radersma, Reinder; Garroway, Colin J; Santure, Anna W; de Cauwer, Isabelle; Farine, Damien R; Slate, Jon; Sheldon, Ben C

2017-10-01

Social interactions are rarely random. In some instances, animals exhibit homophily or heterophily, the tendency to interact with similar or dissimilar conspecifics, respectively. Genetic homophily and heterophily influence the evolutionary dynamics of populations, because they potentially affect sexual and social selection. Here, we investigate the link between social interactions and allele frequencies in foraging flocks of great tits (Parus major) over three consecutive years. We constructed co-occurrence networks which explicitly described the splitting and merging of 85,602 flocks through time (fission-fusion dynamics), at 60 feeding sites. Of the 1,711 birds in those flocks, we genotyped 962 individuals at 4,701 autosomal single nucleotide polymorphisms (SNPs). By combining genomewide genotyping with repeated field observations of the same individuals, we were able to investigate links between social structure and allele frequencies at a much finer scale than was previously possible. We explicitly accounted for potential spatial effects underlying genetic structure at the population level. We modelled social structure and spatial configuration of great tit fission-fusion dynamics with eigenvector maps. Variance partitioning revealed that allele frequencies were strongly affected by group fidelity (explaining 27%-45% of variance) as individuals tended to maintain associations with the same conspecifics. These conspecifics were genetically more dissimilar than expected, shown by genomewide heterophily for pure social (i.e., space-independent) grouping preferences. Genomewide homophily was linked to spatial configuration, indicating spatial segregation of genotypes. We did not find evidence for homophily or heterophily for putative socially relevant candidate genes or any other SNP markers. Together, these results demonstrate the importance of distinguishing social and spatial processes in determining population structure. © 2017 John Wiley & Sons Ltd.

An epidemic model for the interactions between thermal regime of rivers and transmission of Proliferative Kidney Disease in salmonid fish

NASA Astrophysics Data System (ADS)

Carraro, Luca; Bertuzzo, Enrico; Mari, Lorenzo; Gatto, Marino; Strepparava, Nicole; Hartikainen, Hanna; Rinaldo, Andrea

2015-04-01

Proliferative kidney disease (PKD) affects salmonid populations in European and North-American rivers. It is caused by the endoparasitic myxozoan Tetracapsuloides bryosalmonae, which exploits freshwater bryozoans (Fredericella sultana) and salmonids as primary and secondary hosts, respectively. Incidence and mortality, which can reach up to 90-100%, are known to be strongly related to water temperature. PKD has been present in brown trout population for a long time but has recently increased rapidly in incidence and severity causing a decline in fish catches in many countries. In addition, environmental changes are feared to cause PKD outbreaks at higher latitude and altitude regions as warmer temperatures promote disease development. This calls for a better comprehension of the interactions between disease dynamics and the thermal regime of rivers, in order to possibly devise strategies for disease management. In this perspective, a spatially explicit model of PKD epidemiology in riverine host metacommunities is proposed. The model aims at summarizing the knowledge on the modes of transmission of the disease and the life-cycle of the parasite, making the connection between temperature and epidemiological parameters explicit. The model accounts for both local population and disease dynamics of bryozoans and fish and hydrodynamic dispersion of the parasite spores and hosts along the river network. The model is time-hybrid, coupling inter-seasonal and intra-seasonal dynamics, the former being described in a continuous time domain, the latter seen as time steps of a discrete time domain. In order to test the model, a case study is conducted in river Wigger (Cantons of Aargau and Lucerne, Switzerland), where data about water temperature, brown trout and bryozoan populations and PKD prevalence are being collected.

DYNAMO-HIA--a Dynamic Modeling tool for generic Health Impact Assessments.

PubMed

Lhachimi, Stefan K; Nusselder, Wilma J; Smit, Henriette A; van Baal, Pieter; Baili, Paolo; Bennett, Kathleen; Fernández, Esteve; Kulik, Margarete C; Lobstein, Tim; Pomerleau, Joceline; Mackenbach, Johan P; Boshuizen, Hendriek C

2012-01-01

Currently, no standard tool is publicly available that allows researchers or policy-makers to quantify the impact of policies using epidemiological evidence within the causal framework of Health Impact Assessment (HIA). A standard tool should comply with three technical criteria (real-life population, dynamic projection, explicit risk-factor states) and three usability criteria (modest data requirements, rich model output, generally accessible) to be useful in the applied setting of HIA. With DYNAMO-HIA (Dynamic Modeling for Health Impact Assessment), we introduce such a generic software tool specifically designed to facilitate quantification in the assessment of the health impacts of policies. DYNAMO-HIA quantifies the impact of user-specified risk-factor changes on multiple diseases and in turn on overall population health, comparing one reference scenario with one or more intervention scenarios. The Markov-based modeling approach allows for explicit risk-factor states and simulation of a real-life population. A built-in parameter estimation module ensures that only standard population-level epidemiological evidence is required, i.e. data on incidence, prevalence, relative risks, and mortality. DYNAMO-HIA provides a rich output of summary measures--e.g. life expectancy and disease-free life expectancy--and detailed data--e.g. prevalences and mortality/survival rates--by age, sex, and risk-factor status over time. DYNAMO-HIA is controlled via a graphical user interface and is publicly available from the internet, ensuring general accessibility. We illustrate the use of DYNAMO-HIA with two example applications: a policy causing an overall increase in alcohol consumption and quantifying the disease-burden of smoking. By combining modest data needs with general accessibility and user friendliness within the causal framework of HIA, DYNAMO-HIA is a potential standard tool for health impact assessment based on epidemiologic evidence.

Impact of transient climate change upon Grouse population dynamics in the Italian Alps

NASA Astrophysics Data System (ADS)

Pirovano, Andrea; Bocchiola, Daniele

2010-05-01

Understanding the effect of short to medium term weather condition, and of transient global warming upon wildlife species life history is essential to predict the demographic consequences therein, and possibly develop adaptation strategies, especially in game species, where hunting mortality may play an important role in population dynamics. We carried out a preliminary investigation of observed impact of weather variables upon population dynamics indexes of three alpine Grouse species (i.e. Rock Ptarmigan, Lagopus Mutus, Black Grouse, Tetrao Tetrix, Rock Partridge, Alectoris Graeca), nested within central Italian Alps, based upon 15 years (1995-2009) of available censuses data, provided by the Sondrio Province authority. We used a set of climate variables already highlighted within recent literature for carrying considerable bearing on Grouse population dynamics, including e.g. temperature at hatching time and during winter, snow cover at nesting, and precipitation during nursing period. We then developed models of Grouses' population dynamics by explicitly driving population change according to their dependence upon the significant weather variables and population density and we evaluated objective indexes to assess the so obtained predictive power. Eventually, we develop projection of future local climate, based upon locally derived trends, and upon projections from GCMs (A2 IPCC storyline) already validated for the area, to project forward in time (until 2100 or so) the significant climatic variables, which we then use to force population dynamics models of the target species. The projected patterns obtained through this exercise are discussed and compared against those expected under stationary climate conditions at present, and preliminary conclusions are drawn.

Modeling nitrous oxide production and reduction in soil through explicit representation of denitrification enzyme kinetics.

PubMed

Zheng, Jianqiu; Doskey, Paul V

2015-02-17

An enzyme-explicit denitrification model with representations for pre- and de novo synthesized enzymes was developed to improve predictions of nitrous oxide (N2O) accumulations in soil and emissions from the surface. The metabolic model of denitrification is based on dual-substrate utilization and Monod growth kinetics. Enzyme synthesis/activation was incorporated into each sequential reduction step of denitrification to regulate dynamics of the denitrifier population and the active enzyme pool, which controlled the rate function. Parameterizations were developed from observations of the dynamics of N2O production and reduction in soil incubation experiments. The model successfully reproduced the dynamics of N2O and N2 accumulation in the incubations and revealed an important regulatory effect of denitrification enzyme kinetics on the accumulation of denitrification products. Pre-synthesized denitrification enzymes contributed 20, 13, 43, and 62% of N2O that accumulated in 48 h incubations of soil collected from depths of 0-5, 5-10, 10-15, and 15-25 cm, respectively. An enzyme activity function (E) was defined to estimate the relative concentration of active enzymes and variation in response to environmental conditions. The value of E allows for activities of pre-synthesized denitrification enzymes to be differentiated from de novo synthesized enzymes. Incorporating explicit representations of denitrification enzyme kinetics into biogeochemical models is a promising approach for accurately simulating dynamics of the production and reduction of N2O in soils.

How can we model selectively neutral density dependence in evolutionary games.

PubMed

Argasinski, Krzysztof; Kozłowski, Jan

2008-03-01

The problem of density dependence appears in all approaches to the modelling of population dynamics. It is pertinent to classic models (i.e., Lotka-Volterra's), and also population genetics and game theoretical models related to the replicator dynamics. There is no density dependence in the classic formulation of replicator dynamics, which means that population size may grow to infinity. Therefore the question arises: How is unlimited population growth suppressed in frequency-dependent models? Two categories of solutions can be found in the literature. In the first, replicator dynamics is independent of background fitness. In the second type of solution, a multiplicative suppression coefficient is used, as in a logistic equation. Both approaches have disadvantages. The first one is incompatible with the methods of life history theory and basic probabilistic intuitions. The logistic type of suppression of per capita growth rate stops trajectories of selection when population size reaches the maximal value (carrying capacity); hence this method does not satisfy selective neutrality. To overcome these difficulties, we must explicitly consider turn-over of individuals dependent on mortality rate. This new approach leads to two interesting predictions. First, the equilibrium value of population size is lower than carrying capacity and depends on the mortality rate. Second, although the phase portrait of selection trajectories is the same as in density-independent replicator dynamics, pace of selection slows down when population size approaches equilibrium, and then remains constant and dependent on the rate of turn-over of individuals.

Microbial consortia at steady supply

PubMed Central

Taillefumier, Thibaud; Posfai, Anna; Meir, Yigal; Wingreen, Ned S

2017-01-01

Metagenomics has revealed hundreds of species in almost all microbiota. In a few well-studied cases, microbial communities have been observed to coordinate their metabolic fluxes. In principle, microbes can divide tasks to reap the benefits of specialization, as in human economies. However, the benefits and stability of an economy of microbial specialists are far from obvious. Here, we physically model the population dynamics of microbes that compete for steadily supplied resources. Importantly, we explicitly model the metabolic fluxes yielding cellular biomass production under the constraint of a limited enzyme budget. We find that population dynamics generally leads to the coexistence of different metabolic types. We establish that these microbial consortia act as cartels, whereby population dynamics pins down resource concentrations at values for which no other strategy can invade. Finally, we propose that at steady supply, cartels of competing strategies automatically yield maximum biomass, thereby achieving a collective optimum. DOI: http://dx.doi.org/10.7554/eLife.22644.001 PMID:28473032

Mathematical modelling methodologies in predictive food microbiology: a SWOT analysis.

PubMed

Ferrer, Jordi; Prats, Clara; López, Daniel; Vives-Rego, Josep

2009-08-31

Predictive microbiology is the area of food microbiology that attempts to forecast the quantitative evolution of microbial populations over time. This is achieved to a great extent through models that include the mechanisms governing population dynamics. Traditionally, the models used in predictive microbiology are whole-system continuous models that describe population dynamics by means of equations applied to extensive or averaged variables of the whole system. Many existing models can be classified by specific criteria. We can distinguish between survival and growth models by seeing whether they tackle mortality or cell duplication. We can distinguish between empirical (phenomenological) models, which mathematically describe specific behaviour, and theoretical (mechanistic) models with a biological basis, which search for the underlying mechanisms driving already observed phenomena. We can also distinguish between primary, secondary and tertiary models, by examining their treatment of the effects of external factors and constraints on the microbial community. Recently, the use of spatially explicit Individual-based Models (IbMs) has spread through predictive microbiology, due to the current technological capacity of performing measurements on single individual cells and thanks to the consolidation of computational modelling. Spatially explicit IbMs are bottom-up approaches to microbial communities that build bridges between the description of micro-organisms at the cell level and macroscopic observations at the population level. They provide greater insight into the mesoscale phenomena that link unicellular and population levels. Every model is built in response to a particular question and with different aims. Even so, in this research we conducted a SWOT (Strength, Weaknesses, Opportunities and Threats) analysis of the different approaches (population continuous modelling and Individual-based Modelling), which we hope will be helpful for current and future researchers.

On Spatially Explicit Models of Cholera Epidemics: Hydrologic controls, environmental drivers, human-mediated transmissions (Invited)

NASA Astrophysics Data System (ADS)

Rinaldo, A.; Bertuzzo, E.; Mari, L.; Righetto, L.; Gatto, M.; Casagrandi, R.; Rodriguez-Iturbe, I.

2010-12-01

A recently proposed model for cholera epidemics is examined. The model accounts for local communities of susceptibles and infectives in a spatially explicit arrangement of nodes linked by networks having different topologies. The vehicle of infection (Vibrio cholerae) is transported through the network links which are thought of as hydrological connections among susceptible communities. The mathematical tools used are borrowed from general schemes of reactive transport on river networks acting as the environmental matrix for the circulation and mixing of water-borne pathogens. The results of a large-scale application to the Kwa Zulu (Natal) epidemics of 2001-2002 will be discussed. Useful theoretical results derived in the spatially-explicit context will also be reviewed (like e.g. the exact derivation of the speed of propagation for traveling fronts of epidemics on regular lattices endowed with uniform population density). Network effects will be discussed. The analysis of the limit case of uniformly distributed population density proves instrumental in establishing the overall conditions for the relevance of spatially explicit models. To that extent, it is shown that the ratio between spreading and disease outbreak timescales proves the crucial parameter. The relevance of our results lies in the major differences potentially arising between the predictions of spatially explicit models and traditional compartmental models of the SIR-like type. Our results suggest that in many cases of real-life epidemiological interest timescales of disease dynamics may trigger outbreaks that significantly depart from the predictions of compartmental models. Finally, a view on further developments includes: hydrologically improved aquatic reservoir models for pathogens; human mobility patterns affecting disease propagation; double-peak emergence and seasonality in the spatially explicit epidemic context.

A Geographically Explicit Genetic Model of Worldwide Human-Settlement History

PubMed Central

Liu, Hua; Prugnolle, Franck; Manica, Andrea; Balloux, François

2006-01-01

Currently available genetic and archaeological evidence is generally interpreted as supportive of a recent single origin of modern humans in East Africa. However, this is where the near consensus on human settlement history ends, and considerable uncertainty clouds any more detailed aspect of human colonization history. Here, we present a dynamic genetic model of human settlement history coupled with explicit geographical distances from East Africa, the likely origin of modern humans. We search for the best-supported parameter space by fitting our analytical prediction to genetic data that are based on 52 human populations analyzed at 783 autosomal microsatellite markers. This framework allows us to jointly estimate the key parameters of the expansion of modern humans. Our best estimates suggest an initial expansion of modern humans ∼56,000 years ago from a small founding population of ∼1,000 effective individuals. Our model further points to high growth rates in newly colonized habitats. The general fit of the model with the data is excellent. This suggests that coupling analytical genetic models with explicit demography and geography provides a powerful tool for making inferences on human-settlement history. PMID:16826514

Population ecology, nonlinear dynamics, and social evolution. I. Associations among nonrelatives.

PubMed

Avilés, Leticia; Abbot, Patrick; Cutter, Asher D

2002-02-01

Using an individual-based and genetically explicit simulation model, we explore the evolution of sociality within a population-ecology and nonlinear-dynamics framework. Assuming that individual fitness is a unimodal function of group size and that cooperation may carry a relative fitness cost, we consider the evolution of one-generation breeding associations among nonrelatives. We explore how parameters such as the intrinsic rate of growth and group and global carrying capacities may influence social evolution and how social evolution may, in turn, influence and be influenced by emerging group-level and population-wide dynamics. We find that group living and cooperation evolve under a wide range of parameter values, even when cooperation is costly and the interactions can be defined as altruistic. Greater levels of cooperation, however, did evolve when cooperation carried a low or no relative fitness cost. Larger group carrying capacities allowed the evolution of larger groups but also resulted in lower cooperative tendencies. When the intrinsic rate of growth was not too small and control of the global population size was density dependent, the evolution of large cooperative tendencies resulted in dynamically unstable groups and populations. These results are consistent with the existence and typical group sizes of organisms ranging from the pleometrotic ants to the colonial birds and the global population outbreaks and crashes characteristic of organisms such as the migratory locusts and the tree-killing bark beetles.

CDPOP: A spatially explicit cost distance population genetics program

Treesearch

Erin L. Landguth; S. A. Cushman

2010-01-01

Spatially explicit simulation of gene flow in complex landscapes is essential to explain observed population responses and provide a foundation for landscape genetics. To address this need, we wrote a spatially explicit, individual-based population genetics model (CDPOP). The model implements individual-based population modelling with Mendelian inheritance and k-allele...

Five challenges for spatial epidemic models

PubMed Central

Riley, Steven; Eames, Ken; Isham, Valerie; Mollison, Denis; Trapman, Pieter

2015-01-01

Infectious disease incidence data are increasingly available at the level of the individual and include high-resolution spatial components. Therefore, we are now better able to challenge models that explicitly represent space. Here, we consider five topics within spatial disease dynamics: the construction of network models; characterising threshold behaviour; modelling long-distance interactions; the appropriate scale for interventions; and the representation of population heterogeneity. PMID:25843387

The impact of parasitoid emergence time on host-parasitoid population dynamics.

PubMed

Cobbold, Christina A; Roland, Jens; Lewis, Mark A

2009-01-01

We investigate the effect of parasitoid phenology on host-parasitoid population cycles. Recent experimental research has shown that parasitized hosts can continue to interact with their unparasitized counterparts through competition. Parasitoid phenology, in particular the timing of emergence from the host, determines the duration of this competition. We construct a discrete-time host-parasitoid model in which within-generation dynamics associated with parasitoid timing is explicitly incorporated. We found that late-emerging parasitoids induce less severe, but more frequent, host outbreaks, independent of the choice of competition model. The competition experienced by the parasitized host reduces the parasitoids' numerical response to changes in host numbers, preventing the 'boom-bust' dynamics associated with more efficient parasitoids. We tested our findings against experimental data for the forest tent caterpillar (Malacosoma disstria Hübner) system, where a large number of consecutive years at a high host density is synonymous with severe forest damage.

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

Kostova, T; Carlsen, T

We present a study, based on simulations with SERDYCA, a spatially-explicit individual-based model of rodent dynamics, on the relation between population persistence and the presence of numerous isolated disturbances in the habitat. We are specifically interested in the effect of disturbances that do not fragment the environment on population persistence. Our results suggest that the presence of disturbances in the absence of fragmentation can actually increase the average time to extinction of the modeled population. The presence of disturbances decreases population density but can increase the chance for mating in monogamous species and consequently, the ratio of juveniles in themore » population. It thus provides a better chance for the population to restore itself after a severe period with critically low population density. We call this the ''disturbance-forced localization effect''.« less

Accounting for system dynamics in reserve design.

PubMed

Leroux, Shawn J; Schmiegelow, Fiona K A; Cumming, Steve G; Lessard, Robert B; Nagy, John

2007-10-01

Systematic conservation plans have only recently considered the dynamic nature of ecosystems. Methods have been developed to incorporate climate change, population dynamics, and uncertainty in reserve design, but few studies have examined how to account for natural disturbance. Considering natural disturbance in reserve design may be especially important for the world's remaining intact areas, which still experience active natural disturbance regimes. We developed a spatially explicit, dynamic simulation model, CONSERV, which simulates patch dynamics and fire, and used it to evaluate the efficacy of hypothetical reserve networks in northern Canada. We designed six networks based on conventional reserve design methods, with different conservation targets for woodland caribou habitat, high-quality wetlands, vegetation, water bodies, and relative connectedness. We input the six reserve networks into CONSERV and tracked the ability of each to maintain initial conservation targets through time under an active natural disturbance regime. None of the reserve networks maintained all initial targets, and some over-represented certain features, suggesting that both effectiveness and efficiency of reserve design could be improved through use of spatially explicit dynamic simulation during the planning process. Spatial simulation models of landscape dynamics are commonly used in natural resource management, but we provide the first illustration of their potential use for reserve design. Spatial simulation models could be used iteratively to evaluate competing reserve designs and select targets that have a higher likelihood of being maintained through time. Such models could be combined with dynamic planning techniques to develop a general theory for reserve design in an uncertain world.

At the Interface: Dynamic Interactions of Explicit and Implicit Language Knowledge

ERIC Educational Resources Information Center

Ellis, Nick C.

2005-01-01

This paper considers how implicit and explicit knowledge are dissociable but cooperative. It reviews various psychological and neurobiological processes by which explicit knowledge of form-meaning associations impacts upon implicit language learning. The interface is dynamic: It happens transiently during conscious processing, but the influence…

Anthropogenic habitat disturbance and the dynamics of hantavirus using remote sensing, GIS, and a spatially explicit agent-based model

NASA Astrophysics Data System (ADS)

Cao, Lina

Sin Nombre virus (SNV), a strain of hantavirus, causes hantavirus pulmonary syndrome (HPS) in humans, a deadly disease with high mortality rate (>50%). The primary virus host is deer mice, and greater deer mice abundance has been shown to increase the human risk of HPS. There is a great need in understanding the nature of the virus host, its temporal and spatial dynamics, and its relation to the human population with the purpose of predicting human risk of the disease. This research studies SNV dynamics in deer mice in the Great Basin Desert of central Utah, USA using multiyear field data and integrated geospatial approaches including remote sensing, Geographic Information System (GIS), and a spatially explicit agent-based model. The goal is to advance our understanding of the important ecological and demographic factors that affect the dynamics of deer mouse population and SNV prevalence. The primary research question is how climate, habitat disturbance, and deer mouse demographics affect deer mouse population density, its movement, and SNV prevalence in the sagebrush habitat. The results show that the normalized difference vegetation index (NDVI) and the enhanced vegetation index (EVI) can be good predictors of deer mouse density and the number of infected deer mice with a time lag of 1.0 to 1.3 years. This information can be very useful in predicting mouse abundance and SNV risk. The results also showed that climate, mouse density, sex, mass, and SNV infection had significant effects on deer mouse movement. The effect of habitat disturbance on mouse movement varies according to climate conditions with positive relationship in predrought condition and negative association in postdrought condition. The heavier infected deer mice moved the most. Season and disturbance alone had no significant effects. The spatial agent-based model (SABM) simulation results show that prevalence was negatively related to the disturbance levels and the sensitivity analysis showed that population density was one of the most important parameters affecting the SNV dynamics. The results also indicated that habitat disturbance could increase hantavirus transmission likely by increasing the movement and consequently contact rates. However, the model suggested that habitat disturbance had a much stronger effect on prevalence by decreasing population density than by increasing mice movement. Therefore, overall habitat disturbance reduces SNV prevalence.

Collective effects and dynamics of non-adiabatic flame balls

NASA Astrophysics Data System (ADS)

D'Angelo, Yves; Joulin, Guy

2001-03-01

The dynamics of a homogeneous, polydisperse collection of non-adiabatic flame balls (FBs) is investigated by analytical/numerical means. A strongly temperature-dependent Arrhenius reaction rate is assumed, along with a light enough reactant characterized by a markedly less than unity Lewis number (Le). Combining activation-energy asymptotics with a mean-field type of treatment, the analysis yields a nonlinear integro-differential evolution equation (EE) for the FB population. The EE accounts for heat losses inside each FB and unsteadiness around it, as well as for its interactions with the entire FB population, namely mutual heating and faster (Le<1) consumption of the reactant pool. The initial FB number density and size distribution enter the EE explicitly. The latter is studied analytically at early times, then for small total FB number densities; it is subsequently solved numerically, yielding the whole population evolution and its lifetime. Generalizations and open questions relating to `spotty' turbulent combustion are finally evoked.

Nonlinear Fano interferences in open quantum systems: An exactly solvable model

NASA Astrophysics Data System (ADS)

Finkelstein-Shapiro, Daniel; Calatayud, Monica; Atabek, Osman; Mujica, Vladimiro; Keller, Arne

2016-06-01

We obtain an explicit solution for the stationary-state populations of a dissipative Fano model, where a discrete excited state is coupled to a continuum set of states; both excited sets of states are reachable by photoexcitation from the ground state. The dissipative dynamic is described by a Liouville equation in Lindblad form and the field intensity can take arbitrary values within the model. We show that the population of the continuum states as a function of laser frequency can always be expressed as a Fano profile plus a Lorentzian function with effective parameters whose explicit expressions are given in the case of a closed system coupled to a bath as well as for the original Fano scattering framework. Although the solution is intricate, it can be elegantly expressed as a linear transformation of the kernel of a 4 ×4 matrix which has the meaning of an effective Liouvillian. We unveil key notable processes related to the optical nonlinearity and which had not been reported to date: electromagnetic-induced transparency, population inversions, power narrowing and broadening, as well as an effective reduction of the Fano asymmetry parameter.

Forecasting climate change impacts on plant populations over large spatial extents

DOE PAGES

Tredennick, Andrew T.; Hooten, Mevin B.; Aldridge, Cameron L.; ...

2016-10-24

Plant population models are powerful tools for predicting climate change impacts in one location, but are difficult to apply at landscape scales. Here, we overcome this limitation by taking advantage of two recent advances: remotely sensed, species-specific estimates of plant cover and statistical models developed for spatiotemporal dynamics of animal populations. Using computationally efficient model reparameterizations, we fit a spatiotemporal population model to a 28-year time series of sagebrush (Artemisia spp.) percent cover over a 2.5 × 5 km landscape in southwestern Wyoming while formally accounting for spatial autocorrelation. We include interannual variation in precipitation and temperature as covariates inmore » the model to investigate how climate affects the cover of sagebrush. We then use the model to forecast the future abundance of sagebrush at the landscape scale under projected climate change, generating spatially explicit estimates of sagebrush population trajectories that have, until now, been impossible to produce at this scale. Our broadscale and long-term predictions are rooted in small-scale and short-term population dynamics and provide an alternative to predictions offered by species distribution models that do not include population dynamics. Finally, our approach, which combines several existing techniques in a novel way, demonstrates the use of remote sensing data to model population responses to environmental change that play out at spatial scales far greater than the traditional field study plot.« less

Forecasting climate change impacts on plant populations over large spatial extents

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

Tredennick, Andrew T.; Hooten, Mevin B.; Aldridge, Cameron L.

Plant population models are powerful tools for predicting climate change impacts in one location, but are difficult to apply at landscape scales. Here, we overcome this limitation by taking advantage of two recent advances: remotely sensed, species-specific estimates of plant cover and statistical models developed for spatiotemporal dynamics of animal populations. Using computationally efficient model reparameterizations, we fit a spatiotemporal population model to a 28-year time series of sagebrush (Artemisia spp.) percent cover over a 2.5 × 5 km landscape in southwestern Wyoming while formally accounting for spatial autocorrelation. We include interannual variation in precipitation and temperature as covariates inmore » the model to investigate how climate affects the cover of sagebrush. We then use the model to forecast the future abundance of sagebrush at the landscape scale under projected climate change, generating spatially explicit estimates of sagebrush population trajectories that have, until now, been impossible to produce at this scale. Our broadscale and long-term predictions are rooted in small-scale and short-term population dynamics and provide an alternative to predictions offered by species distribution models that do not include population dynamics. Finally, our approach, which combines several existing techniques in a novel way, demonstrates the use of remote sensing data to model population responses to environmental change that play out at spatial scales far greater than the traditional field study plot.« less

Forecasting climate change impacts on plant populations over large spatial extents

USGS Publications Warehouse

Tredennick, Andrew T.; Hooten, Mevin B.; Aldridge, Cameron L.; Homer, Collin G.; Kleinhesselink, Andrew R.; Adler, Peter B.

2016-01-01

Plant population models are powerful tools for predicting climate change impacts in one location, but are difficult to apply at landscape scales. We overcome this limitation by taking advantage of two recent advances: remotely sensed, species-specific estimates of plant cover and statistical models developed for spatiotemporal dynamics of animal populations. Using computationally efficient model reparameterizations, we fit a spatiotemporal population model to a 28-year time series of sagebrush (Artemisia spp.) percent cover over a 2.5 × 5 km landscape in southwestern Wyoming while formally accounting for spatial autocorrelation. We include interannual variation in precipitation and temperature as covariates in the model to investigate how climate affects the cover of sagebrush. We then use the model to forecast the future abundance of sagebrush at the landscape scale under projected climate change, generating spatially explicit estimates of sagebrush population trajectories that have, until now, been impossible to produce at this scale. Our broadscale and long-term predictions are rooted in small-scale and short-term population dynamics and provide an alternative to predictions offered by species distribution models that do not include population dynamics. Our approach, which combines several existing techniques in a novel way, demonstrates the use of remote sensing data to model population responses to environmental change that play out at spatial scales far greater than the traditional field study plot.

Spatial capture-recapture models allowing Markovian transience or dispersal

USGS Publications Warehouse

Royle, J. Andrew; Fuller, Angela K.; Sutherland, Chris

2016-01-01

Spatial capture–recapture (SCR) models are a relatively recent development in quantitative ecology, and they are becoming widely used to model density in studies of animal populations using camera traps, DNA sampling and other methods which produce spatially explicit individual encounter information. One of the core assumptions of SCR models is that individuals possess home ranges that are spatially stationary during the sampling period. For many species, this assumption is unlikely to be met and, even for species that are typically territorial, individuals may disperse or exhibit transience at some life stages. In this paper we first conduct a simulation study to evaluate the robustness of estimators of density under ordinary SCR models when dispersal or transience is present in the population. Then, using both simulated and real data, we demonstrate that such models can easily be described in the BUGS language providing a practical framework for their analysis, which allows us to evaluate movement dynamics of species using capture–recapture data. We find that while estimators of density are extremely robust, even to pathological levels of movement (e.g., complete transience), the estimator of the spatial scale parameter of the encounter probability model is confounded with the dispersal/transience scale parameter. Thus, use of ordinary SCR models to make inferences about density is feasible, but interpretation of SCR model parameters in relation to movement should be avoided. Instead, when movement dynamics are of interest, such dynamics should be parameterized explicitly in the model.

The scaling of geographic ranges: implications for species distribution models

USGS Publications Warehouse

Yackulic, Charles B.; Ginsberg, Joshua R.

2016-01-01

There is a need for timely science to inform policy and management decisions; however, we must also strive to provide predictions that best reflect our understanding of ecological systems. Species distributions evolve through time and reflect responses to environmental conditions that are mediated through individual and population processes. Species distribution models that reflect this understanding, and explicitly model dynamics, are likely to give more accurate predictions.

Patient-Adaptive Reconstruction and Acquisition in Dynamic Imaging with Sensitivity Encoding (PARADISE)

PubMed Central

Sharif, Behzad; Derbyshire, J. Andrew; Faranesh, Anthony Z.; Bresler, Yoram

2010-01-01

MR imaging of the human heart without explicit cardiac synchronization promises to extend the applicability of cardiac MR to a larger patient population and potentially expand its diagnostic capabilities. However, conventional non-gated imaging techniques typically suffer from low image quality or inadequate spatio-temporal resolution and fidelity. Patient-Adaptive Reconstruction and Acquisition in Dynamic Imaging with Sensitivity Encoding (PARADISE) is a highly-accelerated non-gated dynamic imaging method that enables artifact-free imaging with high spatio-temporal resolutions by utilizing novel computational techniques to optimize the imaging process. In addition to using parallel imaging, the method gains acceleration from a physiologically-driven spatio-temporal support model; hence, it is doubly accelerated. The support model is patient-adaptive, i.e., its geometry depends on dynamics of the imaged slice, e.g., subject’s heart-rate and heart location within the slice. The proposed method is also doubly adaptive as it adapts both the acquisition and reconstruction schemes. Based on the theory of time-sequential sampling, the proposed framework explicitly accounts for speed limitations of gradient encoding and provides performance guarantees on achievable image quality. The presented in-vivo results demonstrate the effectiveness and feasibility of the PARADISE method for high resolution non-gated cardiac MRI during a short breath-hold. PMID:20665794

Hierarchical modeling and inference in ecology: The analysis of data from populations, metapopulations and communities

USGS Publications Warehouse

Royle, J. Andrew; Dorazio, Robert M.

2008-01-01

A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics.

Influence of network dynamics on the spread of sexually transmitted diseases.

PubMed

Risau-Gusman, Sebastián

2012-06-07

Network epidemiology often assumes that the relationships defining the social network of a population are static. The dynamics of relationships is only taken indirectly into account by assuming that the relevant information to study epidemic spread is encoded in the network obtained, by considering numbers of partners accumulated over periods of time roughly proportional to the infectious period of the disease. On the other hand, models explicitly including social dynamics are often too schematic to provide a reasonable representation of a real population, or so detailed that no general conclusions can be drawn from them. Here, we present a model of social dynamics that is general enough so its parameters can be obtained by fitting data from surveys about sexual behaviour, but that can still be studied analytically, using mean-field techniques. This allows us to obtain some general results about epidemic spreading. We show that using accumulated network data to estimate the static epidemic threshold lead to a significant underestimation of that threshold. We also show that, for a dynamic network, the relative epidemic threshold is an increasing function of the infectious period of the disease, implying that the static value is a lower bound to the real threshold. A practical example is given of how to apply the model to the study of a real population.

Influence of network dynamics on the spread of sexually transmitted diseases

PubMed Central

Risau-Gusman, Sebastián

2012-01-01

Network epidemiology often assumes that the relationships defining the social network of a population are static. The dynamics of relationships is only taken indirectly into account by assuming that the relevant information to study epidemic spread is encoded in the network obtained, by considering numbers of partners accumulated over periods of time roughly proportional to the infectious period of the disease. On the other hand, models explicitly including social dynamics are often too schematic to provide a reasonable representation of a real population, or so detailed that no general conclusions can be drawn from them. Here, we present a model of social dynamics that is general enough so its parameters can be obtained by fitting data from surveys about sexual behaviour, but that can still be studied analytically, using mean-field techniques. This allows us to obtain some general results about epidemic spreading. We show that using accumulated network data to estimate the static epidemic threshold lead to a significant underestimation of that threshold. We also show that, for a dynamic network, the relative epidemic threshold is an increasing function of the infectious period of the disease, implying that the static value is a lower bound to the real threshold. A practical example is given of how to apply the model to the study of a real population. PMID:22112655

DYNAMO-HIA–A Dynamic Modeling Tool for Generic Health Impact Assessments

PubMed Central

Lhachimi, Stefan K.; Nusselder, Wilma J.; Smit, Henriette A.; van Baal, Pieter; Baili, Paolo; Bennett, Kathleen; Fernández, Esteve; Kulik, Margarete C.; Lobstein, Tim; Pomerleau, Joceline; Mackenbach, Johan P.; Boshuizen, Hendriek C.

2012-01-01

Background Currently, no standard tool is publicly available that allows researchers or policy-makers to quantify the impact of policies using epidemiological evidence within the causal framework of Health Impact Assessment (HIA). A standard tool should comply with three technical criteria (real-life population, dynamic projection, explicit risk-factor states) and three usability criteria (modest data requirements, rich model output, generally accessible) to be useful in the applied setting of HIA. With DYNAMO-HIA (Dynamic Modeling for Health Impact Assessment), we introduce such a generic software tool specifically designed to facilitate quantification in the assessment of the health impacts of policies. Methods and Results DYNAMO-HIA quantifies the impact of user-specified risk-factor changes on multiple diseases and in turn on overall population health, comparing one reference scenario with one or more intervention scenarios. The Markov-based modeling approach allows for explicit risk-factor states and simulation of a real-life population. A built-in parameter estimation module ensures that only standard population-level epidemiological evidence is required, i.e. data on incidence, prevalence, relative risks, and mortality. DYNAMO-HIA provides a rich output of summary measures – e.g. life expectancy and disease-free life expectancy – and detailed data – e.g. prevalences and mortality/survival rates – by age, sex, and risk-factor status over time. DYNAMO-HIA is controlled via a graphical user interface and is publicly available from the internet, ensuring general accessibility. We illustrate the use of DYNAMO-HIA with two example applications: a policy causing an overall increase in alcohol consumption and quantifying the disease-burden of smoking. Conclusion By combining modest data needs with general accessibility and user friendliness within the causal framework of HIA, DYNAMO-HIA is a potential standard tool for health impact assessment based on epidemiologic evidence. PMID:22590491

Understanding African Swine Fever infection dynamics in Sardinia using a spatially explicit transmission model in domestic pig farms.

PubMed

Mur, L; Sánchez-Vizcaíno, J M; Fernández-Carrión, E; Jurado, C; Rolesu, S; Feliziani, F; Laddomada, A; Martínez-López, B

2018-02-01

African swine fever virus (ASFV) has been endemic in Sardinia since 1978, resulting in severe losses for local pig producers and creating important problems for the island's veterinary authorities. This study used a spatially explicit stochastic transmission model followed by two regression models to investigate the dynamics of ASFV spread amongst domestic pig farms, to identify geographic areas at highest risk and determine the role of different susceptible pig populations (registered domestic pigs, non-registered domestic pigs [brado] and wild boar) in ASF occurrence. We simulated transmission within and between farms using an adapted version of the previously described model known as Be-FAST. Results from the model revealed a generally low diffusion of ASF in Sardinia, with only 24% of the simulations resulting in disease spread, and for each simulated outbreak on average only four farms and 66 pigs were affected. Overall, local spread (indirect transmission between farms within a 2 km radius through fomites) was the most common route of transmission, being responsible for 98.6% of secondary cases. The risk of ASF occurrence for each domestic pig farm was estimated from the spread model results and integrated in two regression models together with available data for brado and wild boar populations. There was a significant association between the density of all three populations (domestic pigs, brado, and wild boar) and ASF occurrence in Sardinia. The most significant risk factors were the high densities of brado (OR = 2.2) and wild boar (OR = 2.1). The results of both analyses demonstrated that ASF epidemiology and infection dynamics in Sardinia create a complex and multifactorial disease situation, where all susceptible populations play an important role. To stop ASF transmission in Sardinia, three main factors (improving biosecurity on domestic pig farms, eliminating brado practices and better management of wild boars) need to be addressed. © 2017 Blackwell Verlag GmbH.

The Limits of Natural Selection in a Nonequilibrium World.

PubMed

Brandvain, Yaniv; Wright, Stephen I

2016-04-01

Evolutionary theory predicts that factors such as a small population size or low recombination rate can limit the action of natural selection. The emerging field of comparative population genomics offers an opportunity to evaluate these hypotheses. However, classical theoretical predictions assume that populations are at demographic equilibrium. This assumption is likely to be violated in the very populations researchers use to evaluate selection's limits: populations that have experienced a recent shift in population size and/or effective recombination rates. Here we highlight theory and data analyses concerning limitations on the action of natural selection in nonequilibrial populations and argue that substantial care is needed to appropriately test whether species and populations show meaningful differences in selection efficacy. A move toward model-based inferences that explicitly incorporate nonequilibrium dynamics provides a promising approach to more accurately contrast selection efficacy across populations and interpret its significance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Role of seasonality on predator-prey-subsidy population dynamics.

PubMed

Levy, Dorian; Harrington, Heather A; Van Gorder, Robert A

2016-05-07

The role of seasonality on predator-prey interactions in the presence of a resource subsidy is examined using a system of non-autonomous ordinary differential equations (ODEs). The problem is motivated by the Arctic, inhabited by the ecological system of arctic foxes (predator), lemmings (prey), and seal carrion (subsidy). We construct two nonlinear, nonautonomous systems of ODEs named the Primary Model, and the n-Patch Model. The Primary Model considers spatial factors implicitly, and the n-Patch Model considers space explicitly as a "Stepping Stone" system. We establish the boundedness of the dynamics, as well as the necessity of sufficiently nutritional food for the survival of the predator. We investigate the importance of including the resource subsidy explicitly in the model, and the importance of accounting for predator mortality during migration. We find a variety of non-equilibrium dynamics for both systems, obtaining both limit cycles and chaotic oscillations. We were then able to discuss relevant implications for biologically interesting predator-prey systems including subsidy under seasonal effects. Notably, we can observe the extinction or persistence of a species when the corresponding autonomous system might predict the opposite. Copyright © 2016 Elsevier Ltd. 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.

Linking body mass and group dynamics in an obligate cooperative breeder.

PubMed

Ozgul, Arpat; Bateman, Andrew W; English, Sinead; Coulson, Tim; Clutton-Brock, Tim H

2014-11-01

Social and environmental factors influence key life-history processes and population dynamics by affecting fitness-related phenotypic traits such as body mass. The role of body mass is particularly pronounced in cooperative breeders due to variation in social status and consequent variation in access to resources. Investigating the mechanisms underlying variation in body mass and its demographic consequences can help elucidate how social and environmental factors affect the dynamics of cooperatively breeding populations. In this study, we present an analysis of the effect of individual variation in body mass on the temporal dynamics of group size and structure of a cooperatively breeding mongoose, the Kalahari meerkat, Suricata suricatta. First, we investigate how body mass interacts with social (dominance status and number of helpers) and environmental (rainfall and season) factors to influence key life-history processes (survival, growth, emigration and reproduction) in female meerkats. Next, using an individual-based population model, we show that the models explicitly including individual variation in body mass predict group dynamics better than those ignoring this morphological trait. Body mass influences group dynamics mainly through its effects on helper emigration and dominant reproduction. Rainfall has a trait-mediated, destabilizing effect on group dynamics, whereas the number of helpers has a direct and stabilizing effect. Counteracting effects of number of helpers on different demographic rates, despite generating temporal fluctuations, stabilizes group dynamics in the long term. Our study demonstrates that social and environmental factors interact to produce individual variation in body mass and accounting for this variation helps to explain group dynamics in this cooperatively breeding population. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

The influence of interspecific interactions on species range expansion rates

USGS Publications Warehouse

Svenning, Jens-Christian; Gravel, Dominique; Holt, Robert D.; Schurr, Frank M.; Thuiller, Wilfried; Münkemüller, Tamara; Schiffers, Katja H.; Dullinger, Stefan; Edwards, Thomas C.; Hickler, Thomas; Higgins, Steven I.; Nabel, Julia E.M.S.; Pagel, Jörn; Normand, Signe

2014-01-01

Ongoing and predicted global change makes understanding and predicting species’ range shifts an urgent scientific priority. Here, we provide a synthetic perspective on the so far poorly understood effects of interspecific interactions on range expansion rates. We present theoretical foundations for how interspecific interactions may modulate range expansion rates, consider examples from empirical studies of biological invasions and natural range expansions as well as process-based simulations, and discuss how interspecific interactions can be more broadly represented in process-based, spatiotemporally explicit range forecasts. Theory tells us that interspecific interactions affect expansion rates via alteration of local population growth rates and spatial displacement rates, but also via effects on other demographic parameters. The best empirical evidence for interspecific effects on expansion rates comes from studies of biological invasions. Notably, invasion studies indicate that competitive dominance and release from specialized enemies can enhance expansion rates. Studies of natural range expansions especially point to the potential for competition from resident species to reduce expansion rates. Overall, it is clear that interspecific interactions may have important consequences for range dynamics, but also that their effects have received too little attention to robustly generalize on their importance. We then discuss how interspecific interactions effects can be more widely incorporated in dynamic modeling of range expansions. Importantly, models must describe spatiotemporal variation in both local population dynamics and dispersal. Finally, we derive the following guidelines for when it is particularly important to explicitly represent interspecific interactions in dynamic range expansion forecasts: if most interacting species show correlated spatial or temporal trends in their effects on the target species, if the number of interacting species is low, and if the abundance of one or more strongly interacting species is not closely linked to the abundance of the target species.

The influence of interspecific interactions on species range expansion rates.

PubMed

Svenning, Jens-Christian; Gravel, Dominique; Holt, Robert D; Schurr, Frank M; Thuiller, Wilfried; Münkemüller, Tamara; Schiffers, Katja H; Dullinger, Stefan; Edwards, Thomas C; Hickler, Thomas; Higgins, Steven I; Nabel, Julia E M S; Pagel, Jörn; Normand, Signe

2014-12-01

Ongoing and predicted global change makes understanding and predicting species' range shifts an urgent scientific priority. Here, we provide a synthetic perspective on the so far poorly understood effects of interspecific interactions on range expansion rates. We present theoretical foundations for how interspecific interactions may modulate range expansion rates, consider examples from empirical studies of biological invasions and natural range expansions as well as process-based simulations, and discuss how interspecific interactions can be more broadly represented in process-based, spatiotemporally explicit range forecasts. Theory tells us that interspecific interactions affect expansion rates via alteration of local population growth rates and spatial displacement rates, but also via effects on other demographic parameters. The best empirical evidence for interspecific effects on expansion rates comes from studies of biological invasions. Notably, invasion studies indicate that competitive dominance and release from specialized enemies can enhance expansion rates. Studies of natural range expansions especially point to the potential for competition from resident species to reduce expansion rates. Overall, it is clear that interspecific interactions may have important consequences for range dynamics, but also that their effects have received too little attention to robustly generalize on their importance. We then discuss how interspecific interactions effects can be more widely incorporated in dynamic modeling of range expansions. Importantly, models must describe spatiotemporal variation in both local population dynamics and dispersal. Finally, we derive the following guidelines for when it is particularly important to explicitly represent interspecific interactions in dynamic range expansion forecasts: if most interacting species show correlated spatial or temporal trends in their effects on the target species, if the number of interacting species is low, and if the abundance of one or more strongly interacting species is not closely linked to the abundance of the target species.

The influence of interspecific interactions on species range expansion rates

PubMed Central

Svenning, Jens-Christian; Gravel, Dominique; Holt, Robert D.; Schurr, Frank M.; Thuiller, Wilfried; Münkemüller, Tamara; Schiffers, Katja H.; Dullinger, Stefan; Edwards, Thomas C.; Hickler, Thomas; Higgins, Steven I.; Nabel, Julia E. M. S.; Pagel, Jörn; Normand, Signe

2014-01-01

Ongoing and predicted global change makes understanding and predicting species’ range shifts an urgent scientific priority. Here, we provide a synthetic perspective on the so far poorly understood effects of interspecific interactions on range expansion rates. We present theoretical foundations for how interspecific interactions may modulate range expansion rates, consider examples from empirical studies of biological invasions and natural range expansions as well as process-based simulations, and discuss how interspecific interactions can be more broadly represented in process-based, spatiotemporally explicit range forecasts. Theory tells us that interspecific interactions affect expansion rates via alteration of local population growth rates and spatial displacement rates, but also via effects on other demographic parameters. The best empirical evidence for interspecific effects on expansion rates comes from studies of biological invasions. Notably, invasion studies indicate that competitive dominance and release from specialized enemies can enhance expansion rates. Studies of natural range expansions especially point to the potential for competition from resident species to reduce expansion rates. Overall, it is clear that interspecific interactions may have important consequences for range dynamics, but also that their effects have received too little attention to robustly generalize on their importance. We then discuss how interspecific interactions effects can be more widely incorporated in dynamic modeling of range expansions. Importantly, models must describe spatiotemporal variation in both local population dynamics and dispersal. Finally, we derive the following guidelines for when it is particularly important to explicitly represent interspecific interactions in dynamic range expansion forecasts: if most interacting species show correlated spatial or temporal trends in their effects on the target species, if the number of interacting species is low, and if the abundance of one or more strongly interacting species is not closely linked to the abundance of the target species. PMID:25722537

Five challenges for spatial epidemic models.

PubMed

Riley, Steven; Eames, Ken; Isham, Valerie; Mollison, Denis; Trapman, Pieter

2015-03-01

Infectious disease incidence data are increasingly available at the level of the individual and include high-resolution spatial components. Therefore, we are now better able to challenge models that explicitly represent space. Here, we consider five topics within spatial disease dynamics: the construction of network models; characterising threshold behaviour; modelling long-distance interactions; the appropriate scale for interventions; and the representation of population heterogeneity. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

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.

An agent-based approach for modeling dynamics of contagious disease spread

PubMed Central

Perez, Liliana; Dragicevic, Suzana

2009-01-01

Background The propagation of communicable diseases through a population is an inherent spatial and temporal process of great importance for modern society. For this reason a spatially explicit epidemiologic model of infectious disease is proposed for a greater understanding of the disease's spatial diffusion through a network of human contacts. Objective The objective of this study is to develop an agent-based modelling approach the integrates geographic information systems (GIS) to simulate the spread of a communicable disease in an urban environment, as a result of individuals' interactions in a geospatial context. Methods The methodology for simulating spatiotemporal dynamics of communicable disease propagation is presented and the model is implemented using measles outbreak in an urban environment as a case study. Individuals in a closed population are explicitly represented by agents associated to places where they interact with other agents. They are endowed with mobility, through a transportation network allowing them to move between places within the urban environment, in order to represent the spatial heterogeneity and the complexity involved in infectious diseases diffusion. The model is implemented on georeferenced land use dataset from Metro Vancouver and makes use of census data sets from Statistics Canada for the municipality of Burnaby, BC, Canada study site. Results The results provide insights into the application of the model to calculate ratios of susceptible/infected in specific time frames and urban environments, due to its ability to depict the disease progression based on individuals' interactions. It is demonstrated that the dynamic spatial interactions within the population lead to high numbers of exposed individuals who perform stationary activities in areas after they have finished commuting. As a result, the sick individuals are concentrated in geographical locations like schools and universities. Conclusion The GIS-agent based model designed for this study can be easily customized to study the disease spread dynamics of any other communicable disease by simply adjusting the modeled disease timeline and/or the infection model and modifying the transmission process. This type of simulations can help to improve comprehension of disease spread dynamics and to take better steps towards the prevention and control of an epidemic outbreak. PMID:19656403

Virtual-pulse time integral methodology: A new explicit approach for computational dynamics - Theoretical developments for general nonlinear structural dynamics

NASA Technical Reports Server (NTRS)

Chen, Xiaoqin; Tamma, Kumar K.; Sha, Desong

1993-01-01

The present paper describes a new explicit virtual-pulse time integral methodology for nonlinear structural dynamics problems. The purpose of the paper is to provide the theoretical basis of the methodology and to demonstrate applicability of the proposed formulations to nonlinear dynamic structures. Different from the existing numerical methods such as direct time integrations or mode superposition techniques, the proposed methodology offers new perspectives and methodology of development, and possesses several unique and attractive computational characteristics. The methodology is tested and compared with the implicit Newmark method (trapezoidal rule) through a nonlinear softening and hardening spring dynamic models. The numerical results indicate that the proposed explicit virtual-pulse time integral methodology is an excellent alternative for solving general nonlinear dynamic problems.

Simulations for designing and interpreting intervention trials in infectious diseases.

PubMed

Halloran, M Elizabeth; Auranen, Kari; Baird, Sarah; Basta, Nicole E; Bellan, Steven E; Brookmeyer, Ron; Cooper, Ben S; DeGruttola, Victor; Hughes, James P; Lessler, Justin; Lofgren, Eric T; Longini, Ira M; Onnela, Jukka-Pekka; Özler, Berk; Seage, George R; Smith, Thomas A; Vespignani, Alessandro; Vynnycky, Emilia; Lipsitch, Marc

2017-12-29

Interventions in infectious diseases can have both direct effects on individuals who receive the intervention as well as indirect effects in the population. In addition, intervention combinations can have complex interactions at the population level, which are often difficult to adequately assess with standard study designs and analytical methods. Herein, we urge the adoption of a new paradigm for the design and interpretation of intervention trials in infectious diseases, particularly with regard to emerging infectious diseases, one that more accurately reflects the dynamics of the transmission process. In an increasingly complex world, simulations can explicitly represent transmission dynamics, which are critical for proper trial design and interpretation. Certain ethical aspects of a trial can also be quantified using simulations. Further, after a trial has been conducted, simulations can be used to explore the possible explanations for the observed effects. Much is to be gained through a multidisciplinary approach that builds collaborations among experts in infectious disease dynamics, epidemiology, statistical science, economics, simulation methods, and the conduct of clinical trials.

Macroparasite dynamics of migratory host populations.

PubMed

Peacock, Stephanie J; Bouhours, Juliette; Lewis, Mark A; Molnár, Péter K

2018-03-01

Spatial variability in host density is a key factor affecting disease dynamics of wildlife, and yet there are few spatially explicit models of host-macroparasite dynamics. This limits our understanding of parasitism in migratory hosts, whose densities change considerably in both space and time. In this paper, we develop a model for host-macroparasite dynamics that considers the directional movement of host populations and their associated parasites. We include spatiotemporal changes in the mean and variance in parasite burden per host, as well as parasite-mediated host mortality and parasite-mediated migratory ability. Reduced migratory ability with increasing parasitism results in heavily infested hosts halting their migration, and higher parasite burdens in stationary hosts than in moving hosts. Simulations reveal the potential for positive feedbacks between parasite-reduced migratory ability and increasing parasite burdens at infection hotspots, such as stopover sites, that may lead to parasite-induced migratory stalling. This framework could help understand how global change might influence wildlife disease via changes to migratory patterns and parasite demographic rates. Copyright © 2018 Elsevier Inc. All rights reserved.

Coevolutionary dynamics in large, but finite populations

NASA Astrophysics Data System (ADS)

Traulsen, Arne; Claussen, Jens Christian; Hauert, Christoph

2006-07-01

Coevolving and competing species or game-theoretic strategies exhibit rich and complex dynamics for which a general theoretical framework based on finite populations is still lacking. Recently, an explicit mean-field description in the form of a Fokker-Planck equation was derived for frequency-dependent selection with two strategies in finite populations based on microscopic processes [A. Traulsen, J. C. Claussen, and C. Hauert, Phys. Rev. Lett. 95, 238701 (2005)]. Here we generalize this approach in a twofold way: First, we extend the framework to an arbitrary number of strategies and second, we allow for mutations in the evolutionary process. The deterministic limit of infinite population size of the frequency-dependent Moran process yields the adjusted replicator-mutator equation, which describes the combined effect of selection and mutation. For finite populations, we provide an extension taking random drift into account. In the limit of neutral selection, i.e., whenever the process is determined by random drift and mutations, the stationary strategy distribution is derived. This distribution forms the background for the coevolutionary process. In particular, a critical mutation rate uc is obtained separating two scenarios: above uc the population predominantly consists of a mixture of strategies whereas below uc the population tends to be in homogeneous states. For one of the fundamental problems in evolutionary biology, the evolution of cooperation under Darwinian selection, we demonstrate that the analytical framework provides excellent approximations to individual based simulations even for rather small population sizes. This approach complements simulation results and provides a deeper, systematic understanding of coevolutionary dynamics.

Learning to Estimate Dynamical State with Probabilistic Population Codes.

PubMed

Makin, Joseph G; Dichter, Benjamin K; Sabes, Philip N

2015-11-01

Tracking moving objects, including one's own body, is a fundamental ability of higher organisms, playing a central role in many perceptual and motor tasks. While it is unknown how the brain learns to follow and predict the dynamics of objects, it is known that this process of state estimation can be learned purely from the statistics of noisy observations. When the dynamics are simply linear with additive Gaussian noise, the optimal solution is the well known Kalman filter (KF), the parameters of which can be learned via latent-variable density estimation (the EM algorithm). The brain does not, however, directly manipulate matrices and vectors, but instead appears to represent probability distributions with the firing rates of population of neurons, "probabilistic population codes." We show that a recurrent neural network-a modified form of an exponential family harmonium (EFH)-that takes a linear probabilistic population code as input can learn, without supervision, to estimate the state of a linear dynamical system. After observing a series of population responses (spike counts) to the position of a moving object, the network learns to represent the velocity of the object and forms nearly optimal predictions about the position at the next time-step. This result builds on our previous work showing that a similar network can learn to perform multisensory integration and coordinate transformations for static stimuli. The receptive fields of the trained network also make qualitative predictions about the developing and learning brain: tuning gradually emerges for higher-order dynamical states not explicitly present in the inputs, appearing as delayed tuning for the lower-order states.

Learning to Estimate Dynamical State with Probabilistic Population Codes

PubMed Central

Sabes, Philip N.

2015-01-01

Tracking moving objects, including one’s own body, is a fundamental ability of higher organisms, playing a central role in many perceptual and motor tasks. While it is unknown how the brain learns to follow and predict the dynamics of objects, it is known that this process of state estimation can be learned purely from the statistics of noisy observations. When the dynamics are simply linear with additive Gaussian noise, the optimal solution is the well known Kalman filter (KF), the parameters of which can be learned via latent-variable density estimation (the EM algorithm). The brain does not, however, directly manipulate matrices and vectors, but instead appears to represent probability distributions with the firing rates of population of neurons, “probabilistic population codes.” We show that a recurrent neural network—a modified form of an exponential family harmonium (EFH)—that takes a linear probabilistic population code as input can learn, without supervision, to estimate the state of a linear dynamical system. After observing a series of population responses (spike counts) to the position of a moving object, the network learns to represent the velocity of the object and forms nearly optimal predictions about the position at the next time-step. This result builds on our previous work showing that a similar network can learn to perform multisensory integration and coordinate transformations for static stimuli. The receptive fields of the trained network also make qualitative predictions about the developing and learning brain: tuning gradually emerges for higher-order dynamical states not explicitly present in the inputs, appearing as delayed tuning for the lower-order states. PMID:26540152

Modeling spatial variation in avian survival and residency probabilities

USGS Publications Warehouse

Saracco, James F.; Royle, J. Andrew; DeSante, David F.; Gardner, Beth

2010-01-01

The importance of understanding spatial variation in processes driving animal population dynamics is widely recognized. Yet little attention has been paid to spatial modeling of vital rates. Here we describe a hierarchical spatial autoregressive model to provide spatially explicit year-specific estimates of apparent survival (phi) and residency (pi) probabilities from capture-recapture data. We apply the model to data collected on a declining bird species, Wood Thrush (Hylocichla mustelina), as part of a broad-scale bird-banding network, the Monitoring Avian Productivity and Survivorship (MAPS) program. The Wood Thrush analysis showed variability in both phi and pi among years and across space. Spatial heterogeneity in residency probability was particularly striking, suggesting the importance of understanding the role of transients in local populations. We found broad-scale spatial patterning in Wood Thrush phi and pi that lend insight into population trends and can direct conservation and research. The spatial model developed here represents a significant advance over approaches to investigating spatial pattern in vital rates that aggregate data at coarse spatial scales and do not explicitly incorporate spatial information in the model. Further development and application of hierarchical capture-recapture models offers the opportunity to more fully investigate spatiotemporal variation in the processes that drive population changes.

Development of a dynamic framework to explain population patterns of leisure-time physical activity through agent-based modeling.

PubMed

Garcia, Leandro M T; Diez Roux, Ana V; Martins, André C R; Yang, Yong; Florindo, Alex A

2017-08-22

Despite the increasing body of evidences on the factors influencing leisure-time physical activity, our understanding of the mechanisms and interactions that lead to the formation and evolution of population patterns is still limited. Moreover, most frameworks in this field fail to capture dynamic processes. Our aim was to create a dynamic conceptual model depicting the interaction between key psychological attributes of individuals and main aspects of the built and social environments in which they live. This conceptual model will inform and support the development of an agent-based model aimed to explore how population patterns of LTPA in adults may emerge from the dynamic interplay between psychological traits and built and social environments. We integrated existing theories and models as well as available empirical data (both from literature reviews), and expert opinions (based on a systematic expert assessment of an intermediary version of the model). The model explicitly presents intention as the proximal determinant of leisure-time physical activity, a relationship dynamically moderated by the built environment (access, quality, and available activities) - with the strength of the moderation varying as a function of the person's intention- and influenced both by the social environment (proximal network's and community's behavior) and the person's behavior. Our conceptual model is well supported by evidence and experts' opinions and will inform the design of our agent-based model, as well as data collection and analysis of future investigations on population patterns of leisure-time physical activity among adults.

A multi-model framework for simulating wildlife population response to land-use and climate change

USGS Publications Warehouse

McRae, B.H.; Schumaker, N.H.; McKane, R.B.; Busing, R.T.; Solomon, A.M.; Burdick, C.A.

2008-01-01

Reliable assessments of how human activities will affect wildlife populations are essential for making scientifically defensible resource management decisions. A principle challenge of predicting effects of proposed management, development, or conservation actions is the need to incorporate multiple biotic and abiotic factors, including land-use and climate change, that interact to affect wildlife habitat and populations through time. Here we demonstrate how models of land-use, climate change, and other dynamic factors can be integrated into a coherent framework for predicting wildlife population trends. Our framework starts with land-use and climate change models developed for a region of interest. Vegetation changes through time under alternative future scenarios are predicted using an individual-based plant community model. These predictions are combined with spatially explicit animal habitat models to map changes in the distribution and quality of wildlife habitat expected under the various scenarios. Animal population responses to habitat changes and other factors are then projected using a flexible, individual-based animal population model. As an example application, we simulated animal population trends under three future land-use scenarios and four climate change scenarios in the Cascade Range of western Oregon. We chose two birds with contrasting habitat preferences for our simulations: winter wrens (Troglodytes troglodytes), which are most abundant in mature conifer forests, and song sparrows (Melospiza melodia), which prefer more open, shrubby habitats. We used climate and land-use predictions from previously published studies, as well as previously published predictions of vegetation responses using FORCLIM, an individual-based forest dynamics simulator. Vegetation predictions were integrated with other factors in PATCH, a spatially explicit, individual-based animal population simulator. Through incorporating effects of landscape history and limited dispersal, our framework predicted population changes that typically exceeded those expected based on changes in mean habitat suitability alone. Although land-use had greater impacts on habitat quality than did climate change in our simulations, we found that small changes in vital rates resulting from climate change or other stressors can have large consequences for population trajectories. The ability to integrate bottom-up demographic processes like these with top-down constraints imposed by climate and land-use in a dynamic modeling environment is a key advantage of our approach. The resulting framework should allow researchers to synthesize existing empirical evidence, and to explore complex interactions that are difficult or impossible to capture through piecemeal modeling approaches. ?? 2008 Elsevier B.V.

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective.

PubMed

Lion, Sébastien

2018-01-01

Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory. As a result, theoretical evolutionary ecology tends to be divided among different schools of thought, with different toolboxes and motivations. My aim in this synthesis is to highlight the connections between these different approaches and clarify the current state of theory in evolutionary ecology. Central to this approach is to make explicit the dependence on environmental dynamics of the population and evolutionary dynamics, thereby materializing the eco-evolutionary feedback loop. This perspective sheds light on the interplay between environmental feedback and the timescales of ecological and evolutionary processes. I conclude by discussing some potential extensions and challenges to our current theoretical understanding of eco-evolutionary dynamics.

Assessing hypotheses about nesting site occupancy dynamics

USGS Publications Warehouse

Bled, Florent; Royle, J. Andrew; Cam, Emmanuelle

2011-01-01

Hypotheses about habitat selection developed in the evolutionary ecology framework assume that individuals, under some conditions, select breeding habitat based on expected fitness in different habitat. The relationship between habitat quality and fitness may be reflected by breeding success of individuals, which may in turn be used to assess habitat quality. Habitat quality may also be assessed via local density: if high-quality sites are preferentially used, high density may reflect high-quality habitat. Here we assessed whether site occupancy dynamics vary with site surrogates for habitat quality. We modeled nest site use probability in a seabird subcolony (the Black-legged Kittiwake, Rissa tridactyla) over a 20-year period. We estimated site persistence (an occupied site remains occupied from time t to t + 1) and colonization through two subprocesses: first colonization (site creation at the timescale of the study) and recolonization (a site is colonized again after being deserted). Our model explicitly incorporated site-specific and neighboring breeding success and conspecific density in the neighborhood. Our results provided evidence that reproductively "successful'' sites have a higher persistence probability than "unsuccessful'' ones. Analyses of site fidelity in marked birds and of survival probability showed that high site persistence predominantly reflects site fidelity, not immediate colonization by new owners after emigration or death of previous owners. There is a negative quadratic relationship between local density and persistence probability. First colonization probability decreases with density, whereas recolonization probability is constant. This highlights the importance of distinguishing initial colonization and recolonization to understand site occupancy. All dynamics varied positively with neighboring breeding success. We found evidence of a positive interaction between site-specific and neighboring breeding success. We addressed local population dynamics using a site occupancy approach integrating hypotheses developed in behavioral ecology to account for individual decisions. This allows development of models of population and metapopulation dynamics that explicitly incorporate ecological and evolutionary processes.

Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method

DTIC Science & Technology

2011-12-01

REMD while reproducing the energy landscape of explicit solvent simulations . ’ INTRODUCTION Molecular dynamics (MD) simulations of proteins can pro...Mongan, J.; McCammon, J. A. Accelerated molecular dynamics : a promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120 (24...Chemical Theory and Computation ARTICLE (8) Abraham,M. J.; Gready, J. E. Ensuringmixing efficiency of replica- exchange molecular dynamics simulations . J

Kinetic theory of age-structured stochastic birth-death processes

NASA Astrophysics Data System (ADS)

Greenman, Chris D.; Chou, Tom

2016-01-01

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but are unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Stochastic theories that treat semi-Markov age-dependent processes using, e.g., the Bellman-Harris equation do not resolve a population's age structure and are unable to quantify population-size dependencies. Conversely, current theories that include size-dependent population dynamics (e.g., mathematical models that include carrying capacity such as the logistic equation) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new, fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a Bogoliubov--Born--Green--Kirkwood--Yvon-like hierarchy. Explicit solutions are derived in three limits: no birth, no death, and steady state. These are then compared with their corresponding mean-field results. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution.

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.

Scale-up of ecological experiments: Density variation in the mobile bivalve Macomona liliana

USGS Publications Warehouse

Schneider, Davod C.; Walters, R.; Thrush, S.; Dayton, P.

1997-01-01

At present the problem of scaling up from controlled experiments (necessarily at a small spatial scale) to questions of regional or global importance is perhaps the most pressing issue in ecology. Most of the proposed techniques recommend iterative cycling between theory and experiment. We present a graphical technique that facilitates this cycling by allowing the scope of experiments, surveys, and natural history observations to be compared to the scope of models and theory. We apply the scope analysis to the problem of understanding the population dynamics of a bivalve exposed to environmental stress at the scale of a harbour. Previous lab and field experiments were found not to be 1:1 scale models of harbour-wide processes. Scope analysis allowed small scale experiments to be linked to larger scale surveys and to a spatially explicit model of population dynamics.

Explicit symplectic algorithms based on generating functions for relativistic charged particle dynamics in time-dependent electromagnetic field

NASA Astrophysics Data System (ADS)

Zhang, Ruili; Wang, Yulei; He, Yang; Xiao, Jianyuan; Liu, Jian; Qin, Hong; Tang, Yifa

2018-02-01

Relativistic dynamics of a charged particle in time-dependent electromagnetic fields has theoretical significance and a wide range of applications. The numerical simulation of relativistic dynamics is often multi-scale and requires accurate long-term numerical simulations. Therefore, explicit symplectic algorithms are much more preferable than non-symplectic methods and implicit symplectic algorithms. In this paper, we employ the proper time and express the Hamiltonian as the sum of exactly solvable terms and product-separable terms in space-time coordinates. Then, we give the explicit symplectic algorithms based on the generating functions of orders 2 and 3 for relativistic dynamics of a charged particle. The methodology is not new, which has been applied to non-relativistic dynamics of charged particles, but the algorithm for relativistic dynamics has much significance in practical simulations, such as the secular simulation of runaway electrons in tokamaks.

Meta-Analysis of Explicit Memory Studies in Populations with Intellectual Disability

ERIC Educational Resources Information Center

Lifshitz, Hefziba; Shtein, Sarit; Weiss, Izhak; Vakil, Eli

2011-01-01

This meta-analysis combines the effect size (ES) of 40 explicit memory experiments in populations with intellectual disability (ID). Eight meta-analyses were performed, as well as contrast tests between ES. The explicit memory of participants with ID was inferior to that of participants with typical development (TD). Relatively preserved explicit…

Boundedness and global stability of the two-predator and one-prey models with nonlinear prey-taxis

NASA Astrophysics Data System (ADS)

Wang, Jianping; Wang, Mingxin

2018-06-01

This paper concerns the reaction-diffusion systems modeling the population dynamics of two predators and one prey with nonlinear prey-taxis. We first investigate the global existence and boundedness of the unique classical solution for the general model. Then, we study the global stabilities of nonnegative spatially homogeneous equilibria for an explicit system with type I functional responses and density-dependent death rates for the predators and logistic growth for the prey. Moreover, the convergence rates are also established.

Uncoupling the Effects of Seed Predation and Seed Dispersal by Granivorous Ants on Plant Population Dynamics

PubMed Central

Arnan, Xavier; Molowny-Horas, Roberto; Rodrigo, Anselm; Retana, Javier

2012-01-01

Secondary seed dispersal is an important plant-animal interaction, which is central to understanding plant population and community dynamics. Very little information is still available on the effects of dispersal on plant demography and, particularly, for ant-seed dispersal interactions. As many other interactions, seed dispersal by animals involves costs (seed predation) and benefits (seed dispersal), the balance of which determines the outcome of the interaction. Separate quantification of each of them is essential in order to understand the effects of this interaction. To address this issue, we have successfully separated and analyzed the costs and benefits of seed dispersal by seed-harvesting ants on the plant population dynamics of three shrub species with different traits. To that aim a stochastic, spatially-explicit individually-based simulation model has been implemented based on actual data sets. The results from our simulation model agree with theoretical models of plant response dependent on seed dispersal, for one plant species, and ant-mediated seed predation, for another one. In these cases, model predictions were close to the observed values at field. Nonetheless, these ecological processes did not affect in anyway a third species, for which the model predictions were far from the observed values. This indicates that the balance between costs and benefits associated to secondary seed dispersal is clearly related to specific traits. This study is one of the first works that analyze tradeoffs of secondary seed dispersal on plant population dynamics, by disentangling the effects of related costs and benefits. We suggest analyzing the effects of interactions on population dynamics as opposed to merely analyzing the partners and their interaction strength. PMID:22880125

Fitted Fourier-pseudospectral methods for solving a delayed reaction-diffusion partial differential equation in biology

NASA Astrophysics Data System (ADS)

Adam, A. M. A.; Bashier, E. B. M.; Hashim, M. H. A.; Patidar, K. C.

2017-07-01

In this work, we design and analyze a fitted numerical method to solve a reaction-diffusion model with time delay, namely, a delayed version of a population model which is an extension of the logistic growth (LG) equation for a food-limited population proposed by Smith [F.E. Smith, Population dynamics in Daphnia magna and a new model for population growth, Ecology 44 (1963) 651-663]. Seeing that the analytical solution (in closed form) is hard to obtain, we seek for a robust numerical method. The method consists of a Fourier-pseudospectral semi-discretization in space and a fitted operator implicit-explicit scheme in temporal direction. The proposed method is analyzed for convergence and we found that it is unconditionally stable. Illustrative numerical results will be presented at the conference.

Dynamic Assessment of Writing: The Impact of Implicit/Explicit Mediations on L2 Learners' Internalization of Writing Skills and Strategies

ERIC Educational Resources Information Center

Alavi, Sayyed Mohammad; Taghizadeh, Mahboubeh

2014-01-01

Dynamic assessment is a procedure in which development is simultaneously assessed and improved with regard to the individual's or group's Zone of Proximal Development (ZPD; Lantolf & Poehner, 2004). This study aimed to follow dynamic assessment and investigate the impact of three types of implicit and explicit feedback on the essay writing of…

Spreading dynamics on complex networks: a general stochastic approach.

PubMed

Noël, Pierre-André; Allard, Antoine; Hébert-Dufresne, Laurent; Marceau, Vincent; Dubé, Louis J

2014-12-01

Dynamics on networks is considered from the perspective of Markov stochastic processes. We partially describe the state of the system through network motifs and infer any missing data using the available information. This versatile approach is especially well adapted for modelling spreading processes and/or population dynamics. In particular, the generality of our framework and the fact that its assumptions are explicitly stated suggests that it could be used as a common ground for comparing existing epidemics models too complex for direct comparison, such as agent-based computer simulations. We provide many examples for the special cases of susceptible-infectious-susceptible and susceptible-infectious-removed dynamics (e.g., epidemics propagation) and we observe multiple situations where accurate results may be obtained at low computational cost. Our perspective reveals a subtle balance between the complex requirements of a realistic model and its basic assumptions.

No Need for Conspiracy: Self-Organized Cartel Formation in a Modified Trust Game

NASA Astrophysics Data System (ADS)

Peixoto, Tiago P.; Bornholdt, Stefan

2012-05-01

We investigate the dynamics of a trust game on a mixed population, where individuals with the role of buyers are forced to play against a predetermined number of sellers whom they choose dynamically. Agents with the role of sellers are also allowed to adapt the level of value for money of their products, based on payoff. The dynamics undergoes a transition at a specific value of the strategy update rate, above which an emergent cartel organization is observed, where sellers have similar values of below-optimal value for money. This cartel organization is not due to an explicit collusion among agents; instead, it arises spontaneously from the maximization of the individual payoffs. This dynamics is marked by large fluctuations and a high degree of unpredictability for most of the parameter space and serves as a plausible qualitative explanation for observed elevated levels and fluctuations of certain commodity prices.

Irruptive dynamics of introduced caribou on Adak Island, Alaska: an evaluation of Riney-Caughley model predictions

USGS Publications Warehouse

Ricca, Mark A.; Van Vuren, Dirk H.; Weckerly, Floyd W.; Williams, Jeffrey C.; Miles, A. Keith

2014-01-01

Large mammalian herbivores introduced to islands without predators are predicted to undergo irruptive population and spatial dynamics, but only a few well-documented case studies support this paradigm. We used the Riney-Caughley model as a framework to test predictions of irruptive population growth and spatial expansion of caribou (Rangifer tarandus granti) introduced to Adak Island in the Aleutian archipelago of Alaska in 1958 and 1959. We utilized a time series of spatially explicit counts conducted on this population intermittently over a 54-year period. Population size increased from 23 released animals to approximately 2900 animals in 2012. Population dynamics were characterized by two distinct periods of irruptive growth separated by a long time period of relative stability, and the catalyst for the initial irruption was more likely related to annual variation in hunting pressure than weather conditions. An unexpected pattern resembling logistic population growth occurred between the peak of the second irruption in 2005 and the next survey conducted seven years later in 2012. Model simulations indicated that an increase in reported harvest alone could not explain the deceleration in population growth, yet high levels of unreported harvest combined with increasing density-dependent feedbacks on fecundity and survival were the most plausible explanation for the observed population trend. No studies of introduced island Rangifer have measured a time series of spatial use to the extent described in this study. Spatial use patterns during the post-calving season strongly supported Riney-Caughley model predictions, whereby high-density core areas expanded outwardly as population size increased. During the calving season, caribou displayed marked site fidelity across the full range of population densities despite availability of other suitable habitats for calving. Finally, dispersal and reproduction on neighboring Kagalaska Island represented a new dispersal front for irruptive dynamics and a new challenge for resource managers. The future demography of caribou on both islands is far from certain, yet sustained and significant hunting pressure should be a vital management tool.

Characterization of the Dispersal of Non-Domiciliated Triatoma dimidiata through the Selection of Spatially Explicit Models

PubMed Central

Barbu, Corentin; Dumonteil, Eric; Gourbière, Sébastien

2010-01-01

Background Chagas disease is a major parasitic disease in Latin America, prevented in part by vector control programs that reduce domestic populations of triatomines. However, the design of control strategies adapted to non-domiciliated vectors, such as Triatoma dimidiata, remains a challenge because it requires an accurate description of their spatio-temporal distributions, and a proper understanding of the underlying dispersal processes. Methodology/Principal Findings We combined extensive spatio-temporal data sets describing house infestation dynamics by T. dimidiata within a village, and spatially explicit population dynamics models in a selection model approach. Several models were implemented to provide theoretical predictions under different hypotheses on the origin of the dispersers and their dispersal characteristics, which we compared with the spatio-temporal pattern of infestation observed in the field. The best models fitted the dynamic of infestation described by a one year time-series, and also predicted with a very good accuracy the infestation process observed during a second replicate one year time-series. The parameterized models gave key insights into the dispersal of these vectors. i) About 55% of the triatomines infesting houses came from the peridomestic habitat, the rest corresponding to immigration from the sylvatic habitat, ii) dispersing triatomines were 5–15 times more attracted by houses than by peridomestic area, and iii) the moving individuals spread on average over rather small distances, typically 40–60 m/15 days. Conclusion/Significance Since these dispersal characteristics are associated with much higher abundance of insects in the periphery of the village, we discuss the possibility that spatially targeted interventions allow for optimizing the efficacy of vector control activities within villages. Such optimization could prove very useful in the context of limited resources devoted to vector control. PMID:20689823

A new heterogeneous asynchronous explicit-implicit time integrator for nonsmooth dynamics

NASA Astrophysics Data System (ADS)

Fekak, Fatima-Ezzahra; Brun, Michael; Gravouil, Anthony; Depale, Bruno

2017-07-01

In computational structural dynamics, particularly in the presence of nonsmooth behavior, the choice of the time-step and the time integrator has a critical impact on the feasibility of the simulation. Furthermore, in some cases, as in the case of a bridge crane under seismic loading, multiple time-scales coexist in the same problem. In that case, the use of multi-time scale methods is suitable. Here, we propose a new explicit-implicit heterogeneous asynchronous time integrator (HATI) for nonsmooth transient dynamics with frictionless unilateral contacts and impacts. Furthermore, we present a new explicit time integrator for contact/impact problems where the contact constraints are enforced using a Lagrange multiplier method. In other words, the aim of this paper consists in using an explicit time integrator with a fine time scale in the contact area for reproducing high frequency phenomena, while an implicit time integrator is adopted in the other parts in order to reproduce much low frequency phenomena and to optimize the CPU time. In a first step, the explicit time integrator is tested on a one-dimensional example and compared to Moreau-Jean's event-capturing schemes. The explicit algorithm is found to be very accurate and the scheme has generally a higher order of convergence than Moreau-Jean's schemes and provides also an excellent energy behavior. Then, the two time scales explicit-implicit HATI is applied to the numerical example of a bridge crane under seismic loading. The results are validated in comparison to a fine scale full explicit computation. The energy dissipated in the implicit-explicit interface is well controlled and the computational time is lower than a full-explicit simulation.

Dispersal responses override density effects on genetic diversity during post-disturbance succession

PubMed Central

Landguth, Erin L.; Bull, C. Michael; Banks, Sam C.; Gardner, Michael G.; Driscoll, Don A.

2016-01-01

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus. We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity in N. stellatus. Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics. PMID:27009225

Productivity responses of a widespread marine piscivore, Gadus morhua, to oceanic thermal extremes and trends.

PubMed

Mantzouni, Irene; MacKenzie, Brian R

2010-06-22

Climate change will have major consequences for population dynamics and life histories of marine biota as it progresses in the twenty-first century. These impacts will differ in magnitude and direction for populations within individual marine species whose geographical ranges span large gradients in latitude and temperature. Here we use meta-analytical methods to investigate how recruitment (i.e. the number of new fish produced by spawners in a given year which subsequently grow and survive to become vulnerable to fishing gear) has reacted to temperature fluctuations, and in particular to extremes of temperature, in cod populations throughout the north Atlantic. Temperature has geographically explicit effects on cod recruitment. Impacts differ depending on whether populations are located in the upper (negative effects) or in the lower (positive effects) thermal range. The probabilities of successful year-classes in populations living in warm areas is on average 34 per cent higher in cold compared with warm seasons, whereas opposite patterns exist for populations living in cold areas. These results have implications for cod dynamics, distributions and phenologies under the influence of ocean warming, particularly related to not only changes in the mean temperature, but also its variability (e.g. frequency of exceptionally cold or warm seasons).

Population genetics and demography unite ecology and evolution

USGS Publications Warehouse

Lowe, Winsor H.; Kovach, Ryan; Allendorf, Fred W.

2017-01-01

The interplay of ecology and evolution has been a rich area of research for decades. A surge of interest in this area was catalyzed by the observation that evolution by natural selection can operate at the same contemporary timescales as ecological dynamics. Specifically, recent eco-evolutionary research focuses on how rapid adaptation influences ecology, and vice versa. Evolution by non-adaptive forces also occurs quickly, with ecological consequences, but understanding the full scope of ecology–evolution (eco–evo) interactions requires explicitly addressing population-level processes – genetic and demographic. We show the strong ecological effects of non-adaptive evolutionary forces and, more broadly, the value of population-level research for gaining a mechanistic understanding of eco–evo interactions. The breadth of eco-evolutionary research should expand to incorporate the breadth of evolution itself.

Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution.

PubMed

Nina, Mafalda; Fonné-Pfister, Raymonde; Beaudegnies, Renaud; Chekatt, Habiba; Jung, Pierre M J; Murphy-Kessabi, Fiona; De Mesmaeker, Alain; Wendeborn, Sebastian

2005-04-27

Thermodynamic and structural properties of a chemically modified DNA-RNA hybrid in which a phosphodiester linkage is replaced by a neutral amide-3 linkage (3'-CH(2)-CONH-5') were investigated using UV melting experiments, molecular dynamics simulations in explicit water, and continuum solvent models. van't Hoff analysis of the experimental UV melting curves suggests that the significant increase of the thermodynamic stability of a 15-mer DNA-RNA with seven alternated amide-3 modifications (+11 degrees C) is mainly due to an increased binding enthalpy. To further evaluate the origin in the observed affinities differences, the electrostatic contribution to the binding free energy was calculated by solving the Poisson-Boltzmann equation numerically. The nonelectrostatic contribution was estimated as the product of a hydrophobic surface tension coefficient and the surface area that is buried upon double strand formation. Structures were taken from 10 ns molecular dynamics simulations computed in a consistent fashion using explicit solvent, counterions, and the particle-mesh Ewald procedure. The present preliminary thermodynamic study suggests that the favorable binding free energy of the amide-3 DNA single strand to the complementary RNA is equally driven by electrostatic and nonpolar contributions to the binding compared to their natural analogues. In addition, molecular dynamics simulations in explicit water were performed on an amide-3 DNA single strand and the corresponding natural DNA. Results from the conformations cluster analysis of the simulated amide-3 DNA single strand ensembles suggest that the 25% of the population sampled within 10 ns has a pre-organized conformation where the sugar C3' endo pucker is favored at the 3'-flanking nucleotides. These structural and thermodynamic features contribute to the understanding of the observed increased affinities of the amide-3 DNA-RNA hybrids at the microscopic level.

Multispecies modeling for adaptive management of horseshoe crabs and red knots in the Delaware Bay

USGS Publications Warehouse

McGowan, Conor P.; Smith, David; Sweka, John A.; Martin, Julien; Nichols, James D.; Wong, Richard; Lyons, James E.; Niles, Lawrence J.; Kalasz, Kevin; Brust, Jeffrey; Klopfer, Michelle; Spear, Braddock

2011-01-01

Adaptive management requires that predictive models be explicit and transparent to improve decisions by comparing management actions, directing further research and monitoring, and facilitating learning. The rufa subspecies of red knots (Calidris canutus rufa), which has recently exhibited steep population declines, relies on horseshoe crab (Limulus polyphemus) eggs as their primary food source during stopover in Delaware Bay during spring migration. We present a model with two different parameterizations for use in the adaptive management of horseshoe crab harvests in the Delaware Bay that links red knot mass gain, annual survival, and fecundity to horseshoe crab dynamics. The models reflect prevailing hypotheses regarding ecological links between these two species. When reported crab harvest from 1998 to 2008 was applied, projections corresponded to the observed red knot population abundances depending on strengths of the demographic relationship between these species. We compared different simulated horseshoe crab harvest strategies to evaluate whether, given this model, horseshoe crab harvest management can affect red knot conservation and found that restricting harvest can benefit red knot populations. Our model is the first to explicitly and quantitatively link these two species and will be used within an adaptive management framework to manage the Delaware Bay system and learn more about the specific nature of the linkage between the two species.

Understanding climate impacts on recruitment and spatial dynamics of Atlantic cod in the Gulf of Maine: Integration of observations and modeling

NASA Astrophysics Data System (ADS)

Runge, Jeffrey A.; Kovach, Adrienne I.; Churchill, James H.; Kerr, Lisa A.; Morrison, John R.; Beardsley, Robert C.; Berlinsky, David L.; Chen, Changsheng; Cadrin, Steven X.; Davis, Cabell S.; Ford, Kathryn H.; Grabowski, Jonathan H.; Howell, W. Huntting; Ji, Rubao; Jones, Rebecca J.; Pershing, Andrew J.; Record, Nicholas R.; Thomas, Andrew C.; Sherwood, Graham D.; Tallack, Shelly M. L.; Townsend, David W.

2010-10-01

We put forward a combined observing and modeling strategy for evaluating effects of environmental forcing on the dynamics of spatially structured cod populations spawning in the western Gulf of Maine. Recent work indicates at least two genetically differentiated complexes in this region: a late spring spawning, coastal population centered in Ipswich Bay, and a population that spawns in winter inshore and on nearshore banks in the Gulf of Maine and off southern New England. The two populations likely differ in trophic interactions and in physiological and behavioral responses to different winter and spring environments. Coupled physical-biological modeling has advanced to the point where within-decade forecasting of environmental conditions for recruitment to each of the two populations is feasible. However, the modeling needs to be supported by hydrographic, primary production and zooplankton data collected by buoys, and by data from remote sensing and fixed station sampling. Forecasts of environmentally driven dispersal and growth of planktonic early life stages, combined with an understanding of possible population-specific predator fields, usage of coastal habitat by juveniles and adult resident and migratory patterns, can be used to develop scenarios for spatially explicit population responses to multiple forcings, including climate change, anthropogenic impacts on nearshore juvenile habitat, connectivity among populations and management interventions such as regional fisheries closures.

Logistical constraints lead to an intermediate optimum in outbreak response vaccination

PubMed Central

Shea, Katriona; Ferrari, Matthew

2018-01-01

Dynamic models in disease ecology have historically evaluated vaccination strategies under the assumption that they are implemented homogeneously in space and time. However, this approach fails to formally account for operational and logistical constraints inherent in the distribution of vaccination to the population at risk. Thus, feedback between the dynamic processes of vaccine distribution and transmission might be overlooked. Here, we present a spatially explicit, stochastic Susceptible-Infected-Recovered-Vaccinated model that highlights the density-dependence and spatial constraints of various diffusive strategies of vaccination during an outbreak. The model integrates an agent-based process of disease spread with a partial differential process of vaccination deployment. We characterize the vaccination response in terms of a diffusion rate that describes the distribution of vaccination to the population at risk from a central location. This generates an explicit trade-off between slow diffusion, which concentrates effort near the central location, and fast diffusion, which spreads a fixed vaccination effort thinly over a large area. We use stochastic simulation to identify the optimum vaccination diffusion rate as a function of population density, interaction scale, transmissibility, and vaccine intensity. Our results show that, conditional on a timely response, the optimal strategy for minimizing outbreak size is to distribute vaccination resource at an intermediate rate: fast enough to outpace the epidemic, but slow enough to achieve local herd immunity. If the response is delayed, however, the optimal strategy for minimizing outbreak size changes to a rapidly diffusive distribution of vaccination effort. The latter may also result in significantly larger outbreaks, thus suggesting a benefit of allocating resources to timely outbreak detection and response. PMID:29791432

Advanced hierarchical distance sampling

USGS Publications Warehouse

Royle, Andy

2016-01-01

In this chapter, we cover a number of important extensions of the basic hierarchical distance-sampling (HDS) framework from Chapter 8. First, we discuss the inclusion of “individual covariates,” such as group size, in the HDS model. This is important in many surveys where animals form natural groups that are the primary observation unit, with the size of the group expected to have some influence on detectability. We also discuss HDS integrated with time-removal and double-observer or capture-recapture sampling. These “combined protocols” can be formulated as HDS models with individual covariates, and thus they have a commonality with HDS models involving group structure (group size being just another individual covariate). We cover several varieties of open-population HDS models that accommodate population dynamics. On one end of the spectrum, we cover models that allow replicate distance sampling surveys within a year, which estimate abundance relative to availability and temporary emigration through time. We consider a robust design version of that model. We then consider models with explicit dynamics based on the Dail and Madsen (2011) model and the work of Sollmann et al. (2015). The final major theme of this chapter is relatively newly developed spatial distance sampling models that accommodate explicit models describing the spatial distribution of individuals known as Point Process models. We provide novel formulations of spatial DS and HDS models in this chapter, including implementations of those models in the unmarked package using a hack of the pcount function for N-mixture models.

Explicit filtering in large eddy simulation using a discontinuous Galerkin method

NASA Astrophysics Data System (ADS)

Brazell, Matthew J.

The discontinuous Galerkin (DG) method is a formulation of the finite element method (FEM). DG provides the ability for a high order of accuracy in complex geometries, and allows for highly efficient parallelization algorithms. These attributes make the DG method attractive for solving the Navier-Stokes equations for large eddy simulation (LES). The main goal of this work is to investigate the feasibility of adopting an explicit filter in the numerical solution of the Navier-Stokes equations with DG. Explicit filtering has been shown to increase the numerical stability of under-resolved simulations and is needed for LES with dynamic sub-grid scale (SGS) models. The explicit filter takes advantage of DG's framework where the solution is approximated using a polyno- mial basis where the higher modes of the solution correspond to a higher order polynomial basis. By removing high order modes, the filtered solution contains low order frequency content much like an explicit low pass filter. The explicit filter implementation is tested on a simple 1-D solver with an initial condi- tion that has some similarity to turbulent flows. The explicit filter does restrict the resolution as well as remove accumulated energy in the higher modes from aliasing. However, the ex- plicit filter is unable to remove numerical errors causing numerical dissipation. A second test case solves the 3-D Navier-Stokes equations of the Taylor-Green vortex flow (TGV). The TGV is useful for SGS model testing because it is initially laminar and transitions into a fully turbulent flow. The SGS models investigated include the constant coefficient Smagorinsky model, dynamic Smagorinsky model, and dynamic Heinz model. The constant coefficient Smagorinsky model is over dissipative, this is generally not desirable however it does add stability. The dynamic Smagorinsky model generally performs better, especially during the laminar-turbulent transition region as expected. The dynamic Heinz model which is based on an improved model, handles the laminar-turbulent transition region well while also showing additional robustness.

Modeling the effects of space structure and combination therapies on phenotypic heterogeneity and drug resistance in solid tumors.

PubMed

Lorz, Alexander; Lorenzi, Tommaso; Clairambault, Jean; Escargueil, Alexandre; Perthame, Benoît

2015-01-01

Histopathological evidence supports the idea that the emergence of phenotypic heterogeneity and resistance to cytotoxic drugs can be considered as a process of selection in tumor cell populations. In this framework, can we explain intra-tumor heterogeneity in terms of selection driven by the local cell environment? Can we overcome the emergence of resistance and favor the eradication of cancer cells by using combination therapies? Bearing these questions in mind, we develop a model describing cell dynamics inside a tumor spheroid under the effects of cytotoxic and cytostatic drugs. Cancer cells are assumed to be structured as a population by two real variables standing for space position and the expression level of a phenotype of resistance to cytotoxic drugs. The model takes explicitly into account the dynamics of resources and anticancer drugs as well as their interactions with the cell population under treatment. We analyze the effects of space structure and combination therapies on phenotypic heterogeneity and chemotherapeutic resistance. Furthermore, we study the efficacy of combined therapy protocols based on constant infusion and bang-bang delivery of cytotoxic and cytostatic drugs.

Population structuring of multi-copy, antigen-encoding genes in Plasmodium falciparum

PubMed Central

Artzy-Randrup, Yael; Rorick, Mary M; Day, Karen; Chen, Donald; Dobson, Andrew P; Pascual, Mercedes

2012-01-01

The coexistence of multiple independently circulating strains in pathogen populations that undergo sexual recombination is a central question of epidemiology with profound implications for control. An agent-based model is developed that extends earlier ‘strain theory’ by addressing the var gene family of Plasmodium falciparum. The model explicitly considers the extensive diversity of multi-copy genes that undergo antigenic variation via sequential, mutually exclusive expression. It tracks the dynamics of all unique var repertoires in a population of hosts, and shows that even under high levels of sexual recombination, strain competition mediated through cross-immunity structures the parasite population into a subset of coexisting dominant repertoires of var genes whose degree of antigenic overlap depends on transmission intensity. Empirical comparison of patterns of genetic variation at antigenic and neutral sites supports this role for immune selection in structuring parasite diversity. DOI: http://dx.doi.org/10.7554/eLife.00093.001 PMID:23251784

Fitting a Structured Juvenile-Adult Model for Green Tree Frogs to Population Estimates from Capture-Mark-Recapture Field Data

USGS Publications Warehouse

Ackleh, A.S.; Carter, J.; Deng, K.; Huang, Q.; Pal, N.; Yang, X.

2012-01-01

We derive point and interval estimates for an urban population of green tree frogs (Hyla cinerea) from capture-mark-recapture field data obtained during the years 2006-2009. We present an infinite-dimensional least-squares approach which compares a mathematical population model to the statistical population estimates obtained from the field data. The model is composed of nonlinear first-order hyperbolic equations describing the dynamics of the amphibian population where individuals are divided into juveniles (tadpoles) and adults (frogs). To solve the least-squares problem, an explicit finite difference approximation is developed. Convergence results for the computed parameters are presented. Parameter estimates for the vital rates of juveniles and adults are obtained, and standard deviations for these estimates are computed. Numerical results for the model sensitivity with respect to these parameters are given. Finally, the above-mentioned parameter estimates are used to illustrate the long-time behavior of the population under investigation. ?? 2011 Society for Mathematical Biology.

Foraminifera Record the Good Years More than the Bad

NASA Astrophysics Data System (ADS)

Hull, P. M.

2014-12-01

Past ocean conditions are primarily discerned from geochemical and community-based analyses of fossilized taxa, each of which have unique environmental niches and dynamics. A key requirement of such paleoceanographic studies is that some unbiased or well-constrained record of the living ecosystem and climate is deposited on the sea floor and preserved through the post-depositional processes that act to distort them. It is widely known that foraminiferal species exhibit varying seasonal preferences and that seasonality is a key variable to account for in paleoceanographic reconstructions. However, on longer time scales (> year), it is generally assumed that species record the 'average' environmental conditions or typical variance (e.g., El Nino intensity) that existed in a given, time-averaged sediment sample. Here I examine planktonic foraminiferal population dynamics on yearly and longer time scales, in order to quantify their effect on paleoceanographic reconstructions. Using a previously published record of >250 years of population dynamics in the Santa Barbara Basin sediments, I find that the majority of individuals in a given species lived during a small subset of the total years (~15- 37% of years depending on the species). Populations of shallow, mixed layer species primarily represent the warmest, youngest years, while thermocline species primarily represent the cooler, older years. Importantly, the seasonality of species does not always predict their interannual dynamics. The general importance of long time-scale population dynamics on paleoceanographic reconstructions will also be considered in a theoretical model parameterized with temporally explicit species co-variances and temperature variability. Such modeling is needed to constrain the relative impact that a very good year can have on our interpretation of the 'average' of hundreds to thousands of years.

Structure of Alzheimer's 10-35 β peptide from replica-exchange molecular dynamics simulations in explicit water

NASA Astrophysics Data System (ADS)

Baumketner, Andriy; Shea, Joan-Emma

2006-03-01

We report a replica-exchange molecular dynamics study of the 10-35 fragment of Alzheimer's disease amyloid β peptide, Aβ10-35, in aqueous solution. This fragment was previously seen [J. Str. Biol. 130 (2000) 130] to possess all the most important amyloidogenic properties characteristic of full-length Aβ peptides. Our simulations attempted to fold Aβ10-35 from first principles. The peptide was modeled using all-atom OPLS/AA force field in conjunction with the TIP3P explicit solvent model. A total of 72 replicas were considered and simulated over 40 ns of total time, including 5 ns of initial equilibration. We find that Aβ10-35 does not possess any unique folded state, a 3D structure of predominant population, under normal temperature and pressure. Rather, this peptide exists as a mixture of collapsed globular states that remain in rapid dynamic equilibrium with each other. This conformational ensemble is seen to be dominated by random coil and bend structures with insignificant presence of α-helical or β-sheet structure. We find that, overall, the 3D structure of Aβ10-35 is shaped by salt bridges formed between oppositely charged residues.Of all possible salt bridges, K28-D23 was seen to have the highest formation probability, totaling more than 60% of the time.

Population-level consequences of herbivory, changing climate, and source-sink dynamics on a long-lived invasive shrub.

PubMed

van Klinken, R D; Pichancourt, J B

2015-12-01

Long-lived plant species are highly valued environmentally, economically, and socially, but can also cause substantial harm as invaders. Realistic demographic predictions can guide management decisions, and are particularly valuable for long-lived species where population response times can be long. Long-lived species are also challenging, given population dynamics can be affected by factors as diverse as herbivory, climate, and dispersal. We developed a matrix model to evaluate the effects of herbivory by a leaf-feeding biological control agent released in Australia against a long-lived invasive shrub (mesquite, Leguminoseae: Prosopis spp.). The stage-structured, density-dependent model used an annual time step and 10 climatically diverse years of field data. Mesquite population demography is sensitive to source-sink dynamics as most seeds are consumed and redistributed spatially by livestock. In addition, individual mesquite plants, because they are long lived, experience natural climate variation that cycles over decadal scales, as well as anthropogenic climate change. The model therefore explicitly considered the effects of both net dispersal and climate variation. Herbivory strongly regulated mesquite populations through reduced growth and fertility, but additional mortality of older plants will be required to reach management goals within a reasonable time frame. Growth and survival of seeds and seedlings were correlated with daily soil moisture. As a result, population dynamics were sensitive to rainfall scenario, but population response times were typically slow (20-800 years to reach equilibrium or extinction) due to adult longevity. Equilibrium population densities were expected to remain 5% higher, and be more dynamic, if historical multi-decadal climate patterns persist, the effect being dampened by herbivory suppressing seed production irrespective of preceding rainfall. Dense infestations were unlikely to form under a drier climate, and required net dispersal under the current climate. Seed input wasn't required to form dense infestations under a wetter climate. Each factor we considered (ongoing herbivory, changing climate, and source-sink dynamics) has a strong bearing on how this invasive species should be managed, highlighting the need for considering both ecological context (in this case, source-sink dynamics) and the effect of climate variability at relevant temporal scales (daily, multi-decadal, and anthropogenic) when deriving management recommendations for long-lived species.

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

Lee, Myeong H., E-mail: myeong.lee@warwick.ac.uk; Troisi, Alessandro

Vibronic coupling between the electronic and vibrational degrees of freedom has been reported to play an important role in charge and exciton transport in organic photovoltaic materials, molecular aggregates, and light-harvesting complexes. Explicitly accounting for effective vibrational modes rather than treating them as a thermal environment has been shown to be crucial to describe the effect of vibronic coupling. We present a methodology to study dissipative quantum dynamics of vibronically coupled systems based on a surrogate Hamiltonian approach, which is in principle not limited by Markov approximation or weak system-bath interaction, using a vibronic basis. We apply vibronic surrogate Hamiltonianmore » method to a linear chain system and discuss how different types of relaxation process, intramolecular vibrational relaxation and intermolecular vibronic relaxation, influence population dynamics of dissipative vibronic systems.« less

Dynamic habitat selection by two wading bird species with divergent foraging strategies in a seasonally fluctuating wetland

USGS Publications Warehouse

Beerens, James M.; Gawlik, Dale E.; Herring, Garth; Cook, Mark I.

2011-01-01

Seasonal and annual variation in food availability during the breeding season plays an influential role in the population dynamics of many avian species. In highly dynamic ecosystems like wetlands, finding and exploiting food resources requires a flexible behavioral response that may produce different population trends that vary with a species' foraging strategy. We quantified dynamic foraging-habitat selection by breeding and radiotagged White Ibises (Eudocimus albus) and Great Egrets (Ardea alba) in the Florida Everglades, where fluctuation in food resources is pronounced because of seasonal drying and flooding. The White Ibis is a tactile “searcher” species in population decline that specializes on highly concentrated prey, whereas the Great Egret, in a growing population, is a visual “exploiter” species that requires lower prey concentrations. In a year with high food availability, resource-selection functions for both species included variables that changed over multiannual time scales and were associated with increased prey production. In a year with low food availability, resource-selection functions included short-term variables that concentrated prey (e.g., water recession rates and reversals in drying pattern), which suggests an adaptive response to poor foraging conditions. In both years, the White Ibis was more restricted in its use of habitats than the Great Egret. Real-time species—habitat suitability models were developed to monitor and assess the daily availability and quality of spatially explicit habitat resources for both species. The models, evaluated through hindcasting using independent observations, demonstrated that habitat use of the more specialized White Ibis was more accurately predicted than that of the more generalist Great Egret.

Population Genetics and Demography Unite Ecology and Evolution.

PubMed

Lowe, Winsor H; Kovach, Ryan P; Allendorf, Fred W

2017-02-01

The interplay of ecology and evolution has been a rich area of research for decades. A surge of interest in this area was catalyzed by the observation that evolution by natural selection can operate at the same contemporary timescales as ecological dynamics. Specifically, recent eco-evolutionary research focuses on how rapid adaptation influences ecology, and vice versa. Evolution by non-adaptive forces also occurs quickly, with ecological consequences, but understanding the full scope of ecology-evolution (eco-evo) interactions requires explicitly addressing population-level processes - genetic and demographic. We show the strong ecological effects of non-adaptive evolutionary forces and, more broadly, the value of population-level research for gaining a mechanistic understanding of eco-evo interactions. The breadth of eco-evolutionary research should expand to incorporate the breadth of evolution itself. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modelling the effect of urbanization on the transmission of an infectious disease.

PubMed

Zhang, Ping; Atkinson, Peter M

2008-01-01

This paper models the impact of urbanization on infectious disease transmission by integrating a CA land use development model, population projection matrix model and CA epidemic model in S-Plus. The innovative feature of this model lies in both its explicit treatment of spatial land use development, demographic changes, infectious disease transmission and their combination in a dynamic, stochastic model. Heuristically-defined transition rules in cellular automata (CA) were used to capture the processes of both land use development with urban sprawl and infectious disease transmission. A population surface model and dwelling distribution surface were used to bridge the gap between urbanization and infectious disease transmission. A case study is presented involving modelling influenza transmission in Southampton, a dynamically evolving city in the UK. The simulation results for Southampton over a 30-year period show that the pattern of the average number of infection cases per day can depend on land use and demographic changes. The modelling framework presents a useful tool that may be of use in planning applications.

Algorithms and software for nonlinear structural dynamics

NASA Technical Reports Server (NTRS)

Belytschko, Ted; Gilbertsen, Noreen D.; Neal, Mark O.

1989-01-01

The objective of this research is to develop efficient methods for explicit time integration in nonlinear structural dynamics for computers which utilize both concurrency and vectorization. As a framework for these studies, the program WHAMS, which is described in Explicit Algorithms for the Nonlinear Dynamics of Shells (T. Belytschko, J. I. Lin, and C.-S. Tsay, Computer Methods in Applied Mechanics and Engineering, Vol. 42, 1984, pp 225 to 251), is used. There are two factors which make the development of efficient concurrent explicit time integration programs a challenge in a structural dynamics program: (1) the need for a variety of element types, which complicates the scheduling-allocation problem; and (2) the need for different time steps in different parts of the mesh, which is here called mixed delta t integration, so that a few stiff elements do not reduce the time steps throughout the mesh.

Linking Crystal Populations to Dynamic States: Crystal Dissolution and Growth During an Open-System Event

NASA Astrophysics Data System (ADS)

Bergantz, G. W.; Schleicher, J.; Burgisser, A.

2016-12-01

The identification of shared characteristics in zoned crystals has motivated the definition of crystal populations. These populations reflect the simultaneous transport of crystals, heat and composition during open-system events. An obstacle to interpreting the emergence of a population is the absence of a way to correlate specific dynamic conditions with the characteristic attributes of a population. By combining a boundary-layer diffusion controlled model for crystal growth/dissolution with discrete-element magma dynamics simulations of crystal-bearing magmas, the creation of populations can be simulated. We have implemented a method that decomposes the chemical potential into the thermal and compositional contributions to crystal dissolution/growth. This allows for the explicit treatment of thermal inertia and thermal-compositional decoupling as fluid circulation stirs the system during an open-system event. We have identified three distinct dynamic states producing crystal populations. They are based on the volume fraction of crystals. In a mushy system, thermal and compositional states are tightly linked as the volume involved in the mixing is constrained by the so-called mixing bowl (Bergantz et al., 2015). The mixing bowl volume is a function of the visco-plastic response of the mush and the intrusion width, not by the progressive entrainment of the new intrusion as commonly assumed. Crystal dissolution is the dominate response to input of more primitive magma. At the other endmember, under very dilute conditions, thermal and compositional conditions can become decoupled, and the in-coming magma forms a double-diffusive low-Re jet. This can allow for both dissolution and growth as crystals circulate widely into an increasingly stratified system. A middle range of crystal concentration produces a very complex feedback, as sedimenting crystals form fingers and chains that interact with the incoming magma, break-up the entrainment with chaotic stirring and add a second length scale to the mixing. It simultaneously forms a small mixing bowl in the pile of crystals sedimenting at the base. This can produce very complex populations even in a simple open-system event. Bergantz et al., 2015, Open-system dynamics and mixing in magma mushes, Nature Geosci., DOI: 10.1038/NGEO2534

Bee++: An Object-Oriented, Agent-Based Simulator for Honey Bee Colonies

PubMed Central

Betti, Matthew; LeClair, Josh; Wahl, Lindi M.; Zamir, Mair

2017-01-01

We present a model and associated simulation package (www.beeplusplus.ca) to capture the natural dynamics of a honey bee colony in a spatially-explicit landscape, with temporally-variable, weather-dependent parameters. The simulation tracks bees of different ages and castes, food stores within the colony, pollen and nectar sources and the spatial position of individual foragers outside the hive. We track explicitly the intake of pesticides in individual bees and their ability to metabolize these toxins, such that the impact of sub-lethal doses of pesticides can be explored. Moreover, pathogen populations (in particular, Nosema apis, Nosema cerenae and Varroa mites) have been included in the model and may be introduced at any time or location. The ability to study interactions among pesticides, climate, biodiversity and pathogens in this predictive framework should prove useful to a wide range of researchers studying honey bee populations. To this end, the simulation package is written in open source, object-oriented code (C++) and can be easily modified by the user. Here, we demonstrate the use of the model by exploring the effects of sub-lethal pesticide exposure on the flight behaviour of foragers. PMID:28287445

Invasion and Persistence of Infectious Agents in Fragmented Host Populations

PubMed Central

Jesse, Marieke; Mazzucco, Rupert; Dieckmann, Ulf; Heesterbeek, Hans; Metz, Johan A. J.

2011-01-01

One of the important questions in understanding infectious diseases and their prevention and control is how infectious agents can invade and become endemic in a host population. A ubiquitous feature of natural populations is that they are spatially fragmented, resulting in relatively homogeneous local populations inhabiting patches connected by the migration of hosts. Such fragmented population structures are studied extensively with metapopulation models. Being able to define and calculate an indicator for the success of invasion and persistence of an infectious agent is essential for obtaining general qualitative insights into infection dynamics, for the comparison of prevention and control scenarios, and for quantitative insights into specific systems. For homogeneous populations, the basic reproduction ratio plays this role. For metapopulations, defining such an ‘invasion indicator’ is not straightforward. Some indicators have been defined for specific situations, e.g., the household reproduction number . However, these existing indicators often fail to account for host demography and especially host migration. Here we show how to calculate a more broadly applicable indicator for the invasion and persistence of infectious agents in a host metapopulation of equally connected patches, for a wide range of possible epidemiological models. A strong feature of our method is that it explicitly accounts for host demography and host migration. Using a simple compartmental system as an example, we illustrate how can be calculated and expressed in terms of the key determinants of epidemiological dynamics. PMID:21980339

A functional-dynamic reflection on participatory processes in modeling projects.

PubMed

Seidl, Roman

2015-12-01

The participation of nonscientists in modeling projects/studies is increasingly employed to fulfill different functions. However, it is not well investigated if and how explicitly these functions and the dynamics of a participatory process are reflected by modeling projects in particular. In this review study, I explore participatory modeling projects from a functional-dynamic process perspective. The main differences among projects relate to the functions of participation-most often, more than one per project can be identified, along with the degree of explicit reflection (i.e., awareness and anticipation) on the dynamic process perspective. Moreover, two main approaches are revealed: participatory modeling covering diverse approaches and companion modeling. It becomes apparent that the degree of reflection on the participatory process itself is not always explicit and perfectly visible in the descriptions of the modeling projects. Thus, the use of common protocols or templates is discussed to facilitate project planning, as well as the publication of project results. A generic template may help, not in providing details of a project or model development, but in explicitly reflecting on the participatory process. It can serve to systematize the particular project's approach to stakeholder collaboration, and thus quality management.

CONSTRUCTING, PERTURBATION ANALYSIIS AND TESTING OF A MULTI-HABITAT PERIODIC MATRIX POPULATION MODEL

EPA Science Inventory

We present a matrix model that explicitly incorporates spatial habitat structure and seasonality and discuss preliminary results from a landscape level experimental test. Ecological risk to populations is often modeled without explicit treatment of spatially or temporally distri...

Spatially Explicit Modeling Reveals Cephalopod Distributions Match Contrasting Trophic Pathways in the Western Mediterranean Sea

PubMed Central

Puerta, Patricia; Hunsicker, Mary E.; Quetglas, Antoni; Álvarez-Berastegui, Diego; Esteban, Antonio; González, María; Hidalgo, Manuel

2015-01-01

Populations of the same species can experience different responses to the environment throughout their distributional range as a result of spatial and temporal heterogeneity in habitat conditions. This highlights the importance of understanding the processes governing species distribution at local scales. However, research on species distribution often averages environmental covariates across large geographic areas, missing variability in population-environment interactions within geographically distinct regions. We used spatially explicit models to identify interactions between species and environmental, including chlorophyll a (Chla) and sea surface temperature (SST), and trophic (prey density) conditions, along with processes governing the distribution of two cephalopods with contrasting life-histories (octopus and squid) across the western Mediterranean Sea. This approach is relevant for cephalopods, since their population dynamics are especially sensitive to variations in habitat conditions and rarely stable in abundance and location. The regional distributions of the two cephalopod species matched two different trophic pathways present in the western Mediterranean Sea, associated with the Gulf of Lion upwelling and the Ebro river discharges respectively. The effects of the studied environmental and trophic conditions were spatially variant in both species, with usually stronger effects along their distributional boundaries. We identify areas where prey availability limited the abundance of cephalopod populations as well as contrasting effects of temperature in the warmest regions. Despite distributional patterns matching productive areas, a general negative effect of Chla on cephalopod densities suggests that competition pressure is common in the study area. Additionally, results highlight the importance of trophic interactions, beyond other common environmental factors, in shaping the distribution of cephalopod populations. Our study presents a valuable approach for understanding the spatially variant ecology of cephalopod populations, which is important for fisheries and ecosystem management. PMID:26201075

SPREADING SPEEDS AND TRAVELING WAVES FOR NON-COOPERATIVE INTEGRO-DIFFERENCE SYSTEMS

PubMed Central

Wang, Haiyan; Castillo-Chavez, Carlos

2014-01-01

The study of spatially explicit integro-difference systems when the local population dynamics are given in terms of discrete-time generations models has gained considerable attention over the past two decades. These nonlinear systems arise naturally in the study of the spatial dispersal of organisms. The brunt of the mathematical research on these systems, particularly, when dealing with cooperative systems, has focused on the study of the existence of traveling wave solutions and the characterization of their spreading speed. Here, we characterize the minimum propagation (spreading) speed, via the convergence of initial data to wave solutions, for a large class of non cooperative nonlinear systems of integro-difference equations. The spreading speed turns out to be the slowest speed from a family of non-constant traveling wave solutions. The applicability of these theoretical results is illustrated through the explicit study of an integro-difference system with local population dynamics governed by Hassell and Comins’ non-cooperative competition model (1976). The corresponding integro-difference nonlinear systems that results from the redistribution of individuals via a dispersal kernel is shown to satisfy conditions that guarantee the existence of minimum speeds and traveling waves. This paper is dedicated to Avner Friedman as we celebrate his immense contributions to the fields of partial differential equations, integral equations, mathematical biology, industrial mathematics and applied mathematics in general. His leadership in the mathematical sciences and his mentorship of students and friends over several decades has made a huge difference in the personal and professional lives of many, including both of us. PMID:24899868

DEFINING RECOVERY GOALS AND STRATEGIES FOR ENDANGERED SPECIES USING SPATIALLY-EXPLICIT POPULATION MODELS

EPA Science Inventory

We used a spatially explicit population model of wolves (Canis lupus) to propose a framework for defining rangewide recovery priorities and finer-scale strategies for regional reintroductions. The model predicts that Yellowstone and central Idaho, where wolves have recently been ...

Spatial structure and nutrients promote invasion of IncP-1 plasmids in bacterial populations

PubMed Central

Fox, Randal E; Zhong, Xue; Krone, Stephen M; Top, Eva M

2008-01-01

In spite of the importance of plasmids in bacterial adaptation, we have a poor understanding of their dynamics. It is not known if or how plasmids persist in and spread through (invade) a bacterial population when there is no selection for plasmid-encoded traits. Moreover, the differences in dynamics between spatially structured and mixed populations are poorly understood. Through a joint experimental/theoretical approach, we tested the hypothesis that self-transmissible IncP-1 plasmids can invade a bacterial population in the absence of selection when initially very rare, but only in spatially structured habitats and when nutrients are regularly replenished. Using protocols that differed in the degree of spatial structure and nutrient levels, the invasiveness of plasmid pB10 in Escherichia coli was monitored during at least 15 days, with an initial fraction of plasmid-bearing (p+) cells as low as 10−7. To further explore the mechanisms underlying plasmid dynamics, we developed a spatially explicit mathematical model. When cells were grown on filters and transferred to fresh medium daily, the p+ fraction increased to 13%, whereas almost complete invasion occurred when the population structure was disturbed daily. The plasmid was unable to invade in liquid. When carbon source levels were lower or not replenished, plasmid invasion was hampered. Simulations of the mathematical model closely matched the experimental results and produced estimates of the effects of alternative experimental parameters. This allowed us to isolate the likely mechanisms most responsible for the observations. In conclusion, spatial structure and nutrient availability can be key determinants in the invasiveness of plasmids. PMID:18528415

Evolutionary dynamics of populations with conflicting interactions: Classification and analytical treatment considering asymmetry and power

NASA Astrophysics Data System (ADS)

Helbing, Dirk; Johansson, Anders

2010-01-01

Evolutionary game theory has been successfully used to investigate the dynamics of systems, in which many entities have competitive interactions. From a physics point of view, it is interesting to study conditions under which a coordination or cooperation of interacting entities will occur, be it spins, particles, bacteria, animals, or humans. Here, we analyze the case, where the entities are heterogeneous, particularly the case of two populations with conflicting interactions and two possible states. For such systems, explicit mathematical formulas will be determined for the stationary solutions and the associated eigenvalues, which determine their stability. In this way, four different types of system dynamics can be classified and the various kinds of phase transitions between them will be discussed. While these results are interesting from a physics point of view, they are also relevant for social, economic, and biological systems, as they allow one to understand conditions for (1) the breakdown of cooperation, (2) the coexistence of different behaviors (“subcultures”), (3) the evolution of commonly shared behaviors (“norms”), and (4) the occurrence of polarization or conflict. We point out that norms have a similar function in social systems that forces have in physics.

Implicit–explicit (IMEX) Runge–Kutta methods for non-hydrostatic atmospheric models

DOE PAGES

Gardner, David J.; Guerra, Jorge E.; Hamon, François P.; ...

2018-04-17

The efficient simulation of non-hydrostatic atmospheric dynamics requires time integration methods capable of overcoming the explicit stability constraints on time step size arising from acoustic waves. In this work, we investigate various implicit–explicit (IMEX) additive Runge–Kutta (ARK) methods for evolving acoustic waves implicitly to enable larger time step sizes in a global non-hydrostatic atmospheric model. The IMEX formulations considered include horizontally explicit – vertically implicit (HEVI) approaches as well as splittings that treat some horizontal dynamics implicitly. In each case, the impact of solving nonlinear systems in each implicit ARK stage in a linearly implicit fashion is also explored.The accuracymore » and efficiency of the IMEX splittings, ARK methods, and solver options are evaluated on a gravity wave and baroclinic wave test case. HEVI splittings that treat some vertical dynamics explicitly do not show a benefit in solution quality or run time over the most implicit HEVI formulation. While splittings that implicitly evolve some horizontal dynamics increase the maximum stable step size of a method, the gains are insufficient to overcome the additional cost of solving a globally coupled system. Solving implicit stage systems in a linearly implicit manner limits the solver cost but this is offset by a reduction in step size to achieve the desired accuracy for some methods. Overall, the third-order ARS343 and ARK324 methods performed the best, followed by the second-order ARS232 and ARK232 methods.« less

Implicit-explicit (IMEX) Runge-Kutta methods for non-hydrostatic atmospheric models

NASA Astrophysics Data System (ADS)

Gardner, David J.; Guerra, Jorge E.; Hamon, François P.; Reynolds, Daniel R.; Ullrich, Paul A.; Woodward, Carol S.

2018-04-01

The efficient simulation of non-hydrostatic atmospheric dynamics requires time integration methods capable of overcoming the explicit stability constraints on time step size arising from acoustic waves. In this work, we investigate various implicit-explicit (IMEX) additive Runge-Kutta (ARK) methods for evolving acoustic waves implicitly to enable larger time step sizes in a global non-hydrostatic atmospheric model. The IMEX formulations considered include horizontally explicit - vertically implicit (HEVI) approaches as well as splittings that treat some horizontal dynamics implicitly. In each case, the impact of solving nonlinear systems in each implicit ARK stage in a linearly implicit fashion is also explored. The accuracy and efficiency of the IMEX splittings, ARK methods, and solver options are evaluated on a gravity wave and baroclinic wave test case. HEVI splittings that treat some vertical dynamics explicitly do not show a benefit in solution quality or run time over the most implicit HEVI formulation. While splittings that implicitly evolve some horizontal dynamics increase the maximum stable step size of a method, the gains are insufficient to overcome the additional cost of solving a globally coupled system. Solving implicit stage systems in a linearly implicit manner limits the solver cost but this is offset by a reduction in step size to achieve the desired accuracy for some methods. Overall, the third-order ARS343 and ARK324 methods performed the best, followed by the second-order ARS232 and ARK232 methods.

Implicit–explicit (IMEX) Runge–Kutta methods for non-hydrostatic atmospheric models

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

Gardner, David J.; Guerra, Jorge E.; Hamon, François P.

The efficient simulation of non-hydrostatic atmospheric dynamics requires time integration methods capable of overcoming the explicit stability constraints on time step size arising from acoustic waves. In this work, we investigate various implicit–explicit (IMEX) additive Runge–Kutta (ARK) methods for evolving acoustic waves implicitly to enable larger time step sizes in a global non-hydrostatic atmospheric model. The IMEX formulations considered include horizontally explicit – vertically implicit (HEVI) approaches as well as splittings that treat some horizontal dynamics implicitly. In each case, the impact of solving nonlinear systems in each implicit ARK stage in a linearly implicit fashion is also explored.The accuracymore » and efficiency of the IMEX splittings, ARK methods, and solver options are evaluated on a gravity wave and baroclinic wave test case. HEVI splittings that treat some vertical dynamics explicitly do not show a benefit in solution quality or run time over the most implicit HEVI formulation. While splittings that implicitly evolve some horizontal dynamics increase the maximum stable step size of a method, the gains are insufficient to overcome the additional cost of solving a globally coupled system. Solving implicit stage systems in a linearly implicit manner limits the solver cost but this is offset by a reduction in step size to achieve the desired accuracy for some methods. Overall, the third-order ARS343 and ARK324 methods performed the best, followed by the second-order ARS232 and ARK232 methods.« less

Two-strain competition in quasineutral stochastic disease dynamics.

PubMed

Kogan, Oleg; Khasin, Michael; Meerson, Baruch; Schneider, David; Myers, Christopher R

2014-10-01

We develop a perturbation method for studying quasineutral competition in a broad class of stochastic competition models and apply it to the analysis of fixation of competing strains in two epidemic models. The first model is a two-strain generalization of the stochastic susceptible-infected-susceptible (SIS) model. Here we extend previous results due to Parsons and Quince [Theor. Popul. Biol. 72, 468 (2007)], Parsons et al. [Theor. Popul. Biol. 74, 302 (2008)], and Lin, Kim, and Doering [J. Stat. Phys. 148, 646 (2012)]. The second model, a two-strain generalization of the stochastic susceptible-infected-recovered (SIR) model with population turnover, has not been studied previously. In each of the two models, when the basic reproduction numbers of the two strains are identical, a system with an infinite population size approaches a point on the deterministic coexistence line (CL): a straight line of fixed points in the phase space of subpopulation sizes. Shot noise drives one of the strain populations to fixation, and the other to extinction, on a time scale proportional to the total population size. Our perturbation method explicitly tracks the dynamics of the probability distribution of the subpopulations in the vicinity of the CL. We argue that, whereas the slow strain has a competitive advantage for mathematically "typical" initial conditions, it is the fast strain that is more likely to win in the important situation when a few infectives of both strains are introduced into a susceptible population.

How spatio-temporal habitat connectivity affects amphibian genetic structure.

PubMed

Watts, Alexander G; Schlichting, Peter E; Billerman, Shawn M; Jesmer, Brett R; Micheletti, Steven; Fortin, Marie-Josée; Funk, W Chris; Hapeman, Paul; Muths, Erin; Murphy, Melanie A

2015-01-01

Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.

Distinct spatiotemporal activity in principal neurons of the mouse olfactory bulb in anesthetized and awake states

PubMed Central

Blauvelt, David G.; Sato, Tomokazu F.; Wienisch, Martin; Murthy, Venkatesh N.

2013-01-01

The acquisition of olfactory information and its early processing in mammals are modulated by brain states through sniffing behavior and neural feedback. We imaged the spatiotemporal pattern of odor-evoked activity in a population of output neurons (mitral/tufted cells, MTCs) in the olfactory bulb (OB) of head-restrained mice expressing a genetically-encoded calcium indicator. The temporal dynamics of MTC population activity were relatively simple in anesthetized animals, but were highly variable in awake animals. However, the apparently irregular activity in awake animals could be predicted well using sniff timing measured externally, or inferred through fluctuations in the global responses of MTC population even without explicit knowledge of sniff times. The overall spatial pattern of activity was conserved across states, but odor responses had a diffuse spatial component in anesthetized mice that was less prominent during wakefulness. Multi-photon microscopy indicated that MTC lateral dendrites were the likely source of spatially disperse responses in the anesthetized animal. Our data demonstrate that the temporal and spatial dynamics of MTCs can be significantly modulated by behavioral state, and that the ensemble activity of MTCs can provide information about sniff timing to downstream circuits to help decode odor responses. PMID:23543674

Linear dimension reduction and Bayes classification

NASA Technical Reports Server (NTRS)

Decell, H. P., Jr.; Odell, P. L.; Coberly, W. A.

1978-01-01

An explicit expression for a compression matrix T of smallest possible left dimension K consistent with preserving the n variate normal Bayes assignment of X to a given one of a finite number of populations and the K variate Bayes assignment of TX to that population was developed. The Bayes population assignment of X and TX were shown to be equivalent for a compression matrix T explicitly calculated as a function of the means and covariances of the given populations.

Cancer in light of experimental evolution.

PubMed

Sprouffske, Kathleen; Merlo, Lauren M F; Gerrish, Philip J; Maley, Carlo C; Sniegowski, Paul D

2012-09-11

Cancer initiation, progression, and the emergence of therapeutic resistance are evolutionary phenomena of clonal somatic cell populations. Studies in microbial experimental evolution and the theoretical work inspired by such studies are yielding deep insights into the evolutionary dynamics of clonal populations, yet there has been little explicit consideration of the relevance of this rapidly growing field to cancer biology. Here, we examine how the understanding of mutation, selection, and spatial structure in clonal populations that is emerging from experimental evolution may be applicable to cancer. Along the way, we discuss some significant ways in which cancer differs from the model systems used in experimental evolution. Despite these differences, we argue that enhanced prediction and control of cancer may be possible using ideas developed in the context of experimental evolution, and we point out some prospects for future research at the interface between these traditionally separate areas. Copyright © 2012 Elsevier Ltd. All rights reserved.

Cancer in Light of Experimental Evolution

PubMed Central

Sprouffske, Kathleen; Merlo, Lauren M.F.; Gerrish, Philip J.; Maley, Carlo C.; Sniegowski, Paul D.

2012-01-01

Cancer initiation, progression, and the emergence of therapeutic resistance are evolutionary phenomena of clonal somatic cell populations. Studies in microbial experimental evolution and the theoretical work inspired by such studies are yielding deep insights into the evolutionary dynamics of clonal populations, yet there has been little explicit consideration of the relevance of this rapidly growing field to cancer biology. Here, we examine how the understanding of mutation, selection, and spatial structure in clonal populations that is emerging from experimental evolution may be applicable to cancer. Along the way, we discuss some significant ways in which cancer differs from the model systems used in experimental evolution. Despite these differences, we argue that enhanced prediction and control of cancer may be possible using ideas developed in the context of experimental evolution, and we point out some prospects for future research at the interface between these traditionally separate areas. PMID:22975007

Moran model as a dynamical process on networks and its implications for neutral speciation.

PubMed

de Aguiar, Marcus A M; Bar-Yam, Yaneer

2011-09-01

In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.

Moran model as a dynamical process on networks and its implications for neutral speciation

NASA Astrophysics Data System (ADS)

de Aguiar, Marcus A. M.; Bar-Yam, Yaneer

2011-03-01

In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.

Graph-based analysis of connectivity in spatially-explicit population models: HexSim and the Connectivity Analysis Toolkit

EPA Science Inventory

Background / Question / Methods Planning for the recovery of threatened species is increasingly informed by spatially-explicit population models. However, using simulation model results to guide land management decisions can be difficult due to the volume and complexity of model...

Spatially explicit modelling of cholera epidemics

NASA Astrophysics Data System (ADS)

Finger, F.; Bertuzzo, E.; Mari, L.; Knox, A. C.; Gatto, M.; Rinaldo, A.

2013-12-01

Epidemiological models can provide crucial understanding about the dynamics of infectious diseases. Possible applications range from real-time forecasting and allocation of health care resources to testing alternative intervention mechanisms such as vaccines, antibiotics or the improvement of sanitary conditions. We apply a spatially explicit model to the cholera epidemic that struck Haiti in October 2010 and is still ongoing. The dynamics of susceptibles as well as symptomatic and asymptomatic infectives are modelled at the scale of local human communities. Dissemination of Vibrio cholerae through hydrological transport and human mobility along the road network is explicitly taken into account, as well as the effect of rainfall as a driver of increasing disease incidence. The model is calibrated using a dataset of reported cholera cases. We further model the long term impact of several types of interventions on the disease dynamics by varying parameters appropriately. Key epidemiological mechanisms and parameters which affect the efficiency of treatments such as antibiotics are identified. Our results lead to conclusions about the influence of different intervention strategies on the overall epidemiological dynamics.

Modeling the Impact of Spatial Structure on Growth Dynamics of Invasive Plant Species

NASA Astrophysics Data System (ADS)

Murphy, James T.; Johnson, Mark P.; Walshe, Ray

2013-07-01

Invasive nonindigenous plant species can have potentially serious detrimental effects on local ecosystems and, as a result, costly control efforts often have to be put in place to protect habitats. An example of an invasive problem on a global scale involves the salt marsh grass species from the genus Spartina. The spread of Spartina anglica in Europe and Asia has drawn much concern due to its ability to convert coastal habitats into cord-grass monocultures and to alter the native food webs. However, the patterns of invasion of Spartina species are amenable to spatially-explicit modeling strategies that take into account both temporal and spatio-temporal processes. In this study, an agent-based model of Spartina growth on a simulated mud flat environment was developed in order to study the effects of spatial pattern and initial seedling placement on the invasion dynamics of the population. The spatial pattern of an invasion plays a key role in the rate of spread of the species and understanding this can lead to significant cost savings when designing efficient control strategies. We present here a model framework that can be used to explicitly represent complex spatial and temporal patterns of invasion in order to be able to predict quantitatively the impact of these factors on invasion dynamics. This would be a useful tool for assessing eradication strategies and choosing optimal control solutions in order to be able to minimize future control costs.

Persistence of Rift Valley fever virus in East Africa

NASA Astrophysics Data System (ADS)

Gachohi, J.; Hansen, F.; Bett, B.; Kitala, P.

2012-04-01

Rift Valley fever virus (RVFv) is a mosquito-borne pathogen of livestock, wildlife and humans that causes severe outbreaks in intervals of several years. One of the open questions is how the virus persists between outbreaks. We developed a spatially-explicit, individual-based simulation model of the RVFv transmission dynamics to investigate this question. The model, is based on livestock and mosquito population dynamics. Spatial aspects are explicitly represented by a set of grid cells that represent mosquito breeding sites. A grid cell measures 500 by 500m and the model considers a grid of 100 by 100 grid cells; the model thus operates on the regional scale of 2500km2. Livestock herds move between grid cells, and provide connectivity between the cells. The model is used to explore the spatio-temporal dynamics of RVFv persistence in absence of a wildlife reservoir in an east African semi-arid context. Specifically, the model assesses the importance of local virus persistence in mosquito breeding sites relative to global virus persistence mitigated by movement of hosts. Local persistence is determined by the length of time the virus remains in a mosquito breeding site once introduced. In the model, this is a function of the number of mosquitoes that emerge infected and their lifespan. Global persistence is determined by the level of connectivity between isolated grid cells. Our work gives insights into the ecological and epidemiological conditions under which RVFv persists. The implication for disease surveillance and management are discussed.

Non-Fixed Investment in Voluntary Public Goods Games

NASA Astrophysics Data System (ADS)

Wang, Shuai; Xu, Zhaojin; Zhang, Lianzhong

2018-05-01

In this work, we introduce a non-fixed investment ratio to the public goods games in which players can determine whether or not to participate and how much money to invest into the common pool, and with it a new mechanism has been established. We explicitly demonstrate a different rockscissors- paper dynamics which is a consequence of this model. Meanwhile, it is shown how the mechanism of non-fixed investment ratio influences the players' decision. In addition, we found that the length of memory has an important effect on the average payoff of the population by this introduction.

MULTIGRAIN: a smoothed particle hydrodynamic algorithm for multiple small dust grains and gas

NASA Astrophysics Data System (ADS)

Hutchison, Mark; Price, Daniel J.; Laibe, Guillaume

2018-05-01

We present a new algorithm, MULTIGRAIN, for modelling the dynamics of an entire population of small dust grains immersed in gas, typical of conditions that are found in molecular clouds and protoplanetary discs. The MULTIGRAIN method is more accurate than single-phase simulations because the gas experiences a backreaction from each dust phase and communicates this change to the other phases, thereby indirectly coupling the dust phases together. The MULTIGRAIN method is fast, explicit and low storage, requiring only an array of dust fractions and their derivatives defined for each resolution element.

Protocol and practice in the adaptive management of waterfowl harvests

USGS Publications Warehouse

Johnson, F.; Williams, K.

1999-01-01

Waterfowl harvest management in North America, for all its success, historically has had several shortcomings, including a lack of well-defined objectives, a failure to account for uncertain management outcomes, and inefficient use of harvest regulations to understand the effects of management. To address these and other concerns, the U.S. Fish and Wildlife Service began implementation of adaptive harvest management in 1995. Harvest policies are now developed using a Markov decision process in which there is an explicit accounting for uncontrolled environmental variation, partial controllability of harvest, and structural uncertainty in waterfowl population dynamics. Current policies are passively adaptive, in the sense that any reduction in structural uncertainty is an unplanned by-product of the regulatory process. A generalization of the Markov decision process permits the calculation of optimal actively adaptive policies, but it is not yet clear how state-specific harvest actions differ between passive and active approaches. The Markov decision process also provides managers the ability to explore optimal levels of aggregation or "management scale" for regulating harvests in a system that exhibits high temporal, spatial, and organizational variability. Progress in institutionalizing adaptive harvest management has been remarkable, but some managers still perceive the process as a panacea, while failing to appreciate the challenges presented by this more explicit and methodical approach to harvest regulation. Technical hurdles include the need to develop better linkages between population processes and the dynamics of landscapes, and to model the dynamics of structural uncertainty in a more comprehensive fashion. From an institutional perspective, agreement on how to value and allocate harvests continues to be elusive, and there is some evidence that waterfowl managers have overestimated the importance of achievement-oriented factors in setting hunting regulations. Indeed, it is these unresolved value judgements, and the lack of an effective structure for organizing debate, that present the greatest threat to adaptive harvest management as a viable means for coping with management uncertainty. Copyright ?? 1999 by The Resilience Alliance.

A new solution method for wheel/rail rolling contact.

PubMed

Yang, Jian; Song, Hua; Fu, Lihua; Wang, Meng; Li, Wei

2016-01-01

To solve the problem of wheel/rail rolling contact of nonlinear steady-state curving, a three-dimensional transient finite element (FE) model is developed by the explicit software ANSYS/LS-DYNA. To improve the solving speed and efficiency, an explicit-explicit order solution method is put forward based on analysis of the features of implicit and explicit algorithm. The solution method was first applied to calculate the pre-loading of wheel/rail rolling contact with explicit algorithm, and then the results became the initial conditions in solving the dynamic process of wheel/rail rolling contact with explicit algorithm as well. Simultaneously, the common implicit-explicit order solution method is used to solve the FE model. Results show that the explicit-explicit order solution method has faster operation speed and higher efficiency than the implicit-explicit order solution method while the solution accuracy is almost the same. Hence, the explicit-explicit order solution method is more suitable for the wheel/rail rolling contact model with large scale and high nonlinearity.

Evolution of plant–pollinator mutualisms in response to climate change

PubMed Central

Gilman, R Tucker; Fabina, Nicholas S; Abbott, Karen C; Rafferty, Nicole E

2012-01-01

Climate change has the potential to desynchronize the phenologies of interdependent species, with potentially catastrophic effects on mutualist populations. Phenologies can evolve, but the role of evolution in the response of mutualisms to climate change is poorly understood. We developed a model that explicitly considers both the evolution and the population dynamics of a plant–pollinator mutualism under climate change. How the populations evolve, and thus whether the populations and the mutualism persist, depends not only on the rate of climate change but also on the densities and phenologies of other species in the community. Abundant alternative mutualist partners with broad temporal distributions can make a mutualism more robust to climate change, while abundant alternative partners with narrow temporal distributions can make a mutualism less robust. How community composition and the rate of climate change affect the persistence of mutualisms is mediated by two-species Allee thresholds. Understanding these thresholds will help researchers to identify those mutualisms at highest risk owing to climate change. PMID:25568025

Echinococcosis: Control and Prevention.

PubMed

Craig, P S; Hegglin, D; Lightowlers, M W; Torgerson, P R; Wang, Q

2017-01-01

Human cystic echinococcosis (CE) has been eliminated or significantly reduced as a public health problem in several previously highly endemic regions. This has been achieved by the long-term application of prevention and control measures primarily targeted to deworming dogs, health education, meat inspection, and effective surveillance in livestock and human populations. Human CE, however, remains a serious neglected zoonotic disease in many resource-poor pastoral regions. The incidence of human alveolar echinococcosis (AE) has increased in continental Europe and is a major public health problem in parts of Eurasia. Better understanding of wildlife ecology for fox and small mammal hosts has enabled targeted anthelmintic baiting of fox populations and development of spatially explicit models to predict population dynamics for key intermediate host species and human AE risk in endemic landscapes. Challenges that remain for echinococcosis control include effective intervention in resource-poor communities, better availability of surveillance tools, optimal application of livestock vaccination, and management and ecology of dog and wildlife host populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dielectric response of an inhomogeneous quasi-two-dimensional electron gas

NASA Astrophysics Data System (ADS)

Fernández-Velicia, F. J.; García-Moliner, F.; Velasco, V. R.

1996-01-01

The solution of the integral equation required to invert the dielectric function of a confined quasi-two-dimensional electron gas is studied by means of a formal analysis which yields a convergent algorithm. The dielectric function can then be inverted in real space for an arbitrary number of populated subbands and taking into account the effect of intersubband excitations involving empty subbands to any desired degree of accuracy. Plasma modes and screened potential can then be easily studied by using a basis which bears out explicitly the consequences of symmetry in symmetric systems. A model calculation of dynamical screening at frequencies of the order of those of confined polar optical modes in usual GaAs wells indicates that the empty states may play a quite significant role and the screened potential, explicitly obtained in real space, may exhibit a great variety of behaviors: the sign of the potential may change and its magnitude may be either reduced (ordinary screening) or enhanced (antiscreening).

On common noise-induced synchronization in complex networks with state-dependent noise diffusion processes

NASA Astrophysics Data System (ADS)

Russo, Giovanni; Shorten, Robert

2018-04-01

This paper is concerned with the study of common noise-induced synchronization phenomena in complex networks of diffusively coupled nonlinear systems. We consider the case where common noise propagation depends on the network state and, as a result, the noise diffusion process at the nodes depends on the state of the network. For such networks, we present an algebraic sufficient condition for the onset of synchronization, which depends on the network topology, the dynamics at the nodes, the coupling strength and the noise diffusion. Our result explicitly shows that certain noise diffusion processes can drive an unsynchronized network towards synchronization. In order to illustrate the effectiveness of our result, we consider two applications: collective decision processes and synchronization of chaotic systems. We explicitly show that, in the former application, a sufficiently large noise can drive a population towards a common decision, while, in the latter, we show how common noise can synchronize a network of Lorentz chaotic systems.

The free energy landscape for beta hairpin folding in explicit water.

PubMed

Zhou, R; Berne, B J; Germain, R

2001-12-18

The folding free energy landscape of the C-terminal beta hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and OPLSAA force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the beta strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The beta hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature.

The free energy landscape for hairpin folding in explicit water

NASA Astrophysics Data System (ADS)

Zhou, Ruhong; Berne, Bruce J.; Germain, Robert

2001-12-01

The folding free energy landscape of the C-terminal hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and OPLSAA force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The β hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature.

The free energy landscape for β hairpin folding in explicit water

PubMed Central

Zhou, Ruhong; Berne, Bruce J.; Germain, Robert

2001-01-01

The folding free energy landscape of the C-terminal β hairpin of protein G has been explored in this study with explicit solvent under periodic boundary condition and oplsaa force field. A highly parallel replica exchange method that combines molecular dynamics trajectories with a temperature exchange Monte Carlo process is used for sampling with the help of a new efficient algorithm P3ME/RESPA. The simulation results show that the hydrophobic core and the β strand hydrogen bond form at roughly the same time. The free energy landscape with respect to various reaction coordinates is found to be rugged at low temperatures and becomes a smooth funnel-like landscape at about 360 K. In contrast to some very recent studies, no significant helical content has been found in our simulation at all temperatures studied. The β hairpin population and hydrogen-bond probability are in reasonable agreement with the experiment at biological temperature, but both decay more slowly than the experiment with temperature. PMID:11752441

Human Disturbance Influences Reproductive Success and Growth Rate in California Sea Lions (Zalophus californianus)

PubMed Central

French, Susannah S.; González-Suárez, Manuela; Young, Julie K.; Durham, Susan; Gerber, Leah R.

2011-01-01

The environment is currently undergoing changes at both global (e.g., climate change) and local (e.g., tourism, pollution, habitat modification) scales that have the capacity to affect the viability of animal and plant populations. Many of these changes, such as human disturbance, have an anthropogenic origin and therefore may be mitigated by management action. To do so requires an understanding of the impact of human activities and changing environmental conditions on population dynamics. We investigated the influence of human activity on important life history parameters (reproductive rate, and body condition, and growth rate of neonate pups) for California sea lions (Zalophus californianus) in the Gulf of California, Mexico. Increased human presence was associated with lower reproductive rates, which translated into reduced long-term population growth rates and suggested that human activities are a disturbance that could lead to population declines. We also observed higher body growth rates in pups with increased exposure to humans. Increased growth rates in pups may reflect a density dependent response to declining reproductive rates (e.g., decreased competition for resources). Our results highlight the potentially complex changes in life history parameters that may result from human disturbance, and their implication for population dynamics. We recommend careful monitoring of human activities in the Gulf of California and emphasize the importance of management strategies that explicitly consider the potential impact of human activities such as ecotourism on vertebrate populations. PMID:21436887

Critical factors in the establishment of allopolyploids.

PubMed

Fowler, Norma L; Levin, Donald A

2016-07-01

The growth and spread of new polyploid populations have been explained in terms of fitness advantages over their diploid progenitors. However, a fitness advantage is not sufficient to insure the establishment of a polyploid; it must also overcome the obstacles of demographic stochasticity and minority disadvantage. Several studies have addressed the population dynamics of autopolyploids, but the present study is the first to consider allopolyploids, which are affected by more factors than autopolyploids. We constructed a population dynamic model of four types of plants (two parent species, hybrids, allopolyploids) that also included an explicit breeding system. The numbers of plants of each type were the most important factors determining whether the new allopolyploid would become established. More polyploid plants greatly increased the likelihood of polyploid persistence. More plants of the parent species and more hybrids resulted in more polyploids being produced. The model parameters with the most effect on polyploid establishment were potential population size (K), individual plant fecundity, and niche separation (α). The most important breeding system parameters were selfing rates, which mitigated minority disadvantage imposed by pollen limitation. The importance of population sizes, and the parameters that controlled them, in overcoming demographic stochasticity parallels the well-recognized role of propagule pressure in determining the success of invasive species. We modeled the establishment of a new allopolyploid; analogous considerations would affect the establishment of a new autopolyploid. The critical role of population sizes in polyploid establishment should be more widely recognized. © 2016 Botanical Society of America.

An efficient, explicit finite-rate algorithm to compute flows in chemical nonequilibrium

NASA Technical Reports Server (NTRS)

Palmer, Grant

1989-01-01

An explicit finite-rate code was developed to compute hypersonic viscous chemically reacting flows about three-dimensional bodies. Equations describing the finite-rate chemical reactions were fully coupled to the gas dynamic equations using a new coupling technique. The new technique maintains stability in the explicit finite-rate formulation while permitting relatively large global time steps.

Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes

NASA Astrophysics Data System (ADS)

Cai, Kaicong; Du, Fenfen; Liu, Jia; Su, Tingting

2015-02-01

The solvation effect on the three dimensional structure and the vibrational feature of alanine dipeptide (ALAD) was evaluated by applying the implicit solvents from polarizable continuum solvent model (PCM) through ab initio calculations, by using molecular dynamic (MD) simulations with explicit solvents, and by combining these two approaches. The implicit solvent induced potential energy fluctuations of ALAD in CHCl3, DMSO and H2O are revealed by means of ab initio calculations, and a global view of conformational and solvation environmental dependence of amide I frequencies is achieved. The results from MD simulations with explicit solvents show that ALAD trends to form PPII, αL, αR, and C5 in water, PPII and C5 in DMSO, and C5 in CHCl3, ordered by population, and the demonstration of the solvated structure, the solute-solvent interaction and hydrogen bonding is therefore enhanced. Representative ALAD-solvent clusters were sampled from MD trajectories and undergone ab initio calculations. The explicit solvents reveal the hydrogen bonding between ALAD and solvents, and the correlation between amide I frequencies and the Cdbnd O bond length is built. The implicit solvents applied to the ALAD-solvent clusters further compensate the solvation effect from the bulk, and thus enlarge the degree of structural distortion and the amide I frequency red shift. The combination of explicit solvent in the first hydration shell and implicit solvent in the bulk is helpful for our understanding about the conformational fluctuation of solvated polypeptides through vibrational probes.

Sierra/Solid Mechanics 4.48 User's Guide.

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

Merewether, Mark Thomas; Crane, Nathan K; de Frias, Gabriel Jose

Sierra/SolidMechanics (Sierra/SM) is a Lagrangian, three-dimensional code for finite element analysis of solids and structures. It provides capabilities for explicit dynamic, implicit quasistatic and dynamic analyses. The explicit dynamics capabilities allow for the efficient and robust solution of models with extensive contact subjected to large, suddenly applied loads. For implicit problems, Sierra/SM uses a multi-level iterative solver, which enables it to effectively solve problems with large deformations, nonlinear material behavior, and contact. Sierra/SM has a versatile library of continuum and structural elements, and a large library of material models. The code is written for parallel computing environments enabling scalable solutionsmore » of extremely large problems for both implicit and explicit analyses. It is built on the SIERRA Framework, which facilitates coupling with other SIERRA mechanics codes. This document describes the functionality and input syntax for Sierra/SM.« less

Comparison of Damage Path Predictions for Composite Laminates by Explicit and Standard Finite Element Analysis Tools

NASA Technical Reports Server (NTRS)

Bogert, Philip B.; Satyanarayana, Arunkumar; Chunchu, Prasad B.

2006-01-01

Splitting, ultimate failure load and the damage path in center notched composite specimens subjected to in-plane tension loading are predicted using progressive failure analysis methodology. A 2-D Hashin-Rotem failure criterion is used in determining intra-laminar fiber and matrix failures. This progressive failure methodology has been implemented in the Abaqus/Explicit and Abaqus/Standard finite element codes through user written subroutines "VUMAT" and "USDFLD" respectively. A 2-D finite element model is used for predicting the intra-laminar damages. Analysis results obtained from the Abaqus/Explicit and Abaqus/Standard code show good agreement with experimental results. The importance of modeling delamination in progressive failure analysis methodology is recognized for future studies. The use of an explicit integration dynamics code for simple specimen geometry and static loading establishes a foundation for future analyses where complex loading and nonlinear dynamic interactions of damage and structure will necessitate it.

Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory

NASA Astrophysics Data System (ADS)

Jensen, Christian H.; Nerukh, Dmitry; Glen, Robert C.

2008-03-01

We investigate the sensitivity of a Markov model with states and transition probabilities obtained from clustering a molecular dynamics trajectory. We have examined a 500ns molecular dynamics trajectory of the peptide valine-proline-alanine-leucine in explicit water. The sensitivity is quantified by varying the boundaries of the clusters and investigating the resulting variation in transition probabilities and the average transition time between states. In this way, we represent the effect of clustering using different clustering algorithms. It is found that in terms of the investigated quantities, the peptide dynamics described by the Markov model is sensitive to the clustering; in particular, the average transition times are found to vary up to 46%. Moreover, inclusion of nonphysical sparsely populated clusters can lead to serious errors of up to 814%. In the investigation, the time step used in the transition matrix is determined by the minimum time scale on which the system behaves approximately Markovian. This time step is found to be about 100ps. It is concluded that the description of peptide dynamics with transition matrices should be performed with care, and that using standard clustering algorithms to obtain states and transition probabilities may not always produce reliable results.

Locally adaptive, spatially explicit projection of US population for 2030 and 2050.

PubMed

McKee, Jacob J; Rose, Amy N; Bright, Edward A; Huynh, Timmy; Bhaduri, Budhendra L

2015-02-03

Localized adverse events, including natural hazards, epidemiological events, and human conflict, underscore the criticality of quantifying and mapping current population. Building on the spatial interpolation technique previously developed for high-resolution population distribution data (LandScan Global and LandScan USA), we have constructed an empirically informed spatial distribution of projected population of the contiguous United States for 2030 and 2050, depicting one of many possible population futures. Whereas most current large-scale, spatially explicit population projections typically rely on a population gravity model to determine areas of future growth, our projection model departs from these by accounting for multiple components that affect population distribution. Modeled variables, which included land cover, slope, distances to larger cities, and a moving average of current population, were locally adaptive and geographically varying. The resulting weighted surface was used to determine which areas had the greatest likelihood for future population change. Population projections of county level numbers were developed using a modified version of the US Census's projection methodology, with the US Census's official projection as the benchmark. Applications of our model include incorporating multiple various scenario-driven events to produce a range of spatially explicit population futures for suitability modeling, service area planning for governmental agencies, consequence assessment, mitigation planning and implementation, and assessment of spatially vulnerable populations.

Global change and terrestrial plant community dynamics

DOE PAGES

Franklin, Janet; Serra-Diaz, Josep M.; Syphard, Alexandra D.; ...

2016-02-29

Anthropogenic drivers of global change include rising atmospheric concentrations of carbon dioxide and other greenhouse gasses and resulting changes in the climate, as well as nitrogen deposition, biotic invasions, altered disturbance regimes, and land-use change. Predicting the effects of global change on terrestrial plant communities is crucial because of the ecosystem services vegetation provides, from climate regulation to forest products. In this article, we present a framework for detecting vegetation changes and attributing them to global change drivers that incorporates multiple lines of evidence from spatially extensive monitoring networks, distributed experiments, remotely sensed data, and historical records. Based on amore » literature review, we summarize observed changes and then describe modeling tools that can forecast the impacts of multiple drivers on plant communities in an era of rapid change. Observed responses to changes in temperature, water, nutrients, land use, and disturbance show strong sensitivity of ecosystem productivity and plant population dynamics to water balance and long-lasting effects of disturbance on plant community dynamics. Persistent effects of land-use change and human-altered fire regimes on vegetation can overshadow or interact with climate change impacts. Models forecasting plant community responses to global change incorporate shifting ecological niches, population dynamics, species interactions, spatially explicit disturbance, ecosystem processes, and plant functional responses. Lastly, monitoring, experiments, and models evaluating multiple change drivers are needed to detect and predict vegetation changes in response to 21st century global change.« less

Global change and terrestrial plant community dynamics

PubMed Central

Franklin, Janet; Serra-Diaz, Josep M.; Syphard, Alexandra D.; Regan, Helen M.

2016-01-01

Anthropogenic drivers of global change include rising atmospheric concentrations of carbon dioxide and other greenhouse gasses and resulting changes in the climate, as well as nitrogen deposition, biotic invasions, altered disturbance regimes, and land-use change. Predicting the effects of global change on terrestrial plant communities is crucial because of the ecosystem services vegetation provides, from climate regulation to forest products. In this paper, we present a framework for detecting vegetation changes and attributing them to global change drivers that incorporates multiple lines of evidence from spatially extensive monitoring networks, distributed experiments, remotely sensed data, and historical records. Based on a literature review, we summarize observed changes and then describe modeling tools that can forecast the impacts of multiple drivers on plant communities in an era of rapid change. Observed responses to changes in temperature, water, nutrients, land use, and disturbance show strong sensitivity of ecosystem productivity and plant population dynamics to water balance and long-lasting effects of disturbance on plant community dynamics. Persistent effects of land-use change and human-altered fire regimes on vegetation can overshadow or interact with climate change impacts. Models forecasting plant community responses to global change incorporate shifting ecological niches, population dynamics, species interactions, spatially explicit disturbance, ecosystem processes, and plant functional responses. Monitoring, experiments, and models evaluating multiple change drivers are needed to detect and predict vegetation changes in response to 21st century global change. PMID:26929338

Anticipating the unintended consequences of security dynamics.

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

Backus, George A.; Overfelt, James Robert; Malczynski, Leonard A.

2010-01-01

In a globalized world, dramatic changes within any one nation causes ripple or even tsunamic effects within neighbor nations and nations geographically far removed. Multinational interventions to prevent or mitigate detrimental changes can easily cause secondary unintended consequences more detrimental and enduring than the feared change instigating the intervention. This LDRD research developed the foundations for a flexible geopolitical and socioeconomic simulation capability that focuses on the dynamic national security implications of natural and man-made trauma for a nation-state and the states linked to it through trade or treaty. The model developed contains a database for simulating all 229 recognizedmore » nation-states and sovereignties with the detail of 30 economic sectors including consumers and natural resources. The model explicitly simulates the interactions among the countries and their governments. Decisions among governments and populations is based on expectation formation. In the simulation model, failed expectations are used as a key metric for tension across states, among ethnic groups, and between population factions. This document provides the foundational documentation for the model.« less

Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections.

PubMed

Karslake, Jason; Maltas, Jeff; Brumm, Peter; Wood, Kevin B

2016-10-01

The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments.

Population Density Modulates Drug Inhibition and Gives Rise to Potential Bistability of Treatment Outcomes for Bacterial Infections

PubMed Central

Maltas, Jeff; Brumm, Peter; Wood, Kevin B.

2016-01-01

The inoculum effect (IE) is an increase in the minimum inhibitory concentration (MIC) of an antibiotic as a function of the initial size of a microbial population. The IE has been observed in a wide range of bacteria, implying that antibiotic efficacy may depend on population density. Such density dependence could have dramatic effects on bacterial population dynamics and potential treatment strategies, but explicit measures of per capita growth as a function of density are generally not available. Instead, the IE measures MIC as a function of initial population size, and population density changes by many orders of magnitude on the timescale of the experiment. Therefore, the functional relationship between population density and antibiotic inhibition is generally not known, leaving many questions about the impact of the IE on different treatment strategies unanswered. To address these questions, here we directly measured real-time per capita growth of Enterococcus faecalis populations exposed to antibiotic at fixed population densities using multiplexed computer-automated culture devices. We show that density-dependent growth inhibition is pervasive for commonly used antibiotics, with some drugs showing increased inhibition and others decreased inhibition at high densities. For several drugs, the density dependence is mediated by changes in extracellular pH, a community-level phenomenon not previously linked with the IE. Using a simple mathematical model, we demonstrate how this density dependence can modulate population dynamics in constant drug environments. Then, we illustrate how time-dependent dosing strategies can mitigate the negative effects of density-dependence. Finally, we show that these density effects lead to bistable treatment outcomes for a wide range of antibiotic concentrations in a pharmacological model of antibiotic treatment. As a result, infections exceeding a critical density often survive otherwise effective treatments. PMID:27764095

Transmission intensity and drug resistance in malaria population dynamics: implications for climate change.

PubMed

Artzy-Randrup, Yael; Alonso, David; Pascual, Mercedes

2010-10-26

Although the spread of drug resistance and the influence of climate change on malaria are most often considered separately, these factors have the potential to interact through altered levels of transmission intensity. The influence of transmission intensity on the evolution of drug resistance has been addressed in theoretical studies from a population genetics' perspective; less is known however on how epidemiological dynamics at the population level modulates this influence. We ask from a theoretical perspective, whether population dynamics can explain non-trivial, non-monotonic, patterns of treatment failure with transmission intensity, and, if so, under what conditions. We then address the implications of warmer temperatures in an East African highland, where, as in other similar regions at the altitudinal edge of malaria's distribution, there has been a pronounced increase of cases from the 1970s to the 1990s. Our theoretical analyses, with a transmission model that includes different levels of immunity, demonstrate that an increase in transmission beyond a threshold can lead to a decrease in drug resistance, as previously shown, but that a second threshold may occur and lead to the re-establishment of drug resistance. Estimates of the increase in transmission intensity from the 1970s to the 1990s for the Kenyan time series, obtained by fitting the two-stage version of the model with an explicit representation of vector dynamics, suggest that warmer temperatures are likely to have moved the system towards the first threshold, and in so doing, to have promoted the faster spread of drug resistance. Climate change and drug resistance can interact and need not be considered as alternative explanations for trends in disease incidence in this region. Non-monotonic patterns of treatment failure with transmission intensity similar to those described as the 'valley phenomenon' for Uganda can result from epidemiological dynamics but under poorly understood assumptions.

Global asymptotic stability and hopf bifurcation for a blood cell production model.

PubMed

Crauste, Fabien

2006-04-01

We analyze the asymptotic stability of a nonlinear system of two differential equations with delay, describing the dynamics of blood cell produc- tion. This process takes place in the bone marrow, where stem cells differen- tiate throughout division in blood cells. Taking into account an explicit role of the total population of hematopoietic stem cells in the introduction of cells in cycle, we are led to study a characteristic equation with delay-dependent coefficients. We determine a necessary and sufficient condition for the global stability of the first steady state of our model, which describes the popula- tion's dying out, and we obtain the existence of a Hopf bifurcation for the only nontrivial positive steady state, leading to the existence of periodic solutions. These latter are related to dynamical diseases affecting blood cells known for their cyclic nature.

Fitness in time-dependent environments includes a geometric phase contribution

PubMed Central

Tănase-Nicola, Sorin; Nemenman, Ilya

2012-01-01

Phenotypic evolution implies sequential rise in frequency of new genomic sequences. The speed of the rise depends, in part, on the relative fitness (selection coefficient) of the mutant versus the ancestor. Using a simple population dynamics model, we show that the relative fitness in dynamical environments is not equal to the geometric average of the fitness over individual environments. Instead, it includes a term that explicitly depends on the sequence of the environments. For slowly varying environments, this term depends only on the oriented area enclosed by the trajectory taken by the system in the environment state space. It is closely related to the well-studied geometric phases in classical and quantum physical systems. We discuss possible biological implications of these observations, focusing on evolution of novel metabolic or stress-resistant functions. PMID:22112653

Molecular modelling of protein-protein/protein-solvent interactions

NASA Astrophysics Data System (ADS)

Luchko, Tyler

The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule destabilization. No conformational change was observed but a nucleotide dependent 'softening' of the interaction was found instead, suggesting that an entropic force in a microtubule configuration could be the mechanism of microtubule collapse. Finally, to overcome much of the computational costs associated with explicit soIvent calculations, a new combination of molecular dynamics with the 3D-reference interaction site model (3D-RISM) of solvation was integrated into the Amber molecular dynamics package. Our implementation of 3D-RISM shows excellent agreement with explicit solvent free energy calculations. Several optimisation techniques, including a new multiple time step method, provide a nearly 100 fold performance increase, giving similar computational performance to explicit solvent.

Assessing tiger population dynamics using photographic capture-recapture sampling

USGS Publications Warehouse

Karanth, K.U.; Nichols, J.D.; Kumar, N.S.; Hines, J.E.

2006-01-01

Although wide-ranging, elusive, large carnivore species, such as the tiger, are of scientific and conservation interest, rigorous inferences about their population dynamics are scarce because of methodological problems of sampling populations at the required spatial and temporal scales. We report the application of a rigorous, noninvasive method for assessing tiger population dynamics to test model-based predictions about population viability. We obtained photographic capture histories for 74 individual tigers during a nine-year study involving 5725 trap-nights of effort. These data were modeled under a likelihood-based, ?robust design? capture?recapture analytic framework. We explicitly modeled and estimated ecological parameters such as time-specific abundance, density, survival, recruitment, temporary emigration, and transience, using models that incorporated effects of factors such as individual heterogeneity, trap-response, and time on probabilities of photo-capturing tigers. The model estimated a random temporary emigration parameter of =K' =Y' 0.10 ? 0.069 (values are estimated mean ? SE). When scaled to an annual basis, tiger survival rates were estimated at S = 0.77 ? 0.051, and the estimated probability that a newly caught animal was a transient was = 0.18 ? 0.11. During the period when the sampled area was of constant size, the estimated population size Nt varied from 17 ? 1.7 to 31 ? 2.1 tigers, with a geometric mean rate of annual population change estimated as = 1.03 ? 0.020, representing a 3% annual increase. The estimated recruitment of new animals, Bt, varied from 0 ? 3.0 to 14 ? 2.9 tigers. Population density estimates, D, ranged from 7.33 ? 0.8 tigers/100 km2 to 21.73 ? 1.7 tigers/100 km2 during the study. Thus, despite substantial annual losses and temporal variation in recruitment, the tiger density remained at relatively high levels in Nagarahole. Our results are consistent with the hypothesis that protected wild tiger populations can remain healthy despite heavy mortalities because of their inherently high reproductive potential. The ability to model the entire photographic capture history data set and incorporate reduced-parameter models led to estimates of mean annual population change that were sufficiently precise to be useful. This efficient, noninvasive sampling approach can be used to rigorously investigate the population dynamics of tigers and other elusive, rare, wide-ranging animal species in which individuals can be identified from photographs or other means.

Assessing tiger population dynamics using photographic capture-recapture sampling.

PubMed

Karanth, K Ullas; Nichols, James D; Kumar, N Samba; Hines, James E

2006-11-01

Although wide-ranging, elusive, large carnivore species, such as the tiger, are of scientific and conservation interest, rigorous inferences about their population dynamics are scarce because of methodological problems of sampling populations at the required spatial and temporal scales. We report the application of a rigorous, noninvasive method for assessing tiger population dynamics to test model-based predictions about population viability. We obtained photographic capture histories for 74 individual tigers during a nine-year study involving 5725 trap-nights of effort. These data were modeled under a likelihood-based, "robust design" capture-recapture analytic framework. We explicitly modeled and estimated ecological parameters such as time-specific abundance, density, survival, recruitment, temporary emigration, and transience, using models that incorporated effects of factors such as individual heterogeneity, trap-response, and time on probabilities of photo-capturing tigers. The model estimated a random temporary emigration parameter of gamma" = gamma' = 0.10 +/- 0.069 (values are estimated mean +/- SE). When scaled to an annual basis, tiger survival rates were estimated at S = 0.77 +/- 0.051, and the estimated probability that a newly caught animal was a transient was tau = 0.18 +/- 0.11. During the period when the sampled area was of constant size, the estimated population size N(t) varied from 17 +/- 1.7 to 31 +/- 2.1 tigers, with a geometric mean rate of annual population change estimated as lambda = 1.03 +/- 0.020, representing a 3% annual increase. The estimated recruitment of new animals, B(t), varied from 0 +/- 3.0 to 14 +/- 2.9 tigers. Population density estimates, D, ranged from 7.33 +/- 0.8 tigers/100 km2 to 21.73 +/- 1.7 tigers/100 km2 during the study. Thus, despite substantial annual losses and temporal variation in recruitment, the tiger density remained at relatively high levels in Nagarahole. Our results are consistent with the hypothesis that protected wild tiger populations can remain healthy despite heavy mortalities because of their inherently high reproductive potential. The ability to model the entire photographic capture history data set and incorporate reduced-parameter models led to estimates of mean annual population change that were sufficiently precise to be useful. This efficient, noninvasive sampling approach can be used to rigorously investigate the population dynamics of tigers and other elusive, rare, wide-ranging animal species in which individuals can be identified from photographs or other means.

Natural Human Mobility Patterns and Spatial Spread of Infectious Diseases

NASA Astrophysics Data System (ADS)

Belik, Vitaly; Geisel, Theo; Brockmann, Dirk

2011-08-01

We investigate a model for spatial epidemics explicitly taking into account bidirectional movements between base and destination locations on individual mobility networks. We provide a systematic analysis of generic dynamical features of the model on regular and complex metapopulation network topologies and show that significant dynamical differences exist to ordinary reaction-diffusion and effective force of infection models. On a lattice we calculate an expression for the velocity of the propagating epidemic front and find that, in contrast to the diffusive systems, our model predicts a saturation of the velocity with an increasing traveling rate. Furthermore, we show that a fully stochastic system exhibits a novel threshold for the attack ratio of an outbreak that is absent in diffusion and force of infection models. These insights not only capture natural features of human mobility relevant for the geographical epidemic spread, they may serve as a starting point for modeling important dynamical processes in human and animal epidemiology, population ecology, biology, and evolution.

Achieving Rigorous Accelerated Conformational Sampling in Explicit Solvent.

PubMed

Doshi, Urmi; Hamelberg, Donald

2014-04-03

Molecular dynamics simulations can provide valuable atomistic insights into biomolecular function. However, the accuracy of molecular simulations on general-purpose computers depends on the time scale of the events of interest. Advanced simulation methods, such as accelerated molecular dynamics, have shown tremendous promise in sampling the conformational dynamics of biomolecules, where standard molecular dynamics simulations are nonergodic. Here we present a sampling method based on accelerated molecular dynamics in which rotatable dihedral angles and nonbonded interactions are boosted separately. This method (RaMD-db) is a different implementation of the dual-boost accelerated molecular dynamics, introduced earlier. The advantage is that this method speeds up sampling of the conformational space of biomolecules in explicit solvent, as the degrees of freedom most relevant for conformational transitions are accelerated. We tested RaMD-db on one of the most difficult sampling problems - protein folding. Starting from fully extended polypeptide chains, two fast folding α-helical proteins (Trpcage and the double mutant of C-terminal fragment of Villin headpiece) and a designed β-hairpin (Chignolin) were completely folded to their native structures in very short simulation time. Multiple folding/unfolding transitions could be observed in a single trajectory. Our results show that RaMD-db is a promisingly fast and efficient sampling method for conformational transitions in explicit solvent. RaMD-db thus opens new avenues for understanding biomolecular self-assembly and functional dynamics occurring on long time and length scales.

Regulating energy transfer of excited carriers and the case for excitation-induced hydrogen dissociation on hydrogenated graphene

PubMed Central

Bang, Junhyeok; Meng, Sheng; Sun, Yi-Yang; West, Damien; Wang, Zhiguo; Gao, Fei; Zhang, S. B.

2013-01-01

Understanding and controlling of excited carrier dynamics is of fundamental and practical importance, particularly in photochemistry and solar energy applications. However, theory of energy relaxation of excited carriers is still in its early stage. Here, using ab initio molecular dynamics (MD) coupled with time-dependent density functional theory, we show a coverage-dependent energy transfer of photoexcited carriers in hydrogenated graphene, giving rise to distinctively different ion dynamics. Graphene with sparsely populated H is difficult to dissociate due to inefficient transfer of the excitation energy into kinetic energy of the H. In contrast, H can easily desorb from fully hydrogenated graphane. The key is to bring down the H antibonding state to the conduction band minimum as the band gap increases. These results can be contrasted to those of standard ground-state MD that predict H in the sparse case should be much less stable than that in fully hydrogenated graphane. Our findings thus signify the importance of carrying out explicit electronic dynamics in excited-state simulations. PMID:23277576

Strategy to Conduct Quantitative Ecohydrologic Analysis of a UNESCO World Heritage Site: the Peace-Athabasca Delta, Canada

NASA Astrophysics Data System (ADS)

Ward, E. M.; Gorelick, S.; Hadly, E. A.

2016-12-01

The 6000 km2 Peace-Athabasca Delta ("Delta") in northeastern Alberta, Canada, is a Ramsar Convention Wetland and UNESCO World Heritage Site ("in Danger" status pending) where hydropower development and climate change are creating ecological impacts through desiccation and reduction in Delta shoreline habitat. We focus on ecohydrologic changes and mitigation and adaptation options to advance the field of ecohydrology using interdisciplinary technology by combining, for the first time, satellite remote sensing and hydrologic simulation with individual-based population modeling of muskrat (Ondatra zibethicus), a species native to the Delta whose population dynamics are strongly controlled by the hydrology of floodplain lakes. We are building a conceptual and quantitative modeling framework linking climate change, upstream water demand, and hydrologic change in the floodplain to muskrat population dynamics with the objective of exploring the impacts of these stressors on this ecosystem. We explicitly account for cultural and humanistic influences and are committed to effective communication with the regional subsistence community that depends on muskrat for food and income. Our modeling framework can ultimately serve as the basis for improved stewardship and sustainable development upstream of stressed freshwater deltaic, coastal and lake systems worldwide affected by climate change, providing a predictive tool to quantify population changes of animals relevant to regional subsistence food security and commercial trapping.

Exposing extinction risk analysis to pathogens: Is disease just another form of density dependence?

USGS Publications Warehouse

Gerber, L.R.; McCallum, H.; Lafferty, K.D.; Sabo, J.L.; Dobson, A.

2005-01-01

In the United States and several other countries, the development of population viability analyses (PVA) is a legal requirement of any species survival plan developed for threatened and endangered species. Despite the importance of pathogens in natural populations, little attention has been given to host-pathogen dynamics in PVA. To study the effect of infectious pathogens on extinction risk estimates generated from PVA, we review and synthesize the relevance of host-pathogen dynamics in analyses of extinction risk. We then develop a stochastic, density-dependent host-parasite model to investigate the effects of disease on the persistence of endangered populations. We show that this model converges on a Ricker model of density dependence under a suite of limiting assumptions, including a high probability that epidemics will arrive and occur. Using this modeling framework, we then quantify: (1) dynamic differences between time series generated by disease and Ricker processes with the same parameters; (2) observed probabilities of quasi-extinction for populations exposed to disease or self-limitation; and (3) bias in probabilities of quasi-extinction estimated by density-independent PVAs when populations experience either form of density dependence. Our results suggest two generalities about the relationships among disease, PVA, and the management of endangered species. First, disease more strongly increases variability in host abundance and, thus, the probability of quasi-extinction, than does self-limitation. This result stems from the fact that the effects and the probability of occurrence of disease are both density dependent. Second, estimates of quasi-extinction are more often overly optimistic for populations experiencing disease than for those subject to self-limitation. Thus, although the results of density-independent PVAs may be relatively robust to some particular assumptions about density dependence, they are less robust when endangered populations are known to be susceptible to disease. If potential management actions involve manipulating pathogens, then it may be useful to model disease explicitly. ?? 2005 by the Ecological Society of America.

Effects of wind energy generation and white-nose syndrome on the viability of the Indiana bat

USGS Publications Warehouse

Erickson, Richard A.; Thogmartin, Wayne E.; Diffendorfer, James E.; Russell, Robin E.; Szymanski, Jennifer A.

2016-01-01

Wind energy generation holds the potential to adversely affect wildlife populations. Species-wide effects are difficult to study and few, if any, studies examine effects of wind energy generation on any species across its entire range. One species that may be affected by wind energy generation is the endangered Indiana bat (Myotis sodalis), which is found in the eastern and midwestern United States. In addition to mortality from wind energy generation, the species also faces range-wide threats from the emerging infectious fungal disease, white-nose syndrome (WNS). White-nose syndrome, caused by Pseudogymnoascus destructans, disturbs hibernating bats leading to high levels of mortality. We used a spatially explicit full-annual-cycle model to investigate how wind turbine mortality and WNS may singly and then together affect population dynamics of this species. In the simulation, wind turbine mortality impacted the metapopulation dynamics of the species by causing extirpation of some of the smaller winter colonies. In general, effects of wind turbines were localized and focused on specific spatial subpopulations. Conversely, WNS had a depressive effect on the species across its range. Wind turbine mortality interacted with WNS and together these stressors had a larger impact than would be expected from either alone, principally because these stressors together act to reduce species abundance across the spectrum of population sizes. Our findings illustrate the importance of not only prioritizing the protection of large winter colonies as is currently done, but also of protecting metapopulation dynamics and migratory connectivity.

Effects of wind energy generation and white-nose syndrome on the viability of the Indiana bat.

PubMed

Erickson, Richard A; Thogmartin, Wayne E; Diffendorfer, Jay E; Russell, Robin E; Szymanski, Jennifer A

2016-01-01

Wind energy generation holds the potential to adversely affect wildlife populations. Species-wide effects are difficult to study and few, if any, studies examine effects of wind energy generation on any species across its entire range. One species that may be affected by wind energy generation is the endangered Indiana bat ( Myotis sodalis ), which is found in the eastern and midwestern United States. In addition to mortality from wind energy generation, the species also faces range-wide threats from the emerging infectious fungal disease, white-nose syndrome (WNS). White-nose syndrome, caused by Pseudogymnoascus destructans , disturbs hibernating bats leading to high levels of mortality. We used a spatially explicit full-annual-cycle model to investigate how wind turbine mortality and WNS may singly and then together affect population dynamics of this species. In the simulation, wind turbine mortality impacted the metapopulation dynamics of the species by causing extirpation of some of the smaller winter colonies. In general, effects of wind turbines were localized and focused on specific spatial subpopulations. Conversely, WNS had a depressive effect on the species across its range. Wind turbine mortality interacted with WNS and together these stressors had a larger impact than would be expected from either alone, principally because these stressors together act to reduce species abundance across the spectrum of population sizes. Our findings illustrate the importance of not only prioritizing the protection of large winter colonies as is currently done, but also of protecting metapopulation dynamics and migratory connectivity.

Constant pH Molecular Dynamics of Proteins in Explicit Solvent with Proton Tautomerism

PubMed Central

Goh, Garrett B.; Hulbert, Benjamin S.; Zhou, Huiqing; Brooks, Charles L.

2015-01-01

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMDMSλD). In the CPHMDMSλD framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMDMSλD simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMDMSλD framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules – proteins and nucleic acids is now possible. PMID:24375620

How spatio-temporal habitat connectivity affects amphibian genetic structure

PubMed Central

Watts, Alexander G.; Schlichting, Peter E.; Billerman, Shawn M.; Jesmer, Brett R.; Micheletti, Steven; Fortin, Marie-Josée; Funk, W. Chris; Hapeman, Paul; Muths, Erin; Murphy, Melanie A.

2015-01-01

Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations. PMID:26442094

How spatio-temporal habitat connectivity affects amphibian genetic structure

USGS Publications Warehouse

Watts, Alexander G.; Schlichting, P; Billerman, S; Jesmer, B; Micheletti, S; Fortin, M.-J.; Funk, W.C.; Hapeman, P; Muths, Erin L.; Murphy, M.A.

2015-01-01

Heterogeneous landscapes and fluctuating environmental conditions can affect species dispersal, population genetics, and genetic structure, yet understanding how biotic and abiotic factors affect population dynamics in a fluctuating environment is critical for species management. We evaluated how spatio-temporal habitat connectivity influences dispersal and genetic structure in a population of boreal chorus frogs (Pseudacris maculata) using a landscape genetics approach. We developed gravity models to assess the contribution of various factors to the observed genetic distance as a measure of functional connectivity. We selected (a) wetland (within-site) and (b) landscape matrix (between-site) characteristics; and (c) wetland connectivity metrics using a unique methodology. Specifically, we developed three networks that quantify wetland connectivity based on: (i) P. maculata dispersal ability, (ii) temporal variation in wetland quality, and (iii) contribution of wetland stepping-stones to frog dispersal. We examined 18 wetlands in Colorado, and quantified 12 microsatellite loci from 322 individual frogs. We found that genetic connectivity was related to topographic complexity, within- and between-wetland differences in moisture, and wetland functional connectivity as contributed by stepping-stone wetlands. Our results highlight the role that dynamic environmental factors have on dispersal-limited species and illustrate how complex asynchronous interactions contribute to the structure of spatially-explicit metapopulations.

Computational plasticity algorithm for particle dynamics simulations

NASA Astrophysics Data System (ADS)

Krabbenhoft, K.; Lyamin, A. V.; Vignes, C.

2018-01-01

The problem of particle dynamics simulation is interpreted in the framework of computational plasticity leading to an algorithm which is mathematically indistinguishable from the common implicit scheme widely used in the finite element analysis of elastoplastic boundary value problems. This algorithm provides somewhat of a unification of two particle methods, the discrete element method and the contact dynamics method, which usually are thought of as being quite disparate. In particular, it is shown that the former appears as the special case where the time stepping is explicit while the use of implicit time stepping leads to the kind of schemes usually labelled contact dynamics methods. The framing of particle dynamics simulation within computational plasticity paves the way for new approaches similar (or identical) to those frequently employed in nonlinear finite element analysis. These include mixed implicit-explicit time stepping, dynamic relaxation and domain decomposition schemes.

Dynamics of Small-Scale Perched Aquifers in the Semi-Arid South-Western Region of Madagascar and Implications for the Sustainable Groundwater Exploitation

NASA Astrophysics Data System (ADS)

Englert, A.; Brinkmann, K.; Kobbe, S.; Buerkert, A.

2016-12-01

The south-western region of Madagascar is characterized by limited water resources throughout the year and recurrent droughts, which affect agricultural production and increase the risk of food insecurity. To deliver reliable estimates on the availability and dynamics of water resources, we studied the hydrogeology of several villages in the Mahafaly region. Detailed investigations were conducted for a selected village on a calcareous plateau to predict the local water resources under changing boundary conditions including enhanced water abstraction and changes in groundwater recharge. In 2014 a participatory monitoring network was established, which allowed groundwater level measurements in three wells twice a day. Additional hydrogeological investigations included pumping tests, automatic monitoring of meteorological data, daily groundwater abstraction appraisal and mapping of the spatial extent of the perched aquifer using satellite data. Analysis of the measured data unraveled the aquifer dynamic to be dominated by a groundwater level driven leakage process. The latter is superimposed by groundwater recharge in the rainy season and a daily groundwater abstraction. Based on these findings we developed a model for the aquifer, which allows to predict the duration of groundwater availability as a function of annual precipitation and daily water abstraction. The latter will be implemented in an agent-based land-use model, were groundwater abstraction is a function of population and livestock. The main objective is to model land use scenarios and global trends (climate, market trends and population development) through explicit imbedding of artificial and natural groundwater dynamics. The latter is expected to enable the evaluation of additional water abstraction for agricultural purposes without endangering water supply of the local population and their livestock.

Analysis on Patterns of Globally Coupled Phase Oscillators with Attractive and Repulsive Interactions

NASA Astrophysics Data System (ADS)

Wang, Peng-Fei; Ruan, Xiao-Dong; Xu, Zhong-Bin; Fu, Xin

2015-11-01

The Hong-Strogatz (HS) model of globally coupled phase oscillators with attractive and repulsive interactions reflects the fact that each individual (oscillator) has its own attitude (attractive or repulsive) to the same environment (mean field). Previous studies on HS model focused mainly on the stable states on Ott-Antonsen (OA) manifold. In this paper, the eigenvalues of the Jacobi matrix of each fixed point in HS model are explicitly derived, with the aim to understand the local dynamics around each fixed point. Phase transitions are described according to relative population and coupling strength. Besides, the dynamics off OA manifold is studied. Supported by the National Basic Research Program of China under Grant No. 2015CB057301, the Applied Research Project of Public Welfare Technology of Zhejiang Province under Grant No. 201SC31109 and China Postdoctoral Science Foundation under Grant No. 2014M560483

Species abundance distribution and population dynamics in a two-community model of neutral ecology

NASA Astrophysics Data System (ADS)

Vallade, M.; Houchmandzadeh, B.

2006-11-01

Explicit formulas for the steady-state distribution of species in two interconnected communities of arbitrary sizes are derived in the framework of Hubbell’s neutral model of biodiversity. Migrations of seeds from both communities as well as mutations in both of them are taken into account. These results generalize those previously obtained for the “island-continent” model and they allow an analysis of the influence of the ratio of the sizes of the two communities on the dominance/diversity equilibrium. Exact expressions for species abundance distributions are deduced from a master equation for the joint probability distribution of species in the two communities. Moreover, an approximate self-consistent solution is derived. It corresponds to a generalization of previous results and it proves to be accurate over a broad range of parameters. The dynamical correlations between the abundances of a species in both communities are also discussed.

Modeling trends from North American Breeding Bird Survey data: a spatially explicit approach

USGS Publications Warehouse

Bled, Florent; Sauer, John R.; Pardieck, Keith L.; Doherty, Paul; Royle, J. Andy

2013-01-01

Population trends, defined as interval-specific proportional changes in population size, are often used to help identify species of conservation interest. Efficient modeling of such trends depends on the consideration of the correlation of population changes with key spatial and environmental covariates. This can provide insights into causal mechanisms and allow spatially explicit summaries at scales that are of interest to management agencies. We expand the hierarchical modeling framework used in the North American Breeding Bird Survey (BBS) by developing a spatially explicit model of temporal trend using a conditional autoregressive (CAR) model. By adopting a formal spatial model for abundance, we produce spatially explicit abundance and trend estimates. Analyses based on large-scale geographic strata such as Bird Conservation Regions (BCR) can suffer from basic imbalances in spatial sampling. Our approach addresses this issue by providing an explicit weighting based on the fundamental sample allocation unit of the BBS. We applied the spatial model to three species from the BBS. Species have been chosen based upon their well-known population change patterns, which allows us to evaluate the quality of our model and the biological meaning of our estimates. We also compare our results with the ones obtained for BCRs using a nonspatial hierarchical model (Sauer and Link 2011). Globally, estimates for mean trends are consistent between the two approaches but spatial estimates provide much more precise trend estimates in regions on the edges of species ranges that were poorly estimated in non-spatial analyses. Incorporating a spatial component in the analysis not only allows us to obtain relevant and biologically meaningful estimates for population trends, but also enables us to provide a flexible framework in order to obtain trend estimates for any area.

Estimating survival rates with time series of standing age‐structure data

USGS Publications Warehouse

Udevitz, Mark S.; Gogan, Peter J.

2012-01-01

It has long been recognized that age‐structure data contain useful information for assessing the status and dynamics of wildlife populations. For example, age‐specific survival rates can be estimated with just a single sample from the age distribution of a stable, stationary population. For a population that is not stable, age‐specific survival rates can be estimated using techniques such as inverse methods that combine time series of age‐structure data with other demographic data. However, estimation of survival rates using these methods typically requires numerical optimization, a relatively long time series of data, and smoothing or other constraints to provide useful estimates. We developed general models for possibly unstable populations that combine time series of age‐structure data with other demographic data to provide explicit maximum likelihood estimators of age‐specific survival rates with as few as two years of data. As an example, we applied these methods to estimate survival rates for female bison (Bison bison) in Yellowstone National Park, USA. This approach provides a simple tool for monitoring survival rates based on age‐structure data.

Eco-evolutionary feedbacks drive species interactions

PubMed Central

Andrade-Domínguez, Andrés; Salazar, Emmanuel; del Carmen Vargas-Lagunas, María; Kolter, Roberto; Encarnación, Sergio

2014-01-01

In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions. PMID:24304674

Feed-backs among inbreeding, inbreeding depression in sperm traits, and sperm competition can drive evolution of costly polyandry.

PubMed

Bocedi, Greta; Reid, Jane M

2017-12-01

Ongoing ambitions are to understand the evolution of costly polyandry and its consequences for species ecology and evolution. Emerging patterns could stem from feed-back dynamics between the evolving mating system and its genetic environment, defined by interactions among kin including inbreeding. However, such feed-backs are rarely considered in nonselfing systems. We use a genetically explicit model to demonstrate a mechanism by which inbreeding depression can select for polyandry to mitigate the negative consequences of mating with inbred males, rather than to avoid inbreeding, and to elucidate underlying feed-backs. Specifically, given inbreeding depression in sperm traits, costly polyandry evolved to ensure female fertility, without requiring explicit inbreeding avoidance. Resulting sperm competition caused evolution of sperm traits and further mitigated the negative effect of inbreeding depression on female fertility. The evolving mating system fed back to decrease population-wide homozygosity, and hence inbreeding. However, the net overall decrease was small due to compound effects on the variances in sex-specific reproductive success and paternity skew. Purging of deleterious mutations did not eliminate inbreeding depression in sperm traits or hence selection for polyandry. Overall, our model illustrates that polyandry evolution, both directly and through sperm competition, might facilitate evolutionary rescue for populations experiencing sudden increases in inbreeding. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

PubMed

Goh, Garrett B; Hulbert, Benjamin S; Zhou, Huiqing; Brooks, Charles L

2014-07-01

pH is a ubiquitous regulator of biological activity, including protein-folding, protein-protein interactions, and enzymatic activity. Existing constant pH molecular dynamics (CPHMD) models that were developed to address questions related to the pH-dependent properties of proteins are largely based on implicit solvent models. However, implicit solvent models are known to underestimate the desolvation energy of buried charged residues, increasing the error associated with predictions that involve internal ionizable residue that are important in processes like hydrogen transport and electron transfer. Furthermore, discrete water and ions cannot be modeled in implicit solvent, which are important in systems like membrane proteins and ion channels. We report on an explicit solvent constant pH molecular dynamics framework based on multi-site λ-dynamics (CPHMD(MSλD)). In the CPHMD(MSλD) framework, we performed seamless alchemical transitions between protonation and tautomeric states using multi-site λ-dynamics, and designed novel biasing potentials to ensure that the physical end-states are predominantly sampled. We show that explicit solvent CPHMD(MSλD) simulations model realistic pH-dependent properties of proteins such as the Hen-Egg White Lysozyme (HEWL), binding domain of 2-oxoglutarate dehydrogenase (BBL) and N-terminal domain of ribosomal protein L9 (NTL9), and the pKa predictions are in excellent agreement with experimental values, with a RMSE ranging from 0.72 to 0.84 pKa units. With the recent development of the explicit solvent CPHMD(MSλD) framework for nucleic acids, accurate modeling of pH-dependent properties of both major class of biomolecules-proteins and nucleic acids is now possible. © 2013 Wiley Periodicals, Inc.

Nonadiabatic dynamics of electron transfer in solution: Explicit and implicit solvent treatments that include multiple relaxation time scales

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

Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon, E-mail: shs3@illinois.edu

2014-01-21

The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent. In this theory, the parameters are directly related to the physical properties of the system and can be determined from experimental data or explicit molecular dynamics simulations. Herein, we combine these Langevin equations with surface hopping nonadiabatic dynamics methods to calculate the rate constants for thermal ET reactions in polar solvents formore » a wide range of electronic couplings and reaction free energies. Comparison of explicit and implicit solvent calculations illustrates that the mapping from explicit to implicit solvent models is valid even for solvents exhibiting complex relaxation behavior with multiple relaxation time scales and a short-time inertial response. The rate constants calculated for implicit solvent models with a single solvent relaxation time scale corresponding to water, acetonitrile, and methanol agree well with analytical theories in the Golden rule and solvent-controlled regimes, as well as in the intermediate regime. The implicit solvent models with two relaxation time scales are in qualitative agreement with the analytical theories but quantitatively overestimate the rate constants compared to these theories. Analysis of these simulations elucidates the importance of multiple relaxation time scales and the inertial component of the solvent response, as well as potential shortcomings of the analytical theories based on single time scale solvent relaxation models. This implicit solvent approach will enable the simulation of a wide range of ET reactions via the stochastic dynamics of a single collective solvent coordinate with parameters that are relevant to experimentally accessible systems.« less

Dynamic Target Match Signals in Perirhinal Cortex Can Be Explained by Instantaneous Computations That Act on Dynamic Input from Inferotemporal Cortex

PubMed Central

Pagan, Marino

2014-01-01

Finding sought objects requires the brain to combine visual and target signals to determine when a target is in view. To investigate how the brain implements these computations, we recorded neural responses in inferotemporal cortex (IT) and perirhinal cortex (PRH) as macaque monkeys performed a delayed-match-to-sample target search task. Our data suggest that visual and target signals were combined within or before IT in the ventral visual pathway and then passed onto PRH, where they were reformatted into a more explicit target match signal over ∼10–15 ms. Accounting for these dynamics in PRH did not require proposing dynamic computations within PRH itself but, rather, could be attributed to instantaneous PRH computations performed upon an input representation from IT that changed with time. We found that the dynamics of the IT representation arose from two commonly observed features: individual IT neurons whose response preferences were not simply rescaled with time and variable response latencies across the population. Our results demonstrate that these types of time-varying responses have important consequences for downstream computation and suggest that dynamic representations can arise within a feedforward framework as a consequence of instantaneous computations performed upon time-varying inputs. PMID:25122904

Spatially explicit modeling in ecology: A review

USGS Publications Warehouse

DeAngelis, Donald L.; Yurek, Simeon

2017-01-01

The use of spatially explicit models (SEMs) in ecology has grown enormously in the past two decades. One major advancement has been that fine-scale details of landscapes, and of spatially dependent biological processes, such as dispersal and invasion, can now be simulated with great precision, due to improvements in computer technology. Many areas of modeling have shifted toward a focus on capturing these fine-scale details, to improve mechanistic understanding of ecosystems. However, spatially implicit models (SIMs) have played a dominant role in ecology, and arguments have been made that SIMs, which account for the effects of space without specifying spatial positions, have an advantage of being simpler and more broadly applicable, perhaps contributing more to understanding. We address this debate by comparing SEMs and SIMs in examples from the past few decades of modeling research. We argue that, although SIMs have been the dominant approach in the incorporation of space in theoretical ecology, SEMs have unique advantages for addressing pragmatic questions concerning species populations or communities in specific places, because local conditions, such as spatial heterogeneities, organism behaviors, and other contingencies, produce dynamics and patterns that usually cannot be incorporated into simpler SIMs. SEMs are also able to describe mechanisms at the local scale that can create amplifying positive feedbacks at that scale, creating emergent patterns at larger scales, and therefore are important to basic ecological theory. We review the use of SEMs at the level of populations, interacting populations, food webs, and ecosystems and argue that SEMs are not only essential in pragmatic issues, but must play a role in the understanding of causal relationships on landscapes.

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.

Exploring Hamiltonian dielectric solvent molecular dynamics

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-09-01

Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an α-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation.

Modeling the Effect of Fluid-Structure Interaction on the Impact Dynamics of Pressurized Tank Cars

DOT National Transportation Integrated Search

2009-11-13

This paper presents a computational framework that : analyzes the effect of fluid-structure interaction (FSI) on the : impact dynamics of pressurized commodity tank cars using the : nonlinear dynamic finite element code ABAQUS/Explicit. : There exist...

Hierarchical Structure of the Eysenck Personality Inventory in a Large Population Sample: Goldberg's Trait-Tier Mapping Procedure

PubMed Central

Chapman, Benjamin P.; Weiss, Alexander; Barrett, Paul; Duberstein, Paul

2014-01-01

The structure of the Eysenck Personality Inventory (EPI) is poorly understood, and applications have mostly been confined to the broad Neuroticism, Extraversion, and Lie scales. Using a hierarchical factoring procedure, we mapped the sequential differentiation of EPI scales from broad, molar factors to more specific, molecular factors, in a UK population sample of over 6500 persons. Replicable facets at the lowest tier of Neuroticism included emotional fragility, mood lability, nervous tension, and rumination. The lowest order set of replicable Extraversion facets consisted of social dynamism, sociotropy, decisiveness, jocularity, social information seeking, and impulsivity. The Lie scale consisted of an interpersonal virtue and a behavioral diligence facet. Users of the EPI may be well served in some circumstances by considering its broad Neuroticism, Extraversion, and Lie scales as multifactorial, a feature that was explicitly incorporated into subsequent Eysenck inventories and is consistent with other hierarchical trait structures. PMID:25983361

Explicit Computations of Instantons and Large Deviations in Beta-Plane Turbulence

NASA Astrophysics Data System (ADS)

Laurie, J.; Bouchet, F.; Zaboronski, O.

2012-12-01

We use a path integral formalism and instanton theory in order to make explicit analytical predictions about large deviations and rare events in beta-plane turbulence. The path integral formalism is a concise way to get large deviation results in dynamical systems forced by random noise. In the most simple cases, it leads to the same results as the Freidlin-Wentzell theory, but it has a wider range of applicability. This approach is however usually extremely limited, due to the complexity of the theoretical problems. As a consequence it provides explicit results in a fairly limited number of models, often extremely simple ones with only a few degrees of freedom. Few exception exist outside the realm of equilibrium statistical physics. We will show that the barotropic model of beta-plane turbulence is one of these non-equilibrium exceptions. We describe sets of explicit solutions to the instanton equation, and precise derivations of the action functional (or large deviation rate function). The reason why such exact computations are possible is related to the existence of hidden symmetries and conservation laws for the instanton dynamics. We outline several applications of this apporach. For instance, we compute explicitly the very low probability to observe flows with an energy much larger or smaller than the typical one. Moreover, we consider regimes for which the system has multiple attractors (corresponding to different numbers of alternating jets), and discuss the computation of transition probabilities between two such attractors. These extremely rare events are of the utmost importance as the dynamics undergo qualitative macroscopic changes during such transitions.

Population extinction under bursty reproduction in a time-modulated environment

NASA Astrophysics Data System (ADS)

Vilk, Ohad; Assaf, Michael

2018-06-01

In recent years nondemographic variability has been shown to greatly affect dynamics of stochastic populations. For example, nondemographic noise in the form of a bursty reproduction process with an a priori unknown burst size, or environmental variability in the form of time-varying reaction rates, have been separately found to dramatically impact the extinction risk of isolated populations. In this work we investigate the extinction risk of an isolated population under the combined influence of these two types of nondemographic variation. Using the so-called momentum-space Wentzel-Kramers-Brillouin (WKB) approach and accounting for the explicit time dependence in the reaction rates, we arrive at a set of time-dependent Hamilton equations. To this end, we evaluate the population's extinction risk by finding the instanton of the time-perturbed Hamiltonian numerically, whereas analytical expressions are presented in particular limits using various perturbation techniques. We focus on two classes of time-varying environments: periodically varying rates corresponding to seasonal effects and a sudden decrease in the birth rate corresponding to a catastrophe. All our theoretical results are tested against numerical Monte Carlo simulations with time-dependent rates and also against a numerical solution of the corresponding time-dependent Hamilton equations.

Effects of wind energy generation and white-nose syndrome on the viability of the Indiana bat

PubMed Central

Thogmartin, Wayne E.; Diffendorfer, Jay E.; Russell, Robin E.; Szymanski, Jennifer A.

2016-01-01

Wind energy generation holds the potential to adversely affect wildlife populations. Species-wide effects are difficult to study and few, if any, studies examine effects of wind energy generation on any species across its entire range. One species that may be affected by wind energy generation is the endangered Indiana bat (Myotis sodalis), which is found in the eastern and midwestern United States. In addition to mortality from wind energy generation, the species also faces range-wide threats from the emerging infectious fungal disease, white-nose syndrome (WNS). White-nose syndrome, caused by Pseudogymnoascus destructans, disturbs hibernating bats leading to high levels of mortality. We used a spatially explicit full-annual-cycle model to investigate how wind turbine mortality and WNS may singly and then together affect population dynamics of this species. In the simulation, wind turbine mortality impacted the metapopulation dynamics of the species by causing extirpation of some of the smaller winter colonies. In general, effects of wind turbines were localized and focused on specific spatial subpopulations. Conversely, WNS had a depressive effect on the species across its range. Wind turbine mortality interacted with WNS and together these stressors had a larger impact than would be expected from either alone, principally because these stressors together act to reduce species abundance across the spectrum of population sizes. Our findings illustrate the importance of not only prioritizing the protection of large winter colonies as is currently done, but also of protecting metapopulation dynamics and migratory connectivity. PMID:28028486

Population dynamics can be more important than physiological limits for determining range shifts under climate change.

PubMed

Fordham, Damien A; Mellin, Camille; Russell, Bayden D; Akçakaya, Reşit H; Bradshaw, Corey J A; Aiello-Lammens, Matthew E; Caley, Julian M; Connell, Sean D; Mayfield, Stephen; Shepherd, Scoresby A; Brook, Barry W

2013-10-01

Evidence is accumulating that species' responses to climate changes are best predicted by modelling the interaction of physiological limits, biotic processes and the effects of dispersal-limitation. Using commercially harvested blacklip (Haliotis rubra) and greenlip abalone (Haliotis laevigata) as case studies, we determine the relative importance of accounting for interactions among physiology, metapopulation dynamics and exploitation in predictions of range (geographical occupancy) and abundance (spatially explicit density) under various climate change scenarios. Traditional correlative ecological niche models (ENM) predict that climate change will benefit the commercial exploitation of abalone by promoting increased abundances without any reduction in range size. However, models that account simultaneously for demographic processes and physiological responses to climate-related factors result in future (and present) estimates of area of occupancy (AOO) and abundance that differ from those generated by ENMs alone. Range expansion and population growth are unlikely for blacklip abalone because of important interactions between climate-dependent mortality and metapopulation processes; in contrast, greenlip abalone should increase in abundance despite a contraction in AOO. The strongly non-linear relationship between abalone population size and AOO has important ramifications for the use of ENM predictions that rely on metrics describing change in habitat area as proxies for extinction risk. These results show that predicting species' responses to climate change often require physiological information to understand climatic range determinants, and a metapopulation model that can make full use of this data to more realistically account for processes such as local extirpation, demographic rescue, source-sink dynamics and dispersal-limitation. © 2013 John Wiley & Sons Ltd.

Model structure of the stream salmonid simulator (S3)—A dynamic model for simulating growth, movement, and survival of juvenile salmonids

USGS Publications Warehouse

Perry, Russell W.; Plumb, John M.; Jones, Edward C.; Som, Nicholas A.; Hetrick, Nicholas J.; Hardy, Thomas B.

2018-04-06

Fisheries and water managers often use population models to aid in understanding the effect of alternative water management or restoration actions on anadromous fish populations. We developed the Stream Salmonid Simulator (S3) to help resource managers evaluate the effect of management alternatives on juvenile salmonid populations. S3 is a deterministic stage-structured population model that tracks daily growth, movement, and survival of juvenile salmon. A key theme of the model is that river flow affects habitat availability and capacity, which in turn drives density dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily time series of discharge, water temperature, and usable habitat area or carrying capacity. The physical characteristics of each habitat unit and the number of fish occupying each unit, in turn, drive survival and growth within each habitat unit and movement of fish among habitat units.The purpose of this report is to outline the underlying general structure of the S3 model that is common among different applications of the model. We have developed applications of the S3 model for juvenile fall Chinook salmon (Oncorhynchus tshawytscha) in the lower Klamath River. Thus, this report is a companion to current application of the S3 model to the Trinity River (in review). The general S3 model structure provides a biological and physical framework for the salmonid freshwater life cycle. This framework captures important demographics of juvenile salmonids aimed at translating management alternatives into simulated population responses. Although the S3 model is built on this common framework, the model has been constructed to allow much flexibility in application of the model to specific river systems. The ability for practitioners to include system-specific information for the physical stream structure, survival, growth, and movement processes ensures that simulations provide results that are relevant to the questions asked about the population under study.

Fixation probabilities of evolutionary coordination games on two coupled populations

NASA Astrophysics Data System (ADS)

Zhang, Liye; Ying, Limin; Zhou, Jie; Guan, Shuguang; Zou, Yong

2016-09-01

Evolutionary forces resulted from competitions between different populations are common, which change the evolutionary behavior of a single population. In an isolated population of coordination games of two strategies (e.g., s1 and s2), the previous studies focused on determining the fixation probability that the system is occupied by only one strategy (s1) and their expectation times, given an initial mixture of two strategies. In this work, we propose a model of two interdependent populations, disclosing the effects of the interaction strength on fixation probabilities. In the well-mixing limit, a detailed linear stability analysis is performed, which allows us to find and to classify the different equilibria, yielding a clear picture of the bifurcation patterns in phase space. We demonstrate that the interactions between populations crucially alter the dynamic behavior. More specifically, if the coupling strength is larger than some threshold value, the critical initial density of one strategy (s1) that corresponds to fixation is significantly delayed. Instead, the two populations evolve to the opposite state of all (s2) strategy, which are in favor of the red queen hypothesis. We delineate the extinction time of strategy (s1) explicitly, which is an exponential form. These results are validated by systematic numerical simulations.

Habitat continuity and stepping-stone oceanographic distances explain population genetic connectivity of the brown alga Cystoseira amentacea.

PubMed

Buonomo, Roberto; Assis, Jorge; Fernandes, Francisco; Engelen, Aschwin H; Airoldi, Laura; Serrão, Ester A

2017-02-01

Effective predictive and management approaches for species occurring in a metapopulation structure require good understanding of interpopulation connectivity. In this study, we ask whether population genetic structure of marine species with fragmented distributions can be predicted by stepping-stone oceanographic transport and habitat continuity, using as model an ecosystem-structuring brown alga, Cystoseira amentacea var. stricta. To answer this question, we analysed the genetic structure and estimated the connectivity of populations along discontinuous rocky habitat patches in southern Italy, using microsatellite markers at multiple scales. In addition, we modelled the effect of rocky habitat continuity and ocean circulation on gene flow by simulating Lagrangian particle dispersal based on ocean surface currents allowing multigenerational stepping-stone dynamics. Populations were highly differentiated, at scales from few metres up to thousands of kilometres. The best possible model fit to explain the genetic results combined current direction, rocky habitat extension and distance along the coast among rocky sites. We conclude that a combination of variable suitable habitat and oceanographic transport is a useful predictor of genetic structure. This relationship provides insight into the mechanisms of dispersal and the role of life-history traits. Our results highlight the importance of spatially explicit modelling of stepping-stone dynamics and oceanographic directional transport coupled with habitat suitability, to better describe and predict marine population structure and differentiation. This study also suggests the appropriate spatial scales for the conservation, restoration and management of species that are increasingly affected by habitat modifications. © 2016 John Wiley & Sons Ltd.

Carnivora Population Dynamics Are as Slow and as Fast as Those of Other Mammals: Implications for Their Conservation

PubMed Central

van de Kerk, Madelon; de Kroon, Hans; Conde, Dalia A.; Jongejans, Eelke

2013-01-01

Of the 285 species of Carnivora 71 are threatened, while many of these species fulfill important ecological roles in their ecosystems as top or meso-predators. Population transition matrices make it possible to study how age-specific survival and fecundity affect population growth, extinction risks, and responses to management strategies. Here we review 38 matrix models from 35 studies on 27 Carnivora taxa, covering 11% of the threatened Carnivora species. We show that the elasticity patterns (i.e. distribution over fecundity, juvenile survival and adult survival) in Carnivora cover the same range in triangular elasticity plots as those of other mammal species, despite the specific place of Carnivora in the food chain. Furthermore, reproductive loop elasticity analysis shows that the studied species spread out evenly over a slow-fast continuum, but also quantifies the large variation in the duration of important life cycles and their contributions to population growth rate. These general elasticity patterns among species, and their correlation with simple life history characteristics like body mass, age of first reproduction and life span, enables the extrapolation of population dynamical properties to unstudied species. With several examples we discuss how this slow-fast continuum, and related patterns of variation in reproductive loop elasticity, can be used in the formulation of tentative management plans for threatened species that cannot wait for the results of thorough demographic studies. We argue, however, that such management programs should explicitly include a plan for learning about the key demographic rates and how these are affected by environmental drivers and threats. PMID:23950922

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

Franklin, Janet; Serra-Diaz, Josep M.; Syphard, Alexandra D.

Anthropogenic drivers of global change include rising atmospheric concentrations of carbon dioxide and other greenhouse gasses and resulting changes in the climate, as well as nitrogen deposition, biotic invasions, altered disturbance regimes, and land-use change. Predicting the effects of global change on terrestrial plant communities is crucial because of the ecosystem services vegetation provides, from climate regulation to forest products. In this article, we present a framework for detecting vegetation changes and attributing them to global change drivers that incorporates multiple lines of evidence from spatially extensive monitoring networks, distributed experiments, remotely sensed data, and historical records. Based on amore » literature review, we summarize observed changes and then describe modeling tools that can forecast the impacts of multiple drivers on plant communities in an era of rapid change. Observed responses to changes in temperature, water, nutrients, land use, and disturbance show strong sensitivity of ecosystem productivity and plant population dynamics to water balance and long-lasting effects of disturbance on plant community dynamics. Persistent effects of land-use change and human-altered fire regimes on vegetation can overshadow or interact with climate change impacts. Models forecasting plant community responses to global change incorporate shifting ecological niches, population dynamics, species interactions, spatially explicit disturbance, ecosystem processes, and plant functional responses. Lastly, monitoring, experiments, and models evaluating multiple change drivers are needed to detect and predict vegetation changes in response to 21st century global change.« less

Modeling the population-level effects of hypoxia on a coastal fish: implications of a spatially-explicit individual-based model

NASA Astrophysics Data System (ADS)

Rose, K.; Creekmore, S.; Thomas, P.; Craig, K.; Neilan, R.; Rahman, S.; Wang, L.; Justic, D.

2016-02-01

The northwestern Gulf of Mexico (USA) currently experiences a large hypoxic area ("dead zone") during the summer. The population-level effects of hypoxia on coastal fish are largely unknown. We developed a spatially-explicit, individual-based model to analyze how hypoxia effects on reproduction, growth, and mortality of individual Atlantic croaker could lead to population-level responses. The model follows the hourly growth, mortality, reproduction, and movement of individuals on a 300 x 800 spatial grid of 1 km2 cells for 140 years. Chlorophyll-a concentration and water temperature were specified daily for each grid cell. Dissolved oxygen (DO) was obtained from a 3-D water quality model for four years that differed in their severity of hypoxia. A bioenergetics model was used to represent growth, mortality was assumed stage- and age-dependent, and movement behavior was based on temperature preferences and avoidance of low DO. Hypoxia effects were imposed using exposure-effects sub-models that converted time-varying exposure to DO to reductions in growth and fecundity, and increases in mortality. Using sequences of mild, intermediate, and severe hypoxia years, the model predicted a 20% decrease in population abundance. Additional simulations were performed under the assumption that river-based nutrients loadings that lead to more hypoxia also lead to higher primary production and more food for croaker. Twenty-five percent and 50% nutrient reduction scenarios were simulated by adjusting the cholorphyll-a concentrations used as food proxy for the croaker. We then incrementally increased the DO concentrations to determine how much hypoxia would need to be reduced to offset the lower food production resulting from reduced nutrients. We discuss the generality of our results, the hidden effects of hypoxia on fish, and our overall strategy of combining laboratory and field studies with modeling to produce robust predictions of population responses to stressors under dynamic and multi-stressor conditions.

The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community

NASA Astrophysics Data System (ADS)

Daly, Aisling J.; Baetens, Jan M.; De Baets, Bernard

2016-12-01

Biodiversity has a critical impact on ecosystem functionality and stability, and thus the current biodiversity crisis has motivated many studies of the mechanisms that sustain biodiversity, a notable example being non-transitive or cyclic competition. We therefore extend existing microscopic models of communities with cyclic competition by incorporating resource dependence in demographic processes, characteristics of natural systems often oversimplified or overlooked by modellers. The spatially explicit nature of our individual-based model of three interacting species results in the formation of stable spatial structures, which have significant effects on community functioning, in agreement with experimental observations of pattern formation in microbial communities.

[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.

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides.

PubMed

Frembgen-Kesner, Tamara; Andrews, Casey T; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A; Jain, Aakash; Olayiwola, Oluwatoni J; Weishaar, Mitch R; Elcock, Adrian H

2015-05-12

Recently, we reported the parametrization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral, and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral, and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downward in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multidomain proteins connected by flexible linkers.

Physical, Psychological and Emotional Benefits of Green Physical Activity: An Ecological Dynamics Perspective.

PubMed

Yeh, Hsiao-Pu; Stone, Joseph Antony; Churchill, Sarah May; Wheat, Jonathan Stephen; Brymer, Eric; Davids, Keith

2016-07-01

Increasing evidence supports the multiple benefits to physical, psychological and emotional wellbeing of green physical activity, a topic of increasing interest in the past decade. Research has revealed a synergistic benefit of green physical activity, which includes all aspects of exercise and physical activity in the presence of nature. Our theoretical analysis suggests there are three distinct levels of engagement in green physical activity, with each level reported to have a positive effect on human behaviours. However, the extent to which each level of green physical activity benefits health and wellbeing is assumed to differ, requiring confirmation in future research. This elucidation of understanding is needed because previous literature has tended to focus on recording empirical evidence rather than developing a sound theoretical framework to understand green physical activity effects. Here we propose an ecological dynamics rationale to explain how and why green physical activity might influence health and wellbeing of different population groups. This framework suggests a number of unexplored, interacting constraints related to types of environment and population groups, which shape reported levels of benefit of green physical activity. Further analysis is needed to clarify the explicit relationship between green physical activity and health and wellbeing, including levels of engagement, types of environmental constraints, levels of physical activity, adventure effects, skill effects and sampling of different populations.

Conceptualizing the dynamics of a drought affected agricultural community

NASA Astrophysics Data System (ADS)

Kuil, Linda; Carr, Gemma; Viglione, Alberto; Bloeschl, Guenter

2015-04-01

Climate and especially water availability and variability play an important role in the development of our societies. This can be seen through the vast investments that are made in reaching water security and the economic impact regions experience when the rains fail. However, the limit of available fresh water is increasingly felt as our population increases and the demand for water continues to rise. But how do we as society respond? Are periods of drought making us more resilient? The answer to this question is sought through the development of a stylized model that is built within the spirit of the Easter Island model by Brander and Taylor and aimed at capturing the essence of the dynamics of water supply and demand. By explicitly incorporating feedbacks, but keeping the framework simple, the model seeks to understand qualitative behavior of our socio-hydrological system as opposed to predicting exact pathways. The model shows that carrying capacity dynamics are a determining factor for continued growth. Future work will explore the underlying relationships further, among others, through examination of case studies.

The evolution within us

PubMed Central

Cobey, Sarah; Wilson, Patrick; Matsen, Frederick A.

2015-01-01

The B-cell immune response is a remarkable evolutionary system found in jawed vertebrates. B-cell receptors, the membrane-bound form of antibodies, are capable of evolving high affinity to almost any foreign protein. High germline diversity and rapid evolution upon encounter with antigen explain the general adaptability of B-cell populations, but the dynamics of repertoires are less well understood. These dynamics are scientifically and clinically important. After highlighting the remarkable characteristics of naive and experienced B-cell repertoires, especially biased usage of genes encoding the B-cell receptors, we contrast methods of sequence analysis and their attempts to explain patterns of B-cell evolution. These phylogenetic approaches are currently unlinked to explicit models of B-cell competition, which analyse repertoire evolution at the level of phenotype, the affinities and specificities to particular antigenic sites. The models, in turn, suggest how chance, infection history and other factors contribute to different patterns of immunodominance and protection between people. Challenges in rational vaccine design, specifically vaccines to induce broadly neutralizing antibodies to HIV, underscore critical gaps in our understanding of B cells' evolutionary and ecological dynamics. PMID:26194749

Single-crossover recombination in discrete time.

PubMed

von Wangenheim, Ute; Baake, Ellen; Baake, Michael

2010-05-01

Modelling the process of recombination leads to a large coupled nonlinear dynamical system. Here, we consider a particular case of recombination in discrete time, allowing only for single crossovers. While the analogous dynamics in continuous time admits a closed solution (Baake and Baake in Can J Math 55:3-41, 2003), this no longer works for discrete time. A more general model (i.e. without the restriction to single crossovers) has been studied before (Bennett in Ann Hum Genet 18:311-317, 1954; Dawson in Theor Popul Biol 58:1-20, 2000; Linear Algebra Appl 348:115-137, 2002) and was solved algorithmically by means of Haldane linearisation. Using the special formalism introduced by Baake and Baake (Can J Math 55:3-41, 2003), we obtain further insight into the single-crossover dynamics and the particular difficulties that arise in discrete time. We then transform the equations to a solvable system in a two-step procedure: linearisation followed by diagonalisation. Still, the coefficients of the second step must be determined in a recursive manner, but once this is done for a given system, they allow for an explicit solution valid for all times.

Ultrafast Electronic Relaxation through a Conical Intersection: Nonadiabatic Dynamics Disentangled through an Oscillator Strength-Based Diabatization Framework

DOE PAGES

Medders, Gregory R.; Alguire, Ethan C.; Jain, Amber; ...

2017-01-18

Here, we employ surface hopping trajectories to model the short-time dynamics of gas-phase and partially solvated 4-(N,N-dimethylamino)benzonitrile (DMABN), a dual fluorescent molecule that is known to undergo a nonadiabatic transition through a conical intersection. To compare theory vs time-resolved fluorescence measurements, we calculate the mixed quantum–classical density matrix and the ensemble averaged transition dipole moment. We introduce a diabatization scheme based on the oscillator strength to convert the TDDFT adiabatic states into diabatic states of L a and L b character. Somewhat surprisingly, we find that the rate of relaxation reported by emission to the ground state is almost 50%more » slower than the adiabatic population relaxation. Although our calculated adiabatic rates are largely consistent with previous theoretical calculations and no obvious effects of decoherence are seen, the diabatization procedure introduced here enables an explicit picture of dynamics in the branching plane, raising tantalizing questions about geometric phase effects in systems with dozens of atoms.« less

Fish and fire: Post-wildfire sediment dynamics and implications for the viability of trout populations

NASA Astrophysics Data System (ADS)

Murphy, B. P.; Czuba, J. A.; Belmont, P.; Budy, P.; Finch, C.

2017-12-01

Episodic events in steep landscapes, such as wildfire and mass wasting, contribute large pulses of sediment to rivers and can significantly alter the quality and connectivity of fish habitat. Understanding where these sediment inputs occur, how they are transported and processed through the watershed, and their geomorphic effect on the river network is critical to predicting the impact on ecological aquatic communities. The Tushar Mountains of southern Utah experienced a severe wildfire in 2010, resulting in numerous debris flows and the extirpation of trout populations. Following many years of habitat and ecological monitoring in the field, we have developed a modeling framework that links post-wildfire debris flows, fluvial sediment routing, and population ecology in order to evaluate the impact and response of trout to wildfire. First, using the Tushar topographic and wildfire parameters, as well as stochastic precipitation generation, we predict the post-wildfire debris flow probabilities and volumes of mainstem tributaries using the Cannon et al. [2010] model. This produces episodic hillslope sediment inputs, which are delivered to a fluvial sediment, river-network routing model (modified from Czuba et al. [2017]). In this updated model, sediment transport dynamics are driven by time-varying discharge associated with the stochastic precipitation generation, include multiple grain sizes (including gravel), use mixed-size transport equations (Wilcock & Crowe [2003]), and incorporate channel slope adjustments with aggradation and degradation. Finally, with the spatially explicit adjustments in channel bed elevation and grain size, we utilize a new population viability analysis (PVA) model to predict the impact and recovery of fish populations in response to these changes in habitat. Our model provides a generalizable framework for linking physical and ecological models and for evaluating the extirpation risk of isolated fish populations throughout the Intermountain West to the increasing threat of wildfire.

Implicit and explicit self-esteem in currently depressed individuals with and without suicidal ideation.

PubMed

Franck, Erik; De Raedt, Rudi; Dereu, Mieke; Van den Abbeele, Dirk

2007-03-01

In the present study, we have further explored implicit self-esteem in currently depressed individuals. Since suicidal ideation is associated with lower self-esteem in depressed individuals, we measured both implicit and explicit self-esteem in a population of currently depressed (CD) individuals, with and without suicidal ideation (SI), and in a group of non-depressed controls (ND). The results indicate that only CD individuals with SI show a discrepancy between their implicit and explicit self-esteem: that is, they exhibit high implicit and low explicit self-esteem. CD individuals without SI exhibit both low implicit and low explicit self-esteem; and ND controls exhibit both normal implicit and normal explicit self-esteem. These results provide new insights in the study of implicit self-esteem and the combination of implicit and explicit self-esteem in depression.

L1 Adaptive Control Augmentation System with Application to the X-29 Lateral/Directional Dynamics: A Multi-Input Multi-Output Approach

NASA Technical Reports Server (NTRS)

Griffin, Brian Joseph; Burken, John J.; Xargay, Enric

2010-01-01

This paper presents an L(sub 1) adaptive control augmentation system design for multi-input multi-output nonlinear systems in the presence of unmatched uncertainties which may exhibit significant cross-coupling effects. A piecewise continuous adaptive law is adopted and extended for applicability to multi-input multi-output systems that explicitly compensates for dynamic cross-coupling. In addition, explicit use of high-fidelity actuator models are added to the L1 architecture to reduce uncertainties in the system. The L(sub 1) multi-input multi-output adaptive control architecture is applied to the X-29 lateral/directional dynamics and results are evaluated against a similar single-input single-output design approach.

Fast but fleeting: adaptive motor learning processes associated with aging and cognitive decline.

PubMed

Trewartha, Kevin M; Garcia, Angeles; Wolpert, Daniel M; Flanagan, J Randall

2014-10-01

Motor learning has been shown to depend on multiple interacting learning processes. For example, learning to adapt when moving grasped objects with novel dynamics involves a fast process that adapts and decays quickly-and that has been linked to explicit memory-and a slower process that adapts and decays more gradually. Each process is characterized by a learning rate that controls how strongly motor memory is updated based on experienced errors and a retention factor determining the movement-to-movement decay in motor memory. Here we examined whether fast and slow motor learning processes involved in learning novel dynamics differ between younger and older adults. In addition, we investigated how age-related decline in explicit memory performance influences learning and retention parameters. Although the groups adapted equally well, they did so with markedly different underlying processes. Whereas the groups had similar fast processes, they had different slow processes. Specifically, the older adults exhibited decreased retention in their slow process compared with younger adults. Within the older group, who exhibited considerable variation in explicit memory performance, we found that poor explicit memory was associated with reduced retention in the fast process, as well as the slow process. These findings suggest that explicit memory resources are a determining factor in impairments in the both the fast and slow processes for motor learning but that aging effects on the slow process are independent of explicit memory declines. Copyright © 2014 the authors 0270-6474/14/3413411-11$15.00/0.

Toll-Like Receptor-9-Mediated Invasion in Breast Cancer

DTIC Science & Technology

2011-07-01

Molecular Dynamics Simulations. Theoretical structural models were obtained from molecular dynamics simulations using explicit solvation by...with AMBER by MARDIGRAS. The solution structure was then derived by coupling the resulting NMR distance restraints with a molecular dynamic ...Overlay of NMR restrained structure (red) with theoretical molecular dynamic simulated annealing structure (blue). Energetic stability of the 9-mer

Collaborative Research Program on Advanced Metals and Ceramics for Armor and Anti-Armor Applications Dynamic Behavior of Non-Crystalline and Crystalline Metallic Systems

DTIC Science & Technology

2006-09-01

compression, including real-time cinematography of failure under dynamic compression, was evaluated. The results (figure 10) clearly show that the failure... art of simulations of dynamic failure and damage mechanisms. An explicit dynamic parallel code has been developed to track damage mechanisms in the

Trp-cage: folding free energy landscape in explicit water.

PubMed

Zhou, Ruhong

2003-11-11

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

Trp-cage: Folding free energy landscape in explicit water

NASA Astrophysics Data System (ADS)

Zhou, Ruhong

2003-11-01

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

Trp-cage: Folding free energy landscape in explicit water

PubMed Central

Zhou, Ruhong

2003-01-01

Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle–particle particle–mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å Cα-RMSD (Cα-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence. PMID:14581616

A mechanistic soil biogeochemistry model with explicit representation of microbial and macrofaunal activities and nutrient cycles

NASA Astrophysics Data System (ADS)

Fatichi, Simone; Manzoni, Stefano; Or, Dani; Paschalis, Athanasios

2016-04-01

The potential of a given ecosystem to store and release carbon is inherently linked to soil biogeochemical processes. These processes are deeply connected to the water, energy, and vegetation dynamics above and belowground. Recently, it has been advocated that a mechanistic representation of soil biogeochemistry require: (i) partitioning of soil organic carbon (SOC) pools according to their functional role; (ii) an explicit representation of microbial dynamics; (iii) coupling of carbon and nutrient cycles. While some of these components have been introduced in specialized models, they have been rarely implemented in terrestrial biosphere models and tested in real cases. In this study, we combine a new soil biogeochemistry model with an existing model of land-surface hydrology and vegetation dynamics (T&C). Specifically the soil biogeochemistry component explicitly separates different litter pools and distinguishes SOC in particulate, dissolved and mineral associated fractions. Extracellular enzymes and microbial pools are explicitly represented differentiating the functional roles of bacteria, saprotrophic and mycorrhizal fungi. Microbial activity depends on temperature, soil moisture and litter or SOC stoichiometry. The activity of macrofauna is also modeled. Nutrient dynamics include the cycles of nitrogen, phosphorous and potassium. The model accounts for feedbacks between nutrient limitations and plant growth as well as for plant stoichiometric flexibility. In turn, litter input is a function of the simulated vegetation dynamics. Root exudation and export to mycorrhiza are computed based on a nutrient uptake cost function. The combined model is tested to reproduce respiration dynamics and nitrogen cycle in few sites where data were available to test plausibility of results across a range of different metrics. For instance in a Swiss grassland ecosystem, fine root, bacteria, fungal and macrofaunal respiration account for 40%, 23%, 33% and 4% of total belowground respiration, respectively. Root exudation and carbon export to mycorrhizal represent about 7% of plant Net Primary Production. The model allows exploring the temporal dynamics of respiration fluxes from the different ecosystem components and designing virtual experiments on the controls exerted by environmental variables and/or soil microbes and mycorrhizal associations on soil carbon storage, plant growth, and nutrient leaching.

Measuring Explicit Word Learning of Preschool Children: A Development Study.

PubMed

Kelley, Elizabeth Spencer

2017-08-15

The purpose of this article is to present preliminary results related to the development of a new measure of explicit word learning. The measure incorporated elements of explicit vocabulary instruction and dynamic assessment and was designed to be sensitive to differences in word learning skill and to be feasible for use in clinical settings. The explicit word learning measure included brief teaching trials and repeated fine-grained measurement of semantic knowledge and production of 3 novel words (2 verbs and 1 adjective). Preschool children (N = 23) completed the measure of explicit word learning; standardized, norm-referenced measures of expressive and receptive vocabulary; and an incidental word learning task. The measure of explicit word learning provided meaningful information about word learning. Performance on the explicit measure was related to existing vocabulary knowledge and incidental word learning. Findings from this development study indicate that further examination of the measure of explicit word learning is warranted. The measure may have the potential to identify children who are poor word learners. https://doi.org/10.23641/asha.5170738.

Examining the equivalence of Bakamjian-Thomas mass operators in different forms of dynamics

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

Polyzou, W. N.

We discus the proof of the equivalence of relativistic quantum mechanical models based on the generalized Bakamjian-Thomas construction in all of Dirac's forms of dynamics. Explicit representations of the equivalent mass operators are given in all three of Dirac's forms of dynamics.

Increased gamma band power during movement planning coincides with motor memory retrieval.

PubMed

Thürer, Benjamin; Stockinger, Christian; Focke, Anne; Putze, Felix; Schultz, Tanja; Stein, Thorsten

2016-01-15

The retrieval of motor memory requires a previous memory encoding and subsequent consolidation of the specific motor memory. Previous work showed that motor memory seems to rely on different memory components (e.g., implicit, explicit). However, it is still unknown if explicit components contribute to the retrieval of motor memories formed by dynamic adaptation tasks and which neural correlates are linked to memory retrieval. We investigated the lower and higher gamma bands of subjects' electroencephalography during encoding and retrieval of a dynamic adaptation task. A total of 24 subjects were randomly assigned to a treatment and control group. Both groups adapted to a force field A on day 1 and were re-exposed to the same force field A on day 3 of the experiment. On day 2, treatment group learned an interfering force field B whereas control group had a day rest. Kinematic analyses showed that control group improved their initial motor performance from day 1 to day 3 but treatment group did not. This behavioral result coincided with an increased higher gamma band power in the electrodes over prefrontal areas on the initial trials of day 3 for control but not treatment group. Intriguingly, this effect vanished with the subsequent re-adaptation on day 3. We suggest that improved re-test performance in a dynamic motor adaptation task is contributed by explicit memory and that gamma bands in the electrodes over the prefrontal cortex are linked to these explicit components. Furthermore, we suggest that the contribution of explicit memory vanishes with the subsequent re-adaptation while task automaticity increases. Copyright © 2015 Elsevier Inc. All rights reserved.

From Experiment to Theory: What Can We Learn from Growth Curves?

PubMed

Kareva, Irina; Karev, Georgy

2018-01-01

Finding an appropriate functional form to describe population growth based on key properties of a described system allows making justified predictions about future population development. This information can be of vital importance in all areas of research, ranging from cell growth to global demography. Here, we use this connection between theory and observation to pose the following question: what can we infer about intrinsic properties of a population (i.e., degree of heterogeneity, or dependence on external resources) based on which growth function best fits its growth dynamics? We investigate several nonstandard classes of multi-phase growth curves that capture different stages of population growth; these models include hyperbolic-exponential, exponential-linear, exponential-linear-saturation growth patterns. The constructed models account explicitly for the process of natural selection within inhomogeneous populations. Based on the underlying hypotheses for each of the models, we identify whether the population that it best fits by a particular curve is more likely to be homogeneous or heterogeneous, grow in a density-dependent or frequency-dependent manner, and whether it depends on external resources during any or all stages of its development. We apply these predictions to cancer cell growth and demographic data obtained from the literature. Our theory, if confirmed, can provide an additional biomarker and a predictive tool to complement experimental research.

Persistence of Soil Organic Carbon can be Explained as an Emergent Property of Microbial Ecology and Population Dynamics

NASA Astrophysics Data System (ADS)

Woolf, D.; Lehmann, J.

2016-12-01

The exchange of carbon between soils and the atmosphere represents an important uncertainty in climate predictions. Current Earth system models apply soil organic matter (SOM) models based on independent carbon pools with 1st order decomposition dynamics. It has been widely argued over the last decade that such models do not accurately describe soil processes and mechanisms. For example, the long term persistence of soil organic carbon (SOC) is only adequately described by such models by the post hoc assumption of passive or inert carbon pools. Further, such 1st order models also fail to account for microbially-mediated dynamics such as priming interactions. These shortcomings may limit their applicability to long term predictions under conditions of global environmental change. In addition to incorporating recent conceptual advances in the mechanisms of SOM decomposition and protection, next-generation SOM models intended for use in Earth system models need to meet further quality criteria. Namely, that they should (a) accurately describe historical data from long term trials and the current global distribution of soil organic carbon, (b) be computationally efficient for large number of iterations involved in climate modeling, and (c) have sufficiently simple parameterization that they can be run on spatially-explicit data available at global scale under varying conditions of global change over long time scales. Here we show that linking fundamental ecological principles and microbial population dynamics to SOC turnover rates results in a dynamic model that meets all of these quality criteria. This approach simultaneously eliminates the need to postulate biogeochemically-implausible passive or inert pools, instead showing how SOM persistence emerges from ecological principles, while also reproducing observed priming interactions.

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

PubMed

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

2015-12-01

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

Demographic consequences of climate change and land cover help explain a history of extirpations and range contraction in a declining snake species.

PubMed

Pomara, Lars Y; LeDee, Olivia E; Martin, Karl J; Zuckerberg, Benjamin

2014-07-01

Developing conservation strategies for threatened species increasingly requires understanding vulnerabilities to climate change, in terms of both demographic sensitivities to climatic and other environmental factors, and exposure to variability in those factors over time and space. We conducted a range-wide, spatially explicit climate change vulnerability assessment for Eastern Massasauga (Sistrurus catenatus), a declining endemic species in a region showing strong environmental change. Using active season and winter adult survival estimates derived from 17 data sets throughout the species' range, we identified demographic sensitivities to winter drought, maximum precipitation during the summer, and the proportion of the surrounding landscape dominated by agricultural and urban land cover. Each of these factors was negatively associated with active season adult survival rates in binomial generalized linear models. We then used these relationships to back-cast adult survival with dynamic climate variables from 1950 to 2008 using spatially explicit demographic models. Demographic models for 189 population locations predicted known extant and extirpated populations well (AUC = 0.75), and models based on climate and land cover variables were superior to models incorporating either of those effects independently. These results suggest that increasing frequencies and severities of extreme events, including drought and flooding, have been important drivers of the long-term spatiotemporal variation in a demographic rate. We provide evidence that this variation reflects nonadaptive sensitivity to climatic stressors, which are contributing to long-term demographic decline and range contraction for a species of high-conservation concern. Range-wide demographic modeling facilitated an understanding of spatial shifts in climatic suitability and exposure, allowing the identification of important climate refugia for a dispersal-limited species. Climate change vulnerability assessment provides a framework for linking demographic and distributional dynamics to environmental change, and can thereby provide unique information for conservation planning and management. © 2013 John Wiley & Sons Ltd.

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water.

PubMed

Tamamis, Phanourios; Skourtis, Spiros S; Morikis, Dimitrios; Lambris, John D; Archontis, Georgios

2007-09-01

The cyclic 13-residue peptide compstatin is a potential therapeutic agent against the unregulated activation of the complement system. A thorough knowledge of its structural and dynamical properties in solution may assist the design of improved complement inhibitors. NMR studies have suggested that the 5-8 segment of free compstatin folds into a critical for activity 5-8 beta turn and the rest of the peptide is mainly disordered. Earlier computational studies of compstatin analogues with a polar-hydrogen/generalized-Born approximation reproduced the 5-8 turn, but also indicated the formation of beta-hairpin or alpha-helical elements and the existence of interactions between certain charged or aromatic sidechains. However, these features are absent or partly present in the NMR spectra, due to extensive conformational averaging. In order to check the compstatin properties with a more rigorous model of the intra- and intermolecular interactions, we conduct here 98-ns all-atom/explicit-water simulations of three compstatin analogues with variable activity; a native analogue, the more active mutant V4W/H9A and the inactive mutant Q5G. The 5-8 beta-turn population is in good accord with NMR. For the systems studied here, the simulations suggest that the 5-8 turn population does not correlate strictly with activity, in agreement with earlier mutational studies. Furthermore, they show structural differences among the analogues outside the 5-8 region. The possible role of these differences in activity is discussed. The probability of beta-hairpin or alpha-helix elements is much smaller with respect to the polar-hydrogen/GB simulations, and the persistent Trp4-Trp7 or Asp6-Arg11 sidechain interactions of the earlier GB studies are not reproduced. The present simulations extend the NMR data and improve our understanding of the properties of compstatin and related analogues.

A self-learning rule base for command following in dynamical systems

NASA Technical Reports Server (NTRS)

Tsai, Wei K.; Lee, Hon-Mun; Parlos, Alexander

1992-01-01

In this paper, a self-learning Rule Base for command following in dynamical systems is presented. The learning is accomplished though reinforcement learning using an associative memory called SAM. The main advantage of SAM is that it is a function approximator with explicit storage of training samples. A learning algorithm patterned after the dynamic programming is proposed. Two artificially created, unstable dynamical systems are used for testing, and the Rule Base was used to generate a feedback control to improve the command following ability of the otherwise uncontrolled systems. The numerical results are very encouraging. The controlled systems exhibit a more stable behavior and a better capability to follow reference commands. The rules resulting from the reinforcement learning are explicitly stored and they can be modified or augmented by human experts. Due to overlapping storage scheme of SAM, the stored rules are similar to fuzzy rules.

Dynamic occupancy models for explicit colonization processes

USGS Publications Warehouse

Broms, Kristin M.; Hooten, Mevin B.; Johnson, Devin S.; Altwegg, Res; Conquest, Loveday

2016-01-01

The dynamic, multi-season occupancy model framework has become a popular tool for modeling open populations with occupancies that change over time through local colonizations and extinctions. However, few versions of the model relate these probabilities to the occupancies of neighboring sites or patches. We present a modeling framework that incorporates this information and is capable of describing a wide variety of spatiotemporal colonization and extinction processes. A key feature of the model is that it is based on a simple set of small-scale rules describing how the process evolves. The result is a dynamic process that can account for complicated large-scale features. In our model, a site is more likely to be colonized if more of its neighbors were previously occupied and if it provides more appealing environmental characteristics than its neighboring sites. Additionally, a site without occupied neighbors may also become colonized through the inclusion of a long-distance dispersal process. Although similar model specifications have been developed for epidemiological applications, ours formally accounts for detectability using the well-known occupancy modeling framework. After demonstrating the viability and potential of this new form of dynamic occupancy model in a simulation study, we use it to obtain inference for the ongoing Common Myna (Acridotheres tristis) invasion in South Africa. Our results suggest that the Common Myna continues to enlarge its distribution and its spread via short distance movement, rather than long-distance dispersal. Overall, this new modeling framework provides a powerful tool for managers examining the drivers of colonization including short- vs. long-distance dispersal, habitat quality, and distance from source populations.

Linking Adverse Outcome Pathways to Dynamic Energy Budgets: A Conceptual Model

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

Murphy, Cheryl; Nisbet, Roger; Antczak, Philipp

Ecological risk assessment quantifies the likelihood of undesirable impacts of stressors, primarily at high levels of biological organization. Data used to inform ecological risk assessments come primarily from tests on individual organisms or from suborganismal studies, indicating a disconnect between primary data and protection goals. We know how to relate individual responses to population dynamics using individual-based models, and there are emerging ideas on how to make connections to ecosystem services. However, there is no established methodology to connect effects seen at higher levels of biological organization with suborganismal dynamics, despite progress made in identifying Adverse Outcome Pathways (AOPs) thatmore » link molecular initiating events to ecologically relevant key events. This chapter is a product of a working group at the National Center for Mathematical and Biological Synthesis (NIMBioS) that assessed the feasibility of using dynamic energy budget (DEB) models of individual organisms as a “pivot” connecting suborganismal processes to higher level ecological processes. AOP models quantify explicit molecular, cellular or organ-level processes, but do not offer a route to linking sub-organismal damage to adverse effects on individual growth, reproduction, and survival, which can be propagated to the population level through individual-based models. DEB models describe these processes, but use abstract variables with undetermined connections to suborganismal biology. We propose linking DEB and quantitative AOP models by interpreting AOP key events as measures of damage-inducing processes in a DEB model. Here, we present a conceptual model for linking AOPs to DEB models and review existing modeling tools available for both AOP and DEB.« less

Parameterization of backbone flexibility in a coarse-grained force field for proteins (COFFDROP) derived from all-atom explicit-solvent molecular dynamics simulations of all possible two-residue peptides

PubMed Central

Frembgen-Kesner, Tamara; Andrews, Casey T.; Li, Shuxiang; Ngo, Nguyet Anh; Shubert, Scott A.; Jain, Aakash; Olayiwola, Oluwatoni; Weishaar, Mitch R.; Elcock, Adrian H.

2015-01-01

Recently, we reported the parameterization of a set of coarse-grained (CG) nonbonded potential functions, derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acid pairs, and designed for use in (implicit-solvent) Brownian dynamics (BD) simulations of proteins; this force field was named COFFDROP (COarse-grained Force Field for Dynamic Representations Of Proteins). Here, we describe the extension of COFFDROP to include bonded backbone terms derived from fitting to results of explicit-solvent MD simulations of all possible two-residue peptides containing the 20 standard amino acids, with histidine modeled in both its protonated and neutral forms. The iterative Boltzmann inversion (IBI) method was used to optimize new CG potential functions for backbone-related terms by attempting to reproduce angle, dihedral and distance probability distributions generated by the MD simulations. In a simple test of the transferability of the extended force field, the angle, dihedral and distance probability distributions obtained from BD simulations of 56 three-residue peptides were compared to results from corresponding explicit-solvent MD simulations. In a more challenging test of the COFFDROP force field, it was used to simulate eight intrinsically disordered proteins and was shown to quite accurately reproduce the experimental hydrodynamic radii (Rhydro), provided that the favorable nonbonded interactions of the force field were uniformly scaled downwards in magnitude. Overall, the results indicate that the COFFDROP force field is likely to find use in modeling the conformational behavior of intrinsically disordered proteins and multi-domain proteins connected by flexible linkers. PMID:26574429

Propagation of solutions to the Fisher-KPP equation with slowly decaying initial data

NASA Astrophysics Data System (ADS)

Henderson, Christopher

2016-10-01

The Fisher-KPP equation is a model for population dynamics that has generated a huge amount of interest since its introduction in 1937. The speed with which a population spreads has been computed quite precisely when the initial data, u 0, decays exponentially. More recently, though, the case when the initial data decays more slowly has been studied. In Hamel F and Roques L (2010 J. Differ. Equ. 249 1726-45), the authors show that the level sets of height of m of u move super-linearly and may be bounded above and below by expressions of the form u0-1≤ft({{c}m}{{\\text{e}}-t}\\right) when u 0 decays algebraically of a small enough order. The constants c m for the upper and lower bounds that they obtain are not explicit and do not match. In this paper, we improve their precision for a broader class of initial data and for a broader class of equations. In particular, our approach yields the explicit highest order term in the location of the level sets, which in the most basic setting is given by u0-1≤ft(m{{\\text{e}}-t}/(1-m)\\right) as long as u 0 decays slower than {{\\text{e}}-\\sqrt{x}} . We generalize this to the previously unstudied setting when the nonlinearity is periodic in space. In addition, for large times, we characterize the profile of the solution in terms of a generalized logistic equation.

Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations

PubMed Central

Xiong, Kan; Zwier, Matthew C.; Myshakina, Nataliya S.; Burger, Virginia M.; Asher, Sanford A.; Chong, Lillian T.

2011-01-01

We report the first experimental measurements of Ramachandran Ψ-angle distributions for intrinsically disordered peptides: the N-terminal peptide fragment of tumor suppressor p53 and its P27 mutant form. To provide atomically detailed views of the conformational distributions, we performed classical, explicit-solvent molecular dynamics simulations on the microsecond timescale. Upon binding its partner protein, MDM2, wild-type p53 peptide adopts an α-helical conformation. Mutation of Pro27 to serine results in the highest affinity yet observed for MDM2-binding of the p53 peptide. Both UV resonance Raman spectroscopy (UVRR) and simulations reveal that the P27S mutation decreases the extent of PPII helical content and increases the probability for conformations that are similar to the α-helical MDM2-bound conformation. In addition, UVRR measurements were performed on peptides that were isotopically labeled at the Leu26 residue preceding the Pro27 in order to determine the conformational distributions of Leu26 in the wild-type and mutant peptides. The UVRR and simulation results are in quantitative agreement in terms of the change in the population of non-PPII conformations involving Leu26 upon mutation of Pro27 to serine. Finally, our simulations reveal that the MDM2-bound conformation of the peptide is significantly populated in both the wild-type and mutant isolated peptide ensembles in their unbound states, suggesting that MDM2 binding of the p53 peptides may involve conformational selection. PMID:21528875

Frequency response function-based explicit framework for dynamic identification in human-structure systems

NASA Astrophysics Data System (ADS)

Wei, Xiaojun; Živanović, Stana

2018-05-01

The aim of this paper is to propose a novel theoretical framework for dynamic identification in a structure occupied by a single human. The framework enables the prediction of the dynamics of the human-structure system from the known properties of the individual system components, the identification of human body dynamics from the known dynamics of the empty structure and the human-structure system and the identification of the properties of the structure from the known dynamics of the human and the human-structure system. The novelty of the proposed framework is the provision of closed-form solutions in terms of frequency response functions obtained by curve fitting measured data. The advantages of the framework over existing methods are that there is neither need for nonlinear optimisation nor need for spatial/modal models of the empty structure and the human-structure system. In addition, the second-order perturbation method is employed to quantify the effect of uncertainties in human body dynamics on the dynamic identification of the empty structure and the human-structure system. The explicit formulation makes the method computationally efficient and straightforward to use. A series of numerical examples and experiments are provided to illustrate the working of the method.

Environmental and ecological conditions at Arctic breeding sites have limited effects on true survival rates of adult shorebirds

USGS Publications Warehouse

Weiser, Emily L.; Lanctot, Richard B.; Brown, Stephen C.; Gates, H. River; Bentzen, Rebecca L.; Bêty, Joël; Boldenow, Megan L.; English, Willow B.; Franks, Samantha E.; Koloski, Laura; Kwon, Eunbi; Lamarre, Jean-Francois; Lank, David B.; Liebezeit, Joseph R.; McKinnon, Laura; Nol, Erica; Rausch, Jennie; Saalfeld, Sarah T.; Senner, Nathan R.; Ward, David H.; Woodard, Paul F.; Sandercock, Brett K.

2018-01-01

Many Arctic shorebird populations are declining, and quantifying adult survival and the effects of anthropogenic factors is a crucial step toward a better understanding of population dynamics. We used a recently developed, spatially explicit Cormack–Jolly–Seber model in a Bayesian framework to obtain broad-scale estimates of true annual survival rates for 6 species of shorebirds at 9 breeding sites across the North American Arctic in 2010–2014. We tested for effects of environmental and ecological variables, study site, nest fate, and sex on annual survival rates of each species in the spatially explicit framework, which allowed us to distinguish between effects of variables on site fidelity versus true survival. Our spatially explicit analysis produced estimates of true survival rates that were substantially higher than previously published estimates of apparent survival for most species, ranging from S = 0.72 to 0.98 across 5 species. However, survival was lower for the arcticolasubspecies of Dunlin (Calidris alpina arcticola; S = 0.54), our only study taxon that migrates through the East Asian–Australasian Flyway. Like other species that use that flyway, arcticola Dunlin could be experiencing unsustainably low survival rates as a result of loss of migratory stopover habitat. Survival rates of our study species were not affected by timing of snowmelt or summer temperature, and only 2 species showed minor variation among study sites. Furthermore, although previous reproductive success, predator abundance, and the availability of alternative prey each affected survival of one species, no factors broadly affected survival across species. Overall, our findings of few effects of environmental or ecological variables suggest that annual survival rates of adult shorebirds are generally robust to conditions at Arctic breeding sites. Instead, conditions at migratory stopovers or overwintering sites might be driving adult survival rates and should be the focus of future studies.

Recurrence Quantification of Fractal Structures

PubMed Central

Webber, Charles L.

2012-01-01

By definition, fractal structures possess recurrent patterns. At different levels repeating patterns can be visualized at higher magnifications. The purpose of this chapter is threefold. First, general characteristics of dynamical systems are addressed from a theoretical mathematical perspective. Second, qualitative and quantitative recurrence analyses are reviewed in brief, but the reader is directed to other sources for explicit details. Third, example mathematical systems that generate strange attractors are explicitly defined, giving the reader the ability to reproduce the rich dynamics of continuous chaotic flows or discrete chaotic iterations. The challenge is then posited for the reader to study for themselves the recurrent structuring of these different dynamics. With a firm appreciation of the power of recurrence analysis, the reader will be prepared to turn their sights on real-world systems (physiological, psychological, mechanical, etc.). PMID:23060808

Blue water scarcity and the economic impacts of future agricultural trade and demand

NASA Astrophysics Data System (ADS)

Schmitz, Christoph; Lotze-Campen, Hermann; Gerten, Dieter; Dietrich, Jan Philipp; Bodirsky, Benjamin; Biewald, Anne; Popp, Alexander

2013-06-01

An increasing demand for agricultural goods affects the pressure on global water resources over the coming decades. In order to quantify these effects, we have developed a new agroeconomic water scarcity indicator, considering explicitly economic processes in the agricultural system. The indicator is based on the water shadow price generated by an economic land use model linked to a global vegetation-hydrology model. Irrigation efficiency is implemented as a dynamic input depending on the level of economic development. We are able to simulate the heterogeneous distribution of water supply and agricultural water demand for irrigation through the spatially explicit representation of agricultural production. This allows in identifying regional hot spots of blue water scarcity and explicit shadow prices for water. We generate scenarios based on moderate policies regarding future trade liberalization and the control of livestock-based consumption, dependent on different population and gross domestic product (GDP) projections. Results indicate increased water scarcity in the future, especially in South Asia, the Middle East, and north Africa. In general, water shadow prices decrease with increasing liberalization, foremost in South Asia, Southeast Asia, and the Middle East. Policies to reduce livestock consumption in developed countries not only lower the domestic pressure on water but also alleviate water scarcity to a large extent in developing countries. It is shown that one of the two policy options would be insufficient for most regions to retain water scarcity in 2045 on levels comparable to 2005.

Boosting cooperation by involving extortion in spatial prisoner's dilemma games

NASA Astrophysics Data System (ADS)

Wu, Zhi-Xi; Rong, Zhihai

2014-12-01

We study the evolution of cooperation in spatial prisoner's dilemma games with and without extortion by adopting the aspiration-driven strategy updating rule. We focus explicitly on how the strategy updating manner (whether synchronous or asynchronous) and also the introduction of extortion strategy affect the collective outcome of the games. By means of Monte Carlo simulations as well as dynamical cluster techniques, we find that the involvement of extortioners facilitates the boom of cooperators in the population (and whom can always dominate the population if the temptation to defect is not too large) for both synchronous and asynchronous strategy updating, in stark contrast to the other case, where cooperation is promoted for an intermediate aspiration level with synchronous strategy updating, but is remarkably inhibited if the strategy updating is implemented asynchronously. We explain the results by configurational analysis and find that the presence of extortion leads to the checkerboard-like ordering of cooperators and extortioners, which enable cooperators to prevail in the population with both strategy updating manners. Moreover, extortion itself is evolutionary stable, and therefore acts as the incubator for the evolution of cooperation.

Bayesian population decoding of spiking neurons.

PubMed

Gerwinn, Sebastian; Macke, Jakob; Bethge, Matthias

2009-01-01

The timing of action potentials in spiking neurons depends on the temporal dynamics of their inputs and contains information about temporal fluctuations in the stimulus. Leaky integrate-and-fire neurons constitute a popular class of encoding models, in which spike times depend directly on the temporal structure of the inputs. However, optimal decoding rules for these models have only been studied explicitly in the noiseless case. Here, we study decoding rules for probabilistic inference of a continuous stimulus from the spike times of a population of leaky integrate-and-fire neurons with threshold noise. We derive three algorithms for approximating the posterior distribution over stimuli as a function of the observed spike trains. In addition to a reconstruction of the stimulus we thus obtain an estimate of the uncertainty as well. Furthermore, we derive a 'spike-by-spike' online decoding scheme that recursively updates the posterior with the arrival of each new spike. We use these decoding rules to reconstruct time-varying stimuli represented by a Gaussian process from spike trains of single neurons as well as neural populations.

Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models.

PubMed

Qin, Zhao; Buehler, Markus J

2011-01-01

Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer and the tetramer, however, have remained elusive due to persistent experimental challenges owing to the large size and fibrillar geometry of this protein. We have recently reported an atomistic-level model of the human vimentin dimer and tetramer, obtained through a bottom-up approach based on structural optimization via molecular simulation based on an implicit solvent model (Qin et al. in PLoS ONE 2009 4(10):e7294, 9). Here we present extensive simulations and structural analyses of the model based on ultra large-scale atomistic-level simulations in an explicit solvent model, with system sizes exceeding 500,000 atoms and simulations carried out at 20 ns time-scales. We report a detailed comparison of the structural and dynamical behavior of this large biomolecular model with implicit and explicit solvent models. Our simulations confirm the stability of the molecular model and provide insight into the dynamical properties of the dimer and tetramer. Specifically, our simulations reveal a heterogeneous distribution of the bending stiffness along the molecular axis with the formation of rather soft and highly flexible hinge-like regions defined by non-alpha-helical linker domains. We report a comparison of Ramachandran maps and the solvent accessible surface area between implicit and explicit solvent models, and compute the persistence length of the dimer and tetramer structure of vimentin intermediate filaments for various subdomains of the protein. Our simulations provide detailed insight into the dynamical properties of the vimentin dimer and tetramer intermediate filament building blocks, which may guide the development of novel coarse-grained models of intermediate filaments, and could also help in understanding assembly mechanisms.

Modeling the impacts of hunting on the population dynamics of red howler monkeys (Alouatta seniculus)

USGS Publications Warehouse

Wiederholt, Ruscena; Fernandez-Duque, Eduardo; Diefenbach, Duane R.; Rudran, Rasanayagam

2010-01-01

Overexploitation of wildlife populations occurs across the humid tropics and is a significant threat to the long-term survival of large-bodied primates. To investigate the impacts of hunting on primates and ways to mitigate them, we developed a spatially explicit, individual-based model for a landscape that included hunted and un-hunted areas. We used the large-bodied neotropical red howler monkey (Alouatta seniculus) as our case study species because its life history characteristics make it vulnerable to hunting. We modeled the influence of different rates of harvest and proportions of landscape dedicated to un-hunted reserves on population persistence, population size, social dynamics, and hunting yields of red howler monkeys. In most scenarios, the un-hunted populations maintained a constant density regardless of hunting pressure elsewhere, and allowed the overall population to persist. Therefore, the overall population was quite resilient to extinction; only in scenarios without any un-hunted areas did the population go extinct. However, the total and hunted populations did experience large declines over 100 years under moderate and high hunting pressure. In addition, when reserve area decreased, population losses and losses per unit area increased disproportionately. Furthermore, hunting disrupted the social structure of troops. The number of male turnovers and infanticides increased in hunted populations, while birth rates decreased and exacerbated population losses due to hunting. Finally, our results indicated that when more than 55% of the landscape was harvested at high (30%) rates, hunting yields, as measured by kilograms of biomass, were less than those obtained from moderate harvest rates. Additionally, hunting yields, expressed as the number of individuals hunted/year/km2, increased in proximity to un-hunted areas, and suggested that dispersal from un-hunted areas may have contributed to hunting sustainability. These results indicate that un-hunted areas serve to enhance hunting yields, population size, and population persistence in hunted landscapes. Therefore, spatial regulation of hunting via a reserve system may be an effective management strategy for sustainable hunting, and we recommend it because it may also be more feasible to implement than harvest quotas or restrictions on season length.

Dragging in a Dynamic Geometry Environment through the Lens of Variation

ERIC Educational Resources Information Center

Leung, Allen

2008-01-01

What makes Dynamic Geometry Environment (DGE) a powerful mathematical knowledge acquisition microworld is its ability to visually make explicit the implicit dynamism of thinking about mathematical geometrical concepts. One of DGE's powers is to equip us with the ability to retain the background of a geometrical configuration while we can…

Spatially explicit global population scenarios consistent with the Shared Socioeconomic Pathways

DOE PAGES

Jones, B.; O’Neill, B. C.

2016-07-29

Here we report that the projected size and spatial distribution of the future population are important drivers of global change and key determinants of exposure and vulnerability to hazards. Spatial demographic projections are widely used as inputs to spatial projections of land use, energy use, and emissions, as well as to assessments of the impacts of extreme events, sea level rise, and other climate-related outcomes. To date, however, there are very few global-scale, spatially explicit population projections, and those that do exist are often based on simple scaling or trend extrapolation. Here we present a new set of global, spatiallymore » explicit population scenarios that are consistent with the new Shared Socioeconomic Pathways (SSPs) developed to facilitate global change research. We use a parameterized gravity-based downscaling model to produce projections of spatial population change that are quantitatively consistent with national population and urbanization projections for the SSPs and qualitatively consistent with assumptions in the SSP narratives regarding spatial development patterns. We show that the five SSPs lead to substantially different spatial population outcomes at the continental, national, and sub-national scale. In general, grid cell-level outcomes are most influenced by national-level population change, second by urbanization rate, and third by assumptions about the spatial style of development. However, the relative importance of these factors is a function of the magnitude of the projected change in total population and urbanization for each country and across SSPs. We also demonstrate variation in outcomes considering the example of population existing in a low-elevation coastal zone under alternative scenarios.« less

Spatially explicit global population scenarios consistent with the Shared Socioeconomic Pathways

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

Jones, B.; O’Neill, B. C.

Here we report that the projected size and spatial distribution of the future population are important drivers of global change and key determinants of exposure and vulnerability to hazards. Spatial demographic projections are widely used as inputs to spatial projections of land use, energy use, and emissions, as well as to assessments of the impacts of extreme events, sea level rise, and other climate-related outcomes. To date, however, there are very few global-scale, spatially explicit population projections, and those that do exist are often based on simple scaling or trend extrapolation. Here we present a new set of global, spatiallymore » explicit population scenarios that are consistent with the new Shared Socioeconomic Pathways (SSPs) developed to facilitate global change research. We use a parameterized gravity-based downscaling model to produce projections of spatial population change that are quantitatively consistent with national population and urbanization projections for the SSPs and qualitatively consistent with assumptions in the SSP narratives regarding spatial development patterns. We show that the five SSPs lead to substantially different spatial population outcomes at the continental, national, and sub-national scale. In general, grid cell-level outcomes are most influenced by national-level population change, second by urbanization rate, and third by assumptions about the spatial style of development. However, the relative importance of these factors is a function of the magnitude of the projected change in total population and urbanization for each country and across SSPs. We also demonstrate variation in outcomes considering the example of population existing in a low-elevation coastal zone under alternative scenarios.« less

One hundred and six years of population and community dynamics of Sonoran Desert Laboratory perennials

USGS Publications Warehouse

Rodriguez-Buritica, Susana; Raichle, Helen; Webb, Robert H.; Turner, Raymond M.; Venable, Larry

2013-01-01

This data set constitutes all information associated with the Spalding-Shreve permanent vegetation plots from 1906 through 2012, which is the longest-running plant monitoring program in the world. The program consists of detailed maps of all Sonoran Desert perennial plants in 30 permanent plots located on Tumamoc Hill, near Tucson, Arizona, USA. Most of these plots are 10 m × 10 m quadrats that were established by Volney Spalding and Forrest Shreve between 1906 and 1928. Analyses derived from these data have been pivotal in testing early theories on plant community succession, plant life history traits, plant longevity, and population dynamics. One of the major contributions of this data set is the species-specific demographic traits that derived from estimating individual plant trajectories for more than 106 years. Further use of these data might shed light on spatially explicit population and community dynamics, as well as long-term changes attributable to global change. Data presented here consist of digital versions of original maps created between 1906 and 1984 and digital data from recent censuses between 1993 and 2012. Attributes associated with these maps include location and coverage of all shrubs, and in some cases, plant height. In addition, we present plot-specific summaries of plant cover and density for each census year and all other information collected, including seedling counts, grass coverage, and annual species enumerations. We reference the repeat photography of these plots, which began in 1906; these images are stored at the Desert Laboratory Collection of Repeat Photography in Tucson. Initial data collection consisted of grid-mapping the plots manually on graph paper; starting in 1993, Total Stations (which allow a direct digitalization, and more accurate mapping) were used to survey root crowns and canopies.

On the origin of ultrafast nonradiative transitions in nitro-polycyclic aromatic hydrocarbons: Excited-state dynamics in 1-nitronaphthalene.

PubMed

Reichardt, Christian; Vogt, R Aaron; Crespo-Hernández, Carlos E

2009-12-14

The electronic energy relaxation of 1-nitronaphthalene was studied in nonpolar, aprotic, and protic solvents in the time window from femtoseconds to microseconds. Excitation at 340 or 360 nm populates the Franck-Condon S(1)(pipi( *)) state, which is proposed to bifurcate into two essentially barrierless nonradiative decay channels with sub-200 fs lifetimes. The first main decay channel connects the S(1) state with a receiver T(n) state that has considerable npi( *) character. The receiver T(n) state undergoes internal conversion to populate the vibrationally excited T(1)(pipi( *)) state in 2-4 ps. It is shown that vibrational cooling dynamics in the T(1) state depends on the solvent used, with average lifetimes in the range from 6 to 12 ps. Furthermore, solvation dynamics competes effectively with vibrational cooling in the triplet manifold in primary alcohols. The relaxed T(1) state undergoes intersystem crossing back to the ground state within a few microseconds in N(2)-saturated solutions in all the solvents studied. The second minor channel involves conformational relaxation of the bright S(1) state (primarily rotation of the NO(2)-group) to populate a dissociative singlet state with significant charge-transfer character and negligible oscillator strength. This dissociative channel is proposed to be responsible for the observed photochemistry in 1-nitronaphthalene. Ground- and excited-state calculations at the density functional level of theory that include bulk and explicit solvent effects lend support to the proposed mechanism where the fluorescent S(1) state decays rapidly and irreversibly to dark excited states. A four-state kinetic model is proposed that satisfactorily explains the origin of the nonradiative electronic relaxation pathways in 1-nitronaphthalene.

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.

Exploring the effect of drought extent and interval on the Florida snail kite: Interplay between spatial and temporal scales

USGS Publications Warehouse

Mooij, Wolf M.; Bennetts, Robert E.; Kitchens, Wiley M.; DeAngelis, Donald L.

2002-01-01

The paper aims at exploring the viability of the Florida snail kite population under various drought regimes in its wetland habitat. The population dynamics of snail kites are strongly linked with the hydrology of the system due to the dependence of this bird species on one exclusive prey species, the apple snail, which is negatively affected by a drying out of habitat. Based on empirical evidence, it has been hypothesised that the viability of the snail kite population critically depends not only on the time interval between droughts, but also on the spatial extent of these droughts. A system wide drought is likely to result in reduced reproduction and increased mortality, whereas the birds can respond to local droughts by moving to sites where conditions are still favourable. This paper explores the implications of this hypothesis by means of a spatially-explicit individual-based model. The specific aim of the model is to study in a factorial design the dynamics of the kite population in relation to two scale parameters, the temporal interval between droughts and the spatial correlation between droughts. In the model high drought frequencies led to reduced numbers of kites. Also, habitat degradation due to prolonged periods of inundation led to lower predicted numbers of kites. Another main result was that when the spatial correlation between droughts was low, the model showed little variability in the predicted numbers of kites. But when droughts occurred mostly on a system wide level, environmental stochasticity strongly increased the stochasticity in kite numbers and in the worst case the viability of the kite population was seriously threatened.

The role of spatial dynamics in modulating metabolic interactions in biofilm development

NASA Astrophysics Data System (ADS)

Bocci, Federico; Lu, Mingyang; Suzuki, Yoko; Onuchic, Jose

Cell phenotypic expression is substantially affected by the presence of environmental stresses and cell-cell communication mechanisms. We study the metabolic interactions of the glutamate synthesis pathway to explain the oscillation of growth rate observed in a B. Subtilis colony. Previous modelling schemes had failed in fully reproducing quantitative experimental observations as they did not explicitly address neither the diffusion of small metabolites nor the spatial distribution of phenotypically distinct bacteria inside the colony. We introduce a continuous space-temporal framework to explain how biofilm development dynamics is influenced by the metabolic interplay between two bacterial phenotypes composing the interior and the peripheral layer of the biofilm. Growth oscillations endorse the preservation of a high level of nutrients in the interior through diffusion and colony expansion in the periphery altogether. Our findings point out that perturbations of environmental conditions can result in the interruption of the interplay between cell populations and advocate alternative approaches to biofilm control strategies.

Critical Slowing Down in Time-to-Extinction: An Example of Critical Phenomena in Ecology

NASA Technical Reports Server (NTRS)

Gandhi, Amar; Levin, Simon; Orszag, Steven

1998-01-01

We study a model for two competing species that explicitly accounts for effects due to discreteness, stochasticity and spatial extension of populations. The two species are equally preferred by the environment and do better when surrounded by others of the same species. We observe that the final outcome depends on the initial densities (uniformly distributed in space) of the two species. The observed phase transition is a continuous one and key macroscopic quantities like the correlation length of clusters and the time-to-extinction diverge at a critical point. Away from the critical point, the dynamics can be described by a mean-field approximation. Close to the critical point, however, there is a crossover to power-law behavior because of the gross mismatch between the largest and smallest scales in the system. We have developed a theory based on surface effects, which is in good agreement with the observed behavior. The course-grained reaction-diffusion system obtained from the mean-field dynamics agrees well with the particle system.

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

Implicit-Explicit Time Integration Methods for Non-hydrostatic Atmospheric Models

NASA Astrophysics Data System (ADS)

Gardner, D. J.; Guerra, J. E.; Hamon, F. P.; Reynolds, D. R.; Ullrich, P. A.; Woodward, C. S.

2016-12-01

The Accelerated Climate Modeling for Energy (ACME) project is developing a non-hydrostatic atmospheric dynamical core for high-resolution coupled climate simulations on Department of Energy leadership class supercomputers. An important factor in computational efficiency is avoiding the overly restrictive time step size limitations of fully explicit time integration methods due to the stiffest modes present in the model (acoustic waves). In this work we compare the accuracy and performance of different Implicit-Explicit (IMEX) splittings of the non-hydrostatic equations and various Additive Runge-Kutta (ARK) time integration methods. Results utilizing the Tempest non-hydrostatic atmospheric model and the ARKode package show that the choice of IMEX splitting and ARK scheme has a significant impact on the maximum stable time step size as well as solution quality. Horizontally Explicit Vertically Implicit (HEVI) approaches paired with certain ARK methods lead to greatly improved runtimes. With effective preconditioning IMEX splittings that incorporate some implicit horizontal dynamics can be competitive with HEVI results. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-699187

Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Watanabe, Yukihisa S.; Kim, Jae Gil; Fukunishi, Yoshifumi; Nakamura, Haruki

2004-12-01

In order to investigate whether the implicit solvent (GB/SA) model could reproduce the free energy landscapes of peptides, the potential of mean forces (PMFs) of eight tripeptides was examined and compared with the PMFs of the explicit water model. The force-biased multicanonical molecular dynamics method was used for the enhanced conformational sampling. Consequently, the GB/SA model reproduced almost all the global and local minima in the PMFs observed with the explicit water model. However, the GB/SA model overestimated frequencies of the structures that are stabilized by intra-peptide hydrogen bonds.

Current capabilities for simulating the extreme distortion of thin structures subjected to severe impacts

NASA Technical Reports Server (NTRS)

Key, Samuel W.

1993-01-01

The explicit transient dynamics technology in use today for simulating the impact and subsequent transient dynamic response of a structure has its origins in the 'hydrocodes' dating back to the late 1940's. The growth in capability in explicit transient dynamics technology parallels the growth in speed and size of digital computers. Computer software for simulating the explicit transient dynamic response of a structure is characterized by algorithms that use a large number of small steps. In explicit transient dynamics software there is a significant emphasis on speed and simplicity. The finite element technology used to generate the spatial discretization of a structure is based on a compromise between completeness of the representation for the physical processes modelled and speed in execution. That is, since it is expected in every calculation that the deformation will be finite and the material will be strained beyond the elastic range, the geometry and the associated gradient operators must be reconstructed, as well as complex stress-strain models evaluated at every time step. As a result, finite elements derived for explicit transient dynamics software use the simplest and barest constructions possible for computational efficiency while retaining an essential representation of the physical behavior. The best example of this technology is the four-node bending quadrilateral derived by Belytschko, Lin and Tsay. Today, the speed, memory capacity and availability of computer hardware allows a number of the previously used algorithms to be 'improved.' That is, it is possible with today's computing hardware to modify many of the standard algorithms to improve their representation of the physical process at the expense of added complexity and computational effort. The purpose is to review a number of these algorithms and identify the improvements possible. In many instances, both the older, faster version of the algorithm and the improved and somewhat slower version of the algorithm are found implemented together in software. Specifically, the following seven algorithmic items are examined: the invariant time derivatives of stress used in material models expressed in rate form; incremental objectivity and strain used in the numerical integration of the material models; the use of one-point element integration versus mean quadrature; shell elements used to represent the behavior of thin structural components; beam elements based on stress-resultant plasticity versus cross-section integration; the fidelity of elastic-plastic material models in their representation of ductile metals; and the use of Courant subcycling to reduce computational effort.

Extinction debt from climate change for frogs in the wet tropics

PubMed Central

Brook, Barry W.; Hoskin, Conrad J.; Pressey, Robert L.; VanDerWal, Jeremy; Williams, Stephen E.

2016-01-01

The effect of twenty-first-century climate change on biodiversity is commonly forecast based on modelled shifts in species ranges, linked to habitat suitability. These projections have been coupled with species–area relationships (SAR) to infer extinction rates indirectly as a result of the loss of climatically suitable areas and associated habitat. This approach does not model population dynamics explicitly, and so accepts that extinctions might occur after substantial (but unknown) delays—an extinction debt. Here we explicitly couple bioclimatic envelope models of climate and habitat suitability with generic life-history models for 24 species of frogs found in the Australian Wet Tropics (AWT). We show that (i) as many as four species of frogs face imminent extinction by 2080, due primarily to climate change; (ii) three frogs face delayed extinctions; and (iii) this extinction debt will take at least a century to be realized in full. Furthermore, we find congruence between forecast rates of extinction using SARs, and demographic models with an extinction lag of 120 years. We conclude that SAR approaches can provide useful advice to conservation on climate change impacts, provided there is a good understanding of the time lags over which delayed extinctions are likely to occur. PMID:27729484

Estimating the short-term recovery potential of little brown bats in the eastern United States in the face of White-nose syndrome

USGS Publications Warehouse

Russell, Robin E.; Thogmartin, Wayne E.; Erickson, Richard A.; Szymanski, Jennifer A.; Tinsley, Karl

2015-01-01

White-nose syndrome (WNS) was first detected in North American bats in New York in 2006. Since that time WNS has spread throughout the northeastern United States, southeastern Canada, and southwest across Pennsylvania and as far west as Missouri. Suspect WNS cases have been identified in Minnesota and Iowa, and the causative agent of WNS (Pseudogymnoascus destructans) has recently been detected in Mississippi. The impact of WNS is devastating for little brown bats (Myotis lucifugus), causing up to 100% mortality in some overwintering populations, and previous research has forecast the extirpation of the species due to the disease. Recent evidence indicates that remnant populations may persist in areas where WNS is endemic. We developed a spatially explicit model of little brown bat population dynamics to investigate the potential for populations to recover under alternative scenarios. We used these models to investigate how starting population sizes, potential changes in the number of bats overwintering successfully in hibernacula, and potential changes in demographic rates of the population post WNS may influence the ability of the bats to recover to former levels of abundance. We found that populations of the little brown bat and other species that are highly susceptible to WNS are unlikely to return to pre-WNS levels in the near future under any of the scenarios we examined.

Toward accurate and precise estimates of lion density.

PubMed

Elliot, Nicholas B; Gopalaswamy, Arjun M

2017-08-01

Reliable estimates of animal density are fundamental to understanding ecological processes and population dynamics. Furthermore, their accuracy is vital to conservation because wildlife authorities rely on estimates to make decisions. However, it is notoriously difficult to accurately estimate density for wide-ranging carnivores that occur at low densities. In recent years, significant progress has been made in density estimation of Asian carnivores, but the methods have not been widely adapted to African carnivores, such as lions (Panthera leo). Although abundance indices for lions may produce poor inferences, they continue to be used to estimate density and inform management and policy. We used sighting data from a 3-month survey and adapted a Bayesian spatially explicit capture-recapture (SECR) model to estimate spatial lion density in the Maasai Mara National Reserve and surrounding conservancies in Kenya. Our unstructured spatial capture-recapture sampling design incorporated search effort to explicitly estimate detection probability and density on a fine spatial scale, making our approach robust in the context of varying detection probabilities. Overall posterior mean lion density was estimated to be 17.08 (posterior SD 1.310) lions >1 year old/100 km 2 , and the sex ratio was estimated at 2.2 females to 1 male. Our modeling framework and narrow posterior SD demonstrate that SECR methods can produce statistically rigorous and precise estimates of population parameters, and we argue that they should be favored over less reliable abundance indices. Furthermore, our approach is flexible enough to incorporate different data types, which enables robust population estimates over relatively short survey periods in a variety of systems. Trend analyses are essential to guide conservation decisions but are frequently based on surveys of differing reliability. We therefore call for a unified framework to assess lion numbers in key populations to improve management and policy decisions. © 2016 Society for Conservation Biology.

Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission

PubMed Central

Perkins, T. Alex; Scott, Thomas W.; Le Menach, Arnaud; Smith, David L.

2013-01-01

The Ross-Macdonald model has dominated theory for mosquito-borne pathogen transmission dynamics and control for over a century. The model, like many other basic population models, makes the mathematically convenient assumption that populations are well mixed; i.e., that each mosquito is equally likely to bite any vertebrate host. This assumption raises questions about the validity and utility of current theory because it is in conflict with preponderant empirical evidence that transmission is heterogeneous. Here, we propose a new dynamic framework that is realistic enough to describe biological causes of heterogeneous transmission of mosquito-borne pathogens of humans, yet tractable enough to provide a basis for developing and improving general theory. The framework is based on the ecological context of mosquito blood meals and the fine-scale movements of individual mosquitoes and human hosts that give rise to heterogeneous transmission. Using this framework, we describe pathogen dispersion in terms of individual-level analogues of two classical quantities: vectorial capacity and the basic reproductive number, . Importantly, this framework explicitly accounts for three key components of overall heterogeneity in transmission: heterogeneous exposure, poor mixing, and finite host numbers. Using these tools, we propose two ways of characterizing the spatial scales of transmission—pathogen dispersion kernels and the evenness of mixing across scales of aggregation—and demonstrate the consequences of a model's choice of spatial scale for epidemic dynamics and for estimation of , both by a priori model formulas and by inference of the force of infection from time-series data. PMID:24348223

The time course of explicit and implicit categorization.

PubMed

Smith, J David; Zakrzewski, Alexandria C; Herberger, Eric R; Boomer, Joseph; Roeder, Jessica L; Ashby, F Gregory; Church, Barbara A

2015-10-01

Contemporary theory in cognitive neuroscience distinguishes, among the processes and utilities that serve categorization, explicit and implicit systems of category learning that learn, respectively, category rules by active hypothesis testing or adaptive behaviors by association and reinforcement. Little is known about the time course of categorization within these systems. Accordingly, the present experiments contrasted tasks that fostered explicit categorization (because they had a one-dimensional, rule-based solution) or implicit categorization (because they had a two-dimensional, information-integration solution). In Experiment 1, participants learned categories under unspeeded or speeded conditions. In Experiment 2, they applied previously trained category knowledge under unspeeded or speeded conditions. Speeded conditions selectively impaired implicit category learning and implicit mature categorization. These results illuminate the processing dynamics of explicit/implicit categorization.

Disentangling polydispersity in the PCNA−p15PAF complex, a disordered, transient and multivalent macromolecular assembly

PubMed Central

Cordeiro, Tiago N.; Chen, Po-chia; De Biasio, Alfredo; Sibille, Nathalie; Blanco, Francisco J.; Hub, Jochen S.; Crehuet, Ramon

2017-01-01

Abstract The intrinsically disordered p15PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15PAF and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling. By using explicit ensemble descriptions for the individual species, built using integrative approaches and molecular dynamics (MD) simulations, we collectively interpreted multiple SAXS profiles as population-weighted thermodynamic mixtures. The analysis demonstrates that the N-terminus of p15PAF penetrates the PCNA ring and emerges on the back face. This observation substantiates the role of p15PAF as a drag regulating PCNA processivity during DNA repair. Our study reveals the power of ensemble-based approaches to decode structural, dynamic, and thermodynamic information from SAXS data. This strategy paves the way for deciphering the structural bases of flexible, transient and multivalent macromolecular assemblies involved in pivotal biological processes. PMID:28180305

Analytic derivation of bacterial growth laws from a simple model of intracellular chemical dynamics.

PubMed

Pandey, Parth Pratim; Jain, Sanjay

2016-09-01

Experiments have found that the growth rate and certain other macroscopic properties of bacterial cells in steady-state cultures depend upon the medium in a surprisingly simple manner; these dependencies are referred to as 'growth laws'. Here we construct a dynamical model of interacting intracellular populations to understand some of the growth laws. The model has only three population variables: an amino acid pool, a pool of enzymes that transport an external nutrient and produce the amino acids, and ribosomes that catalyze their own and the enzymes' production from the amino acids. We assume that the cell allocates its resources between the enzyme sector and the ribosomal sector to maximize its growth rate. We show that the empirical growth laws follow from this assumption and derive analytic expressions for the phenomenological parameters in terms of the more basic model parameters. Interestingly, the maximization of the growth rate of the cell as a whole implies that the cell allocates resources to the enzyme and ribosomal sectors in inverse proportion to their respective 'efficiencies'. The work introduces a mathematical scheme in which the cellular growth rate can be explicitly determined and shows that two large parameters, the number of amino acid residues per enzyme and per ribosome, are useful for making approximations.

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.

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

PubMed

Naujokaitis-Lewis, Ilona; Curtis, Janelle M R

2016-01-01

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

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

PubMed Central

Curtis, Janelle M.R.

2016-01-01

Developing a rigorous understanding of multiple global threats to species persistence requires the use of integrated modeling methods that capture processes which influence species distributions. Species distribution models (SDMs) coupled with population dynamics models can incorporate relationships between changing environments and demographics and are increasingly used to quantify relative extinction risks associated with climate and land-use changes. Despite their appeal, uncertainties associated with complex models can undermine their usefulness for advancing predictive ecology and informing conservation management decisions. We developed a computationally-efficient and freely available tool (GRIP 2.0) that implements and automates a global sensitivity analysis of coupled SDM-population dynamics models for comparing the relative influence of demographic parameters and habitat attributes on predicted extinction risk. Advances over previous global sensitivity analyses include the ability to vary habitat suitability across gradients, as well as habitat amount and configuration of spatially-explicit suitability maps of real and simulated landscapes. Using GRIP 2.0, we carried out a multi-model global sensitivity analysis of a coupled SDM-population dynamics model of whitebark pine (Pinus albicaulis) in Mount Rainier National Park as a case study and quantified the relative influence of input parameters and their interactions on model predictions. Our results differed from the one-at-time analyses used in the original study, and we found that the most influential parameters included the total amount of suitable habitat within the landscape, survival rates, and effects of a prevalent disease, white pine blister rust. Strong interactions between habitat amount and survival rates of older trees suggests the importance of habitat in mediating the negative influences of white pine blister rust. Our results underscore the importance of considering habitat attributes along with demographic parameters in sensitivity routines. GRIP 2.0 is an important decision-support tool that can be used to prioritize research, identify habitat-based thresholds and management intervention points to improve probability of species persistence, and evaluate trade-offs of alternative management options. PMID:27547529

Simulating the effects of the southern pine beetle on regional dynamics 60 years into the future

Treesearch

Jennifer K. Costanza; Jiri Hulcr; Frank H. Koch; Todd Earnhardt; Alexa J. McKerrow; Rob R. Dunn; Jaime A. Collazo

2012-01-01

We developed a spatially explicit model that simulated future southern pine beetle (Dendroctonus frontalis, SPB) dynamics and pine forest management for a real landscape over 60 years to inform regional forest management. The SPB has a considerable effect on forest dynamics in the Southeastern United States, especially in loblolly pine (...

A Novel Approach to Teaching and Understanding Transformations of Matter in Dynamic Earth Systems

ERIC Educational Resources Information Center

Clark, Scott K.; Sibley, Duncan F.; Libarkin, Julie C.; Heidemann, Merle

2009-01-01

The need to engage K-12 and post-secondary students in considering the Earth as a dynamic system requires explicit discussion of system characteristics. Fundamentally, dynamic systems involve the movement and change of matter, often through processes that are difficult to see and comprehend. We introduce a novel instructional method, termed…

EVALUATING HABITAT AS A SURROGATE FOR POPULATION VIABILITY USING A SPATIALLY EXPLICIT POPULATION MODEL

EPA Science Inventory

Because data for conservation planning are always limited, surrogates are often substituted for intractable measurements such as species richness or population viability. We examined the ability of habitat quality to act as a surrogate for population performance for both Red-sho...

Extraordinary Sex Ratios: Cultural Effects on Ecological Consequences

PubMed Central

Molnár, Ferenc; Caraco, Thomas; Korniss, Gyorgy

2012-01-01

We model sex-structured population dynamics to analyze pairwise competition between groups differing both genetically and culturally. A sex-ratio allele is expressed in the heterogametic sex only, so that assumptions of Fisher’s analysis do not apply. Sex-ratio evolution drives cultural evolution of a group-associated trait governing mortality in the homogametic sex. The two-sex dynamics under resource limitation induces a strong Allee effect that depends on both sex ratio and cultural trait values. We describe the resulting threshold, separating extinction from positive growth, as a function of female and male densities. When initial conditions avoid extinction due to the Allee effect, different sex ratios cannot coexist; in our model, greater female allocation always invades and excludes a lesser allocation. But the culturally transmitted trait interacts with the sex ratio to determine the ecological consequences of successful invasion. The invading female allocation may permit population persistence at self-regulated equilibrium. For this case, the resident culture may be excluded, or may coexist with the invader culture. That is, a single sex-ratio allele in females and a cultural dimorphism in male mortality can persist; a low-mortality resident trait is maintained by father-to-son cultural transmission. Otherwise, the successfully invading female allocation excludes the resident allele and culture and then drives the population to extinction via a shortage of males. Finally, we show that the results obtained under homogeneous mixing hold, with caveats, in a spatially explicit model with local mating and diffusive dispersal in both sexes. PMID:22952669

Extraordinary sex ratios: cultural effects on ecological consequences.

PubMed

Molnár, Ferenc; Caraco, Thomas; Korniss, Gyorgy

2012-01-01

We model sex-structured population dynamics to analyze pairwise competition between groups differing both genetically and culturally. A sex-ratio allele is expressed in the heterogametic sex only, so that assumptions of Fisher's analysis do not apply. Sex-ratio evolution drives cultural evolution of a group-associated trait governing mortality in the homogametic sex. The two-sex dynamics under resource limitation induces a strong Allee effect that depends on both sex ratio and cultural trait values. We describe the resulting threshold, separating extinction from positive growth, as a function of female and male densities. When initial conditions avoid extinction due to the Allee effect, different sex ratios cannot coexist; in our model, greater female allocation always invades and excludes a lesser allocation. But the culturally transmitted trait interacts with the sex ratio to determine the ecological consequences of successful invasion. The invading female allocation may permit population persistence at self-regulated equilibrium. For this case, the resident culture may be excluded, or may coexist with the invader culture. That is, a single sex-ratio allele in females and a cultural dimorphism in male mortality can persist; a low-mortality resident trait is maintained by father-to-son cultural transmission. Otherwise, the successfully invading female allocation excludes the resident allele and culture and then drives the population to extinction via a shortage of males. Finally, we show that the results obtained under homogeneous mixing hold, with caveats, in a spatially explicit model with local mating and diffusive dispersal in both sexes.

Population modeling for pesticide risk assessment of threatened species-A case study of a terrestrial plant, Boltonia decurrens.

PubMed

Schmolke, Amelie; Brain, Richard; Thorbek, Pernille; Perkins, Daniel; Forbes, Valery

2017-02-01

Although population models are recognized as necessary tools in the ecological risk assessment of pesticides, particularly for species listed under the Endangered Species Act, their application in this context is currently limited to very few cases. The authors developed a detailed, individual-based population model for a threatened plant species, the decurrent false aster (Boltonia decurrens), for application in pesticide risk assessment. Floods and competition with other plant species are known factors that drive the species' population dynamics and were included in the model approach. The authors use the model to compare the population-level effects of 5 toxicity surrogates applied to B. decurrens under varying environmental conditions. The model results suggest that the environmental conditions under which herbicide applications occur may have a higher impact on populations than organism-level sensitivities to an herbicide within a realistic range. Indirect effects may be as important as the direct effects of herbicide applications by shifting competition strength if competing species have different sensitivities to the herbicide. The model approach provides a case study for population-level risk assessments of listed species. Population-level effects of herbicides can be assessed in a realistic and species-specific context, and uncertainties can be addressed explicitly. The authors discuss how their approach can inform the future development and application of modeling for population-level risk assessments of listed species, and ecological risk assessment in general. Environ Toxicol Chem 2017;36:480-491. © 2016 SETAC. © 2016 SETAC.

Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

DOE PAGES

Conlisk, Erin; Castanha, Cristina; Germino, Matthew J.; ...

2017-02-08

Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long life spans, the importance of climate-sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively. Using spatially explicit, stochastic population models combined with data from long-term forest surveys, we explored whether the climate-sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two widely distributed, high-elevation North American conifers. Empirically observed, warming-driven declines in recruitment led to rapid modelled population declines at the low-elevation, ‘warm edge’ of subalpine forestmore » and slow emergence of populations beyond the high-elevation, ‘cool edge’. Because population declines in the forest occurred much faster than population emergence in the alpine, we observed range contraction for both species. For Engelmann spruce, this contraction was permanent over the modelled time horizon, even in the presence of increased moisture. For limber pine, lower sensitivity to warming may facilitate persistence at low elevations – especially in the presence of increased moisture – and rapid establishment above tree line, and, ultimately, expansion into the alpine. Synthesis. Assuming 21st century warming and no additional moisture, population dynamics in high-elevation forests led to transient range contractions for limber pine and potentially permanent range contractions for Engelmann spruce. Thus, limitations to seedling recruitment with warming can constrain the pace of subalpine tree range shifts.« less

Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

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

Conlisk, Erin; Castanha, Cristina; Germino, Matthew J.

Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long life spans, the importance of climate-sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively. Using spatially explicit, stochastic population models combined with data from long-term forest surveys, we explored whether the climate-sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two widely distributed, high-elevation North American conifers. Empirically observed, warming-driven declines in recruitment led to rapid modelled population declines at the low-elevation, ‘warm edge’ of subalpine forestmore » and slow emergence of populations beyond the high-elevation, ‘cool edge’. Because population declines in the forest occurred much faster than population emergence in the alpine, we observed range contraction for both species. For Engelmann spruce, this contraction was permanent over the modelled time horizon, even in the presence of increased moisture. For limber pine, lower sensitivity to warming may facilitate persistence at low elevations – especially in the presence of increased moisture – and rapid establishment above tree line, and, ultimately, expansion into the alpine. Synthesis. Assuming 21st century warming and no additional moisture, population dynamics in high-elevation forests led to transient range contractions for limber pine and potentially permanent range contractions for Engelmann spruce. Thus, limitations to seedling recruitment with warming can constrain the pace of subalpine tree range shifts.« less

Declines in low-elevation subalpine tree populations outpace growth in high-elevation populations with warming

USGS Publications Warehouse

Conlisk, Erin; Castanha, Cristina; Germino, Matthew J.; Veblen, Thomas T; Smith, Jeremy M.; Kueppers, Lara M.

2017-01-01

Species distribution shifts in response to climate change require that recruitment increase beyond current range boundaries. For trees with long life spans, the importance of climate-sensitive seedling establishment to the pace of range shifts has not been demonstrated quantitatively.Using spatially explicit, stochastic population models combined with data from long-term forest surveys, we explored whether the climate-sensitivity of recruitment observed in climate manipulation experiments was sufficient to alter populations and elevation ranges of two widely distributed, high-elevation North American conifers.Empirically observed, warming-driven declines in recruitment led to rapid modelled population declines at the low-elevation, ‘warm edge’ of subalpine forest and slow emergence of populations beyond the high-elevation, ‘cool edge’. Because population declines in the forest occurred much faster than population emergence in the alpine, we observed range contraction for both species. For Engelmann spruce, this contraction was permanent over the modelled time horizon, even in the presence of increased moisture. For limber pine, lower sensitivity to warming may facilitate persistence at low elevations – especially in the presence of increased moisture – and rapid establishment above tree line, and, ultimately, expansion into the alpine.Synthesis. Assuming 21st century warming and no additional moisture, population dynamics in high-elevation forests led to transient range contractions for limber pine and potentially permanent range contractions for Engelmann spruce. Thus, limitations to seedling recruitment with warming can constrain the pace of subalpine tree range shifts.

Influence of climate drivers on colonization and extinction dynamics of wetland-dependent species

USGS Publications Warehouse

Ray, Andrew M.; Gould, William R.; Hossack, Blake R.; Sepulveda, Adam; Thoma, David P.; Patla, Debra A.; Daley, Rob; Al-Chokhachy, Robert K.

2016-01-01

Freshwater wetlands are particularly vulnerable to climate change. Specifically, changes in temperature, precipitation, and evapotranspiration (i.e., climate drivers) are likely to alter flooding regimes of wetlands and affect the vital rates, abundance, and distributions of wetland-dependent species. Amphibians may be among the most climate-sensitive wetland-dependent groups, as many species rely on shallow or intermittently flooded wetland habitats for breeding. Here, we integrated multiple years of high-resolution gridded climate and amphibian monitoring data from Grand Teton and Yellowstone National Parks to explicitly model how variations in climate drivers and habitat conditions affect the occurrence and breeding dynamics (i.e., annual extinction and colonization rates) of amphibians. Our results showed that models incorporating climate drivers outperformed models of amphibian breeding dynamics that were exclusively habitat based. Moreover, climate-driven variation in extinction rates, but not colonization rates, disproportionately influenced amphibian occupancy in monitored wetlands. Long-term monitoring from national parks coupled with high-resolution climate data sets will be crucial to describing population dynamics and characterizing the sensitivity of amphibians and other wetland-dependent species to climate change. Further, long-term monitoring of wetlands in national parks will help reduce uncertainty surrounding wetland resources and strengthen opportunities to make informed, science-based decisions that have far-reaching benefits.

A mathematical study of a model for childhood diseases with non-permanent immunity

NASA Astrophysics Data System (ADS)

Moghadas, S. M.; Gumel, A. B.

2003-08-01

Protecting children from diseases that can be prevented by vaccination is a primary goal of health administrators. Since vaccination is considered to be the most effective strategy against childhood diseases, the development of a framework that would predict the optimal vaccine coverage level needed to prevent the spread of these diseases is crucial. This paper provides this framework via qualitative and quantitative analysis of a deterministic mathematical model for the transmission dynamics of a childhood disease in the presence of a preventive vaccine that may wane over time. Using global stability analysis of the model, based on constructing a Lyapunov function, it is shown that the disease can be eradicated from the population if the vaccination coverage level exceeds a certain threshold value. It is also shown that the disease will persist within the population if the coverage level is below this threshold. These results are verified numerically by constructing, and then simulating, a robust semi-explicit second-order finite-difference method.

Nonlinearity in bacterial population dynamics: Proposal for experiments for the observation of abrupt transitions in patches

PubMed Central

Kenkre, V. M.; Kumar, Niraj

2008-01-01

An explicit proposal for experiments leading to abrupt transitions in spatially extended bacterial populations in a Petri dish is presented on the basis of an exact formula obtained through an analytic theory. The theory provides accurately the transition expressions despite the fact that the actual solutions, which involve strong nonlinearity, are inaccessible to it. The analytic expressions are verified through numerical solutions of the relevant nonlinear equation. The experimental setup suggested uses opaque masks in a Petri dish bathed in ultraviolet radiation [Lin A-L, et al. (2004) Biophys J 87:75–80 and Perry N (2005) J R Soc Interface 2:379–387], but is based on the interplay of two distances the bacteria must traverse, one of them favorable and the other adverse. As a result of this interplay feature, the experiments proposed introduce highly enhanced reliability in interpretation of observations and in the potential for extraction of system parameters. PMID:19033185

Opposing effects of floral visitors and soil conditions on the determinants of competitive outcomes maintain species diversity in heterogeneous landscapes.

PubMed

Lanuza, Jose B; Bartomeus, Ignasi; Godoy, Oscar

2018-06-01

Theory argues that both soil conditions and aboveground trophic interactions have equivalent potential to limit or promote plant diversity. However, it remains unexplored how they jointly modify the niche differences stabilising species coexistence and the average fitness differences driving competitive dominance. We conducted a field study in Mediterranean annual grasslands to parameterise population models of six competing plant species. Spatially explicit floral visitor assemblages and soil salinity variation were characterised for each species. Both floral visitors and soil salinity modified species population dynamics via direct changes in seed production and indirect changes in competitive responses. Although the magnitude and sign of these changes were species-specific, floral visitors promoted coexistence at neighbourhood scales, while soil salinity did so over larger scales by changing the superior competitors' identity. Our results show how below and aboveground interactions maintain diversity in heterogeneous landscapes through their opposing effects on the determinants of competitive outcomes. © 2018 John Wiley & Sons Ltd/CNRS.

Survival in patchy landscapes: the interplay between dispersal, habitat loss and fragmentation

PubMed Central

Niebuhr, Bernardo B. S.; Wosniack, Marina E.; Santos, Marcos C.; Raposo, Ernesto P.; Viswanathan, Gandhimohan M.; da Luz, Marcos G. E.; Pie, Marcio R.

2015-01-01

Habitat loss and fragmentation are important factors determining animal population dynamics and spatial distribution. Such landscape changes can lead to the deleterious impact of a significant drop in the number of species, caused by critically reduced survival rates for organisms. In order to obtain a deeper understanding of the threeway interplay between habitat loss, fragmentation and survival rates, we propose here a spatially explicit multi-scaled movement model of individuals that search for habitat. By considering basic ecological processes, such as predation, starvation (outside the habitat area), and competition, together with dispersal movement as a link among habitat areas, we show that a higher survival rate is achieved in instances with a lower number of patches of larger areas. Our results demonstrate how movement may counterbalance the effects of habitat loss and fragmentation in altered landscapes. In particular, they have important implications for conservation planning and ecosystem management, including the design of specific features of conservation areas in order to enhance landscape connectivity and population viability. PMID:26148488

Explicit Low-Thrust Guidance for Reference Orbit Targeting

NASA Technical Reports Server (NTRS)

Lam, Try; Udwadia, Firdaus E.

2013-01-01

The problem of a low-thrust spacecraft controlled to a reference orbit is addressed in this paper. A simple and explicit low-thrust guidance scheme with constrained thrust magnitude is developed by combining the fundamental equations of motion for constrained systems from analytical dynamics with a Lyapunov-based method. Examples are given for a spacecraft controlled to a reference trajectory in the circular restricted three body problem.

A stochastic and dynamical view of pluripotency in mouse embryonic stem cells

PubMed Central

Lee, Esther J.

2018-01-01

Pluripotent embryonic stem cells are of paramount importance for biomedical sciences because of their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent state is regulated by complex genetic regulatory networks. The rapid growth of single-cell sequencing data has greatly stimulated applications of statistical and machine learning methods for inferring topologies of pluripotency regulating genetic networks. The inferred network topologies, however, often only encode Boolean information while remaining silent about the roles of dynamics and molecular stochasticity inherent in gene expression. Herein we develop a framework for systematically extending Boolean-level network topologies into higher resolution models of networks which explicitly account for the promoter architectures and gene state switching dynamics. We show the framework to be useful for disentangling the various contributions that gene switching, external signaling, and network topology make to the global heterogeneity and dynamics of transcription factor populations. We find the pluripotent state of the network to be a steady state which is robust to global variations of gene switching rates which we argue are a good proxy for epigenetic states of individual promoters. The temporal dynamics of exiting the pluripotent state, on the other hand, is significantly influenced by the rates of genetic switching which makes cells more responsive to changes in extracellular signals. PMID:29451874

Dynamics of Coupled Electron-Boson Systems with the Multiple Davydov D1 Ansatz and the Generalized Coherent State.

PubMed

Chen, Lipeng; Borrelli, Raffaele; Zhao, Yang

2017-11-22

The dynamics of a coupled electron-boson system is investigated by employing a multitude of the Davydov D 1 trial states, also known as the multi-D 1 Ansatz, and a second trial state based on a superposition of the time-dependent generalized coherent state (GCS Ansatz). The two Ansätze are applied to study population dynamics in the spin-boson model and the Holstein molecular crystal model, and a detailed comparison with numerically exact results obtained by the (multilayer) multiconfiguration time-dependent Hartree method and the hierarchy equations of motion approach is drawn. It is found that the two methodologies proposed here have significantly improved over that with the single D 1 Ansatz, yielding quantitatively accurate results even in the critical cases of large energy biases and large transfer integrals. The two methodologies provide new effective tools for accurate, efficient simulation of many-body quantum dynamics thanks to a relatively small number of parameters which characterize the electron-nuclear wave functions. The wave-function-based approaches are capable of tracking explicitly detailed bosonic dynamics, which is absent by construct in approaches based on the reduced density matrix. The efficiency and flexibility of our methods are also advantages as compared with numerically exact approaches such as QUAPI and HEOM, especially at low temperatures and in the strong coupling regime.

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.

Alternative Stable States, Coral Reefs, and Smooth Dynamics with a Kick.

PubMed

Ippolito, Stephen; Naudot, Vincent; Noonburg, Erik G

2016-03-01

We consider a computer simulation, which was found to be faithful to time series data for Caribbean coral reefs, and an analytical model to help understand the dynamics of the simulation. The analytical model is a system of ordinary differential equations (ODE), and the authors claim this model demonstrates the existence of alternative stable states. The existence of an alternative stable state should consider a sudden shift in coral and macroalgae populations, while the grazing rate remains constant. The results of such shifts, however, are often confounded by changes in grazing rate. Although the ODE suggest alternative stable states, the ODE need modification to explicitly account for shifts or discrete events such as hurricanes. The goal of this paper will be to study the simulation dynamics through a simplified analytical representation. We proceed by modifying the original analytical model through incorporating discrete changes into the ODE. We then analyze the resulting dynamics and their bifurcations with respect to changes in grazing rate and hurricane frequency. In particular, a "kick" enabling the ODE to consider impulse events is added. Beyond adding a "kick" we employ the grazing function that is suggested by the simulation. The extended model was fit to the simulation data to support its use and predicts the existence cycles depending nonlinearly on grazing rates and hurricane frequency. These cycles may bring new insights into consideration for reef health, restoration and dynamics.

Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins.

PubMed

Eriksson, Anders; Manica, Andrea

2012-08-28

Recent comparisons between anatomically modern humans and ancient genomes of other hominins have raised the tantalizing, and hotly debated, possibility of hybridization. Although several tests of hybridization have been devised, they all rely on the degree to which different modern populations share genetic polymorphisms with the ancient genomes of other hominins. However, spatial population structure is expected to generate genetic patterns similar to those that might be attributed to hybridization. To investigate this problem, we take Neanderthals as a case study, and build a spatially explicit model of the shared history of anatomically modern humans and this hominin. We show that the excess polymorphism shared between Eurasians and Neanderthals is compatible with scenarios in which no hybridization occurred, and is strongly linked to the strength of population structure in ancient populations. Thus, we recommend caution in inferring admixture from geographic patterns of shared polymorphisms, and argue that future attempts to investigate ancient hybridization between humans and other hominins should explicitly account for population structure.

Testing the Use of Implicit Solvent in the Molecular Dynamics Modelling of DNA Flexibility

NASA Astrophysics Data System (ADS)

Mitchell, J.; Harris, S.

DNA flexibility controls packaging, looping and in some cases sequence specific protein binding. Molecular dynamics simulations carried out with a computationally efficient implicit solvent model are potentially a powerful tool for studying larger DNA molecules than can be currently simulated when water and counterions are represented explicitly. In this work we compare DNA flexibility at the base pair step level modelled using an implicit solvent model to that previously determined from explicit solvent simulations and database analysis. Although much of the sequence dependent behaviour is preserved in implicit solvent, the DNA is considerably more flexible when the approximate model is used. In addition we test the ability of the implicit solvent to model stress induced DNA disruptions by simulating a series of DNA minicircle topoisomers which vary in size and superhelical density. When compared with previously run explicit solvent simulations, we find that while the levels of DNA denaturation are similar using both computational methodologies, the specific structural form of the disruptions is different.

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...

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics.

PubMed

Armen, Roger S; Chen, Jianhan; Brooks, Charles L

2009-10-13

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and "noise" that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds.

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

PubMed Central

Armen, Roger S.; Chen, Jianhan; Brooks, Charles L.

2009-01-01

Incorporating receptor flexibility into molecular docking should improve results for flexible proteins. However, the incorporation of explicit all-atom flexibility with molecular dynamics for the entire protein chain may also introduce significant error and “noise” that could decrease docking accuracy and deteriorate the ability of a scoring function to rank native-like poses. We address this apparent paradox by comparing the success of several flexible receptor models in cross-docking and multiple receptor ensemble docking for p38α mitogen-activated protein (MAP) kinase. Explicit all-atom receptor flexibility has been incorporated into a CHARMM-based molecular docking method (CDOCKER) using both molecular dynamics (MD) and torsion angle molecular dynamics (TAMD) for the refinement of predicted protein-ligand binding geometries. These flexible receptor models have been evaluated, and the accuracy and efficiency of TAMD sampling is directly compared to MD sampling. Several flexible receptor models are compared, encompassing flexible side chains, flexible loops, multiple flexible backbone segments, and treatment of the entire chain as flexible. We find that although including side chain and some backbone flexibility is required for improved docking accuracy as expected, docking accuracy also diminishes as additional and unnecessary receptor flexibility is included into the conformational search space. Ensemble docking results demonstrate that including protein flexibility leads to to improved agreement with binding data for 227 active compounds. This comparison also demonstrates that a flexible receptor model enriches high affinity compound identification without significantly increasing the number of false positives from low affinity compounds. PMID:20160879

Hacking DNA copy number for circuit engineering.

PubMed

Wu, Feilun; You, Lingchong

2017-07-27

DNA copy number represents an essential parameter in the dynamics of synthetic gene circuits but typically is not explicitly considered. A new study demonstrates how dynamic control of DNA copy number can serve as an effective strategy to program robust oscillations in gene expression circuits.

Modular and Spatially Explicit: A Novel Approach to System Dynamics

EPA Science Inventory

The Open Modeling Environment (OME) is an open-source System Dynamics (SD) simulation engine which has been created as a joint project between Oregon State University and the US Environmental Protection Agency. It is designed around a modular implementation, and provides a standa...

Mapping and spatial-temporal modeling of Bromus tectorum invasion in central Utah

NASA Astrophysics Data System (ADS)

Jin, Zhenyu

Cheatgrass, or Downy Brome, is an exotic winter annual weed native to the Mediterranean region. Since its introduction to the U.S., it has become a significant weed and aggressive invader of sagebrush, pinion-juniper, and other shrub communities, where it can completely out-compete native grasses and shrubs. In this research, remotely sensed data combined with field collected data are used to investigate the distribution of the cheatgrass in Central Utah, to characterize the trend of the NDVI time-series of cheatgrass, and to construct a spatially explicit population-based model to simulate the spatial-temporal dynamics of the cheatgrass. This research proposes a method for mapping the canopy closure of invasive species using remotely sensed data acquired at different dates. Different invasive species have their own distinguished phenologies and the satellite images in different dates could be used to capture the phenology. The results of cheatgrass abundance prediction have a good fit with the field data for both linear regression and regression tree models, although the regression tree model has better performance than the linear regression model. To characterize the trend of NDVI time-series of cheatgrass, a novel smoothing algorithm named RMMEH is presented in this research to overcome some drawbacks of many other algorithms. By comparing the performance of RMMEH in smoothing a 16-day composite of the MODIS NDVI time-series with that of two other methods, which are the 4253EH, twice and the MVI, we have found that RMMEH not only keeps the original valid NDVI points, but also effectively removes the spurious spikes. The reconstructed NDVI time-series of different land covers are of higher quality and have smoother temporal trend. To simulate the spatial-temporal dynamics of cheatgrass, a spatially explicit population-based model is built applying remotely sensed data. The comparison between the model output and the ground truth of cheatgrass closure demonstrates that the model could successfully simulate the spatial-temporal dynamics of cheatgrass in a simple cheatgrass-dominant environment. The simulation of the functional response of different prescribed fire rates also shows that this model is helpful to answer management questions like, "What are the effects of prescribed fire to invasive species?" It demonstrates that a medium fire rate of 10% can successfully prevent cheatgrass invasion.

Nonlinear amplitude dynamics in flagellar beating

NASA Astrophysics Data System (ADS)

Oriola, David; Gadêlha, Hermes; Casademunt, Jaume

2017-03-01

The physical basis of flagellar and ciliary beating is a major problem in biology which is still far from completely understood. The fundamental cytoskeleton structure of cilia and flagella is the axoneme, a cylindrical array of microtubule doublets connected by passive cross-linkers and dynein motor proteins. The complex interplay of these elements leads to the generation of self-organized bending waves. Although many mathematical models have been proposed to understand this process, few attempts have been made to assess the role of dyneins on the nonlinear nature of the axoneme. Here, we investigate the nonlinear dynamics of flagella by considering an axonemal sliding control mechanism for dynein activity. This approach unveils the nonlinear selection of the oscillation amplitudes, which are typically either missed or prescribed in mathematical models. The explicit set of nonlinear equations are derived and solved numerically. Our analysis reveals the spatio-temporal dynamics of dynein populations and flagellum shape for different regimes of motor activity, medium viscosity and flagellum elasticity. Unstable modes saturate via the coupling of dynein kinetics and flagellum shape without the need of invoking a nonlinear axonemal response. Hence, our work reveals a novel mechanism for the saturation of unstable modes in axonemal beating.

Nonlinear amplitude dynamics in flagellar beating.

PubMed

Oriola, David; Gadêlha, Hermes; Casademunt, Jaume

2017-03-01

The physical basis of flagellar and ciliary beating is a major problem in biology which is still far from completely understood. The fundamental cytoskeleton structure of cilia and flagella is the axoneme, a cylindrical array of microtubule doublets connected by passive cross-linkers and dynein motor proteins. The complex interplay of these elements leads to the generation of self-organized bending waves. Although many mathematical models have been proposed to understand this process, few attempts have been made to assess the role of dyneins on the nonlinear nature of the axoneme. Here, we investigate the nonlinear dynamics of flagella by considering an axonemal sliding control mechanism for dynein activity. This approach unveils the nonlinear selection of the oscillation amplitudes, which are typically either missed or prescribed in mathematical models. The explicit set of nonlinear equations are derived and solved numerically. Our analysis reveals the spatio-temporal dynamics of dynein populations and flagellum shape for different regimes of motor activity, medium viscosity and flagellum elasticity. Unstable modes saturate via the coupling of dynein kinetics and flagellum shape without the need of invoking a nonlinear axonemal response. Hence, our work reveals a novel mechanism for the saturation of unstable modes in axonemal beating.

Nonlinear amplitude dynamics in flagellar beating

PubMed Central

Casademunt, Jaume

2017-01-01

The physical basis of flagellar and ciliary beating is a major problem in biology which is still far from completely understood. The fundamental cytoskeleton structure of cilia and flagella is the axoneme, a cylindrical array of microtubule doublets connected by passive cross-linkers and dynein motor proteins. The complex interplay of these elements leads to the generation of self-organized bending waves. Although many mathematical models have been proposed to understand this process, few attempts have been made to assess the role of dyneins on the nonlinear nature of the axoneme. Here, we investigate the nonlinear dynamics of flagella by considering an axonemal sliding control mechanism for dynein activity. This approach unveils the nonlinear selection of the oscillation amplitudes, which are typically either missed or prescribed in mathematical models. The explicit set of nonlinear equations are derived and solved numerically. Our analysis reveals the spatio-temporal dynamics of dynein populations and flagellum shape for different regimes of motor activity, medium viscosity and flagellum elasticity. Unstable modes saturate via the coupling of dynein kinetics and flagellum shape without the need of invoking a nonlinear axonemal response. Hence, our work reveals a novel mechanism for the saturation of unstable modes in axonemal beating. PMID:28405357

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

PubMed

Higo, Junichi; Umezawa, Koji

2014-01-01

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

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms☆

PubMed Central

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-01-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov. PMID:26766517

FATE-HD: A spatially and temporally explicit integrated model for predicting vegetation structure and diversity at regional scale

PubMed Central

Isabelle, Boulangeat; Damien, Georges; Wilfried, Thuiller

2014-01-01

During the last decade, despite strenuous efforts to develop new models and compare different approaches, few conclusions have been drawn on their ability to provide robust biodiversity projections in an environmental change context. The recurring suggestions are that models should explicitly (i) include spatiotemporal dynamics; (ii) consider multiple species in interactions; and (iii) account for the processes shaping biodiversity distribution. This paper presents a biodiversity model (FATE-HD) that meets this challenge at regional scale by combining phenomenological and process-based approaches and using well-defined plant functional groups. FATE-HD has been tested and validated in a French National Park, demonstrating its ability to simulate vegetation dynamics, structure and diversity in response to disturbances and climate change. The analysis demonstrated the importance of considering biotic interactions, spatio-temporal dynamics, and disturbances in addition to abiotic drivers to simulate vegetation dynamics. The distribution of pioneer trees was particularly improved, as were all undergrowth functional groups. PMID:24214499

Mathematical Model of Bubble Sloshing Dynamics for Cryogenic Liquid Helium in Orbital Spacecraft Dewar Container

NASA Technical Reports Server (NTRS)

Hung, R. J.; Pan, H. L.

1995-01-01

A generalized mathematical model is investigated of sloshing dynamics for dewar containers, partially filled with a liquid of cryogenic superfluid helium 2, driven by both gravity gradient and jitter accelerations applicable to two types of scientific spacecrafts, which are eligible to carry out spinning motion and/or slew motion to perform scientific observations during normal spacecraft operation. Two examples are given for the Gravity Probe-B (GP-B) with spinning motion, and the Advanced X-Ray Astrophysics Facility-Spectroscopy (AXAF-S) with slew motion, which are responsible for the sloshing dynamics. Explicit mathematical expressions for the modelling of sloshing dynamics to cover these forces acting on the spacecraft fluid systems are derived. The numerical computation of sloshing dynamics will be based on the noninertial frame spacecraft bound coordinate, and we will solve the time-dependent three-dimensional formulations of partial differential equations subject to initial and boundary conditions. Explicit mathematical expressions of boundary conditions lo cover capillary force effects on the liquid-vapor interface in microgravity environments are also derived. Results of the simulations of the mathematical model are illustrated.

A coarse-grained polarizable force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate

NASA Astrophysics Data System (ADS)

Zeman, Johannes; Uhlig, Frank; Smiatek, Jens; Holm, Christian

2017-12-01

We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such as mass density, enthalpy of vaporization, diffusion coefficients, or electrical conductivity in the relevant temperature range. In situations where an explicit treatment of electronic polarizability might be crucial, we expect the force field to be an improvement over non-polarizable models, while still profiting from the reduction of computational cost due to the coarse-grained representation.

The Time Course of Explicit and Implicit Categorization

PubMed Central

Zakrzewski, Alexandria C.; Herberger, Eric; Boomer, Joseph; Roeder, Jessica; Ashby, F. Gregory; Church, Barbara A.

2015-01-01

Contemporary theory in cognitive neuroscience distinguishes, among the processes and utilities that serve categorization, explicit and implicit systems of category learning that learn, respectively, category rules by active hypothesis testing or adaptive behaviors by association and reinforcement. Little is known about the time course of categorization within these systems. Accordingly, the present experiments contrasted tasks that fostered explicit categorization (because they had a one-dimensional, rule-based solution) or implicit categorization (because they had a two-dimensional, information-integration solution). In Experiment 1, participants learned categories under unspeeded or speeded conditions. In Experiment 2, they applied previously trained category knowledge under unspeeded or speeded conditions. Speeded conditions selectively impaired implicit category learning and implicit mature categorization. These results illuminate the processing dynamics of explicit/implicit categorization. PMID:26025556

Dynamic population mapping using mobile phone data.

PubMed

Deville, Pierre; Linard, Catherine; Martin, Samuel; Gilbert, Marius; Stevens, Forrest R; Gaughan, Andrea E; Blondel, Vincent D; Tatem, Andrew J

2014-11-11

During the past few decades, technologies such as remote sensing, geographical information systems, and global positioning systems have transformed the way the distribution of human population is studied and modeled in space and time. However, the mapping of populations remains constrained by the logistics of censuses and surveys. Consequently, spatially detailed changes across scales of days, weeks, or months, or even year to year, are difficult to assess and limit the application of human population maps in situations in which timely information is required, such as disasters, conflicts, or epidemics. Mobile phones (MPs) now have an extremely high penetration rate across the globe, and analyzing the spatiotemporal distribution of MP calls geolocated to the tower level may overcome many limitations of census-based approaches, provided that the use of MP data is properly assessed and calibrated. Using datasets of more than 1 billion MP call records from Portugal and France, we show how spatially and temporarily explicit estimations of population densities can be produced at national scales, and how these estimates compare with outputs produced using alternative human population mapping methods. We also demonstrate how maps of human population changes can be produced over multiple timescales while preserving the anonymity of MP users. With similar data being collected every day by MP network providers across the world, the prospect of being able to map contemporary and changing human population distributions over relatively short intervals exists, paving the way for new applications and a near real-time understanding of patterns and processes in human geography.

Dynamic population mapping using mobile phone data

PubMed Central

Deville, Pierre; Martin, Samuel; Gilbert, Marius; Stevens, Forrest R.; Gaughan, Andrea E.; Blondel, Vincent D.; Tatem, Andrew J.

2014-01-01

During the past few decades, technologies such as remote sensing, geographical information systems, and global positioning systems have transformed the way the distribution of human population is studied and modeled in space and time. However, the mapping of populations remains constrained by the logistics of censuses and surveys. Consequently, spatially detailed changes across scales of days, weeks, or months, or even year to year, are difficult to assess and limit the application of human population maps in situations in which timely information is required, such as disasters, conflicts, or epidemics. Mobile phones (MPs) now have an extremely high penetration rate across the globe, and analyzing the spatiotemporal distribution of MP calls geolocated to the tower level may overcome many limitations of census-based approaches, provided that the use of MP data is properly assessed and calibrated. Using datasets of more than 1 billion MP call records from Portugal and France, we show how spatially and temporarily explicit estimations of population densities can be produced at national scales, and how these estimates compare with outputs produced using alternative human population mapping methods. We also demonstrate how maps of human population changes can be produced over multiple timescales while preserving the anonymity of MP users. With similar data being collected every day by MP network providers across the world, the prospect of being able to map contemporary and changing human population distributions over relatively short intervals exists, paving the way for new applications and a near real-time understanding of patterns and processes in human geography. PMID:25349388

Nonadiabatic Dynamics of Photoinduced Proton-Coupled Electron Transfer Processes

DTIC Science & Technology

devices and photoelectrochemical cells. Theoretical methodology for simulating the nonadiabatic dynamics of photoinduced PCET reactions in solution has...tuning and control of the ultrafast dynamics is crucial for designing renewable and sustainable energy sources, such as artificial photosynthesis...describes the solute with a multiconfigurational method in a bath of explicit solvent molecules. The transferring hydrogen nucleus is represented as a

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...

Spreading of Cholera through Surface Water

NASA Astrophysics Data System (ADS)

Bertuzzo, E.; Casagrandi, R.; Gatto, M.; Rodriguez-Iturbe, I.; Rinaldo, A.

2009-12-01

Cholera epidemics are still a major public health concern to date in many areas of the world. In order to understand and forecast cholera outbreaks, one of the most important factors is the role played by the environmental matrix in which the disease spreads. We study how river networks, acting as environmental corridors for pathogens, affect the spreading of cholera epidemics. The environmental matrix in which the disease spreads is constituted by different human communities and their hydrologic interconnections. Each community is characterized by its spatial position, population size, water resources availability and hygiene conditions. By implementing a spatially explicit cholera model we seek the effects on epidemic dynamics of: i) the topology and metrics of the pathogens pathways that connect different communities; ii) the spatial distribution of the population size; and iii) the spatial distributions and quality of surface water resources and public health conditions, and how they vary with population size. The model has been applied to study the space-time evolution of a well documented cholera epidemic occurred in the KwaZulu-Natal province of South Africa. The epidemic lasted for two years and involved about 140,000 confirmed cholera cases. The model does well in reproducing the distribution of the cholera cases during the two outbreaks as well as their spatial spreading. We further extend the model by deriving the speed of propagation of traveling fronts in the case of uniformly distributed systems for different topologies: one and two dimensional lattices and river networks. The derivation of the spreading celerity proves instrumental in establishing the overall conditions for the relevance of spatially explicit models. The conditions are sought by comparison between spreading and disease timescales. Consider a cholera epidemic that starts from a point and spreads throughout a finite size system, it is possible to identify two different timescales: i) the spreading timescale, that is the time needed for the disease to spread and involve all the communities in the system; and ii) the epidemic timescale, defined by the duration of the epidemic in a single community. Our results suggest that in many cases of real-life epidemiological interest, timescales of disease dynamics may trigger outbreaks that significantly depart from the predictions of classical space-implicit compartmental models.

Transport theory and fluid dynamics

NASA Astrophysics Data System (ADS)

Greenberg, W.; Zweifel, P. F.

We report progress in various areas of applied mathematics relevant to transport theory under the subjects: abstract transport theory, explicit transport models and computation, and fluid dynamics. We present a brief review of progress during the past year and personnel supported, and we indicate the direction of our future research.

Spatial Patterns in Alternative States and Thresholds: A Missing Link for Management of Landscapes?

USDA-ARS?s Scientific Manuscript database

The detection of threshold dynamics (and other dynamics of interest) would benefit from explicit representations of spatial patterns of disturbance, spatial dependence in responses to disturbance, and the spatial structure of feedbacks in the design of monitoring and management strategies. Spatially...

Spatializing 6,000 years of global urbanization from 3700 BC to AD 2000

NASA Astrophysics Data System (ADS)

Reba, Meredith; Reitsma, Femke; Seto, Karen C.

2016-06-01

How were cities distributed globally in the past? How many people lived in these cities? How did cities influence their local and regional environments? In order to understand the current era of urbanization, we must understand long-term historical urbanization trends and patterns. However, to date there is no comprehensive record of spatially explicit, historic, city-level population data at the global scale. Here, we developed the first spatially explicit dataset of urban settlements from 3700 BC to AD 2000, by digitizing, transcribing, and geocoding historical, archaeological, and census-based urban population data previously published in tabular form by Chandler and Modelski. The dataset creation process also required data cleaning and harmonization procedures to make the data internally consistent. Additionally, we created a reliability ranking for each geocoded location to assess the geographic uncertainty of each data point. The dataset provides the first spatially explicit archive of the location and size of urban populations over the last 6,000 years and can contribute to an improved understanding of contemporary and historical urbanization trends.

Spatializing 6,000 years of global urbanization from 3700 BC to AD 2000

PubMed Central

Reba, Meredith; Reitsma, Femke; Seto, Karen C.

2016-01-01

How were cities distributed globally in the past? How many people lived in these cities? How did cities influence their local and regional environments? In order to understand the current era of urbanization, we must understand long-term historical urbanization trends and patterns. However, to date there is no comprehensive record of spatially explicit, historic, city-level population data at the global scale. Here, we developed the first spatially explicit dataset of urban settlements from 3700 BC to AD 2000, by digitizing, transcribing, and geocoding historical, archaeological, and census-based urban population data previously published in tabular form by Chandler and Modelski. The dataset creation process also required data cleaning and harmonization procedures to make the data internally consistent. Additionally, we created a reliability ranking for each geocoded location to assess the geographic uncertainty of each data point. The dataset provides the first spatially explicit archive of the location and size of urban populations over the last 6,000 years and can contribute to an improved understanding of contemporary and historical urbanization trends. PMID:27271481

Chained Aggregation and Control System Design:; A Geometric Approach.

DTIC Science & Technology

1982-10-01

Furthermore, it explicitly identifies a reduced order modal used to meet the design goals. This results in an interactive design pro- cedure which allows...same framework. This leads directly to dynamic compen- sator design. The results are applied to decentralized control problems, non interactive ...goals. Furthermore, it explicitly identifies a reduced order model used to meet the design goals. This results in an interactive design procedure which

Finite Element Modeling of Coupled Flexible Multibody Dynamics and Liquid Sloshing

DTIC Science & Technology

2006-09-01

tanks is presented. The semi-discrete combined solid and fluid equations of motions are integrated using a time- accurate parallel explicit solver...Incompressible fluid flow in a moving/deforming container including accurate modeling of the free-surface, turbulence, and viscous effects ...paper, a single computational code which uses a time- accurate explicit solution procedure is used to solve both the solid and fluid equations of

Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations

PubMed Central

van Albada, Sacha Jennifer; Helias, Moritz; Diesmann, Markus

2015-01-01

Network models are routinely downscaled compared to nature in terms of numbers of nodes or edges because of a lack of computational resources, often without explicit mention of the limitations this entails. While reliable methods have long existed to adjust parameters such that the first-order statistics of network dynamics are conserved, here we show that limitations already arise if also second-order statistics are to be maintained. The temporal structure of pairwise averaged correlations in the activity of recurrent networks is determined by the effective population-level connectivity. We first show that in general the converse is also true and explicitly mention degenerate cases when this one-to-one relationship does not hold. The one-to-one correspondence between effective connectivity and the temporal structure of pairwise averaged correlations implies that network scalings should preserve the effective connectivity if pairwise averaged correlations are to be held constant. Changes in effective connectivity can even push a network from a linearly stable to an unstable, oscillatory regime and vice versa. On this basis, we derive conditions for the preservation of both mean population-averaged activities and pairwise averaged correlations under a change in numbers of neurons or synapses in the asynchronous regime typical of cortical networks. We find that mean activities and correlation structure can be maintained by an appropriate scaling of the synaptic weights, but only over a range of numbers of synapses that is limited by the variance of external inputs to the network. Our results therefore show that the reducibility of asynchronous networks is fundamentally limited. PMID:26325661

Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

PubMed Central

2012-01-01

Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

Testing the nature of reaction coordinate describing interaction of H2 with carbonyl carbon, activated by Lewis acid complexation, and the Lewis basic solvent: A Born-Oppenheimer molecular dynamics study with explicit solvent

NASA Astrophysics Data System (ADS)

Heshmat, Mojgan; Privalov, Timofei

2017-09-01

Using Born-Oppenheimer molecular dynamics (BOMD), we explore the nature of interactions between H2 and the activated carbonyl carbon, C(carbonyl), of the acetone-B(C6F5)3 adduct surrounded by an explicit solvent (1,4-dioxane). BOMD simulations at finite (non-zero) temperature with an explicit solvent produced long-lasting instances of significant vibrational perturbation of the H—H bond and H2-polarization at C(carbonyl). As far as the characteristics of H2 are concerned, the dynamical transient state approximates the transition-state of the heterolytic H2-cleavage. The culprit is the concerted interactions of H2 with C(carbonyl) and a number of Lewis basic solvent molecules—i.e., the concerted C(carbonyl)⋯H2⋯solvent interactions. On one hand, the results presented herein complement the mechanistic insight gained from our recent transition-state calculations, reported separately from this article. But on the other hand, we now indicate that an idea of the sufficiency of just one simple reaction coordinate in solution-phase reactions can be too simplistic and misleading. This article goes in the footsteps of the rapidly strengthening approach of investigating molecular interactions in large molecular systems via "computational experimentation" employing, primarily, ab initio molecular dynamics describing reactants-interaction without constraints of the preordained reaction coordinate and/or foreknowledge of the sampling order parameters.

Market-based demand forecasting promotes informed strategic financial planning.

PubMed

Beech, A J

2001-11-01

Market-based demand forecasting is a method of estimating future demand for a healthcare organization's services by using a broad range of data that describe the nature of demand within the organization's service area. Such data include the primary and secondary service areas, the service-area populations by various demographic groupings, discharge utilization rates, market size, and market share by service line and organizationwide. Based on observable market dynamics, strategic planners can make a variety of explicit assumptions about future trends regarding these data to develop scenarios describing potential future demand. Financial planners then can evaluate each scenario to determine its potential effect on selected financial and operational measures, such as operating margin, days cash on hand, and debt-service coverage, and develop a strategic financial plan that covers a range of contingencies.

Larval Connectivity and the International Management of Fisheries

PubMed Central

Kough, Andrew S.; Paris, Claire B.; Butler, Mark J.

2013-01-01

Predicting the oceanic dispersal of planktonic larvae that connect scattered marine animal populations is difficult, yet crucial for management of species whose movements transcend international boundaries. Using multi-scale biophysical modeling techniques coupled with empirical estimates of larval behavior and gamete production, we predict and empirically verify spatio-temporal patterns of larval supply and describe the Caribbean-wide pattern of larval connectivity for the Caribbean spiny lobster (Panulirus argus), an iconic coral reef species whose commercial value approaches $1 billion USD annually. Our results provide long sought information needed for international cooperation in the management of marine resources by identifying lobster larval connectivity and dispersal pathways throughout the Caribbean. Moreover, we outline how large-scale fishery management could explicitly recognize metapopulation structure by considering larval transport dynamics and pelagic larval sanctuaries. PMID:23762273

The urban health transition hypothesis: empirical evidence of an avian influenza Kuznets curve in Vietnam?

PubMed

Spencer, James Herbert

2013-04-01

The literature on development has focused on the concept of transition in understanding the emergent challenges facing poor but rapidly developing countries. Scholars have focused extensively on the health and urban transitions associated with this change and, in particular, its use for understanding emerging infectious diseases. However, few have developed explicit empirical measures to quantify the extent to which a transitions focus is useful for theory, policy, and practice. Using open source data on avian influenza in 2004 and 2005 and the Vietnam Census of Population and Housing, this paper introduces the Kuznets curve as a tool for empirically estimating transition and disease. Findings suggest that the Kuznets curve is a viable tool for empirically assessing the role of transitional dynamics in the emergence of new infectious diseases.

Characterization and solvability of quasipolynomial symplectic mappings

NASA Astrophysics Data System (ADS)

Hernández-Bermejo, Benito; Brenig, Léon

2004-02-01

Quasipolynomial (or QP) mappings constitute a wide generalization of the well-known Lotka-Volterra mappings, of importance in different fields such as population dynamics, physics, chemistry or economy. In addition, QP mappings are a natural discrete-time analogue of the continuous QP systems, which have been extensively used in different pure and applied domains. After presenting the basic definitions and properties of QP mappings in a previous paper [1], the purpose of this work is to focus on their characterization by considering the existence of symplectic QP mappings. In what follows such QP symplectic maps are completely characterized. Moreover, use of the QP formalism can be made in order to demonstrate that all QP symplectic mappings have an analytical solution that is explicitly and generally constructed. Examples are given.

Study of the stability of a SEIRS model for computer worm propagation

NASA Astrophysics Data System (ADS)

Hernández Guillén, J. D.; Martín del Rey, A.; Hernández Encinas, L.

2017-08-01

Nowadays, malware is the most important threat to information security. In this sense, several mathematical models to simulate malware spreading have appeared. They are compartmental models where the population of devices is classified into different compartments: susceptible, exposed, infectious, recovered, etc. The main goal of this work is to propose an improved SEIRS (Susceptible-Exposed-Infectious-Recovered-Susceptible) mathematical model to simulate computer worm propagation. It is a continuous model whose dynamic is ruled by means of a system of ordinary differential equations. It considers more realistic parameters related to the propagation; in fact, a modified incidence rate has been used. Moreover, the equilibrium points are computed and their local and global stability analyses are studied. From the explicit expression of the basic reproductive number, efficient control measures are also obtained.

A dynamic appearance descriptor approach to facial actions temporal modeling.

PubMed

Jiang, Bihan; Valstar, Michel; Martinez, Brais; Pantic, Maja

2014-02-01

Both the configuration and the dynamics of facial expressions are crucial for the interpretation of human facial behavior. Yet to date, the vast majority of reported efforts in the field either do not take the dynamics of facial expressions into account, or focus only on prototypic facial expressions of six basic emotions. Facial dynamics can be explicitly analyzed by detecting the constituent temporal segments in Facial Action Coding System (FACS) Action Units (AUs)-onset, apex, and offset. In this paper, we present a novel approach to explicit analysis of temporal dynamics of facial actions using the dynamic appearance descriptor Local Phase Quantization from Three Orthogonal Planes (LPQ-TOP). Temporal segments are detected by combining a discriminative classifier for detecting the temporal segments on a frame-by-frame basis with Markov Models that enforce temporal consistency over the whole episode. The system is evaluated in detail over the MMI facial expression database, the UNBC-McMaster pain database, the SAL database, the GEMEP-FERA dataset in database-dependent experiments, in cross-database experiments using the Cohn-Kanade, and the SEMAINE databases. The comparison with other state-of-the-art methods shows that the proposed LPQ-TOP method outperforms the other approaches for the problem of AU temporal segment detection, and that overall AU activation detection benefits from dynamic appearance information.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.

PubMed

Andrews, Casey T; Elcock, Adrian H

2014-11-11

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions-which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)-quantitatively reproduced all of the "target" MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic ( PLoS Comput. Biol. 2014 , 5 , e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP's nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins.

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

PubMed Central

2015-01-01

We describe the derivation of a set of bonded and nonbonded coarse-grained (CG) potential functions for use in implicit-solvent Brownian dynamics (BD) simulations of proteins derived from all-atom explicit-solvent molecular dynamics (MD) simulations of amino acids. Bonded potential functions were derived from 1 μs MD simulations of each of the 20 canonical amino acids, with histidine modeled in both its protonated and neutral forms; nonbonded potential functions were derived from 1 μs MD simulations of every possible pairing of the amino acids (231 different systems). The angle and dihedral probability distributions and radial distribution functions sampled during MD were used to optimize a set of CG potential functions through use of the iterative Boltzmann inversion (IBI) method. The optimized set of potential functions—which we term COFFDROP (COarse-grained Force Field for Dynamic Representation Of Proteins)—quantitatively reproduced all of the “target” MD distributions. In a first test of the force field, it was used to predict the clustering behavior of concentrated amino acid solutions; the predictions were directly compared with the results of corresponding all-atom explicit-solvent MD simulations and found to be in excellent agreement. In a second test, BD simulations of the small protein villin headpiece were carried out at concentrations that have recently been studied in all-atom explicit-solvent MD simulations by Petrov and Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions seen in the MD study were reproduced in the COFFDROP simulations; a simple scaling of COFFDROP’s nonbonded parameters, however, produced results in better accordance with experiment. Overall, our results suggest that potential functions derived from simulations of pairwise amino acid interactions might be of quite broad applicability, with COFFDROP likely to be especially useful for modeling unfolded or intrinsically disordered proteins. PMID:25400526

Simulating mechanisms for dispersal, production and stranding of small forage fish in temporary wetland habitats

USGS Publications Warehouse

Yurek, Simeon; DeAngelis, Donald L.; Trexler, Joel C.; Jopp, Fred; Donalson, Douglas D.

2013-01-01

Movement strategies of small forage fish (<8 cm total length) between temporary and permanent wetland habitats affect their overall population growth and biomass concentrations, i.e., availability to predators. These fish are often the key energy link between primary producers and top predators, such as wading birds, which require high concentrations of stranded fish in accessible depths. Expansion and contraction of seasonal wetlands induce a sequential alternation between rapid biomass growth and concentration, creating the conditions for local stranding of small fish as they move in response to varying water levels. To better understand how landscape topography, hydrology, and fish behavior interact to create high densities of stranded fish, we first simulated population dynamics of small fish, within a dynamic food web, with different traits for movement strategy and growth rate, across an artificial, spatially explicit, heterogeneous, two-dimensional marsh slough landscape, using hydrologic variability as the driver for movement. Model output showed that fish with the highest tendency to invade newly flooded marsh areas built up the largest populations over long time periods with stable hydrologic patterns. A higher probability to become stranded had negative effects on long-term population size, and offset the contribution of that species to stranded biomass. The model was next applied to the topography of a 10 km × 10 km area of Everglades landscape. The details of the topography were highly important in channeling fish movements and creating spatiotemporal patterns of fish movement and stranding. This output provides data that can be compared in the future with observed locations of fish biomass concentrations, or such surrogates as phosphorus ‘hotspots’ in the marsh.

The dynamics of architectural complexity on coral reefs under climate change.

PubMed

Bozec, Yves-Marie; Alvarez-Filip, Lorenzo; Mumby, Peter J

2015-01-01

One striking feature of coral reef ecosystems is the complex benthic architecture which supports diverse and abundant fauna, particularly of reef fish. Reef-building corals are in decline worldwide, with a corresponding loss of live coral cover resulting in a loss of architectural complexity. Understanding the dynamics of the reef architecture is therefore important to envision the ability of corals to maintain functional habitats in an era of climate change. Here, we develop a mechanistic model of reef topographical complexity for contemporary Caribbean reefs. The model describes the dynamics of corals and other benthic taxa under climate-driven disturbances (hurricanes and coral bleaching). Corals have a simplified shape with explicit diameter and height, allowing species-specific calculation of their colony surface and volume. Growth and the mechanical (hurricanes) and biological erosion (parrotfish) of carbonate skeletons are important in driving the pace of extension/reduction in the upper reef surface, the net outcome being quantified by a simple surface roughness index (reef rugosity). The model accurately simulated the decadal changes of coral cover observed in Cozumel (Mexico) between 1984 and 2008, and provided a realistic hindcast of coral colony-scale (1-10 m) changing rugosity over the same period. We then projected future changes of Caribbean reef rugosity in response to global warming. Under severe and frequent thermal stress, the model predicted a dramatic loss of rugosity over the next two or three decades. Critically, reefs with managed parrotfish populations were able to delay the general loss of architectural complexity, as the benefits of grazing in maintaining living coral outweighed the bioerosion of dead coral skeletons. Overall, this model provides the first explicit projections of reef rugosity in a warming climate, and highlights the need of combining local (protecting and restoring high grazing) to global (mitigation of greenhouse gas emissions) interventions for the persistence of functional reef habitats. © 2014 John Wiley & Sons Ltd.

Effects of Explicit Vocabulary Videos Delivered through iPods on Students with Language Impairments

ERIC Educational Resources Information Center

Lowman, J. Joneen; Dressler, Emily V.

2016-01-01

Poor word learning is a hallmark characteristic of students with specific language impairment (SLI). Explicit vocabulary instruction has shown to positively improve word learning in this population. Mobile technology has many advantages making it conducive for addressing the word learning needs of students with SLI. The current study utilized a…

Explicit Memory among Individuals with Mild and Moderate Intellectual Disability: Educational Implications

ERIC Educational Resources Information Center

Lifshitz, Hefziba; Shtein, Sarit; Weiss, Itzhak; Svisrsky, Naama

2011-01-01

We previously reported a meta-analysis of explicit memory studies in populations with intellectual disability (ID). The current study discusses the educational implications of this meta-analysis. The main factors at the core of these implications can be divided into two categories: those related to task characteristics (e.g., depth of processing,…

A Characterization of Dynamic Reasoning: Reasoning with Time as Parameter

ERIC Educational Resources Information Center

Keene, Karen Allen

2007-01-01

Students incorporate and use the implicit and explicit parameter time to support their mathematical reasoning and deepen their understandings as they participate in a differential equations class during instruction on solutions to systems of differential equations. Therefore, dynamic reasoning is defined as developing and using conceptualizations…

Complex life cycles and density dependence: assessing the contribution of egg mortality to amphibian declines.

PubMed

Vonesh, James R; De la Cruz, Omar

2002-11-01

In the last decade there has been increasing evidence of amphibian declines from relatively pristine areas. Some declines are hypothesized to be the result of egg mortality caused by factors such as elevated solar UV-B irradiation, chemical pollutants, pathogenic fungi, and climate change. However, the population-level consequences of egg mortality have not been examined explicitly, and may be complicated by density dependence in intervening life-history stages. Here we develop a demographic model for two amphibians with contrasting life-history strategies, Bufo boreas and Ambystoma macrodactylum. We then use the complementary approaches of elasticity and limitation to examine the relationships among stage-specific survival rates, larval-stage density dependence and amphibian population dynamics. Elasticity analyses showed that for a range of density dependence scenarios both species were more sensitive to changes in post-embryonic survival parameters, particularly juvenile survival, than to egg survival, suggesting that mortality of later stages may play an important role in driving declines. Limitation analyses revealed that larval density dependence can dramatically alter the consequences of early mortality, reducing or even reversing the expected population-level effects of egg mortality. Thus, greater focus on later life stages and density dependence is called for to accurately assess how stressors are likely to affect amphibian populations of conservation concern.

Competitive intransitivity, population interaction structure, and strategy coexistence.

PubMed

Laird, Robert A; Schamp, Brandon S

2015-01-21

Intransitive competition occurs when competing strategies cannot be listed in a hierarchy, but rather form loops-as in the game rock-paper-scissors. Due to its cyclic competitive replacement, competitive intransitivity promotes strategy coexistence, both in rock-paper-scissors and in higher-richness communities. Previous work has shown that this intransitivity-mediated coexistence is strongly influenced by spatially explicit interactions, compared to when populations are well mixed. Here, we extend and broaden this line of research and examine the impact on coexistence of intransitive competition taking place on a continuum of small-world networks linking spatial lattices and regular random graphs. We use simulations to show that the positive effect of competitive intransitivity on strategy coexistence holds when competition occurs on networks toward the spatial end of the continuum. However, in networks that are sufficiently disordered, increasingly violent fluctuations in strategy frequencies can lead to extinctions and the prevalence of monocultures. We further show that the degree of disorder that leads to the transition between these two regimes is positively dependent on population size; indeed for very large populations, intransitivity-mediated strategy coexistence may even be possible in regular graphs with completely random connections. Our results emphasize the importance of interaction structure in determining strategy dynamics and diversity. Copyright © 2014 Elsevier Ltd. All rights reserved.

Latitude delineates patterns of biogeography in terrestrial Streptomyces.

PubMed

Choudoir, Mallory J; Doroghazi, James R; Buckley, Daniel H

2016-12-01

The biogeography of Streptomyces was examined at regional spatial scales to identify factors that govern patterns of microbial diversity. Streptomyces are spore forming filamentous bacteria which are widespread in soil. Streptomyces strains were isolated from perennial grass habitats sampled across a spatial scale of more than 6000 km. Previous analysis of this geographically explicit culture collection provided evidence for a latitudinal diversity gradient in Streptomyces species. Here the hypothesis that this latitudinal diversity gradient is a result of evolutionary dynamics associated with historical demographic processes was evaluated. Historical demographic phenomena have genetic consequences that can be evaluated through analysis of population genetics. Population genetic approaches were applied to analyze population structure in six of the most numerically abundant and geographically widespread Streptomyces phylogroups from our culture collection. Streptomyces population structure varied at regional spatial scales, and allelic diversity correlated with geographic distance. In addition, allelic diversity and gene flow are partitioned by latitude. Finally, it was found that nucleotide diversity within phylogroups was negatively correlated with latitude. These results indicate that phylogroup diversification is constrained by dispersal limitation at regional spatial scales, and they are consistent with the hypothesis that historical demographic processes have influenced the contemporary biogeography of Streptomyces. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparing Two Forms of Dynamic Assessment and Traditional Assessment of Preschool Phonological Awareness

ERIC Educational Resources Information Center

Kantor, Patricia Thatcher; Wagner, Richard K.; Torgesen, Joseph K.; Rashotte, Carol A.

2011-01-01

The goal of the current study was to compare two forms of dynamic assessment and standard assessment of preschool children's phonological awareness. The first form of dynamic assessment was a form of scaffolding in which item formats were modified in response to an error so as to make the task easier or more explicit. The second form of dynamic…

Quantification of live aboveground forest biomass dynamics with Landsat time-series and field inventory data: A comparison of empirical modeling approaches

Treesearch

Scott L. Powell; Warren B. Cohen; Sean P. Healey; Robert E. Kennedy; Gretchen G. Moisen; Kenneth B. Pierce; Janet L. Ohmann

2010-01-01

Spatially and temporally explicit knowledge of biomass dynamics at broad scales is critical to understanding how forest disturbance and regrowth processes influence carbon dynamics. We modeled live, aboveground tree biomass using Forest Inventory and Analysis (FIA) field data and applied the models to 20+ year time-series of Landsat satellite imagery to...

Coevolution in host-parasite systems: behavioural strategies of slave-making ants and their hosts.

PubMed

Foitzik, S; DeHeer, C J; Hunjan, D N; Herbers, J M

2001-06-07

Recently, avian brood parasites and their hosts have emerged as model systems for the study of host-parasite coevolution. However, empirical studies of the highly analogous social parasites, which use the workers of another eusocial species to raise their own young, have never explicitly examined the dynamics of these systems from a coevolutionary perspective. Here, we demonstrate interpopulational variation in behavioural interactions between a socially parasitic slave-maker ant and its host that is consistent with the expectations of host-parasite coevolution. Parasite pressure, as inferred by the size, abundance and raiding frequency of Protomognathus americanus colonies, was highest in a New York population of the host Leptothorax longispinosus and lowest in a West Virginia population. As host-parasite coevolutionary theory would predict, we found that the slave-makers and the hosts from New York were more effective at raiding and defending against raiders, respectively, than were conspecifics from the West Virginia population. Some of these variations in efficacy were brought about by apparently simple shifts in behaviour. These results demonstrate that defence mechanisms against social parasites can evolve, and they give the first indications of the existence of a coevolutionary arms race between a social parasite and its host.

Application of the Hughes-LIU algorithm to the 2-dimensional heat equation

NASA Technical Reports Server (NTRS)

Malkus, D. S.; Reichmann, P. I.; Haftka, R. T.

1982-01-01

An implicit explicit algorithm for the solution of transient problems in structural dynamics is described. The method involved dividing the finite elements into implicit and explicit groups while automatically satisfying the conditions. This algorithm is applied to the solution of the linear, transient, two dimensional heat equation subject to an initial condition derived from the soluton of a steady state problem over an L-shaped region made up of a good conductor and an insulating material. Using the IIT/PRIME computer with virtual memory, a FORTRAN computer program code was developed to make accuracy, stability, and cost comparisons among the fully explicit Euler, the Hughes-Liu, and the fully implicit Crank-Nicholson algorithms. The Hughes-Liu claim that the explicit group governs the stability of the entire region while maintaining the unconditional stability of the implicit group is illustrated.

Contact structure, mobility, environmental impact and behaviour: the importance of social forces to infectious disease dynamics and disease ecology

PubMed Central

Gurley, Emily S.

2017-01-01

Human factors, including contact structure, movement, impact on the environment and patterns of behaviour, can have significant influence on the emergence of novel infectious diseases and the transmission and amplification of established ones. As anthropogenic climate change alters natural systems and global economic forces drive land-use and land-cover change, it becomes increasingly important to understand both the ecological and social factors that impact infectious disease outcomes for human populations. While the field of disease ecology explicitly studies the ecological aspects of infectious disease transmission, the effects of the social context on zoonotic pathogen spillover and subsequent human-to-human transmission are comparatively neglected in the literature. The social sciences encompass a variety of disciplines and frameworks for understanding infectious diseases; however, here we focus on four primary areas of social systems that quantitatively and qualitatively contribute to infectious diseases as social–ecological systems. These areas are social mixing and structure, space and mobility, geography and environmental impact, and behaviour and behaviour change. Incorporation of these social factors requires empirical studies for parametrization, phenomena characterization and integrated theoretical modelling of social–ecological interactions. The social–ecological system that dictates infectious disease dynamics is a complex system rich in interacting variables with dynamically significant heterogeneous properties. Future discussions about infectious disease spillover and transmission in human populations need to address the social context that affects particular disease systems by identifying and measuring qualitatively important drivers. This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’. PMID:28289265

Multi-Scale Ballistic Material Modeling of Cross-Plied Compliant Composites

DTIC Science & Technology

2009-01-01

PERFORMING ORGANIZATION REPORT NUMBER 19a. NAME OF RESPONSIBLE PERSON 19b. TELEPHONE NUMBER Mica Grujicic 864-656-5639 3. DATES COVERED (From - To...Autodyn [ANSYS/Autodyn version 11.0, User Documentation, Century Dynamics Inc. a subsidiary of ANSYS Inc. (2007)] and ABA- QUS /Explicit [ABAQUS...matrix, Fig. 3(b). Bonding between the matrix and the filaments is represented using 7056 ‘‘cohesive” elements, (ABA- QUS /Explicit designation COH3D6

Biomass and fire dynamics in a temperate forest-grassland mosaic: Integrating multi-species herbivory, climate, and fire with the FireBGCv2/GrazeBGC system

Treesearch

Robert A. Riggs; Robert E. Keane; Norm Cimon; Rachel Cook; Lisa Holsinger; John Cook; Timothy DelCurto; L.Scott Baggett; Donald Justice; David Powell; Martin Vavra; Bridgett Naylor

2015-01-01

Landscape fire succession models (LFSMs) predict spatially-explicit interactions between vegetation succession and disturbance, but these models have yet to fully integrate ungulate herbivory as a driver of their processes. We modified a complex LFSM, FireBGCv2, to include a multi-species herbivory module, GrazeBGC. The system is novel in that it explicitly...

White-nose syndrome is likely to extirpate the endangered Indiana bat over large parts of its range

USGS Publications Warehouse

Thogmartin, Wayne E.; Sanders-Reed, Carol A.; Szymanski, Jennifer A.; McKann, Patrick C.; Pruitt, Lori; King, R. Andrew; Runge, Michael C.; Russell, Robin E.

2013-01-01

White-nose syndrome, a novel fungal pathogen spreading quickly through cave-hibernating bat species in east and central North America, is responsible for killing millions of bats. We developed a stochastic, stage-based population model to forecast the population dynamics of the endangered Indiana bat (Myotis sodalis) subject to white-nose syndrome. Our population model explicitly incorporated environmentally imposed annual variability in survival and reproductive rates and demographic stochasticity in predictions of extinction. With observed rates of disease spread, >90% of wintering populations were predicted to experience white-nose syndrome within 20 years, causing the proportion of populations at the quasi-extinction threshold of less than 250 females to increase by 33.9% over 50 years. At the species’ lowest median population level, ca. year 2022, we predicted 13.7% of the initial population to remain, totaling 28,958 females (95% CI = 13,330; 92,335). By 2022, only 12 of the initial 52 wintering populations were expected to possess wintering populations of >250 females. If the species can acquire immunity to the disease, we predict 3.7% of wintering populations to be above 250 females after 50 years (year 2057) after a 69% decline in abundance (from 210,741 to 64,768 [95% CI = 49,386; 85,360] females). At the nadir of projections, we predicted regional quasi-extirpation of wintering populations in 2 of 4 Recovery Units while in a third region, where the species is currently most abundant, >95% of the wintering populations were predicted to be below 250 females. Our modeling suggests white-nose syndrome is capable of bringing about severe numerical reduction in population size and local and regional extirpation of the Indiana bat.

The nonlinear modified equation approach to analyzing finite difference schemes

NASA Technical Reports Server (NTRS)

Klopfer, G. H.; Mcrae, D. S.

1981-01-01

The nonlinear modified equation approach is taken in this paper to analyze the generalized Lax-Wendroff explicit scheme approximation to the unsteady one- and two-dimensional equations of gas dynamics. Three important applications of the method are demonstrated. The nonlinear modified equation analysis is used to (1) generate higher order accurate schemes, (2) obtain more accurate estimates of the discretization error for nonlinear systems of partial differential equations, and (3) generate an adaptive mesh procedure for the unsteady gas dynamic equations. Results are obtained for all three areas. For the adaptive mesh procedure, mesh point requirements for equal resolution of discontinuities were reduced by a factor of five for a 1-D shock tube problem solved by the explicit MacCormack scheme.

Flux and Hall states in ABJM with dynamical flavors

NASA Astrophysics Data System (ADS)

Bea, Yago; Jokela, Niko; Lippert, Matthew; Ramallo, Alfonso V.; Zoakos, Dimitrios

2015-03-01

We study the physics of probe D6-branes with quantized internal worldvolume flux in the ABJM background with unquenched massless flavors. This flux breaks parity in the (2+1)-dimensional gauge theory and allows quantum Hall states. Parity breaking is also explicitly demonstrated via the helicity dependence of the meson spectrum. We obtain general expressions for the conductivities, both in the gapped Minkowski embeddings and in the compressible black hole ones. These conductivities depend on the flux and contain a contribution from the dynamical flavors which can be regarded as an effect of intrinsic disorder due to quantum fluctuations of the fundamentals. We present an explicit, analytic family of supersymmetric solutions with nonzero charge density, electric, and magnetic fields.

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

PubMed Central

Good, Benjamin H.; Rouzine, Igor M.; Balick, Daniel J.; Hallatschek, Oskar; Desai, Michael M.

2012-01-01

When large asexual populations adapt, competition between simultaneously segregating mutations slows the rate of adaptation and restricts the set of mutations that eventually fix. This phenomenon of interference arises from competition between mutations of different strengths as well as competition between mutations that arise on different fitness backgrounds. Previous work has explored each of these effects in isolation, but the way they combine to influence the dynamics of adaptation remains largely unknown. Here, we describe a theoretical model to treat both aspects of interference in large populations. We calculate the rate of adaptation and the distribution of fixed mutational effects accumulated by the population. We focus particular attention on the case when the effects of beneficial mutations are exponentially distributed, as well as on a more general class of exponential-like distributions. In both cases, we show that the rate of adaptation and the influence of genetic background on the fixation of new mutants is equivalent to an effective model with a single selection coefficient and rescaled mutation rate, and we explicitly calculate these effective parameters. We find that the effective selection coefficient exactly coincides with the most common fixed mutational effect. This equivalence leads to an intuitive picture of the relative importance of different types of interference effects, which can shift dramatically as a function of the population size, mutation rate, and the underlying distribution of fitness effects. PMID:22371564

Model-based scenario planning to develop climate change adaptation strategies for rare plant populations in grassland reserves

Treesearch

Laura Phillips-Mao; Susan M. Galatowitsch; Stephanie A. Snyder; Robert G. Haight

2016-01-01

Incorporating climate change into conservation decision-making at site and population scales is challenging due to uncertainties associated with localized climate change impacts and population responses to multiple interacting impacts and adaptation strategies. We explore the use of spatially explicit population models to facilitate scenario analysis, a conservation...

Using occupancy and population models to assess habitat conservation opportunities for an isolated carnivore population

Treesearch

Wayne Spencer; Heather Rustigian-Romsos; James Strittholt; Robert Scheller; William Zielinski; Richard Truex

2011-01-01

An isolated population of the fisher (Martes pennanti) in the southern Sierra Nevada, California, is threatened by small size and habitat alteration from wildfires, fuels management, and other factors. We assessed the population’s status and conservation options for its habitat using a spatially explicit population model coupled with a...

Feed‐backs among inbreeding, inbreeding depression in sperm traits, and sperm competition can drive evolution of costly polyandry

PubMed Central

Bocedi, Greta; Reid, Jane M.

2017-01-01

Abstract Ongoing ambitions are to understand the evolution of costly polyandry and its consequences for species ecology and evolution. Emerging patterns could stem from feed‐back dynamics between the evolving mating system and its genetic environment, defined by interactions among kin including inbreeding. However, such feed‐backs are rarely considered in nonselfing systems. We use a genetically explicit model to demonstrate a mechanism by which inbreeding depression can select for polyandry to mitigate the negative consequences of mating with inbred males, rather than to avoid inbreeding, and to elucidate underlying feed‐backs. Specifically, given inbreeding depression in sperm traits, costly polyandry evolved to ensure female fertility, without requiring explicit inbreeding avoidance. Resulting sperm competition caused evolution of sperm traits and further mitigated the negative effect of inbreeding depression on female fertility. The evolving mating system fed back to decrease population‐wide homozygosity, and hence inbreeding. However, the net overall decrease was small due to compound effects on the variances in sex‐specific reproductive success and paternity skew. Purging of deleterious mutations did not eliminate inbreeding depression in sperm traits or hence selection for polyandry. Overall, our model illustrates that polyandry evolution, both directly and through sperm competition, might facilitate evolutionary rescue for populations experiencing sudden increases in inbreeding. PMID:28895138

Extinction debt from climate change for frogs in the wet tropics.

PubMed

Fordham, Damien A; Brook, Barry W; Hoskin, Conrad J; Pressey, Robert L; VanDerWal, Jeremy; Williams, Stephen E

2016-10-01

The effect of twenty-first-century climate change on biodiversity is commonly forecast based on modelled shifts in species ranges, linked to habitat suitability. These projections have been coupled with species-area relationships (SAR) to infer extinction rates indirectly as a result of the loss of climatically suitable areas and associated habitat. This approach does not model population dynamics explicitly, and so accepts that extinctions might occur after substantial (but unknown) delays-an extinction debt. Here we explicitly couple bioclimatic envelope models of climate and habitat suitability with generic life-history models for 24 species of frogs found in the Australian Wet Tropics (AWT). We show that (i) as many as four species of frogs face imminent extinction by 2080, due primarily to climate change; (ii) three frogs face delayed extinctions; and (iii) this extinction debt will take at least a century to be realized in full. Furthermore, we find congruence between forecast rates of extinction using SARs, and demographic models with an extinction lag of 120 years. We conclude that SAR approaches can provide useful advice to conservation on climate change impacts, provided there is a good understanding of the time lags over which delayed extinctions are likely to occur. © 2016 The Author(s).

Emergence of increased frequency and severity of multiple infections by viruses due to spatial clustering of hosts

NASA Astrophysics Data System (ADS)

Taylor, Bradford P.; Penington, Catherine J.; Weitz, Joshua S.

2016-12-01

Multiple virus particles can infect a target host cell. Such multiple infections (MIs) have significant and varied ecological and evolutionary consequences for both virus and host populations. Yet, the in situ rates and drivers of MIs in virus-microbe systems remain largely unknown. Here, we develop an individual-based model (IBM) of virus-microbe dynamics to probe how spatial interactions drive the frequency and nature of MIs. In our IBMs, we identify increasingly spatially correlated clusters of viruses given sufficient decreases in viral movement. We also identify increasingly spatially correlated clusters of viruses and clusters of hosts given sufficient increases in viral infectivity. The emergence of clusters is associated with an increase in multiply infected hosts as compared to expectations from an analogous mean field model. We also observe long-tails in the distribution of the multiplicity of infection in contrast to mean field expectations that such events are exponentially rare. We show that increases in both the frequency and severity of MIs occur when viruses invade a cluster of uninfected microbes. We contend that population-scale enhancement of MI arises from an aggregate of invasion dynamics over a distribution of microbe cluster sizes. Our work highlights the need to consider spatially explicit interactions as a potentially key driver underlying the ecology and evolution of virus-microbe communities.

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations.

PubMed

Kortkhonjia, Ekaterine; Brandman, Relly; Zhou, Joe Zhongxiang; Voelz, Vincent A; Chorny, Ilya; Kabakoff, Bruce; Patapoff, Thomas W; Dill, Ken A; Swartz, Trevor E

2013-01-01

The solution dynamics of antibodies are critical to antibody function. We explore the internal solution dynamics of antibody molecules through the combination of time-resolved fluorescence anisotropy experiments on IgG1 with more than two microseconds of all-atom molecular dynamics (MD) simulations in explicit water, an order of magnitude more than in previous simulations. We analyze the correlated motions with a mutual information entropy quantity, and examine state transition rates in a Markov-state model, to give coarse-grained descriptors of the motions. Our MD simulations show that while there are many strongly correlated motions, antibodies are highly flexible, with F(ab) and F(c) domains constantly forming and breaking contacts, both polar and non-polar. We find that salt bridges break and reform, and not always with the same partners. While the MD simulations in explicit water give the right time scales for the motions, the simulated motions are about 3-fold faster than the experiments. Overall, the picture that emerges is that antibodies do not simply fluctuate around a single state of atomic contacts. Rather, in these large molecules, different atoms come in contact during different motions.

Free vibration of functionally graded beams and frameworks using the dynamic stiffness method

NASA Astrophysics Data System (ADS)

Banerjee, J. R.; Ananthapuvirajah, A.

2018-05-01

The free vibration analysis of functionally graded beams (FGBs) and frameworks containing FGBs is carried out by applying the dynamic stiffness method and deriving the elements of the dynamic stiffness matrix in explicit algebraic form. The usually adopted rule that the material properties of the FGB vary continuously through the thickness according to a power law forms the fundamental basis of the governing differential equations of motion in free vibration. The differential equations are solved in closed analytical form when the free vibratory motion is harmonic. The dynamic stiffness matrix is then formulated by relating the amplitudes of forces to those of the displacements at the two ends of the beam. Next, the explicit algebraic expressions for the dynamic stiffness elements are derived with the help of symbolic computation. Finally the Wittrick-Williams algorithm is applied as solution technique to solve the free vibration problems of FGBs with uniform cross-section, stepped FGBs and frameworks consisting of FGBs. Some numerical results are validated against published results, but in the absence of published results for frameworks containing FGBs, consistency checks on the reliability of results are performed. The paper closes with discussion of results and conclusions.

Simulation of rapid ecological change in Lake Ontario

USGS Publications Warehouse

McKenna, James E.; Chalupnicki, Marc; Dittman, Dawn E.; Watkins, James M.

2017-01-01

Lower trophic level processes are integral to proper functioning of large aquatic ecosystems and have been disturbed in Lake Ontario by various stressors including exotic species. The invasion of benthic habitats by dreissenid mussels has led to systemic changes and native faunal declines. Size-dependent physiological rates, spatial differences and connectivity, competition, and differential population dynamics among invertebrate groups contributed to the change and system complexity. We developed a spatially explicit, individual-based mechanistic model of the benthic ecosystem in Lake Ontario, with coupling to the pelagic system, to examine ecosystem dynamics and effects of dreissenid mussel invasion and native fauna losses. Benthic organisms were represented by functional groups; filter-feeders (i.e., dreissenid mussels), surface deposit-feeders (e.g., native amphipod Diporeia spp.), and deposit-feeders (e.g., oligochaetes and other burrowers). The model was stable, represented ecological structure and function effectively, and reproduced observed effects of the mussel invasion. Two hypotheses for causes of Diporeia loss, competition or disease-like mortality, were tested. Simple competition for food did not explain observed declines in native surface deposit-feeders during the filter-feeder invasion. However, the elevated mortality scenario supports a disease-like cause for loss of the native amphipod, with population changes in various lake areas and altered benthic biomass transfers. Stabilization of mussel populations and possible recovery of the native, surface-deposit feeding amphipod were predicted. Although further research is required on forcing functions, model parameters, and natural conditions, the model provides a valuable tool to help managers understand the benthic system and plan for response to future disruptions.

The Role of Climatic and Density Dependent Factors in Shaping Mosquito Population Dynamics: The Case of Culex pipiens in Northwestern Italy

PubMed Central

Giacobini, Mario; Pugliese, Andrea; Merler, Stefano; Rosà, Roberto

2016-01-01

Culex pipiens mosquito is a species widely spread across Europe and represents a competent vector for many arboviruses such as West Nile virus (WNV), which has been recently circulating in many European countries, causing hundreds of human cases. In order to identify the main determinants of the high heterogeneity in Cx. pipiens abundance observed in Piedmont region (Northwestern Italy) among different seasons, we developed a density-dependent stochastic model that takes explicitly into account the role played by temperature, which affects both developmental and mortality rates of different life stages. The model was calibrated with a Markov chain Monte Carlo approach exploring the likelihood of recorded capture data gathered in the study area from 2000 to 2011; in this way, we disentangled the role played by different seasonal eco-climatic factors in shaping the vector abundance. Illustrative simulations have been performed to forecast likely changes if temperature or density–dependent inputs would change. Our analysis suggests that inter-seasonal differences in the mosquito dynamics are largely driven by different temporal patterns of temperature and seasonal-specific larval carrying capacities. Specifically, high temperatures during early spring hasten the onset of the breeding season and increase population abundance in that period, while, high temperatures during the summer can decrease population size by increasing adult mortality. Higher densities of adult mosquitoes are associated with higher larval carrying capacities, which are positively correlated with spring precipitations. Finally, an increase in larval carrying capacity is expected to proportionally increase adult mosquito abundance. PMID:27105065

A virtual-system coupled multicanonical molecular dynamics simulation: Principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent

NASA Astrophysics Data System (ADS)

Higo, Junichi; Umezawa, Koji; Nakamura, Haruki

2013-05-01

We propose a novel generalized ensemble method, a virtual-system coupled multicanonical molecular dynamics (V-McMD), to enhance conformational sampling of biomolecules expressed by an all-atom model in an explicit solvent. In this method, a virtual system, of which physical quantities can be set arbitrarily, is coupled with the biomolecular system, which is the target to be studied. This method was applied to a system of an Endothelin-1 derivative, KR-CSH-ET1, known to form an antisymmetric homodimer at room temperature. V-McMD was performed starting from a configuration in which two KR-CSH-ET1 molecules were mutually distant in an explicit solvent. The lowest free-energy state (the most thermally stable state) at room temperature coincides with the experimentally determined native complex structure. This state was separated to other non-native minor clusters by a free-energy barrier, although the barrier disappeared with elevated temperature. V-McMD produced a canonical ensemble faster than a conventional McMD method.

Interface Metaphors for Interactive Machine Learning

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

Jasper, Robert J.; Blaha, Leslie M.

To promote more interactive and dynamic machine learn- ing, we revisit the notion of user-interface metaphors. User-interface metaphors provide intuitive constructs for supporting user needs through interface design elements. A user-interface metaphor provides a visual or action pattern that leverages a user’s knowledge of another domain. Metaphors suggest both the visual representations that should be used in a display as well as the interactions that should be afforded to the user. We argue that user-interface metaphors can also offer a method of extracting interaction-based user feedback for use in machine learning. Metaphors offer indirect, context-based information that can be usedmore » in addition to explicit user inputs, such as user-provided labels. Implicit information from user interactions with metaphors can augment explicit user input for active learning paradigms. Or it might be leveraged in systems where explicit user inputs are more challenging to obtain. Each interaction with the metaphor provides an opportunity to gather data and learn. We argue this approach is especially important in streaming applications, where we desire machine learning systems that can adapt to dynamic, changing data.« less

Interactions between Nanoparticles and Polymer Brushes: Molecular Dynamics Simulations and Self-consistent Field Theory Calculations

NASA Astrophysics Data System (ADS)

Cheng, Shengfeng; Wen, Chengyuan; Egorov, Sergei

2015-03-01

Molecular dynamics simulations and self-consistent field theory calculations are employed to study the interactions between a nanoparticle and a polymer brush at various densities of chains grafted to a plane. Simulations with both implicit and explicit solvent are performed. In either case the nanoparticle is loaded to the brush at a constant velocity. Then a series of simulations are performed to compute the force exerted on the nanoparticle that is fixed at various distances from the grafting plane. The potential of mean force is calculated and compared to the prediction based on a self-consistent field theory. Our simulations show that the explicit solvent leads to effects that are not captured in simulations with implicit solvent, indicating the importance of including explicit solvent in molecular simulations of such systems. Our results also demonstrate an interesting correlation between the force on the nanoparticle and the density profile of the brush. We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Tesla K40 GPU used for this research.

Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.

PubMed

Bureau, Hailey R; Merz, Dale R; Hershkovits, Eli; Quirk, Stephen; Hernandez, Rigoberto

2015-01-01

Steered Molecular Dynamics (SMD) has been seen to provide the potential of mean force (PMF) along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD) has been seen to provide a significant computational advantage by limiting the spread of the trajectories in a staged approach. The contraction of the trajectories at the end of each stage can be performed by taking a structure whose nonequilibrium work is closest to the Jarzynski average (in naive ASMD) or by relaxing the trajectories under a no-work condition (in full-relaxation ASMD--namely, FR-ASMD). Both approaches have been used to determine the energetics and hydrogen-bonding structure along the pathway for unfolding of a benchmark peptide initially constrained as an α-helix in a water environment. The energetics are quite different to those in vacuum, but are found to be similar between implicit and explicit solvents. Surprisingly, the hydrogen-bonding pathways are also similar in the implicit and explicit solvents despite the fact that the solvent contact plays an important role in opening the helix.

Potential impacts of climate change on the ecology of dengue and its mosquito vector the Asian tiger mosquito (Aedes albopictus)

NASA Astrophysics Data System (ADS)

Erickson, R. A.; Hayhoe, K.; Presley, S. M.; Allen, L. J. S.; Long, K. R.; Cox, S. B.

2012-09-01

Shifts in temperature and precipitation patterns caused by global climate change may have profound impacts on the ecology of certain infectious diseases. We examine the potential impacts of climate change on the transmission and maintenance dynamics of dengue, a resurging mosquito-vectored infectious disease. In particular, we project changes in dengue season length for three cities: Atlanta, GA; Chicago, IL and Lubbock, TX. These cities are located on the edges of the range of the Asian tiger mosquito within the United States of America and were chosen as test cases. We use a disease model that explicitly incorporates mosquito population dynamics and high-resolution climate projections. Based on projected changes under the Special Report on Emissions Scenarios (SRES) A1fi (higher) and B1 (lower) emission scenarios as simulated by four global climate models, we found that the projected warming shortened mosquito lifespan, which in turn decreased the potential dengue season. These results illustrate the difficulty in predicting how climate change may alter complex systems.

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences.

PubMed

Best, Robert B; Mittal, Jeetain

2011-04-01

Although it is now possible to fold peptides and miniproteins in molecular dynamics simulations, it is well appreciated that force fields are not all transferable to different proteins. Here, we investigate the influence of the protein force field and the solvent model on the folding energy landscape of a prototypical two-state folder, the GB1 hairpin. We use extensive replica-exchange molecular dynamics simulations to characterize the free-energy surface as a function of temperature. Most of these force fields appear similar at a global level, giving a fraction folded at 300 K between 0.2 and 0.8 in all cases, which is a difference in stability of 2.8 kT, and are generally consistent with experimental data at this temperature. The most significant differences appear in the unfolded state, where there are different residual secondary structures which are populated, and the overall dimensions of the unfolded states, which in most of the force fields are too collapsed relative to experimental Förster Resonance Energy Transfer (FRET) data.

The evolutionary language game: an orthogonal approach.

PubMed

Lenaerts, Tom; Jansen, Bart; Tuyls, Karl; De Vylder, Bart

2005-08-21

Evolutionary game dynamics have been proposed as a mathematical framework for the cultural evolution of language and more specifically the evolution of vocabulary. This article discusses a model that is mutually exclusive in its underlying principals with some previously suggested models. The model describes how individuals in a population culturally acquire a vocabulary by actively participating in the acquisition process instead of passively observing and communicate through peer-to-peer interactions instead of vertical parent-offspring relations. Concretely, a notion of social/cultural learning called the naming game is first abstracted using learning theory. This abstraction defines the required cultural transmission mechanism for an evolutionary process. Second, the derived transmission system is expressed in terms of the well-known selection-mutation model defined in the context of evolutionary dynamics. In this way, the analogy between social learning and evolution at the level of meaning-word associations is made explicit. Although only horizontal and oblique transmission structures will be considered, extensions to vertical structures over different genetic generations can easily be incorporated. We provide a number of simplified experiments to clarify our reasoning.

Finite BRST-BFV transformations for dynamical systems with second-class constraints

NASA Astrophysics Data System (ADS)

Batalin, Igor A.; Lavrov, Peter M.; Tyutin, Igor V.

2015-06-01

We study finite field-dependent BRST-BFV transformations for dynamical systems with first- and second-class constraints within the generalized Hamiltonian formalism. We find explicitly their Jacobians and the form of a solution to the compensation equation necessary for generating an arbitrary finite change of gauge-fixing functionals in the path integral.

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...

Parallel computational fluid dynamics '91; Conference Proceedings, Stuttgart, Germany, Jun. 10-12, 1991

NASA Technical Reports Server (NTRS)

Reinsch, K. G. (Editor); Schmidt, W. (Editor); Ecer, A. (Editor); Haeuser, Jochem (Editor); Periaux, J. (Editor)

1992-01-01

A conference was held on parallel computational fluid dynamics and produced related papers. Topics discussed in these papers include: parallel implicit and explicit solvers for compressible flow, parallel computational techniques for Euler and Navier-Stokes equations, grid generation techniques for parallel computers, and aerodynamic simulation om massively parallel systems.

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

PubMed

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-07-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Past and future perspectives on mathematical models of tick-borne pathogens.

PubMed

Norman, R A; Worton, A J; Gilbert, L

2016-06-01

Ticks are vectors of pathogens which are important both with respect to human health and economically. They have a complex life cycle requiring several blood meals throughout their life. These blood meals take place on different individual hosts and potentially on different host species. Their life cycle is also dependent on environmental conditions such as the temperature and habitat type. Mathematical models have been used for the more than 30 years to help us understand how tick dynamics are dependent on these environmental factors and host availability. In this paper, we review models of tick dynamics and summarize the main results. This summary is split into two parts, one which looks at tick dynamics and one which looks at tick-borne pathogens. In general, the models of tick dynamics are used to determine when the peak in tick densities is likely to occur in the year and how that changes with environmental conditions. The models of tick-borne pathogens focus more on the conditions under which the pathogen can persist and how host population densities might be manipulated to control these pathogens. In the final section of the paper, we identify gaps in the current knowledge and future modelling approaches. These include spatial models linked to environmental information and Geographic Information System maps, and development of new modelling techniques which model tick densities per host more explicitly.

[The health system of Chile].

PubMed

Becerril-Montekio, Víctor; Reyes, Juan de Dios; Manuel, Annick

2011-01-01

This paper describes the Chilean health system, including its structure, financing, beneficiaries, and its physical, material and human resources. This system has two sectors, public and private. The public sector comprises all the organisms that constitute the National System of Health Services, which covers 70% of the population, including the rural and urban poor, the low middle-class, the retired, and the self-employed professionals and technicians.The private sector covers 17.5% of the population, mostly the upper middle-class and the high-income population. A small proportion of the population uses private health services and pays for them out-of-pocket. Around l0% of the population is covered by other public agencies, basically the Health Services for the Armed Forces. The system was recently reformed with the establishment of a Universal System of Explicit Entitlements, which operates through a Universal Plan of Explicit Entitlements (AUGE), which guarantees timely access to treatment for 56 health problems, including cancer in children, breast cancer, ischaemic heart disease, HIV/AIDS and diabetes.

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

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.

Algorithms for the explicit computation of Penrose diagrams

NASA Astrophysics Data System (ADS)

Schindler, J. C.; Aguirre, A.

2018-05-01

An algorithm is given for explicitly computing Penrose diagrams for spacetimes of the form . The resulting diagram coordinates are shown to extend the metric continuously and nondegenerately across an arbitrary number of horizons. The method is extended to include piecewise approximations to dynamically evolving spacetimes using a standard hypersurface junction procedure. Examples generated by an implementation of the algorithm are shown for standard and new cases. In the appendix, this algorithm is compared to existing methods.

The Value of Learning about Natural History in Biodiversity Markets

PubMed Central

Bruggeman, Douglas J.

2015-01-01

Markets for biodiversity have generated much controversy because of the often unstated and untested assumptions included in transactions rules. Simple trading rules are favored to reduce transaction costs, but others have argued that this leads to markets that favor development and erode biodiversity. Here, I describe how embracing complexity and uncertainty within a tradable credit system for the Red-cockaded Woodpecker (Picoides borealis) creates opportunities to achieve financial and conservation goals simultaneously. Reversing the effects of habitat fragmentation is one of the main reasons for developing markets. I include uncertainty in habitat fragmentation effects by evaluating market transactions using five alternative dispersal models that were able to approximate observed patterns of occupancy and movement. Further, because dispersal habitat is often not included in market transactions, I contrast how changes in breeding versus dispersal habitat affect credit values. I use an individually-based, spatially-explicit population model for the Red-cockaded Woodpecker (Picoides borealis) to predict spatial- and temporal- influences of landscape change on species occurrence and genetic diversity. Results indicated that the probability of no net loss of abundance and genetic diversity responded differently to the transient dynamics in breeding and dispersal habitat. Trades that do not violate the abundance cap may simultaneously violate the cap for the erosion of genetic diversity. To highlight how economic incentives may help reduce uncertainty, I demonstrate tradeoffs between the value of tradable credits and the value of information needed to predict the influence of habitat trades on population viability. For the trade with the greatest uncertainty regarding the change in habitat fragmentation, I estimate that the value of using 13-years of data to reduce uncertainty in dispersal behaviors is $6.2 million. Future guidance for biodiversity markets should at least encourage the use of spatially- and temporally-explicit techniques that include population genetic estimates and the influence of uncertainty. PMID:26675488

The Value of Learning about Natural History in Biodiversity Markets.

PubMed

Bruggeman, Douglas J

2015-01-01

Markets for biodiversity have generated much controversy because of the often unstated and untested assumptions included in transactions rules. Simple trading rules are favored to reduce transaction costs, but others have argued that this leads to markets that favor development and erode biodiversity. Here, I describe how embracing complexity and uncertainty within a tradable credit system for the Red-cockaded Woodpecker (Picoides borealis) creates opportunities to achieve financial and conservation goals simultaneously. Reversing the effects of habitat fragmentation is one of the main reasons for developing markets. I include uncertainty in habitat fragmentation effects by evaluating market transactions using five alternative dispersal models that were able to approximate observed patterns of occupancy and movement. Further, because dispersal habitat is often not included in market transactions, I contrast how changes in breeding versus dispersal habitat affect credit values. I use an individually-based, spatially-explicit population model for the Red-cockaded Woodpecker (Picoides borealis) to predict spatial- and temporal- influences of landscape change on species occurrence and genetic diversity. Results indicated that the probability of no net loss of abundance and genetic diversity responded differently to the transient dynamics in breeding and dispersal habitat. Trades that do not violate the abundance cap may simultaneously violate the cap for the erosion of genetic diversity. To highlight how economic incentives may help reduce uncertainty, I demonstrate tradeoffs between the value of tradable credits and the value of information needed to predict the influence of habitat trades on population viability. For the trade with the greatest uncertainty regarding the change in habitat fragmentation, I estimate that the value of using 13-years of data to reduce uncertainty in dispersal behaviors is $6.2 million. Future guidance for biodiversity markets should at least encourage the use of spatially- and temporally-explicit techniques that include population genetic estimates and the influence of uncertainty.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory

NASA Astrophysics Data System (ADS)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-01

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory.

PubMed

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-13

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

EXTINCTION DEBT OF PROTECTED AREAS IN DEVELOPING LANDSCAPES

EPA Science Inventory

To conserve biological diversity, protected-area networks must be based not only upon current species distributions but also the landscape's long-term capacity to support populations. We used spatially-explicit population models requiring detailed habitat and demographic data to ...

Applying the Explicit Time Central Difference Method for Numerical Simulation of the Dynamic Behavior of Elastoplastic Flexible Reinforced Plates

NASA Astrophysics Data System (ADS)

Yankovskii, A. P.

2017-12-01

Based on a stepwise algorithm involving central finite differences for the approximation in time, a mathematical model is developed for elastoplastic deformation of cross-reinforced plates with isotropically hardening materials of components of the composition. The model allows obtaining the solution of elastoplastic problems at discrete points in time by an explicit scheme. The initial boundary value problem of the dynamic behavior of flexible plates reinforced in their own plane is formulated in the von Kármán approximation with allowance for their weakened resistance to the transverse shear. With a common approach, the resolving equations corresponding to two variants of the Timoshenko theory are obtained. An explicit "cross" scheme for numerical integration of the posed initial boundary value problem has been constructed. The scheme is consistent with the incremental algorithm used for simulating the elastoplastic behavior of a reinforced medium. Calculations of the dynamic behavior have been performed for elastoplastic cylindrical bending of differently reinforced fiberglass rectangular elongated plates. It is shown that the reinforcement structure significantly affects their elastoplastic dynamic behavior. It has been found that the classical theory of plates is as a rule unacceptable for carrying out the required calculations (except for very thin plates), and the first version of the Timoshenko theory yields reasonable results only in cases of relatively thin constructions reinforced by lowmodulus fibers. Proceeding from the results of the work, it is recommended to use the second variant of the Timoshenko theory (as a more accurate one) for calculations of the elastoplastic behavior of reinforced plates.

A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection.

PubMed

Song, Yun S; Steinrücken, Matthias

2012-03-01

The transition density function of the Wright-Fisher diffusion describes the evolution of population-wide allele frequencies over time. This function has important practical applications in population genetics, but finding an explicit formula under a general diploid selection model has remained a difficult open problem. In this article, we develop a new computational method to tackle this classic problem. Specifically, our method explicitly finds the eigenvalues and eigenfunctions of the diffusion generator associated with the Wright-Fisher diffusion with recurrent mutation and arbitrary diploid selection, thus allowing one to obtain an accurate spectral representation of the transition density function. Simplicity is one of the appealing features of our approach. Although our derivation involves somewhat advanced mathematical concepts, the resulting algorithm is quite simple and efficient, only involving standard linear algebra. Furthermore, unlike previous approaches based on perturbation, which is applicable only when the population-scaled selection coefficient is small, our method is nonperturbative and is valid for a broad range of parameter values. As a by-product of our work, we obtain the rate of convergence to the stationary distribution under mutation-selection balance.

A Simple Method for Finding Explicit Analytic Transition Densities of Diffusion Processes with General Diploid Selection

PubMed Central

Song, Yun S.; Steinrücken, Matthias

2012-01-01

The transition density function of the Wright–Fisher diffusion describes the evolution of population-wide allele frequencies over time. This function has important practical applications in population genetics, but finding an explicit formula under a general diploid selection model has remained a difficult open problem. In this article, we develop a new computational method to tackle this classic problem. Specifically, our method explicitly finds the eigenvalues and eigenfunctions of the diffusion generator associated with the Wright–Fisher diffusion with recurrent mutation and arbitrary diploid selection, thus allowing one to obtain an accurate spectral representation of the transition density function. Simplicity is one of the appealing features of our approach. Although our derivation involves somewhat advanced mathematical concepts, the resulting algorithm is quite simple and efficient, only involving standard linear algebra. Furthermore, unlike previous approaches based on perturbation, which is applicable only when the population-scaled selection coefficient is small, our method is nonperturbative and is valid for a broad range of parameter values. As a by-product of our work, we obtain the rate of convergence to the stationary distribution under mutation–selection balance. PMID:22209899

Improved global simulation of groundwater-ecosystem interactions via tight coupling of a dynamic global ecosystem model and a global hydrological model

NASA Astrophysics Data System (ADS)

Braakhekke, Maarten; Rebel, Karin; Dekker, Stefan; Smith, Benjamin; Sutanudjaja, Edwin; van Beek, Rens; van Kampenhout, Leo; Wassen, Martin

2017-04-01

In up to 30% of the global land surface ecosystems are potentially influenced by the presence of a shallow groundwater table. In these regions upward water flux by capillary rise increases soil moisture availability in the root zone, which has a strong effect on evapotranspiration, vegetation dynamics, and fluxes of carbon and nitrogen. Most global hydrological models and several land surface models simulate groundwater table dynamics and their effects on land surface processes. However, these models typically have relatively simplistic representation of vegetation and do not consider changes in vegetation type and structure. Dynamic global vegetation models (DGVMs), describe land surface from an ecological perspective, combining detailed description of vegetation dynamics and structure, and biogeochemical processes and are thus more appropriate to simulate the ecological and biogeochemical effects of groundwater interactions. However, currently virtually all DGVMs ignore these effects, assuming that water tables are too deep to affect soil moisture in the root zone. We have implemented a tight coupling between the dynamic global ecosystem model LPJ-GUESS and the global hydrological model PCR-GLOBWB, which explicitly simulates groundwater dynamics. This coupled model allows us to explicitly account for groundwater effects on terrestrial ecosystem processes at global scale. Results of global simulations indicate that groundwater strongly influences fluxes of water, carbon and nitrogen, in many regions, adding up to a considerable effect at the global scale.

Spatially-explicit estimation of Wright's neighborhood size in continuous populations

Treesearch

Andrew J. Shirk; Samuel A. Cushman

2014-01-01

Effective population size (Ne) is an important parameter in conservation genetics because it quantifies a population's capacity to resist loss of genetic diversity due to inbreeding and drift. The classical approach to estimate Ne from genetic data involves grouping sampled individuals into discretely defined subpopulations assumed to be panmictic. Importantly,...

sGD software for estimating spatially explicit indices of genetic diversity

Treesearch

A. J. Shirk; Samuel Cushman

2011-01-01

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is...

Forest Management Under Uncertainty for Multiple Bird Population Objectives

Treesearch

Clinton T. Moore; W. Todd Plummer; Michael J. Conroy

2005-01-01

We advocate adaptive programs of decision making and monitoring for the management of forest birds when responses by populations to management, and particularly management trade-offs among populations, are uncertain. Models are necessary components of adaptive management. Under this approach, uncertainty about the behavior of a managed system is explicitly captured in...

Knowledge translation within a population health study: how do you do it?

PubMed Central

2013-01-01

Background Despite the considerable and growing body of knowledge translation (KT) literature, there are few methodologies sufficiently detailed to guide an integrated KT research approach for a population health study. This paper argues for a clearly articulated collaborative KT approach to be embedded within the research design from the outset. Discussion Population health studies are complex in their own right, and strategies to engage the local community in adopting new interventions are often fraught with considerable challenges. In order to maximise the impact of population health research, more explicit KT strategies need to be developed from the outset. We present four propositions, arising from our work in developing a KT framework for a population health study. These cover the need for an explicit theory-informed conceptual framework; formalizing collaborative approaches within the design; making explicit the roles of both the stakeholders and the researchers; and clarifying what counts as evidence. From our deliberations on these propositions, our own co-creating (co-KT) Framework emerged in which KT is defined as both a theoretical and practical framework for actioning the intent of researchers and communities to co-create, refine, implement and evaluate the impact of new knowledge that is sensitive to the context (values, norms and tacit knowledge) where it is generated and used. The co-KT Framework has five steps. These include initial contact and framing the issue; refining and testing knowledge; interpreting, contextualising and adapting knowledge to the local context; implementing and evaluating; and finally, the embedding and translating of new knowledge into practice. Summary Although descriptions of how to incorporate KT into research designs are increasing, current theoretical and operational frameworks do not generally span a holistic process from knowledge co-creation to knowledge application and implementation within one project. Population health studies may have greater health impact when KT is incorporated early and explicitly into the research design. This, we argue, will require that particular attention be paid to collaborative approaches, stakeholder identification and engagement, the nature and sources of evidence used, and the role of the research team working with the local study community. PMID:23694753

Spatially explicit modeling of greater sage-grouse (Centrocercus urophasianus) habitat in Nevada and northeastern California: a decision-support tool for management

USGS Publications Warehouse

Coates, Peter S.; Casazza, Michael L.; Brussee, Brianne E.; Ricca, Mark A.; Gustafson, K. Benjamin; Overton, Cory T.; Sanchez-Chopitea, Erika; Kroger, Travis; Mauch, Kimberly; Niell, Lara; Howe, Kristy; Gardner, Scott; Espinosa, Shawn; Delehanty, David J.

2014-01-01

Greater sage-grouse (Centrocercus urophasianus, hereafter referred to as “sage-grouse”) populations are declining throughout the sagebrush (Artemisia spp.) ecosystem, including millions of acres of potential habitat across the West. Habitat maps derived from empirical data are needed given impending listing decisions that will affect both sage-grouse population dynamics and human land-use restrictions. This report presents the process for developing spatially explicit maps describing relative habitat suitability for sage-grouse in Nevada and northeastern California. Maps depicting habitat suitability indices (HSI) values were generated based on model-averaged resource selection functions informed by more than 31,000 independent telemetry locations from more than 1,500 radio-marked sage-grouse across 12 project areas in Nevada and northeastern California collected during a 15-year period (1998–2013). Modeled habitat covariates included land cover composition, water resources, habitat configuration, elevation, and topography, each at multiple spatial scales that were relevant to empirically observed sage-grouse movement patterns. We then present an example of how the HSI can be delineated into categories. Specifically, we demonstrate that the deviation from the mean can be used to classify habitat suitability into three categories of habitat quality (high, moderate, and low) and one non-habitat category. The classification resulted in an agreement of 93–97 percent for habitat versus non-habitat across a suite of independent validation datasets. Lastly, we provide an example of how space use models can be integrated with habitat models to help inform conservation planning. In this example, we combined probabilistic breeding density with a non-linear probability of occurrence relative to distance to nearest lek (traditional breeding ground) using count data to calculate a composite space use index (SUI). The SUI was then classified into two categories of use (high and low-to-no) and intersected with the HSI categories to create potential management prioritization scenarios based oninformation about sage-grouse occupancy coupled with habitat suitability. This provided an example of a conservation planning application that uses the intersection of the spatially-explicit HSI and empirically-based SUI to identify potential spatially explicit strategies for sage-grouse management. Importantly, the reported categories for the HSI and SUI can be reclassified relatively easily to employ alternative conservation thresholds that may be identified through decision-making processes with stake-holders, managers, and biologists. Moreover, the HSI/SUI interface map can be updated readily as new data become available.

MULTISCALE MODEL OF CRISPR-INDUCED COEVOLUTIONARY DYNAMICS: DIVERSIFICATION AT THE INTERFACE OF LAMARCK AND DARWIN

PubMed Central

Childs, Lauren M; Held, Nicole L; Young, Mark J; Whitaker, Rachel J; Weitz, Joshua S

2012-01-01

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes. Here, we introduce a multiscale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and the maintenance of many coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities. We observe the punctuated replacement of existent strains, such that populations have very low similarity compared over the long term. However, in the short term, we observe evolutionary dynamics consistent with both incomplete selective sweeps of novel strains (as single strains and coalitions) and the recurrence of previously rare strains. Coalitions of multiple dominant host strains are predicted to arise because host strains can have nearly identical immune phenotypes mediated by CRISPR defense albeit with different genotypes. We close by discussing how our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active. PMID:22759281

Spatially structured superinfection and the evolution of disease virulence.

PubMed

Caraco, Thomas; Glavanakov, Stephan; Li, Shengua; Maniatty, William; Szymanski, Boleslaw K

2006-06-01

When pathogen strains differing in virulence compete for hosts, spatial structuring of disease transmission can govern both evolved levels of virulence and patterns in strain coexistence. We develop a spatially detailed model of superinfection, a form of contest competition between pathogen strains; the probability of superinfection depends explicitly on the difference in levels of virulence. We apply methods of adaptive dynamics to address the interplay of spatial dynamics and evolution. The mean-field approximation predicts evolution to criticality; any small increase in virulence capable of dynamical persistence is favored. Both pair approximation and simulation of the detailed model indicate that spatial structure constrains disease virulence. Increased spatial clustering reduces the maximal virulence capable of single-strain persistence and, more importantly, reduces the convergent-stable virulence level under strain competition. The spatially detailed model predicts that increasing the probability of superinfection, for given difference in virulence, increases the likelihood of between-strain coexistence. When strains differing in virulence can coexist ecologically, our results may suggest policies for managing diseases with localized transmission. Comparing equilibrium densities from the pair approximation, we find that introducing a more virulent strain into a host population infected by a less virulent strain can sometimes reduce total host mortality and increase global host density.

A genetic approach to the rock-paper-scissors game.

PubMed

Barreto, Wendell P; Marquitti, Flavia M D; de Aguiar, Marcus A M

2017-05-21

Polymorphisms are usually associated with defenses and mating strategies, affecting the individual's fitness. Coexistence of different morphs is, therefore, not expected, since the fittest morph should outcompete the others. Nevertheless, coexistence is observed in many natural systems. For instance, males of the side-blotched lizards (Uta stansburiana) present three morphs with throat colors orange, yellow and blue, which are associated with mating strategies and territorial behavior. The three male morphs compete for females in a system that is well described by the rock-paper-scissors dynamics of game theory. Previous studies have modeled the lizards as hermaphroditic populations whose individual's behavior were determined only by their phenotypes. Here we consider an extension of this dynamical system where diploidy and sexual reproduction are explicitly taken into account. Similarly to the lizards we represent the genetic system by a single locus with three alleles, o, y, and b in a diploid chromosome with dominance of o over y and of y over b. We show that this genotypic description of the dynamics results in the same equilibrium phenotype frequencies as the phenotypic models, but affects the stability of the system, changing the parameter region where coexistence of the three morphs is possible in a rock-paper-scissors game. Copyright © 2017 Elsevier Ltd. All rights reserved.

A multi-event capture-recapture analysis of Toxoplasma gondii seroconversion dynamics in farm cats.

PubMed

Simon, Julie Alice; Pradel, Roger; Aubert, Dominique; Geers, Régine; Villena, Isabelle; Poulle, Marie-Lazarine

2018-06-08

Domestic cats play a key role in the epidemiology of the parasite Toxoplasma gondii by excreting environmentally-resistant oocysts that may infect humans and other warm-blooded animals. The dynamics of Toxoplasma gondii seroconversion, used as a proxy for primo-infection dynamics, was investigated in five cat populations living on farms. Serological tests on blood samples from cats were performed every three months over a period of two years, for a total of 400 serological tests performed on 130 cats. Variations in seroconversion rates and associated factors were investigated using a multi-event capture-recapture modelling approach that explicitly accounted for uncertainties in cat age and serological status. Seroprevalence varied between farms, from 15 to 73%, suggesting differential exposure of cats to T. gondii. In farms with high exposure, cats could become infected before reaching the age of six months. Seroconversion rates varied from 0.42 to 0.96 seroconversions per cat per year and were higher in autumn and winter than in spring and summer. Our results suggest inter-farm and seasonal variations in the risks of exposure to T. gondii oocysts for humans and livestock living on farms. The paper also discusses the role of young cats in the maintenance of environmental contamination by T. gondii oocysts on farms.

Simulations of Long-Term Community Dynamics in Coral Reefs - How Perturbations Shape Trajectories

PubMed Central

Kubicek, Andreas; Muhando, Christopher; Reuter, Hauke

2012-01-01

Tropical coral reefs feature extraordinary biodiversity and high productivity rates in oligotrophic waters. Due to increasing frequencies of perturbations – anthropogenic and natural – many reefs are under threat. Such perturbations often have devastating effects on these unique ecosystems and especially if they occur simultaneously and amplify each other's impact, they might trigger a phase shift and create irreversible conditions. We developed a generic, spatially explicit, individual-based model in which competition drives the dynamics of a virtual benthic reef community – comprised of scleractinian corals and algae – under different environmental settings. Higher system properties, like population dynamics or community composition arise through self-organization as emergent properties. The model was parameterized for a typical coral reef site at Zanzibar, Tanzania and features coral bleaching and physical disturbance regimes as major sources of perturbations. Our results show that various types and modes (intensities and frequencies) of perturbations create diverse outcomes and that the switch from high diversity to single species dominance can be evoked by small changes in a key parameter. Here we extend the understanding of coral reef resilience and the identification of key processes, drivers and respective thresholds, responsible for changes in local situations. One future goal is to provide a tool which may aid decision making processes in management of coral reefs. PMID:23209397

Rethinking the dispersal of Homo sapiens out of Africa.

PubMed

Groucutt, Huw S; Petraglia, Michael D; Bailey, Geoff; Scerri, Eleanor M L; Parton, Ash; Clark-Balzan, Laine; Jennings, Richard P; Lewis, Laura; Blinkhorn, James; Drake, Nick A; Breeze, Paul S; Inglis, Robyn H; Devès, Maud H; Meredith-Williams, Matthew; Boivin, Nicole; Thomas, Mark G; Scally, Aylwyn

2015-01-01

Current fossil, genetic, and archeological data indicate that Homo sapiens originated in Africa in the late Middle Pleistocene. By the end of the Late Pleistocene, our species was distributed across every continent except Antarctica, setting the foundations for the subsequent demographic and cultural changes of the Holocene. The intervening processes remain intensely debated and a key theme in hominin evolutionary studies. We review archeological, fossil, environmental, and genetic data to evaluate the current state of knowledge on the dispersal of Homo sapiens out of Africa. The emerging picture of the dispersal process suggests dynamic behavioral variability, complex interactions between populations, and an intricate genetic and cultural legacy. This evolutionary and historical complexity challenges simple narratives and suggests that hybrid models and the testing of explicit hypotheses are required to understand the expansion of Homo sapiens into Eurasia. © 2015 Wiley Periodicals, Inc.

Modeling Wood Encroachment in Abandoned Grasslands in the Eifel National Park – Model Description and Testing

PubMed Central

Hudjetz, Silvana; Lennartz, Gottfried; Krämer, Klara; Roß-Nickoll, Martina; Gergs, André; Preuss, Thomas G.

2014-01-01

The degradation of natural and semi-natural landscapes has become a matter of global concern. In Germany, semi-natural grasslands belong to the most species-rich habitat types but have suffered heavily from changes in land use. After abandonment, the course of succession at a specific site is often difficult to predict because many processes interact. In order to support decision making when managing semi-natural grasslands in the Eifel National Park, we built the WoodS-Model (Woodland Succession Model). A multimodeling approach was used to integrate vegetation dynamics in both the herbaceous and shrub/tree layer. The cover of grasses and herbs was simulated in a compartment model, whereas bushes and trees were modelled in an individual-based manner. Both models worked and interacted in a spatially explicit, raster-based landscape. We present here the model description, parameterization and testing. We show highly detailed projections of the succession of a semi-natural grassland including the influence of initial vegetation composition, neighborhood interactions and ungulate browsing. We carefully weighted the single processes against each other and their relevance for landscape development under different scenarios, while explicitly considering specific site conditions. Model evaluation revealed that the model is able to emulate successional patterns as observed in the field as well as plausible results for different population densities of red deer. Important neighborhood interactions such as seed dispersal, the protection of seedlings from browsing ungulates by thorny bushes, and the inhibition of wood encroachment by the herbaceous layer, have been successfully reproduced. Therefore, not only a detailed model but also detailed initialization turned out to be important for spatially explicit projections of a given site. The advantage of the WoodS-Model is that it integrates these many mutually interacting processes of succession. PMID:25494057

Fluctuations in food supply drive recruitment variation in a marine fish.

PubMed

Okamoto, Daniel K; Schmitt, Russell J; Holbrook, Sally J; Reed, Daniel C

2012-11-22

Reproductive rates and survival of young in animal populations figure centrally in generating management and conservation strategies. Model systems suggest that food supply can drive these often highly variable properties, yet for many wild species, quantifying such effects and assessing their implications have been challenging. We used spatially explicit time series of a well-studied marine reef fish (black surfperch Embiotoca jacksoni) and its known prey resources to evaluate the extent to which fluctuations in food supply influenced production of young by adults and survival of young to subadulthood. Our analyses reveal: (i) variable food available to both adults and to their offspring directly produced an order of magnitude variation in the number of young-of-year (YOY) produced per adult and (ii) food available to YOY produced a similar magnitude of variation in their subsequent survival. We also show that such large natural variation in vital rates can significantly alter decision thresholds (biological reference points) important for precautionary management. These findings reveal how knowledge of food resources can improve understanding of population dynamics and reduce risk of overharvest by more accurately identifying periods of low recruitment.

The effect of loss of immunity on noise-induced sustained oscillations in epidemics.

PubMed

Chaffee, J; Kuske, R

2011-11-01

The effect of loss of immunity on sustained population oscillations about an endemic equilibrium is studied via a multiple scales analysis of a SIRS model. The analysis captures the key elements supporting the nearly regular oscillations of the infected and susceptible populations, namely, the interaction of the deterministic and stochastic dynamics together with the separation of time scales of the damping and the period of these oscillations. The derivation of a nonlinear stochastic amplitude equation describing the envelope of the oscillations yields two criteria providing explicit parameter ranges where they can be observed. These conditions are similar to those found for other applications in the context of coherence resonance, in which noise drives nearly regular oscillations in a system that is quiescent without noise. In this context the criteria indicate how loss of immunity and other factors can lead to a significant increase in the parameter range for prevalence of the sustained oscillations, without any external driving forces. Comparison of the power spectral densities of the full model and the approximation confirms that the multiple scales analysis captures nonlinear features of the oscillations.

Constant-pH Molecular Dynamics Study of Kyotorphin in an Explicit Bilayer

PubMed Central

Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.

2015-01-01

To our knowledge, we present the first constant-pH molecular dynamics study of the neuropeptide kyotorphin in the presence of an explicit lipid bilayer. The overall conformation freedom of the peptide was found to be affected by the interaction with the membrane, in accordance with previous results using different methodologies. Analysis of the interactions between the N-terminus amine group of the peptide and several lipid atoms shows that the membrane is able to stabilize both ionized and neutral forms of kyotorphin, resulting in a pKa value that is similar to the one obtained in water. This illustrates how a detailed molecular model of the membrane leads to rather different results than would be expected from simply regarding it as a low-dielectric slab. PMID:25954885

On the effect of the degeneracy among dark energy parameters

NASA Astrophysics Data System (ADS)

Gong, Yungui; Gao, Qing

2014-01-01

The dynamics of scalar fields as dark energy is well approximated by some general relations between the equation of state parameter and the fractional energy density . Based on the approximation, for slowly rolling scalar fields, we derived the analytical expressions of which reduce to the popular Chevallier-Polarski-Linder parametrization with an explicit degeneracy relation between and . The models approximate the dynamics of scalar fields well and help eliminate the degeneracies among , , and . With the explicit degeneracy relations, we test their effects on the constraints of the cosmological parameters. We find that: (1) The analytical relations between and for the two models are consistent with observational data. (2) The degeneracies have little effect on . (3) The error of was reduced about 30 % with the degeneracy relations.

The Importance of Explicitly Representing Soil Carbon with Depth over the Permafrost Region in Earth System Models: Implications for Atmospheric Carbon Dynamics at Multiple Temporal Scales between 1960 and 2300.

NASA Astrophysics Data System (ADS)

McGuire, A. D.

2014-12-01

We conducted an assessment of changes in permafrost area and carbon storage simulated by process-based models between 1960 and 2300. The models participating in this comparison were those that had joined the model integration team of the Vulnerability of Permafrost Carbon Research Coordination Network (see http://www.biology.ufl.edu/permafrostcarbon/). Each of the models in this comparison conducted simulations over the permafrost land region in the Northern Hemisphere driven by CCSM4-simulated climate for RCP 4.5 and 8.5 scenarios. Among the models, the area of permafrost (defined as the area for which active layer thickness was less than 3 m) ranged between 13.2 and 20.0 million km2. Between 1960 and 2300, models indicated the loss of permafrost area between 5.1 to 6.0 million km2 for RCP 4.5 and between 7.1 and 15.2 million km2 for RCP 8.5. Among the models, the density of soil carbon storage in 1960 ranged between 13 and 42 thousand g C m-2; models that explicitly represented carbon with depth had estimates greater than 27 thousand g C m-2. For the RCP 4.5 scenario, changes in soil carbon between 1960 and 2300 ranged between losses of 32 Pg C to gains of 58 Pg C, in which models that explicitly represent soil carbon with depth simulated losses or lower gains of soil carbon in comparison with those that did not. For the RCP 8.5 scenario, changes in soil carbon between 1960 and 2300 ranged between losses of 642 Pg C to gains of 66 Pg C, in which those models that represent soil carbon explicitly with depth all simulated losses, while those that do not all simulated gains. These results indicate that there are substantial differences in responses of carbon dynamics between model that do and do not explicitly represent soil carbon with depth in the permafrost region. We present analyses of the implications of the differences for atmospheric carbon dynamics at multiple temporal scales between 1960 and 2300.

Sampling the multiple folding mechanisms of Trp-cage in explicit solvent

PubMed Central

Juraszek, J.; Bolhuis, P. G.

2006-01-01

We investigate the kinetic pathways of folding and unfolding of the designed miniprotein Trp- cage in explicit solvent. Straightforward molecular dynamics and replica exchange methods both have severe convergence problems, whereas transition path sampling allows us to sample unbiased dynamical pathways between folded and unfolded states and leads to deeper understanding of the mechanisms of (un)folding. In contrast to previous predictions employing an implicit solvent, we find that Trp-cage folds primarily (80% of the paths) via a pathway forming the tertiary contacts and the salt bridge, before helix formation. The remaining 20% of the paths occur in the opposite order, by first forming the helix. The transition states of the rate-limiting steps are solvated native-like structures. Water expulsion is found to be the last step upon folding for each route. Committor analysis suggests that the dynamics of the solvent is not part of the reaction coordinate. Nevertheless, during the transition, specific water molecules are strongly bound and can play a structural role in the folding. PMID:17035504

Equilibrium distribution of heavy quarks in fokker-planck dynamics

PubMed

Walton; Rafelski

2000-01-03

We obtain an explicit generalization, within Fokker-Planck dynamics, of Einstein's relation between drag, diffusion, and the equilibrium distribution for a spatially homogeneous system, considering both the transverse and longitudinal diffusion for dimension n>1. We provide a complete characterization of the equilibrium distribution in terms of the drag and diffusion transport coefficients. We apply this analysis to charm quark dynamics in a thermal quark-gluon plasma for the case of collisional equilibration.

(Re)politicising and (re)positioning prevention: community mobilisations and AIDS prevention in the new AIDS era.

PubMed

Rolston, Imara Ajani

2016-07-01

An increasing focus on the relationship between AIDS prevalence and socio-economic inequality signals the need for a revaluation of the role of "politics" and "power" in AIDS prevention. This revaluation bears great significance when considering the future trajectories of the AIDS prevention efforts that target highly marginalised populations with high prevalence rates. An emphasis on intersecting forms of inequality has direct implications for the future of AIDS prevention practice. This study explores the experiences of participants, facilitators and local stakeholders applying the United Nations Development Programme (UNDP) Community Capacity Enhancement-Community Conversations (CCE-CC) approach to AIDS prevention in the Eastern Cape province of South Africa. It uses the political narrative analysis of life histories and semi-structured interviews as a means to interrogate the lived experiences of local actors participating in or influenced by this popularised form of community mobilisation used throughout sub-Saharan Africa. Findings suggest the need for a more explicit and intentional valuation for the intersection between the social and political determinants of health in programmes that use community mobilisation as prevention. They also signal a need to critically re-evaluate "community mobilisation" as an AIDS prevention tradition. Intersecting social and political power dynamics play a significant role in both opening up and constraining community mobilisation efforts. This paper proposes the need for a pedagogical turn to "deep organising" and "participatory forms of democracy", as a necessary frontier for programmes working with highly marginalised populations with high prevalence rates. Programmes need to more explicitly support, protect, and advocate for the ability of affected communities to engage in political processes, discourse and long-term organising.

Phenology and trend indicators derived from spatially dynamic bi-weekly satellite imagery to support ecosystem monitoring

Treesearch

Barron J. Orr; Grant M. Casady; Daniel G. Tuttle; Willem J. D. van Leeuwen; Laura E. Baker; Colleen I. McDonald; Stuart E. Marsh

2005-01-01

Ground-based ecosystem monitoring presents some practical challenges to natural resource managers and ecologists tasked with assessing vegetation dynamics across large areas through time. RangeView (http://rangeview.arizona.edu) provides online access to spatially and temporally explicit biweekly vegetation indices derived from satellite data. It also permits side-by-...

Deconstructing the core dynamics from a complex time-lagged regulatory biological circuit.

PubMed

Eriksson, O; Brinne, B; Zhou, Y; Björkegren, J; Tegnér, J

2009-03-01

Complex regulatory dynamics is ubiquitous in molecular networks composed of genes and proteins. Recent progress in computational biology and its application to molecular data generate a growing number of complex networks. Yet, it has been difficult to understand the governing principles of these networks beyond graphical analysis or extensive numerical simulations. Here the authors exploit several simplifying biological circumstances which thereby enable to directly detect the underlying dynamical regularities driving periodic oscillations in a dynamical nonlinear computational model of a protein-protein network. System analysis is performed using the cell cycle, a mathematically well-described complex regulatory circuit driven by external signals. By introducing an explicit time delay and using a 'tearing-and-zooming' approach the authors reduce the system to a piecewise linear system with two variables that capture the dynamics of this complex network. A key step in the analysis is the identification of functional subsystems by identifying the relations between state-variables within the model. These functional subsystems are referred to as dynamical modules operating as sensitive switches in the original complex model. By using reduced mathematical representations of the subsystems the authors derive explicit conditions on how the cell cycle dynamics depends on system parameters, and can, for the first time, analyse and prove global conditions for system stability. The approach which includes utilising biological simplifying conditions, identification of dynamical modules and mathematical reduction of the model complexity may be applicable to other well-characterised biological regulatory circuits. [Includes supplementary material].

New Approaches to Final Cooling

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

Neuffer, David

2014-11-10

A high-energy muon collider scenario require a “final cooling” system that reduces transverse emittances by a factor of ~10 while allowing longitudinal emittance increase. The baseline approach has low-energy transverse cooling within high-field solenoids, with strong longitudinal heating. This approach and its recent simulation are discussed. Alternative approaches which more explicitly include emittance exchange are also presented. Round-to-flat beam transform, transverse slicing, and longitudinal bunch coalescence are possible components of the alternative approach. A more explicit understanding of solenoidal cooling beam dynamics is introduced.

Using effort information with change-in-ratio data for population estimation

USGS Publications Warehouse

Udevitz, Mark S.; Pollock, Kenneth H.

1995-01-01

Most change-in-ratio (CIR) methods for estimating fish and wildlife population sizes have been based only on assumptions about how encounter probabilities vary among population subclasses. When information on sampling effort is available, it is also possible to derive CIR estimators based on assumptions about how encounter probabilities vary over time. This paper presents a generalization of previous CIR models that allows explicit consideration of a range of assumptions about the variation of encounter probabilities among subclasses and over time. Explicit estimators are derived under this model for specific sets of assumptions about the encounter probabilities. Numerical methods are presented for obtaining estimators under the full range of possible assumptions. Likelihood ratio tests for these assumptions are described. Emphasis is on obtaining estimators based on assumptions about variation of encounter probabilities over time.

Estimating connectivity in marine populations: an empirical evaluation of assignment tests and parentage analysis under different gene flow scenarios.

PubMed

Saenz-Agudelo, P; Jones, G P; Thorrold, S R; Planes, S

2009-04-01

The application of spatially explicit models of population dynamics to fisheries management and the design marine reserve network systems has been limited due to a lack of empirical estimates of larval dispersal. Here we compared assignment tests and parentage analysis for examining larval retention and connectivity under two different gene flow scenarios using panda clownfish (Amphiprion polymnus) in Papua New Guinea. A metapopulation of panda clownfish in Bootless Bay with little or no genetic differentiation among five spatially discrete locations separated by 2-6 km provided the high gene flow scenario. The low gene flow scenario compared the Bootless Bay metapopulation with a genetically distinct population (F(ST )= 0.1) located at Schumann Island, New Britain, 1500 km to the northeast. We used assignment tests and parentage analysis based on microsatellite DNA data to identify natal origins of 177 juveniles in Bootless Bay and 73 juveniles at Schumann Island. At low rates of gene flow, assignment tests correctly classified juveniles to their source population. On the other hand, parentage analysis led to an overestimate of self-recruitment within the two populations due to the significant deviation from panmixia when both populations were pooled. At high gene flow (within Bootless Bay), assignment tests underestimated self-recruitment and connectivity among subpopulations, and grossly overestimated self-recruitment within the overall metapopulation. However, the assignment tests did identify immigrants from distant (genetically distinct) populations. Parentage analysis clearly provided the most accurate estimates of connectivity in situations of high gene flow.

Organism and population-level ecological models for ...

EPA Pesticide Factsheets

Ecological risk assessment typically focuses on animal populations as endpoints for regulatory ecotoxicology. Scientists at USEPA are developing models for animal populations exposed to a wide range of chemicals from pesticides to emerging contaminants. Modeled taxa include aquatic and terrestrial invertebrates, fish, amphibians, and birds, and employ a wide range of methods, from matrix-based projection models to mechanistic bioenergetics models and spatially explicit population models. not applicable

Resolvent-Techniques for Multiple Exercise Problems

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

Christensen, Sören, E-mail: christensen@math.uni-kiel.de; Lempa, Jukka, E-mail: jukka.lempa@hioa.no

2015-02-15

We study optimal multiple stopping of strong Markov processes with random refraction periods. The refraction periods are assumed to be exponentially distributed with a common rate and independent of the underlying dynamics. Our main tool is using the resolvent operator. In the first part, we reduce infinite stopping problems to ordinary ones in a general strong Markov setting. This leads to explicit solutions for wide classes of such problems. Starting from this result, we analyze problems with finitely many exercise rights and explain solution methods for some classes of problems with underlying Lévy and diffusion processes, where the optimal characteristicsmore » of the problems can be identified more explicitly. We illustrate the main results with explicit examples.« less

The development of an explicit thermochemical nonequilibrium algorithm and its application to compute three dimensional AFE flowfields

NASA Technical Reports Server (NTRS)

Palmer, Grant

1989-01-01

This study presents a three-dimensional explicit, finite-difference, shock-capturing numerical algorithm applied to viscous hypersonic flows in thermochemical nonequilibrium. The algorithm employs a two-temperature physical model. Equations governing the finite-rate chemical reactions are fully-coupled to the gas dynamic equations using a novel coupling technique. The new coupling method maintains stability in the explicit, finite-rate formulation while allowing relatively large global time steps. The code uses flux-vector accuracy. Comparisons with experimental data and other numerical computations verify the accuracy of the present method. The code is used to compute the three-dimensional flowfield over the Aeroassist Flight Experiment (AFE) vehicle at one of its trajectory points.

Water Dynamics at Protein-Protein Interfaces: Molecular Dynamics Study of Virus-Host Receptor Complexes.

PubMed

Dutta, Priyanka; Botlani, Mohsen; Varma, Sameer

2014-12-26

The dynamical properties of water at protein-water interfaces are unlike those in the bulk. Here we utilize molecular dynamics simulations to study water dynamics in interstitial regions between two proteins. We consider two natural protein-protein complexes, one in which the Nipah virus G protein binds to cellular ephrin B2 and the other in which the same G protein binds to ephrin B3. While the two complexes are structurally similar, the two ephrins share only a modest sequence identity of ∼50%. X-ray crystallography also suggests that these interfaces are fairly extensive and contain exceptionally large amounts of waters. We find that while the interstitial waters tend to occupy crystallographic sites, almost all waters exhibit residence times of less than hundred picoseconds in the interstitial region. We also find that while the differences in the sequence of the two ephrins result in quantitative differences in the dynamics of interstitial waters, the trends in the shifts with respect to bulk values are similar. Despite the high wetness of the protein-protein interfaces, the dynamics of interstitial waters are considerably slower compared to the bulk-the interstitial waters diffuse an order of magnitude slower and have 2-3 fold longer hydrogen bond lifetimes and 2-1000 fold slower dipole relaxation rates. To understand the role of interstitial waters, we examine how implicit solvent models compare against explicit solvent models in producing ephrin-induced shifts in the G conformational density. Ephrin-induced shifts in the G conformational density are critical to the allosteric activation of another viral protein that mediates fusion. We find that in comparison with the explicit solvent model, the implicit solvent model predicts a more compact G-B2 interface, presumably because of the absence of discrete waters at the G-B2 interface. Simultaneously, we find that the two models yield strikingly different induced changes in the G conformational density, even for those residues whose conformational densities in the apo state are unaffected by the treatment of the bulk solvent. Together, these results show that the explicit treatment of interstitial water molecules is necessary for a proper description of allosteric transitions.

PopHR: a knowledge-based platform to support integration, analysis, and visualization of population health data.

PubMed

Shaban-Nejad, Arash; Lavigne, Maxime; Okhmatovskaia, Anya; Buckeridge, David L

2017-01-01

Population health decision makers must consider complex relationships between multiple concepts measured with differential accuracy from heterogeneous data sources. Population health information systems are currently limited in their ability to integrate data and present a coherent portrait of population health. Consequentially, these systems can provide only basic support for decision makers. The Population Health Record (PopHR) is a semantic web application that automates the integration and extraction of massive amounts of heterogeneous data from multiple distributed sources (e.g., administrative data, clinical records, and survey responses) to support the measurement and monitoring of population health and health system performance for a defined population. The design of the PopHR draws on the theories of the determinants of health and evidence-based public health to harmonize and explicitly link information about a population with evidence about the epidemiology and control of chronic diseases. Organizing information in this manner and linking it explicitly to evidence is expected to improve decision making related to the planning, implementation, and evaluation of population health and health system interventions. In this paper, we describe the PopHR platform and discuss the architecture, design, key modules, and its implementation and use. © 2016 New York Academy of Sciences.

Locally-Adaptive, Spatially-Explicit Projection of U.S. Population for 2030 and 2050

DOE PAGES

McKee, Jacob J.; Rose, Amy N.; Bright, Eddie A.; ...

2015-02-03

Localized adverse events, including natural hazards, epidemiological events, and human conflict, underscore the criticality of quantifying and mapping current population. Moreover, knowing the spatial distribution of future population allows for increased preparation in the event of an emergency. Building on the spatial interpolation technique previously developed for high resolution population distribution data (LandScan Global and LandScan USA), we have constructed an empirically-informed spatial distribution of the projected population of the contiguous U.S. for 2030 and 2050. Whereas most current large-scale, spatially explicit population projections typically rely on a population gravity model to determine areas of future growth, our projection modelmore » departs from these by accounting for multiple components that affect population distribution. Modelled variables, which included land cover, slope, distances to larger cities, and a moving average of current population, were locally adaptive and geographically varying. The resulting weighted surface was used to determine which areas had the greatest likelihood for future population change. Population projections of county level numbers were developed using a modified version of the U.S. Census s projection methodology with the U.S. Census s official projection as the benchmark. Applications of our model include, but are not limited to, suitability modelling, service area planning for governmental agencies, consequence assessment, mitigation planning and implementation, and assessment of spatially vulnerable populations.« less

Locally-Adaptive, Spatially-Explicit Projection of U.S. Population for 2030 and 2050

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

McKee, Jacob J.; Rose, Amy N.; Bright, Eddie A.

Localized adverse events, including natural hazards, epidemiological events, and human conflict, underscore the criticality of quantifying and mapping current population. Moreover, knowing the spatial distribution of future population allows for increased preparation in the event of an emergency. Building on the spatial interpolation technique previously developed for high resolution population distribution data (LandScan Global and LandScan USA), we have constructed an empirically-informed spatial distribution of the projected population of the contiguous U.S. for 2030 and 2050. Whereas most current large-scale, spatially explicit population projections typically rely on a population gravity model to determine areas of future growth, our projection modelmore » departs from these by accounting for multiple components that affect population distribution. Modelled variables, which included land cover, slope, distances to larger cities, and a moving average of current population, were locally adaptive and geographically varying. The resulting weighted surface was used to determine which areas had the greatest likelihood for future population change. Population projections of county level numbers were developed using a modified version of the U.S. Census s projection methodology with the U.S. Census s official projection as the benchmark. Applications of our model include, but are not limited to, suitability modelling, service area planning for governmental agencies, consequence assessment, mitigation planning and implementation, and assessment of spatially vulnerable populations.« less

Class of self-limiting growth models in the presence of nonlinear diffusion

NASA Astrophysics Data System (ADS)

Kar, Sandip; Banik, Suman Kumar; Ray, Deb Shankar

2002-06-01

The source term in a reaction-diffusion system, in general, does not involve explicit time dependence. A class of self-limiting growth models dealing with animal and tumor growth and bacterial population in a culture, on the other hand, are described by kinetics with explicit functions of time. We analyze a reaction-diffusion system to study the propagation of spatial front for these models.

A watershed-based spatially-explicit demonstration of an integrated environmental modeling framework for ecosystem services in the Coal River Basin (WV, USA)

Treesearch

John M. Johnston; Mahion C. Barber; Kurt Wolfe; Mike Galvin; Mike Cyterski; Rajbir Parmar; Luis Suarez

2016-01-01

We demonstrate a spatially-explicit regional assessment of current condition of aquatic ecoservices in the Coal River Basin (CRB), with limited sensitivity analysis for the atmospheric contaminant mercury. The integrated modeling framework (IMF) forecasts water quality and quantity, habitat suitability for aquatic biota, fish biomasses, population densities, ...

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.

Contact structure, mobility, environmental impact and behaviour: the importance of social forces to infectious disease dynamics and disease ecology.

PubMed

Arthur, Ronan F; Gurley, Emily S; Salje, Henrik; Bloomfield, Laura S P; Jones, James H

2017-05-05

Human factors, including contact structure, movement, impact on the environment and patterns of behaviour, can have significant influence on the emergence of novel infectious diseases and the transmission and amplification of established ones. As anthropogenic climate change alters natural systems and global economic forces drive land-use and land-cover change, it becomes increasingly important to understand both the ecological and social factors that impact infectious disease outcomes for human populations. While the field of disease ecology explicitly studies the ecological aspects of infectious disease transmission, the effects of the social context on zoonotic pathogen spillover and subsequent human-to-human transmission are comparatively neglected in the literature. The social sciences encompass a variety of disciplines and frameworks for understanding infectious diseases; however, here we focus on four primary areas of social systems that quantitatively and qualitatively contribute to infectious diseases as social-ecological systems. These areas are social mixing and structure, space and mobility, geography and environmental impact, and behaviour and behaviour change. Incorporation of these social factors requires empirical studies for parametrization, phenomena characterization and integrated theoretical modelling of social-ecological interactions. The social-ecological system that dictates infectious disease dynamics is a complex system rich in interacting variables with dynamically significant heterogeneous properties. Future discussions about infectious disease spillover and transmission in human populations need to address the social context that affects particular disease systems by identifying and measuring qualitatively important drivers.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'. © 2017 The Author(s).

Using a model comparison approach to describe the assembly pathway for histone H1

PubMed Central

Contreras, Carlos; Villasana, Minaya; Hendzel, Michael J.

2018-01-01

Histones H1 or linker histones are highly dynamic proteins that diffuse throughout the cell nucleus and associate with chromatin (DNA and associated proteins). This binding interaction of histone H1 with the chromatin is thought to regulate chromatin organization and DNA accessibility to transcription factors and has been proven to involve a kinetic process characterized by a population that associates weakly with chromatin and rapidly dissociates and another population that resides at a binding site for up to several minutes before dissociating. When considering differences between these two classes of interactions in a mathematical model for the purpose of describing and quantifying the dynamics of histone H1, it becomes apparent that there could be several assembly pathways that explain the kinetic data obtained in living cells. In this work, we model these different pathways using systems of reaction-diffusion equations and carry out a model comparison analysis using FRAP (fluorescence recovery after photobleaching) experimental data from different histone H1 variants to determine the most feasible mechanism to explain histone H1 binding to chromatin. The analysis favors four different chromatin assembly pathways for histone H1 which share common features and provide meaningful biological information on histone H1 dynamics. We show, using perturbation analysis, that the explicit consideration of high- and low-affinity associations of histone H1 with chromatin in the favored assembly pathways improves the interpretation of histone H1 experimental FRAP data. To illustrate the results, we use one of the favored models to assess the kinetic changes of histone H1 after core histone hyperacetylation, and conclude that this post-transcriptional modification does not affect significantly the transition of histone H1 from a weakly bound state to a tightly bound state. PMID:29352283

A model for global diversity in response to temperature change over geological time scales, with reference to planktic organisms.

PubMed

De Blasio, Fabio Vittorio; Liow, Lee Hsiang; Schweder, Tore; De Blasio, Birgitte Freiesleben

2015-01-21

There are strong propositions in the literature that abiotic factors override biotic drivers of diversity on time scales of the fossil record. In order to study the interaction of biotic and abiotic forces on long term changes, we devise a spatio-temporal discrete-time Markov process model of macroevolution featuring population formation, speciation, migration and extinction, where populations are free to migrate. In our model, the extinction probability of these populations is controlled by latitudinally and temporally varying environment (temperature) and competition. Although our model is general enough to be applicable to disparate taxa, we explicitly address planktic organisms, which are assumed to disperse freely without barriers over the Earth's oceans. While rapid and drastic environmental changes tend to eliminate many species, generalists preferentially survive and hence leave generalist descendants. In other words, environmental fluctuations result in generalist descendants which are resilient to future environmental changes. Periods of stable or slow environmental changes lead to more specialist species and higher population numbers. Simulating Cenozoic diversity dynamics with both competition and the environmental component of our model produces diversity curves that reflect current empirical knowledge, which cannot be obtained with just one component. Our model predicts that the average temperature optimum at which planktic species thrive best has declined over the Neogene, following the trend of global average temperatures. Copyright © 2014 Elsevier Ltd. All rights reserved.

Sloshing dynamics on rotating helium dewar tank

NASA Technical Reports Server (NTRS)

Hung, R. J.

1993-01-01

The generalized mathematical formulation of sloshing dynamics for partially filled liquid of cryogenic superfluid helium II in dewar containers driven by both the gravity gradient and jitter accelerations applicable to scientific spacecraft which is eligible to carry out spinning motion and/or slew motion for the purpose to perform scientific observation during the normal spacecraft operation are investigated. An example is given with Gravity Probe-B (GP-B) spacecraft which is responsible for the sloshing dynamics. The jitter accelerations include slew motion, spinning motion, atmospheric drag on the spacecraft, spacecraft attitude motions arising from machinery vibrations, thruster firing, pointing control of spacecraft, crew motion, etc. Explicit mathematical expressions to cover these forces acting on the spacecraft fluid systems are derived. The numerical computation of sloshing dynamics were based on the non-inertia frame spacecraft bound coordinate, and solve time dependent, three-dimensional formulations of partial differential equations subject to initial and boundary conditions. The explicit mathematical expressions of boundary conditions to cover capillary force effect on the liquid vapor interface in microgravity environments are also derived. The formulations of fluid moment and angular moment fluctuations in fluid profiles induced by the sloshing dynamics, together with fluid stress and moment fluctuations exerted on the spacecraft dewar containers were derived. Results were widely published in the open journals.

Development of 1D Liner Compression Code for IDL

NASA Astrophysics Data System (ADS)

Shimazu, Akihisa; Slough, John; Pancotti, Anthony

2015-11-01

A 1D liner compression code is developed to model liner implosion dynamics in the Inductively Driven Liner Experiment (IDL) where FRC plasmoid is compressed via inductively-driven metal liners. The driver circuit, magnetic field, joule heating, and liner dynamics calculations are performed at each time step in sequence to couple these effects in the code. To obtain more realistic magnetic field results for a given drive coil geometry, 2D and 3D effects are incorporated into the 1D field calculation through use of correction factor table lookup approach. Commercial low-frequency electromagnetic fields solver, ANSYS Maxwell 3D, is used to solve the magnetic field profile for static liner condition at various liner radius in order to derive correction factors for the 1D field calculation in the code. The liner dynamics results from the code is verified to be in good agreement with the results from commercial explicit dynamics solver, ANSYS Explicit Dynamics, and previous liner experiment. The developed code is used to optimize the capacitor bank and driver coil design for better energy transfer and coupling. FRC gain calculations are also performed using the liner compression data from the code for the conceptual design of the reactor sized system for fusion energy gains.

Velocity Gradient Power Functional for Brownian Dynamics.

PubMed

de Las Heras, Daniel; Schmidt, Matthias

2018-01-12

We present an explicit and simple approximation for the superadiabatic excess (over ideal gas) free power functional, admitting the study of the nonequilibrium dynamics of overdamped Brownian many-body systems. The functional depends on the local velocity gradient and is systematically obtained from treating the microscopic stress distribution as a conjugate field. The resulting superadiabatic forces are beyond dynamical density functional theory and are of a viscous nature. Their high accuracy is demonstrated by comparison to simulation results.

Velocity Gradient Power Functional for Brownian Dynamics

NASA Astrophysics Data System (ADS)

de las Heras, Daniel; Schmidt, Matthias

2018-01-01

We present an explicit and simple approximation for the superadiabatic excess (over ideal gas) free power functional, admitting the study of the nonequilibrium dynamics of overdamped Brownian many-body systems. The functional depends on the local velocity gradient and is systematically obtained from treating the microscopic stress distribution as a conjugate field. The resulting superadiabatic forces are beyond dynamical density functional theory and are of a viscous nature. Their high accuracy is demonstrated by comparison to simulation results.

Prediction of Protein-Peptide Interactions: Application of the XPairIT to Anthrax Lethal Factor and Substrates

DTIC Science & Technology

2013-09-01

hydrogen bonds in Tyrosine-containing peptides. Dalkas et al[7] used docking and molecular dynamics simulations to study a variety of MAPKK-based... simulated using NAMD molecular dynamics and the CHARMM[20] forcefield at 300K and employing the Generalized Born Implicit Solvent (GBIS[21]) with the...which were reported in Section 2. Specifically, after a ~10ns molecular dynamics simulation in TIP3 explicit water, significant motion of domains III

A Bayesian state-space formulation of dynamic occupancy models

USGS Publications Warehouse

Royle, J. Andrew; Kery, M.

2007-01-01

Species occurrence and its dynamic components, extinction and colonization probabilities, are focal quantities in biogeography and metapopulation biology, and for species conservation assessments. It has been increasingly appreciated that these parameters must be estimated separately from detection probability to avoid the biases induced by nondetection error. Hence, there is now considerable theoretical and practical interest in dynamic occupancy models that contain explicit representations of metapopulation dynamics such as extinction, colonization, and turnover as well as growth rates. We describe a hierarchical parameterization of these models that is analogous to the state-space formulation of models in time series, where the model is represented by two components, one for the partially observable occupancy process and another for the observations conditional on that process. This parameterization naturally allows estimation of all parameters of the conventional approach to occupancy models, but in addition, yields great flexibility and extensibility, e.g., to modeling heterogeneity or latent structure in model parameters. We also highlight the important distinction between population and finite sample inference; the latter yields much more precise estimates for the particular sample at hand. Finite sample estimates can easily be obtained using the state-space representation of the model but are difficult to obtain under the conventional approach of likelihood-based estimation. We use R and Win BUGS to apply the model to two examples. In a standard analysis for the European Crossbill in a large Swiss monitoring program, we fit a model with year-specific parameters. Estimates of the dynamic parameters varied greatly among years, highlighting the irruptive population dynamics of that species. In the second example, we analyze route occupancy of Cerulean Warblers in the North American Breeding Bird Survey (BBS) using a model allowing for site-specific heterogeneity in model parameters. The results indicate relatively low turnover and a stable distribution of Cerulean Warblers which is in contrast to analyses of counts of individuals from the same survey that indicate important declines. This discrepancy illustrates the inertia in occupancy relative to actual abundance. Furthermore, the model reveals a declining patch survival probability, and increasing turnover, toward the edge of the range of the species, which is consistent with metapopulation perspectives on the genesis of range edges. Given detection/non-detection data, dynamic occupancy models as described here have considerable potential for the study of distributions and range dynamics.

Building the Foundation for International Conservation Planning for Breeding Ducks across the U.S. and Canadian Border

PubMed Central

Doherty, Kevin E.; Evans, Jeffrey S.; Walker, Johann; Devries, James H.; Howerter, David W.

2015-01-01

We used publically available data on duck breeding distribution and recently compiled geospatial data on upland habitat and environmental conditions to develop a spatially explicit model of breeding duck populations across the entire Prairie Pothole Region (PPR). Our spatial population models were able to identify key areas for duck conservation across the PPR and predict between 62.1 – 79.1% (68.4% avg.) of the variation in duck counts by year from 2002 – 2010. The median difference in observed vs. predicted duck counts at a transect segment level was 4.6 ducks. Our models are the first seamless spatially explicit models of waterfowl abundance across the entire PPR and represent an initial step toward joint conservation planning between Prairie Pothole and Prairie Habitat Joint Ventures. Our work demonstrates that when spatial and temporal variation for highly mobile birds is incorporated into conservation planning it will likely increase the habitat area required to support defined population goals. A major goal of the current North American Waterfowl Management Plan and subsequent action plan is the linking of harvest and habitat management. We contend incorporation of spatial aspects will increase the likelihood of coherent joint harvest and habitat management decisions. Our results show at a minimum, it is possible to produce spatially explicit waterfowl abundance models that when summed across survey strata will produce similar strata level population estimates as the design-based Waterfowl Breeding Pair and Habitat Survey (r2 = 0.977). This is important because these design-based population estimates are currently used to set duck harvest regulations and to set duck population and habitat goals for the North American Waterfowl Management Plan. We hope this effort generates discussion on the important linkages between spatial and temporal variation in population size, and distribution relative to habitat quantity and quality when linking habitat and population goals across this important region. PMID:25714747

Multibody dynamics model building using graphical interfaces

NASA Technical Reports Server (NTRS)

Macala, Glenn A.

1989-01-01

In recent years, the extremely laborious task of manually deriving equations of motion for the simulation of multibody spacecraft dynamics has largely been eliminated. Instead, the dynamicist now works with commonly available general purpose dynamics simulation programs which generate the equations of motion either explicitly or implicitly via computer codes. The user interface to these programs has predominantly been via input data files, each with its own required format and peculiarities, causing errors and frustrations during program setup. Recent progress in a more natural method of data input for dynamics programs: the graphical interface, is described.

A decoupled recursive approach for constrained flexible multibody system dynamics

NASA Technical Reports Server (NTRS)

Lai, Hao-Jan; Kim, Sung-Soo; Haug, Edward J.; Bae, Dae-Sung

1989-01-01

A variational-vector calculus approach is employed to derive a recursive formulation for dynamic analysis of flexible multibody systems. Kinematic relationships for adjacent flexible bodies are derived in a companion paper, using a state vector notation that represents translational and rotational components simultaneously. Cartesian generalized coordinates are assigned for all body and joint reference frames, to explicitly formulate deformation kinematics under small deformation kinematics and an efficient flexible dynamics recursive algorithm is developed. Dynamic analysis of a closed loop robot is performed to illustrate efficiency of the algorithm.

Exploring a multi-scale method for molecular simulation in continuum solvent model: Explicit simulation of continuum solvent as an incompressible fluid.

PubMed

Xiao, Li; Luo, Ray

2017-12-07

We explored a multi-scale algorithm for the Poisson-Boltzmann continuum solvent model for more robust simulations of biomolecules. In this method, the continuum solvent/solute interface is explicitly simulated with a numerical fluid dynamics procedure, which is tightly coupled to the solute molecular dynamics simulation. There are multiple benefits to adopt such a strategy as presented below. At this stage of the development, only nonelectrostatic interactions, i.e., van der Waals and hydrophobic interactions, are included in the algorithm to assess the quality of the solvent-solute interface generated by the new method. Nevertheless, numerical challenges exist in accurately interpolating the highly nonlinear van der Waals term when solving the finite-difference fluid dynamics equations. We were able to bypass the challenge rigorously by merging the van der Waals potential and pressure together when solving the fluid dynamics equations and by considering its contribution in the free-boundary condition analytically. The multi-scale simulation method was first validated by reproducing the solute-solvent interface of a single atom with analytical solution. Next, we performed the relaxation simulation of a restrained symmetrical monomer and observed a symmetrical solvent interface at equilibrium with detailed surface features resembling those found on the solvent excluded surface. Four typical small molecular complexes were then tested, both volume and force balancing analyses showing that these simple complexes can reach equilibrium within the simulation time window. Finally, we studied the quality of the multi-scale solute-solvent interfaces for the four tested dimer complexes and found that they agree well with the boundaries as sampled in the explicit water simulations.

Theory of wavelet-based coarse-graining hierarchies for molecular dynamics.

PubMed

Rinderspacher, Berend Christopher; Bardhan, Jaydeep P; Ismail, Ahmed E

2017-07-01

We present a multiresolution approach to compressing the degrees of freedom and potentials associated with molecular dynamics, such as the bond potentials. The approach suggests a systematic way to accelerate large-scale molecular simulations with more than two levels of coarse graining, particularly applications of polymeric materials. In particular, we derive explicit models for (arbitrarily large) linear (homo)polymers and iterative methods to compute large-scale wavelet decompositions from fragment solutions. This approach does not require explicit preparation of atomistic-to-coarse-grained mappings, but instead uses the theory of diffusion wavelets for graph Laplacians to develop system-specific mappings. Our methodology leads to a hierarchy of system-specific coarse-grained degrees of freedom that provides a conceptually clear and mathematically rigorous framework for modeling chemical systems at relevant model scales. The approach is capable of automatically generating as many coarse-grained model scales as necessary, that is, to go beyond the two scales in conventional coarse-grained strategies; furthermore, the wavelet-based coarse-grained models explicitly link time and length scales. Furthermore, a straightforward method for the reintroduction of omitted degrees of freedom is presented, which plays a major role in maintaining model fidelity in long-time simulations and in capturing emergent behaviors.

Cognitive conflict without explicit conflict monitoring in a dynamical agent.

PubMed

Ward, Robert; Ward, Ronnie

2006-11-01

We examine mechanisms for resolving cognitive conflict in an embodied, situated, and dynamic agent, developed through an evolutionary learning process. The agent was required to solve problems of response conflict in a dual-target "catching" task, focusing response on one of the targets while ignoring the other. Conflict in the agent was revealed at the behavioral level in terms of increased latencies to the second target. This behavioral interference was correlated to peak violations of the network's stable state equation. At the level of the agent's neural network, peak violations were also correlated to periods of disagreement in source inputs to the agent's motor effectors. Despite observing conflict at these numerous levels, we did not find any explicit conflict monitoring mechanisms within the agent. We instead found evidence of a distributed conflict management system, characterized by competitive sources within the network. In contrast to the conflict monitoring hypothesis [Botvinick, M. M., Braver, T. S., Barch, D. M., Carter, C. S., & Cohen, J. D. (2001). Conflict monitoring and cognitive control. Psychological Review, 108(3), 624-652], this agent demonstrates that resolution of cognitive conflict does not require explicit conflict monitoring. We consider the implications of our results for the conflict monitoring hypothesis.

Solvent effects on the properties of hyperbranched polythiophenes.

PubMed

Torras, Juan; Zanuy, David; Aradilla, David; Alemán, Carlos

2016-09-21

The structural and electronic properties of all-thiophene dendrimers and dendrons in solution have been evaluated using very different theoretical approaches based on quantum mechanical (QM) and hybrid QM/molecular mechanics (MM) methodologies: (i) calculations on minimum energy conformations using an implicit solvation model in combination with density functional theory (DFT) or time-dependent DFT (TD-DFT) methods; (ii) hybrid QM/MM calculations, in which the solute and solvent molecules are represented at the DFT level as point charges, respectively, on snapshots extracted from classical molecular dynamics (MD) simulations using explicit solvent molecules, and (iii) QM/MM-MD trajectories in which the solute is described at the DFT or TD-DFT level and the explicit solvent molecules are represented using classical force-fields. Calculations have been performed in dichloromethane, tetrahydrofuran and dimethylformamide. A comparison of the results obtained using the different approaches with the available experimental data indicates that the incorporation of effects associated with both the conformational dynamics of the dendrimer and the explicit solvent molecules is strictly necessary to satisfactorily reproduce the properties of the investigated systems. Accordingly, QM/MM-MD simulations are able to capture such effects providing a reliable description of electronic properties-conformational flexibility relationships in all-Th dendrimers.

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...

Computer-Aided Group Problem Solving for Unified Life Cycle Engineering (ULCE)

DTIC Science & Technology

1989-02-01

defining the problem, generating alternative solutions, evaluating alternatives, selecting alternatives, and implementing the solution. Systems...specialist in group dynamics, assists the group in formulating the problem and selecting a model framework. The analyst provides the group with computer...allocating resources, evaluating and selecting options, making judgments explicit, and analyzing dynamic systems. c. University of Rhode Island Drs. Geoffery

Parametrizing linear generalized Langevin dynamics from explicit molecular dynamics simulations

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

Gottwald, Fabian; Karsten, Sven; Ivanov, Sergei D., E-mail: sergei.ivanov@uni-rostock.de

2015-06-28

Fundamental understanding of complex dynamics in many-particle systems on the atomistic level is of utmost importance. Often the systems of interest are of macroscopic size but can be partitioned into a few important degrees of freedom which are treated most accurately and others which constitute a thermal bath. Particular attention in this respect attracts the linear generalized Langevin equation, which can be rigorously derived by means of a linear projection technique. Within this framework, a complicated interaction with the bath can be reduced to a single memory kernel. This memory kernel in turn is parametrized for a particular system studied,more » usually by means of time-domain methods based on explicit molecular dynamics data. Here, we discuss that this task is more naturally achieved in frequency domain and develop a Fourier-based parametrization method that outperforms its time-domain analogues. Very surprisingly, the widely used rigid bond method turns out to be inappropriate in general. Importantly, we show that the rigid bond approach leads to a systematic overestimation of relaxation times, unless the system under study consists of a harmonic bath bi-linearly coupled to the relevant degrees of freedom.« less

Reproducing kernel potential energy surfaces in biomolecular simulations: Nitric oxide binding to myoglobin

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

Soloviov, Maksym; Meuwly, Markus, E-mail: m.meuwly@unibas.ch

2015-09-14

Multidimensional potential energy surfaces based on reproducing kernel-interpolation are employed to explore the energetics and dynamics of free and bound nitric oxide in myoglobin (Mb). Combining a force field description for the majority of degrees of freedom and the higher-accuracy representation for the NO ligand and the Fe out-of-plane motion allows for a simulation approach akin to a mixed quantum mechanics/molecular mechanics treatment. However, the kernel-representation can be evaluated at conventional force-field speed. With the explicit inclusion of the Fe-out-of-plane (Fe-oop) coordinate, the dynamics and structural equilibrium after photodissociation of the ligand are correctly described compared to experiment. Experimentally, themore » Fe-oop coordinate plays an important role for the ligand dynamics. This is also found here where the isomerization dynamics between the Fe–ON and Fe–NO state is significantly affected whether or not this co-ordinate is explicitly included. Although the Fe–ON conformation is metastable when considering only the bound {sup 2}A state, it may disappear once the {sup 4}A state is included. This explains the absence of the Fe–ON state in previous experimental investigations of MbNO.« less

Estimating the population density of the Asian tapir (Tapirus indicus) in a selectively logged forest in Peninsular Malaysia.

PubMed

Rayan, D Mark; Mohamad, Shariff Wan; Dorward, Leejiah; Aziz, Sheema Abdul; Clements, Gopalasamy Reuben; Christopher, Wong Chai Thiam; Traeholt, Carl; Magintan, David

2012-12-01

The endangered Asian tapir (Tapirus indicus) is threatened by large-scale habitat loss, forest fragmentation and increased hunting pressure. Conservation planning for this species, however, is hampered by a severe paucity of information on its ecology and population status. We present the first Asian tapir population density estimate from a camera trapping study targeting tigers in a selectively logged forest within Peninsular Malaysia using a spatially explicit capture-recapture maximum likelihood based framework. With a trap effort of 2496 nights, 17 individuals were identified corresponding to a density (standard error) estimate of 9.49 (2.55) adult tapirs/100 km(2) . Although our results include several caveats, we believe that our density estimate still serves as an important baseline to facilitate the monitoring of tapir population trends in Peninsular Malaysia. Our study also highlights the potential of extracting vital ecological and population information for other cryptic individually identifiable animals from tiger-centric studies, especially with the use of a spatially explicit capture-recapture maximum likelihood based framework. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

Conservation physiology for applied management of marine fish: an overview with perspectives on the role and value of telemetry

PubMed Central

Metcalfe, J. D.; Le Quesne, W. J. F.; Cheung, W. W. L.; Righton, D. A.

2012-01-01

Physiological studies focus on the responses of cells, tissues and individuals to stressors, usually in laboratory situations. Conservation and management, on the other hand, focus on populations. The field of conservation physiology addresses the question of how abiotic drivers of physiological responses at the level of the individual alter requirements for successful conservation and management of populations. To achieve this, impacts of physiological effects at the individual level need to be scaled to impacts on population dynamics, which requires consideration of ecology. Successfully realizing the potential of conservation physiology requires interdisciplinary studies incorporating physiology and ecology, and requires that a constructive dialogue develops between these traditionally disparate fields. To encourage this dialogue, we consider the increasingly explicit incorporation of physiology into ecological models applied to marine fish conservation and management. Conservation physiology is further challenged as the physiology of an individual revealed under laboratory conditions is unlikely to reflect realized responses to the complex variable stressors to which it is exposed in the wild. Telemetry technology offers the capability to record an animal's behaviour while simultaneously recording environmental variables to which it is exposed. We consider how the emerging insights from telemetry can strengthen the incorporation of physiology into ecology. PMID:22566680

Assessing the Effects of Disease and Bleaching on Florida ...

EPA Pesticide Factsheets

Coral diseases have increased in frequency over the past few decades and have important influences on the structure and composition of coral reef communities. However, there is limited information on the etiologies of many coral diseases, and pathways via which coral diseases are acquired and transmitted are still in question. Furthermore, it is difficult to assess the impacts of disease on coral populations because outbreaks often co-occur with temperature-induced bleaching and anthropogenic stressors. We developed spatially-explicit population models of coral disease and bleaching dynamics to quantify the impact of six common diseases on Florida Keys corals, including aspergillosis, dark spots, white band, white plague, white patch, and yellow band. Models were fit to an 8-year data set of coral abundance, disease prevalence, and bleaching prevalence. Model selection was used to assess alternative pathways for disease transmission, and the influence of environmental stressors, including sea temperature and human population density, on disease prevalence and coral mortality. Classic disease transmission from contagious to susceptible colonies provided the best model only for aspergillosis. For other diseases, direct transmission from the external environment provided the best fit to observed data. Estimates of disease reproductive ratio values (R0) were less than one for each disease, indicating coral colonies were below densities required for diseases

Coevolution in host-parasite systems: behavioural strategies of slave-making ants and their hosts.

PubMed Central

Foitzik, S.; DeHeer, C. J.; Hunjan, D. N.; Herbers, J. M.

2001-01-01

Recently, avian brood parasites and their hosts have emerged as model systems for the study of host-parasite coevolution. However, empirical studies of the highly analogous social parasites, which use the workers of another eusocial species to raise their own young, have never explicitly examined the dynamics of these systems from a coevolutionary perspective. Here, we demonstrate interpopulational variation in behavioural interactions between a socially parasitic slave-maker ant and its host that is consistent with the expectations of host-parasite coevolution. Parasite pressure, as inferred by the size, abundance and raiding frequency of Protomognathus americanus colonies, was highest in a New York population of the host Leptothorax longispinosus and lowest in a West Virginia population. As host-parasite coevolutionary theory would predict, we found that the slave-makers and the hosts from New York were more effective at raiding and defending against raiders, respectively, than were conspecifics from the West Virginia population. Some of these variations in efficacy were brought about by apparently simple shifts in behaviour. These results demonstrate that defence mechanisms against social parasites can evolve, and they give the first indications of the existence of a coevolutionary arms race between a social parasite and its host. PMID:11375101

Modelling the impact of co-circulating low pathogenic avian influenza viruses on epidemics of highly pathogenic avian influenza in poultry.

PubMed

Nickbakhsh, Sema; Hall, Matthew D; Dorigatti, Ilaria; Lycett, Samantha J; Mulatti, Paolo; Monne, Isabella; Fusaro, Alice; Woolhouse, Mark E J; Rambaut, Andrew; Kao, Rowland R

2016-12-01

It is well known that highly pathogenic avian influenza (HPAI) viruses emerge through mutation of precursor low pathogenic avian influenza (LPAI) viruses in domestic poultry populations. The potential for immunological cross-protection between these pathogenic variants is recognised but the epidemiological impact during co-circulation is not well understood. Here we use mathematical models to investigate whether altered flock infection parameters consequent to primary LPAI infections can impact on the spread of HPAI at the population level. First we used mechanistic models reflecting the co-circulatory dynamics of LPAI and HPAI within a single commercial poultry flock. We found that primary infections with LPAI led to HPAI prevalence being maximised under a scenario of high but partial cross-protection. We then tested the population impact in spatially-explicit simulations motivated by a major avian influenza A(H7N1) epidemic that afflicted the Italian poultry industry in 1999-2001. We found that partial cross-protection can lead to a prolongation of HPAI epidemic duration. Our findings have implications for the control of HPAI in poultry particularly for settings in which LPAI and HPAI frequently co-circulate. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

INDIVIDUAL BASED MODELLING APPROACH TO THERMAL ...

EPA Pesticide Factsheets

Diadromous fish populations in the Pacific Northwest face challenges along their migratory routes from declining habitat quality, harvest, and barriers to longitudinal connectivity. Changes in river temperature regimes are producing an additional challenge for upstream migrating adult salmon and steelhead, species that are sensitive to absolute and cumulative thermal exposure. Adult salmon populations have been shown to utilize cold water patches along migration routes when mainstem river temperatures exceed thermal optimums. We are employing an individual based model (IBM) to explore the costs and benefits of spatially-distributed cold water refugia for adult migrating salmon. Our model, developed in the HexSim platform, is built around a mechanistic behavioral decision tree that drives individual interactions with their spatially explicit simulated environment. Population-scale responses to dynamic thermal regimes, coupled with other stressors such as disease and harvest, become emergent properties of the spatial IBM. Other model outputs include arrival times, species-specific survival rates, body energetic content, and reproductive fitness levels. Here, we discuss the challenges associated with parameterizing an individual based model of salmon and steelhead in a section of the Columbia River. Many rivers and streams in the Pacific Northwest are currently listed as impaired under the Clean Water Act as a result of high summer water temperatures. Adverse effec

Restoring Resiliency: Case Studies from Pacific Northwest Estuarine Eelgrass (Zostera marina L.) Ecosystems

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

Thom, Ronald M.; Diefenderfer, Heida L.; Vavrinec, John

2012-01-01

The purpose of many ecological restoration projects is to establish an ecosystem with fully developed structure and function that exhibits resistance to and resilience from disturbances. Coastal restoration projects in the Pacific Northwest provide opportunities to understand what is required to restore the resilience of eelgrass (Zostera marina L.) populations. Factors influencing resilience observed in three case studies of eelgrass restoration include minimum viable population, adaptations of transplant populations, and natural and anthropogenic disturbances at restoration sites. The evaluation of resiliency depends on selecting appropriate monitoring metrics and the frequency and duration of monitoring. Eelgrass area, cover and shoot densitymore » provide useful and reliable metrics for quantifying resilience of restored meadows. Further, five years of monitoring of these metrics provides data that can reasonably predict the long-term viability of a planted plot. Eelgrass appears to be a resilient ecosystem in general, though one that data suggest may exhibit tipping points brought about by compounded environmental conditions outside of its tolerance ranges. Explicit inclusion of resilience in the planning and practice of habitat restoration may reduce uncertainties and improve the performance of restored systems by increasing buffering capacity, nurturing sources of renewal (e.g., seeds and rhizomes), and managing for habitat forming and maintaining processes (e.g., sediment dynamics) at multiple scales.« less

Learning Natural Selection in 4th Grade with Multi-Agent-Based Computational Models

NASA Astrophysics Data System (ADS)

Dickes, Amanda Catherine; Sengupta, Pratim

2013-06-01

In this paper, we investigate how elementary school students develop multi-level explanations of population dynamics in a simple predator-prey ecosystem, through scaffolded interactions with a multi-agent-based computational model (MABM). The term "agent" in an MABM indicates individual computational objects or actors (e.g., cars), and these agents obey simple rules assigned or manipulated by the user (e.g., speeding up, slowing down, etc.). It is the interactions between these agents, based on the rules assigned by the user, that give rise to emergent, aggregate-level behavior (e.g., formation and movement of the traffic jam). Natural selection is such an emergent phenomenon, which has been shown to be challenging for novices (K16 students) to understand. Whereas prior research on learning evolutionary phenomena with MABMs has typically focused on high school students and beyond, we investigate how elementary students (4th graders) develop multi-level explanations of some introductory aspects of natural selection—species differentiation and population change—through scaffolded interactions with an MABM that simulates predator-prey dynamics in a simple birds-butterflies ecosystem. We conducted a semi-clinical interview based study with ten participants, in which we focused on the following: a) identifying the nature of learners' initial interpretations of salient events or elements of the represented phenomena, b) identifying the roles these interpretations play in the development of their multi-level explanations, and c) how attending to different levels of the relevant phenomena can make explicit different mechanisms to the learners. In addition, our analysis also shows that although there were differences between high- and low-performing students (in terms of being able to explain population-level behaviors) in the pre-test, these differences disappeared in the post-test.

Persistent oscillations and backward bifurcation in a malaria model with varying human and mosquito populations: implications for control.

PubMed

Ngonghala, Calistus N; Teboh-Ewungkem, Miranda I; Ngwa, Gideon A

2015-06-01

We derive and study a deterministic compartmental model for malaria transmission with varying human and mosquito populations. Our model considers disease-related deaths, asymptomatic immune humans who are also infectious, as well as mosquito demography, reproduction and feeding habits. Analysis of the model reveals the existence of a backward bifurcation and persistent limit cycles whose period and size is determined by two threshold parameters: the vectorial basic reproduction number Rm, and the disease basic reproduction number R0, whose size can be reduced by reducing Rm. We conclude that malaria dynamics are indeed oscillatory when the methodology of explicitly incorporating the mosquito's demography, feeding and reproductive patterns is considered in modeling the mosquito population dynamics. A sensitivity analysis reveals important control parameters that can affect the magnitudes of Rm and R0, threshold quantities to be taken into consideration when designing control strategies. Both Rm and the intrinsic period of oscillation are shown to be highly sensitive to the mosquito's birth constant λm and the mosquito's feeding success probability pw. Control of λm can be achieved by spraying, eliminating breeding sites or moving them away from human habitats, while pw can be controlled via the use of mosquito repellant and insecticide-treated bed-nets. The disease threshold parameter R0 is shown to be highly sensitive to pw, and the intrinsic period of oscillation is also sensitive to the rate at which reproducing mosquitoes return to breeding sites. A global sensitivity and uncertainty analysis reveals that the ability of the mosquito to reproduce and uncertainties in the estimations of the rates at which exposed humans become infectious and infectious humans recover from malaria are critical in generating uncertainties in the disease classes.

A longitudinal cohort study of malaria exposure and changing serostatus in a malaria endemic area of rural Tanzania.

PubMed

Simmons, Ryan A; Mboera, Leonard; Miranda, Marie Lynn; Morris, Alison; Stresman, Gillian; Turner, Elizabeth L; Kramer, Randall; Drakeley, Chris; O'Meara, Wendy P

2017-08-02

Measurements of anti-malarial antibodies are increasingly used as a proxy of transmission intensity. Most serological surveys are based on the use of cross-sectional data that, when age-stratified, approximates historical patterns of transmission within a population. Comparatively few studies leverage longitudinal data to explicitly relate individual infection events with subsequent antibody responses. The occurrence of seroconversion and seroreversion events for two Plasmodium falciparum asexual stage antigens (MSP-1 and AMA-1) was examined using three annual measurements of 691 individuals from a cohort of individuals in a malaria-endemic area of rural east-central Tanzania. Mixed-effect logistic regression models were employed to determine factors associated with changes in serostatus over time. While the expected population-level relationship between seroprevalence and disease incidence was observed, on an individual level the relationship between individual infections and the antibody response was complex. MSP-1 antibody responses were more dynamic in response to the occurrence and resolution of infection events than AMA-1, while the latter was more correlated with consecutive infections. The MSP-1 antibody response to an observed infection seemed to decay faster over time than the corresponding AMA-1 response. Surprisingly, there was no evidence of an age effect on the occurrence of a conversion or reversion event. While the population-level results concur with previously published sero-epidemiological surveys, the individual-level results highlight the more complex relationship between detected infections and antibody dynamics than can be analysed using cross-sectional data. The longitudinal analysis of serological data may provide a powerful tool for teasing apart the complex relationship between infection events and the corresponding immune response, thereby improving the ability to rapidly assess the success or failure of malaria control programmes.

Implicit attitudes to sexual partner concurrency vary by sexual orientation but not by gender-A cross sectional study of Belgian students.

PubMed

Kenyon, Chris R; Wolfs, Kenny; Osbak, Kara; van Lankveld, Jacques; Van Hal, Guido

2018-01-01

High rates of sexual partner concurrency have been shown to facilitate the spread of various sexually transmitted infections. Assessments of explicit attitudes to concurrency have however found little difference between populations. Implicit attitudes to concurrency may vary between populations and play a role in generating differences in the prevalence of concurrency. We developed a concurrency implicit associations test (C-IAT) to assess if implicit attitudes towards concurrency may vary between individuals and populations and what the correlates of these variations are. A sample of 869 Belgian students (mean age 23, SD 5.1) completed an online version of the C-IAT together with a questionnaire concerning sexual behavior and explicit attitudes to concurrency. The study participants C-IATs demonstrated a strong preference for monogamy (-0.78, SD = 0.41). 93.2% of participants had a pro-monogamy C-IAT. There was no difference in this implicit preference for monogamy between heterosexual men and women. Men who have sex with men and women who have sex with women were more likely to exhibit implicit but not explicit preferences for concurrency compared to heterosexual men and women. Correlates of the C-IAT varied between men and women.

Virtual prototyping of drop test using explicit analysis

NASA Astrophysics Data System (ADS)

Todorov, Georgi; Kamberov, Konstantin

2017-12-01

Increased requirements for reliability and safety, included in contemporary standards and norms, has high impact over new product development. New numerical techniques based on virtual prototyping technology, facilitates imrpoving product development cycle, resutling in reduced time/money spent for this stage as well as increased knowledge about certain failure mechanism. So called "drop test" became nearly a "must" step in development of any human operated product. This study aims to demonstrate dynamic behaviour assessment of a structure under impact loads, based on virtual prototyping using a typical nonlinear analysis - explicit dynamics. An example is presneted, based on a plastic container that is used as cartridge for a dispenser machine exposed to various work conditions. Different drop orientations were analyzed and critical load cases and design weaknesses have been found. Several design modifications have been proposed, based on detailed analyses results review.

The simple rules of social contagion.

PubMed

Hodas, Nathan O; Lerman, Kristina

2014-03-11

It is commonly believed that information spreads between individuals like a pathogen, with each exposure by an informed friend potentially resulting in a naive individual becoming infected. However, empirical studies of social media suggest that individual response to repeated exposure to information is far more complex. As a proxy for intervention experiments, we compare user responses to multiple exposures on two different social media sites, Twitter and Digg. We show that the position of exposing messages on the user-interface strongly affects social contagion. Accounting for this visibility significantly simplifies the dynamics of social contagion. The likelihood an individual will spread information increases monotonically with exposure, while explicit feedback about how many friends have previously spread it increases the likelihood of a response. We provide a framework for unifying information visibility, divided attention, and explicit social feedback to predict the temporal dynamics of user behavior.

The Simple Rules of Social Contagion

NASA Astrophysics Data System (ADS)

Hodas, Nathan O.; Lerman, Kristina

2014-03-01

It is commonly believed that information spreads between individuals like a pathogen, with each exposure by an informed friend potentially resulting in a naive individual becoming infected. However, empirical studies of social media suggest that individual response to repeated exposure to information is far more complex. As a proxy for intervention experiments, we compare user responses to multiple exposures on two different social media sites, Twitter and Digg. We show that the position of exposing messages on the user-interface strongly affects social contagion. Accounting for this visibility significantly simplifies the dynamics of social contagion. The likelihood an individual will spread information increases monotonically with exposure, while explicit feedback about how many friends have previously spread it increases the likelihood of a response. We provide a framework for unifying information visibility, divided attention, and explicit social feedback to predict the temporal dynamics of user behavior.

On the Nexus of the Spatial Dynamics of Global Urbanization and the Age of the City

PubMed Central

Scheuer, Sebastian; Haase, Dagmar; Volk, Martin

2016-01-01

A number of concepts exist regarding how urbanization can be described as a process. Understanding this process that affects billions of people and its future development in a spatial manner is imperative to address related issues such as human quality of life. In the focus of spatially explicit studies on urbanization is typically a city, a particular urban region, an agglomeration. However, gaps remain in spatially explicit global models. This paper addresses that issue by examining the spatial dynamics of urban areas over time, for a full coverage of the world. The presented model identifies past, present and potential future hotspots of urbanization as a function of an urban area's spatial variation and age, whose relation could be depicted both as a proxy and as a path of urban development. PMID:27490199

On the Nexus of the Spatial Dynamics of Global Urbanization and the Age of the City.

PubMed

Scheuer, Sebastian; Haase, Dagmar; Volk, Martin

2016-01-01

A number of concepts exist regarding how urbanization can be described as a process. Understanding this process that affects billions of people and its future development in a spatial manner is imperative to address related issues such as human quality of life. In the focus of spatially explicit studies on urbanization is typically a city, a particular urban region, an agglomeration. However, gaps remain in spatially explicit global models. This paper addresses that issue by examining the spatial dynamics of urban areas over time, for a full coverage of the world. The presented model identifies past, present and potential future hotspots of urbanization as a function of an urban area's spatial variation and age, whose relation could be depicted both as a proxy and as a path of urban development.

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

Whicker, Jeffrey J; Field, Jason P; Belnap, Jayne

Emission and redistribution of dust due to wind erosion in drylands drives major biogeochemical dynamics and provides important aeolian environmental connectivity at scales from individual plants up to the global scale. Yet, perhaps because most relevant research on aeolian processes has been presented in a geosciences rather than ecological context, most ecological studies do not explicitly consider dust-driven processes. To bridge this disciplinary gap, we provide a general overview of the ecological importance of dust, examine complex interactions between wind erosion and ecosystem dynamics from the plant-interspace scale to regional and global scales, and highlight specific examples of how disturbancemore » affects these interactions and their consequences. Changes in climate and intensification of land use will both likely lead to increased dust production. To address these challenges, environmental scientists, land managers and policy makers need to more explicitly consider dust in resource management decisions.« less

Knowledge exchange and integrated services: experiences from an integrated community intellectual (learning) disability service for adults.

PubMed

Farrington, C; Clare, I C H; Holland, A J; Barrett, M; Oborn, E

2015-03-01

This paper examines knowledge exchange dynamics in a specialist integrated intellectual (learning) disability service, comprising specialist healthcare provision with social care commissioning and management, and considers their significance in terms of integrated service delivery. A qualitative study focusing on knowledge exchange and integrated services. Semi-structured interviews (n = 25) were conducted with members of an integrated intellectual disability service in England regarding their perceptions of knowledge exchange within the service and the way in which knowledge exchange impinges on the operation of the integrated service. Exchange of 'explicit' (codifiable) knowledge between health and care management components of the service is problematic because of a lack of integrated clinical governance and related factors such as IT and care record systems and office arrangements. Team meetings and workplace interactions allowed for informal exchange of explicit and 'tacit' (non-codifiable) knowledge, but presented challenges in terms of knowledge exchange completeness and sustainability. Knowledge exchange processes play an important role in the functioning of integrated services incorporating health and care management components. Managers need to ensure that knowledge exchange processes facilitate both explicit and tacit knowledge exchange and do not rely excessively on informal, 'ad hoc' interactions. Research on integrated services should take account of micro-scale knowledge exchange dynamics and relationships between social dynamics and physical factors. © 2014 MENCAP and International Association of the Scientific Study of Intellectual and Developmental Disabilities and John Wiley & Sons Ltd.

Novel application of explicit dynamics occupancy models to ongoing aquatic invasions

USGS Publications Warehouse

Sepulveda, Adam J.

2018-01-01

Identification of suitable habitats, where invasive species can establish, is an important step towards controlling their spread. Accurate identification is difficult for new or slow invaders because unoccupied habitats may be suitable, given enough time for dispersal, while occupied habitats may prove to be unsuitable for establishment.To identify the suitable habitat of a recent invader, I used an explicit dynamics occupancy modelling framework to evaluate habitat covariates related to successful and failed establishments of American bullfrogs (Lithobates catesbeianus) within the Yellowstone River floodplain of Montana, USA from 2012-2016.During this five-year period, bullfrogs failed to establish at most sites they colonized. Bullfrog establishment was most likely to occur and least likely to fail at sites closest to human-modified ponds and lakes and those with emergent vegetation. These habitat covariates were generally associated with the presence of permanent water.Suitable habitat for bullfrog establishment is abundant in the Yellowstone River floodplain, though many sites with suitable habitat remain uncolonized. Thus, the maximum distribution of bullfrogs is much greater than their current distribution.Synthesis and applications. Focused control efforts on habitats with or proximate to permanent waters are most likely to reduce the potential for invasive bullfrog establishment and spread in the Yellowstone River. The novel application of explicit dynamics occupancy models is a useful and widely applicable tool for guiding management efforts towards those habitats where new or slow invaders are most likely to establish and persist.

Vibrotactile Feedback Alters Dynamics Of Static Postural Control In Persons With Parkinson's Disease But Not Older Adults At High Fall Risk.

PubMed

High, Carleigh M; McHugh, Hannah F; Mills, Stephen C; Amano, Shinichi; Freund, Jane E; Vallabhajosula, Srikant

2018-06-01

Aging and Parkinson's disease are often associated with impaired postural control. Providing extrinsic feedback via vibrotactile sensation could supplement intrinsic feedback to maintain postural control. We investigated the postural control response to vibrotactile feedback provided at the trunk during challenging stance conditions in older adults at high fall risk and individuals with Parkinson's disease compared to healthy older adults. Nine older adults at high fall risk, 9 persons with Parkinson's disease and 10 healthy older adults performed 30s quiet standing on a force platform under five challenging stance conditions with eyes open/closed and standing on firm/foam surface with feet together, each with and without vibrotactile feedback. During vibrotactile feedback trials, feedback was provided when participants swayed >10% over the center of their base of support. Participants were instructed vibrations would be in response to their movement. Magnitude of postural sway was estimated using center of pressure path length, velocity, and sway area. Dynamics of individuals' postural control was evaluated using detrended fluctuation analysis. Results showed that vibrotactile feedback induced a change in postural control dynamics among persons with Parkinson's disease when standing with intact intrinsic visual input and altered intrinsic somatosensory input, but there was no change in sway magnitude. However, use of vibrotactile feedback did not significantly alter dynamics of postural control in older adults with high risk of falling or reduce the magnitude of sway. Considering the effects of vibrotactile feedback were dependent on the population and stance condition, designing an optimal therapeutic regimen for balance training should be carefully considered and be specific to a target population. Furthermore, our results suggest that explicit instructions on how to respond to the vibrotactile feedback could affect training outcome. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

A Systematic Bayesian Integration of Epidemiological and Genetic Data

PubMed Central

Lau, Max S. Y.; Marion, Glenn; Streftaris, George; Gibson, Gavin

2015-01-01

Genetic sequence data on pathogens have great potential to inform inference of their transmission dynamics ultimately leading to better disease control. Where genetic change and disease transmission occur on comparable timescales additional information can be inferred via the joint analysis of such genetic sequence data and epidemiological observations based on clinical symptoms and diagnostic tests. Although recently introduced approaches represent substantial progress, for computational reasons they approximate genuine joint inference of disease dynamics and genetic change in the pathogen population, capturing partially the joint epidemiological-evolutionary dynamics. Improved methods are needed to fully integrate such genetic data with epidemiological observations, for achieving a more robust inference of the transmission tree and other key epidemiological parameters such as latent periods. Here, building on current literature, a novel Bayesian framework is proposed that infers simultaneously and explicitly the transmission tree and unobserved transmitted pathogen sequences. Our framework facilitates the use of realistic likelihood functions and enables systematic and genuine joint inference of the epidemiological-evolutionary process from partially observed outbreaks. Using simulated data it is shown that this approach is able to infer accurately joint epidemiological-evolutionary dynamics, even when pathogen sequences and epidemiological data are incomplete, and when sequences are available for only a fraction of exposures. These results also characterise and quantify the value of incomplete and partial sequence data, which has important implications for sampling design, and demonstrate the abilities of the introduced method to identify multiple clusters within an outbreak. The framework is used to analyse an outbreak of foot-and-mouth disease in the UK, enhancing current understanding of its transmission dynamics and evolutionary process. PMID:26599399

Applying metapopulation theory to conservation of migratory birds

USGS Publications Warehouse

Esler, Daniel N.

2000-01-01

Metapopulation theory has proven useful for understanding the population structure and dynamics of many species of conservation concern. The metapopulation concept has been applied almost exclusively to nonmigratory species, however, for which subpopulation demographic independence—a requirement for a classically defined metapopulation - is explicitly related to geographic distribution and dispersal probabilities. Defining the degree of demographic independence among subpopulations of migratory animals, and thus the applicability of metapopulation theory as a conceptual framework for understanding population dynamics, is much more difficult. Unlike nonmigratory species, subpopulations of migratory animals cannot be defined as synonymous with geographic areas. Groups of migratory birds that are geographically separate at one part of the annual cycle may occur together at others, but co-occurrence in time and space does not preclude the demographic independence of subpopulations. I suggest that metapopulation theory can be applied to migratory species but that understanding the degree of subpopulation independence may require information about both spatial distribution throughout the annual cycle and behavioral mechanisms that may lead to subpopulation demographic independence. The key for applying metapopulation theory to migratory animals lies in identifying demographically independent subpopulations, even as they move during the annual cycle and potentially co-occur with other subpopulations. Using examples of migratory bird species, I demonstrate that spatial and temporal modes of subpopulation independence can interact with behavioral mechanisms to create demographically independent subpopulations, including cases in which subpopulations are not spatially distinct in some parts of the annual cycle.

Proline zwitterion dynamics in solution, glass, and crystalline state.

PubMed

Kapitán, Josef; Baumruk, Vladimír; Kopecký, Vladimír; Pohl, Radek; Bour, Petr

2006-10-18

Raman and Raman optical activity spectra of L- and D-proline zwitterionic (PROZW) forms were recorded for H(2)O and D(2)O solutions in a wide frequency range and analyzed with respect to the motion of the proline ring and rotation of the carbonyl group. The solution spectra were additionally compared to Raman scattering of glass and crystalline powder proline. Solution and glass spectral band broadenings are similar and reveal information about the extent of internal molecular motion. Two distinct but equally populated flexible forms were found in the glass and the solution. The equal population is consistent with NMR data, temperature, and concentration dependencies. The molecular flexibility is reduced significantly in the crystal, however, where only one conformer is present. Consequently, the crystal bands are narrow and exhibit minor frequency shifts. The spectra were interpreted with the aid of density functional theory computations involving both continuum and explicit solvent. A two-dimensional potential energy surface pertaining to the five-member ring puckering coordinates was constructed and used for dynamical averaging of spectral properties. Comparison of the computed and experimental bandwidths suggests that the puckering is strongly correlated with the carbonyl rotation. An averaging over these two motions produces similar results. The interpretation of the Raman experiments with the aid of the simulation techniques also indicates that the environment modulates properties of the hydrophobic part of the molecule indirectly by interacting with the ionic group. Such behavior may be important for the reactivity and biological activity of proline-containing peptides and proteins.

Subjective visual perception: from local processing to emergent phenomena of brain activity.

PubMed

Panagiotaropoulos, Theofanis I; Kapoor, Vishal; Logothetis, Nikos K

2014-05-05

The combination of electrophysiological recordings with ambiguous visual stimulation made possible the detection of neurons that represent the content of subjective visual perception and perceptual suppression in multiple cortical and subcortical brain regions. These neuronal populations, commonly referred to as the neural correlates of consciousness, are more likely to be found in the temporal and prefrontal cortices as well as the pulvinar, indicating that the content of perceptual awareness is represented with higher fidelity in higher-order association areas of the cortical and thalamic hierarchy, reflecting the outcome of competitive interactions between conflicting sensory information resolved in earlier stages. However, despite the significant insights into conscious perception gained through monitoring the activities of single neurons and small, local populations, the immense functional complexity of the brain arising from correlations in the activity of its constituent parts suggests that local, microscopic activity could only partially reveal the mechanisms involved in perceptual awareness. Rather, the dynamics of functional connectivity patterns on a mesoscopic and macroscopic level could be critical for conscious perception. Understanding these emergent spatio-temporal patterns could be informative not only for the stability of subjective perception but also for spontaneous perceptual transitions suggested to depend either on the dynamics of antagonistic ensembles or on global intrinsic activity fluctuations that may act upon explicit neural representations of sensory stimuli and induce perceptual reorganization. Here, we review the most recent results from local activity recordings and discuss the potential role of effective, correlated interactions during perceptual awareness.

Subjective visual perception: from local processing to emergent phenomena of brain activity

PubMed Central

Panagiotaropoulos, Theofanis I.; Kapoor, Vishal; Logothetis, Nikos K.

2014-01-01

The combination of electrophysiological recordings with ambiguous visual stimulation made possible the detection of neurons that represent the content of subjective visual perception and perceptual suppression in multiple cortical and subcortical brain regions. These neuronal populations, commonly referred to as the neural correlates of consciousness, are more likely to be found in the temporal and prefrontal cortices as well as the pulvinar, indicating that the content of perceptual awareness is represented with higher fidelity in higher-order association areas of the cortical and thalamic hierarchy, reflecting the outcome of competitive interactions between conflicting sensory information resolved in earlier stages. However, despite the significant insights into conscious perception gained through monitoring the activities of single neurons and small, local populations, the immense functional complexity of the brain arising from correlations in the activity of its constituent parts suggests that local, microscopic activity could only partially reveal the mechanisms involved in perceptual awareness. Rather, the dynamics of functional connectivity patterns on a mesoscopic and macroscopic level could be critical for conscious perception. Understanding these emergent spatio-temporal patterns could be informative not only for the stability of subjective perception but also for spontaneous perceptual transitions suggested to depend either on the dynamics of antagonistic ensembles or on global intrinsic activity fluctuations that may act upon explicit neural representations of sensory stimuli and induce perceptual reorganization. Here, we review the most recent results from local activity recordings and discuss the potential role of effective, correlated interactions during perceptual awareness. PMID:24639588

COMPARING ECOLOGICALLY SCALED LANDSCAPE INDICES WITH A SPATIALLY EXPLICIT POPULATION MODEL

EPA Science Inventory

Vos et al. (2001) proposed a class of landscape indices they called ecologically scaled. By this they meant that the indices incorporate species-specific characteristics that are assumed to be important for population viability. I used their two ideas of species carrying capaci...

Influence of Pleistocene glacial/interglacial cycles on the genetic structure of the mistletoe cactus Rhipsalis baccifera (Cactaceae) in Mesoamerica.

PubMed

Ornelas, Juan Francisco; Rodríguez-Gómez, Flor

2015-01-01

Phylogeographical work on cloud forest-adapted species provides inconsistent evidence on cloud forest dynamics during glacial cycles. A study of Rhipsalis baccifera (Cactaceae), a bird-dispersed epiphytic mistletoe cactus, was conducted to investigate genetic variation at sequence data from nuclear [internal transcribed spacer (ITS), 677 bp] and chloroplast (rpl32-trnL, 1092bp) DNA for 154 individuals across the species range in Mesoamerica to determine if such patterns are consistent with the expansion/contraction model of cloud forest during glacial cycles. We conducted population and spatial genetic analyses as well as gene flow and divergence time estimates between 24 populations comprising the distribution of R. baccifera in Mexico and Guatemala to gain insight of the evolutionary history of these populations, and a complementary species distribution modeling approach to frame information derived from the genetic analyses into an explicit paleoecological context. The results revealed a phylogeographical break at the Isthmus of Tehuantepec, and high levels of genetic diversity among populations and cloud forest areas. Despite the genetic differentiation of some R. baccifera populations, the widespread ITS ribotypes suggest effective nuclear gene flow via pollen and population differentiation shown by the rpl32-trnL suggests more restricted seed flow. Predictions of species distribution models under past last glacial maximum (LGM) climatic conditions and a significant signal of demographic expansion suggest that R. baccifera populations experienced a range expansion tracking the conditions of the cloud forest distribution and shifted to the lowlands with population connectivity during the LGM. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Decision or no decision: how do patient-physician interactions end and what matters?

PubMed

Tai-Seale, Ming; Bramson, Rachel; Bao, Xiaoming

2007-03-01

A clearly stated clinical decision can induce a cognitive closure in patients and is an important investment in the end of patient-physician communications. Little is known about how often explicit decisions are made in primary care visits. To use an innovative videotape analysis approach to assess physicians' propensity to state decisions explicitly, and to examine the factors influencing decision patterns. We coded topics discussed in 395 videotapes of primary care visits, noting the number of instances and the length of discussions on each topic, and how discussions ended. A regression analysis tested the relationship between explicit decisions and visit factors such as the nature of topics under discussion, instances of discussion, the amount of time the patient spoke, and competing demands from other topics. About 77% of topics ended with explicit decisions. Patients spoke for an average of 58 seconds total per topic. Patients spoke more during topics that ended with an explicit decision, (67 seconds), compared with 36 seconds otherwise. The number of instances of a topic was associated with higher odds of having an explicit decision (OR = 1.73, p < 0.01). Increases in the number of topics discussed in visits (OR = 0.95, p < .05), and topics on lifestyle and habits (OR = 0.60, p < .01) were associated with lower odds of explicit decisions. Although discussions often ended with explicit decisions, there were variations related to the content and dynamics of interactions. We recommend strengthening patients' voice and developing clinical tools, e.g., an "exit prescription," to improving decision making.

sGD: software for estimating spatially explicit indices of genetic diversity.

PubMed

Shirk, A J; Cushman, S A

2011-09-01

Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial species. The small local effective population size of remnant populations favours loss of genetic diversity leading to reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the multilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Importantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic factors to influence the viability of clinal populations and guide appropriate conservation plans. © 2011 Blackwell Publishing Ltd.

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems

PubMed Central

Sauterey, Boris; Ward, Ben A.; Follows, Michael J.; Bowler, Chris; Claessen, David

2015-01-01

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that “Everything is everywhere, but the environment selects”, we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean. PMID:25852217

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems.

PubMed

Sauterey, Boris; Ward, Ben A; Follows, Michael J; Bowler, Chris; Claessen, David

2015-01-01

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that "Everything is everywhere, but the environment selects", we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean.

Ecological theatre and the evolutionary game: how environmental and demographic factors determine payoffs in evolutionary games.

PubMed

Argasinski, K; Broom, M

2013-10-01

In the standard approach to evolutionary games and replicator dynamics, differences in fitness can be interpreted as an excess from the mean Malthusian growth rate in the population. In the underlying reasoning, related to an analysis of "costs" and "benefits", there is a silent assumption that fitness can be described in some type of units. However, in most cases these units of measure are not explicitly specified. Then the question arises: are these theories testable? How can we measure "benefit" or "cost"? A natural language, useful for describing and justifying comparisons of strategic "cost" versus "benefits", is the terminology of demography, because the basic events that shape the outcome of natural selection are births and deaths. In this paper, we present the consequences of an explicit analysis of births and deaths in an evolutionary game theoretic framework. We will investigate different types of mortality pressures, their combinations and the possibility of trade-offs between mortality and fertility. We will show that within this new approach it is possible to model how strictly ecological factors such as density dependence and additive background fitness, which seem neutral in classical theory, can affect the outcomes of the game. We consider the example of the Hawk-Dove game, and show that when reformulated in terms of our new approach new details and new biological predictions are produced.

Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

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

Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn

2015-03-28

The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much lessmore » computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.« less

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function

PubMed Central

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A.

2012-01-01

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that the functional evolution can be inferred from the changes in the protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced Cα representation of the protein structure while enzymatic function is described by Enzyme Commission (EC) numbers. Similarity of the binding pocket dynamics at each branch of the protein family’s phylogeny was analyzed in two ways: 1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and 2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the alpha-amylase, D-isomer specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal modes analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. PMID:22651983