Science.gov

Sample records for dynamic species exchange

  1. The Dynamics of Multilateral Exchange

    NASA Astrophysics Data System (ADS)

    Hausken, Kjell; Moxnes, John F.

    The article formulates a dynamic mathematical model where arbitrarily many players produce, consume, exchange, loan, and deposit arbitrarily many goods over time to maximize utility. Consuming goods constitutes a benefit, and producing, exporting, and loaning away goods constitute a cost. Utilities are benefits minus costs, which depend on the exchange ratios and bargaining functions. Three-way exchange occurs when one player acquires, through exchange, one good from another player with the sole purpose of using this good to exchange against the desired good from a third player. Such a triple handshake is not merely a set of double handshakes since the player assigns no interest to the first good in his benefit function. Cognitive and organization costs increase dramatically for higher order exchanges. An exchange theory accounting for media of exchange follows from simple generalization of two-way exchange. The examples of r-way exchange are the triangle trade between Africa, the USA, and England in the 17th and 18th centuries, the hypothetical hypercycle involving RNAs as players and enzymes as goods, and reaction-diffusion processes. The emergence of exchange, and the role of trading agents are discussed. We simulate an example where two-way exchange gives zero production and zero utility, while three-way exchange causes considerable production and positive utility. Maximum utility for each player is reached when exchanges of the same order as the number of players in society are allowed. The article merges micro theory and macro theory within the social, natural, and physical sciences.

  2. Nonadiabatic exchange dynamics during adiabatic frequency sweeps

    NASA Astrophysics Data System (ADS)

    Barbara, Thomas M.

    2016-04-01

    A Bloch equation analysis that includes relaxation and exchange effects during an adiabatic frequency swept pulse is presented. For a large class of sweeps, relaxation can be incorporated using simple first order perturbation theory. For anisochronous exchange, new expressions are derived for exchange augmented rotating frame relaxation. For isochronous exchange between sites with distinct relaxation rate constants outside the extreme narrowing limit, simple criteria for adiabatic exchange are derived and demonstrate that frequency sweeps commonly in use may not be adiabatic with regard to exchange unless the exchange rates are much larger than the relaxation rates. Otherwise, accurate assessment of the sensitivity to exchange dynamics will require numerical integration of the rate equations. Examples of this situation are given for experimentally relevant parameters believed to hold for in-vivo tissue. These results are of significance in the study of exchange induced contrast in magnetic resonance imaging.

  3. Marriage exchanges, seed exchanges, and the dynamics of manioc diversity

    PubMed Central

    Delêtre, Marc; McKey, Doyle B.; Hodkinson, Trevor R.

    2011-01-01

    The conservation of crop genetic resources requires understanding the different variables—cultural, social, and economic—that impinge on crop diversity. In small-scale farming systems, seed exchanges represent a key mechanism in the dynamics of crop genetic diversity, and analyzing the rules that structure social networks of seed exchange between farmer communities can help decipher patterns of crop genetic diversity. Using a combination of ethnobotanical and molecular genetic approaches, we investigated the relationships between regional patterns of manioc genetic diversity in Gabon and local networks of seed exchange. Spatially explicit Bayesian clustering methods showed that geographical discontinuities of manioc genetic diversity mirror major ethnolinguistic boundaries, with a southern matrilineal domain characterized by high levels of varietal diversity and a northern patrilineal domain characterized by low varietal diversity. Borrowing concepts from anthropology—kinship, bridewealth, and filiation—we analyzed the relationships between marriage exchanges and seed exchange networks in patrilineal and matrilineal societies. We demonstrate that, by defining marriage prohibitions, kinship systems structure social networks of exchange between farmer communities and influence the movement of seeds in metapopulations, shaping crop diversity at local and regional levels. PMID:22042843

  4. Pion double charge exchange and hadron dynamics

    SciTech Connect

    Johnson, M.B.

    1991-01-01

    This paper will review theoretical results to show how pion double charge exchange is contributing to our understanding of hadron dynamics in nuclei. The exploitation of the nucleus as a filter is shown to be essential in facilitating the comparison between theory and experiment. 23 refs., 3 figs., 2 tabs.

  5. Spread dynamics of invasive species

    PubMed Central

    Arim, Matías; Abades, Sebastián R.; Neill, Paula E.; Lima, Mauricio; Marquet, Pablo A.

    2006-01-01

    Species invasions are a principal component of global change, causing large losses in biodiversity as well as economic damage. Invasion theory attempts to understand and predict invasion success and patterns of spread. However, there is no consensus regarding which species or community attributes enhance invader success or explain spread dynamics. Experimental and theoretical studies suggest that regulation of spread dynamics is possible; however, the conditions for its existence have not yet been empirically demonstrated. If invasion spread is a regulated process, the structure that accounts for this regulation will be a main determinant of invasion dynamics. Here we explore the existence of regulation underlying changes in the rate of new site colonization. We employ concepts and analytical tools from the study of abundance dynamics and show that spread dynamics are, in fact, regulated processes and that the regulation structure is notably consistent among invasions occurring in widely different contexts. We base our conclusions on the analysis of the spread dynamics of 30 species invasions, including birds, amphibians, fish, invertebrates, plants, and a virus, all of which exhibited similar regulation structures. In contrast to current beliefs that species invasions are idiosyncratic phenomena, here we provide evidence that general patterns do indeed exist. PMID:16387862

  6. Exchange of Standardized Flight Dynamics Data

    NASA Technical Reports Server (NTRS)

    Martin-Mur, Tomas J.; Berry, David; Flores-Amaya, Felipe; Folliard, J.; Kiehling, R.; Ogawa, M.; Pallaschke, S.

    2004-01-01

    Spacecraft operations require the knowledge of the vehicle trajectory and attitude and also that of other spacecraft or natural bodies. This knowledge is normally provided by the Flight Dynamics teams of the different space organizations and, as very often spacecraft operations involve more than one organization, this information needs to be exchanged between Agencies. This is why the Navigation Working Group within the CCSDS (Consultative Committee for Space Data Systems), has been instituted with the task of establishing standards for the exchange of Flight Dynamics data. This exchange encompasses trajectory data, attitude data, and tracking data. The Navigation Working Group includes regular members and observers representing the participating Space Agencies. Currently the group includes representatives from CNES, DLR, ESA, NASA and JAXA. This Working Group meets twice per year in order to devise standardized language, methods, and formats for the description and exchange of Navigation data. Early versions of some of these standards have been used to support mutual tracking of ESA and NASA interplanetary spacecraft, especially during the arrival of the 2003 missions to Mars. This paper provides a summary of the activities carried out by the group, briefly outlines the current and envisioned standards, describes the tests and operational activities that have been performed using the standards, and lists and discusses the lessons learned from these activities.

  7. Molecular Exchange Dynamics in Block Copolymer Micelles

    NASA Astrophysics Data System (ADS)

    Bates, Frank; Lu, Jie; Choi, Soohyung; Lodge, Timothy

    2012-02-01

    Poly(styrene-b-ethylene propylene) (PS-PEP) diblock copolymers were mixed with squalane (C30H62) at 1% by weight resulting in the formation of spherical micelles. The structure and dynamics of molecular exchange were characterized by synchrotron small-angle x-ray scattering (SAXS) and time resolved small-angle neutron scattering (TR-SANS), respectively, between 100 C and 160 C. TR-SANS measurements were performed with solutions initially containing deuterium labeled micelle cores and normal cores dispersed in a contrast matched squalane. Monitoring the reduction in scattering intensity as a function of time at various temperatures revealed molecular exchange dynamics highly sensitive to the core molecular weight and molecular weight distribution. Time-temperature superposition of data acquired at different temperatures produced a single master curve for all the mixtures. Experiments conducted with isotopically labeled micelle cores, each formed from two different but relatively mondisperse PS blocks, confirmed a simple dynamical model based on first order kinetics and core Rouse single chain relaxation. These findings demonstrate a dramatic transition to nonergodicity with increasing micelle core molecular weight and confirm the origins of the logarithmic exchange kinetics in such systems.

  8. Do Heliconius butterfly species exchange mimicry alleles?

    PubMed

    Smith, Joel; Kronforst, Marcus R

    2013-08-23

    Hybridization has the potential to transfer beneficial alleles across species boundaries, and there are a growing number of examples in which this has apparently occurred. Recent studies suggest that Heliconius butterflies have transferred wing pattern mimicry alleles between species via hybridization, but ancestral polymorphism could also produce a signature of shared ancestry around mimicry genes. To distinguish between these alternative hypotheses, we measured DNA sequence divergence around putatively introgressed mimicry loci and compared this with the rest of the genome. Our results reveal that putatively introgressed regions show strongly reduced sequence divergence between co-mimetic species, suggesting that their divergence times are younger than the rest of the genome. This is consistent with introgression and not ancestral variation. We further show that this signature of introgression occurs at sites throughout the genome, not just around mimicry genes.

  9. Dynamic Analysis of Capture Devices for Momentum Exchange with Tethers

    NASA Technical Reports Server (NTRS)

    Canfield, Stephen

    2002-01-01

    One of the significant challenges in developing a momentum exchange / electrodynamic reboost tether system is in the analysis and design of the capture device and its effects on the overall dynamics of the system. The goal of this work is to develop appropriate tether momentum exchange models that can simulate and evaluate the requirements of such a system, and be used to create specifications on the design of a capture device. This report briefly describes dynamic model development, simulation of the momentum exchange process, evaluation of dynamic effects of errors in the momentum exchange process, and the development of guidelines in selecting dynamic properties in the design of a capture device.

  10. Wealth distribution of simple exchange models coupled with extremal dynamics

    NASA Astrophysics Data System (ADS)

    Bagatella-Flores, N.; Rodríguez-Achach, M.; Coronel-Brizio, H. F.; Hernández-Montoya, A. R.

    2015-01-01

    Punctuated Equilibrium (PE) states that after long periods of evolutionary quiescence, species evolution can take place in short time intervals, where sudden differentiation makes new species emerge and some species extinct. In this paper, we introduce and study the effect of punctuated equilibrium on two different asset exchange models: the yard sale model (YS, winner gets a random fraction of a poorer player's wealth) and the theft and fraud model (TF, winner gets a random fraction of the loser's wealth). The resulting wealth distribution is characterized using the Gini index. In order to do this, we consider PE as a perturbation with probability ρ of being applied. We compare the resulting values of the Gini index at different increasing values of ρ in both models. We found that in the case of the TF model, the Gini index reduces as the perturbation ρ increases, not showing dependence with the agents number. While for YS we observe a phase transition which happens around ρc = 0.79. For perturbations ρ <ρc the Gini index reaches the value of one as time increases (an extreme wealth condensation state), whereas for perturbations greater than or equal to ρc the Gini index becomes different to one, avoiding the system reaches this extreme state. We show that both simple exchange models coupled with PE dynamics give more realistic results. In particular for YS, we observe a power low decay of wealth distribution.

  11. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species

    PubMed Central

    Dasmahapatra, Kanchon K; Walters, James R.; Briscoe, Adriana D.; Davey, John W.; Whibley, Annabel; Nadeau, Nicola J.; Zimin, Aleksey V.; Hughes, Daniel S. T.; Ferguson, Laura C.; Martin, Simon H.; Salazar, Camilo; Lewis, James J.; Adler, Sebastian; Ahn, Seung-Joon; Baker, Dean A.; Baxter, Simon W.; Chamberlain, Nicola L.; Chauhan, Ritika; Counterman, Brian A.; Dalmay, Tamas; Gilbert, Lawrence E.; Gordon, Karl; Heckel, David G.; Hines, Heather M.; Hoff, Katharina J.; Holland, Peter W.H.; Jacquin-Joly, Emmanuelle; Jiggins, Francis M.; Jones, Robert T.; Kapan, Durrell D.; Kersey, Paul; Lamas, Gerardo; Lawson, Daniel; Mapleson, Daniel; Maroja, Luana S.; Martin, Arnaud; Moxon, Simon; Palmer, William J.; Papa, Riccardo; Papanicolaou, Alexie; Pauchet, Yannick; Ray, David A.; Rosser, Neil; Salzberg, Steven L.; Supple, Megan A.; Surridge, Alison; Tenger-Trolander, Ayse; Vogel, Heiko; Wilkinson, Paul A.; Wilson, Derek; Yorke, James A.; Yuan, Furong; Balmuth, Alexi L.; Eland, Cathlene; Gharbi, Karim; Thomson, Marian; Gibbs, Richard A.; Han, Yi; Jayaseelan, Joy C.; Kovar, Christie; Mathew, Tittu; Muzny, Donna M.; Ongeri, Fiona; Pu, Ling-Ling; Qu, Jiaxin; Thornton, Rebecca L.; Worley, Kim C.; Wu, Yuan-Qing; Linares, Mauricio; Blaxter, Mark L.; Constant, Richard H. ffrench; Joron, Mathieu; Kronforst, Marcus R.; Mullen, Sean P.; Reed, Robert D.; Scherer, Steven E.; Richards, Stephen; Mallet, James; McMillan, W. Owen; Jiggins, Chris D.

    2012-01-01

    The evolutionary importance of hybridization and introgression has long been debated1. We used genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2-5 . We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,657 predicted genes for Heliconius, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organisation has remained broadly conserved since the Cretaceous, when butterflies split from the silkmoth lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, H. melpomene, H. timareta, and H. elevatus, especially at two genomic regions that control mimicry pattern. Closely related Heliconius species clearly exchange protective colour pattern genes promiscuously, implying a major role for hybridization in adaptive radiation. PMID:22722851

  12. Extensions to the Dynamic Aerospace Vehicle Exchange Markup Language

    NASA Technical Reports Server (NTRS)

    Brian, Geoffrey J.; Jackson, E. Bruce

    2011-01-01

    The Dynamic Aerospace Vehicle Exchange Markup Language (DAVE-ML) is a syntactical language for exchanging flight vehicle dynamic model data. It provides a framework for encoding entire flight vehicle dynamic model data packages for exchange and/or long-term archiving. Version 2.0.1 of DAVE-ML provides much of the functionality envisioned for exchanging aerospace vehicle data; however, it is limited in only supporting scalar time-independent data. Additional functionality is required to support vector and matrix data, abstracting sub-system models, detailing dynamics system models (both discrete and continuous), and defining a dynamic data format (such as time sequenced data) for validation of dynamics system models and vehicle simulation packages. Extensions to DAVE-ML have been proposed to manage data as vectors and n-dimensional matrices, and record dynamic data in a compatible form. These capabilities will improve the clarity of data being exchanged, simplify the naming of parameters, and permit static and dynamic data to be stored using a common syntax within a single file; thereby enhancing the framework provided by DAVE-ML for exchanging entire flight vehicle dynamic simulation models.

  13. Spatial variability in plant species composition and peatland carbon exchange

    NASA Astrophysics Data System (ADS)

    Goud, E.; Moore, T. R.; Roulet, N. T.

    2015-12-01

    Plant species shifts in response to global change will have significant impacts on ecosystem carbon (C) exchange and storage arising from changes in hydrology. Spatial variation in peatland C fluxes have largely been attributed to the spatial distribution of microhabitats that arise from variation in surface topography and water table depth, but little is known about how plant species composition impacts peatland C cycling or how these impacts will be influenced by changing environmental conditions. We quantified the effect of species composition and environmental variables on carbon dioxide (CO2) and methane (CH4) fluxes over 2 years in a temperate peatland for four plant communities situated along a water table gradient from ombrotrophic bog to beaver pond. We hypothesized that (i) spatial heterogeneity in species composition would drive predictable spatial heterogeneity in C fluxes due to variation in plant traits and ecological tolerances, and (ii) increases in peat temperature would increase C fluxes. Species had different effects on C fluxes primarily due to differences in leaf traits. Differences in ecological tolerances among communities resulted in different rates of CO2 exchange in response to changes in water table depth. There was an overall reduction in ecosystem respiration (ER), gross primary productivity (GPP) and CH4 flux in response to colder peat temperatures in the second year, and the additive effects of a deeper water table in the bog margin and pond sites further reduced flux rates in these areas. These results demonstrate that different plant species can increase or decrease the flux of C into and out of peatlands based on differences in leaf traits and ecological tolerances, and that CO2 and CH4 fluxes are sensitive to changes in soil temperature, especially when coupled with changes in moisture availability.

  14. Reactive oxygen species production and discontinuous gas exchange in insects

    PubMed Central

    Boardman, Leigh; Terblanche, John S.; Hetz, Stefan K.; Marais, Elrike; Chown, Steven L.

    2012-01-01

    While biochemical mechanisms are typically used by animals to reduce oxidative damage, insects are suspected to employ a higher organizational level, discontinuous gas exchange mechanism to do so. Using a combination of real-time, flow-through respirometry and live-cell fluorescence microscopy, we show that spiracular control associated with the discontinuous gas exchange cycle (DGC) in Samia cynthia pupae is related to reactive oxygen species (ROS). Hyperoxia fails to increase mean ROS production, although minima are elevated above normoxic levels. Furthermore, a negative relationship between mean and mean ROS production indicates that higher ROS production is generally associated with lower . Our results, therefore, suggest a possible signalling role for ROS in DGC, rather than supporting the idea that DGC acts to reduce oxidative damage by regulating ROS production. PMID:21865257

  15. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species.

    PubMed

    2012-07-01

    The evolutionary importance of hybridization and introgression has long been debated. Hybrids are usually rare and unfit, but even infrequent hybridization can aid adaptation by transferring beneficial traits between species. Here we use genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation. We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,669 predicted genes, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organization has remained broadly conserved since the Cretaceous period, when butterflies split from the Bombyx (silkmoth) lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, Heliconius melpomene, Heliconius timareta and Heliconius elevatus, especially at two genomic regions that control mimicry pattern. We infer that closely related Heliconius species exchange protective colour-pattern genes promiscuously, implying that hybridization has an important role in adaptive radiation. PMID:22722851

  16. Water exchange dynamics around H3O+ and OH- ions

    NASA Astrophysics Data System (ADS)

    Roy, Santanu; Dang, Liem X.

    2015-05-01

    In this letter, we report the first computer simulation of the dynamics of water exchanging between the first and second solvation shells of H3O+. Employing different rate theories for chemical reactions such as the transition state theory, the Grote-Hynes theory, the reactive flux method, and the Impey-Madden-McDonald method, we calculate the solvent exchange rates from molecular dynamics simulations that account for explicit polarization effects. In addition, we also study water exchanges around OH- and find that the corresponding time scale is much smaller than that for H3O+.

  17. Dynamic enhancement of the exchange bias training effect

    NASA Astrophysics Data System (ADS)

    Sahoo, Sarbeswar; Berger, Andreas; Polisetty, Srinivas; Binek, Christian

    2007-03-01

    Exchange bias in coupled magnetic films and its accompanying training effect are fundamental interface phenomena which impact spintronic applications. Training is referred to as a gradual change of the bias field, which evolves upon cycling the soft layer through consecutive hysteresis loops. We report on its dynamic enhancement in exchange coupled bilayers of soft and hard ferromagnetic materials. Dynamic effects are induced with increasing sweep rate of the applied magnetic field from quasi-static to the fully dynamic range. A dynamically generalized theory based on triggered and partially truncated relaxation is in excellent agreement with the data. Remarkable universality of our theoretical approach is evidenced when applying the approach to the dynamic training effect of a conventional exchange bias system involving an antiferromagnetic pinning layer.

  18. Complex dynamical behaviors of daily data series in stock exchange

    NASA Astrophysics Data System (ADS)

    Wang, Hongchun; Chen, Guanrong; Lü, Jinhu

    2004-12-01

    It is well known that many economic data series show chaotic behaviors. In this Letter, we further investigate the complex dynamical behaviors of the daily data series, including opening quotation, closing quotation, maximum price, minimum price, and total exchange quantum, in Shenzhen stock exchange and Shanghai stock exchange, which are two representative stock exchanges in mainland China. The maximum Lyapunov exponents, correlation dimensions, and frequency spectra are calculated for these time series. Our results indicate that some daily data series of stock exchanges display low-dimensional chaotic behaviors, and some other daily data series do not show any chaotic behavior. Moreover, we introduce a weighted one-rank local-region approach for predicting short-term daily data series of stock exchange.

  19. Reversible Control of Nanoparticle Functionalization and Physicochemical Properties by Dynamic Covalent Exchange**

    PubMed Central

    della Sala, Flavio; Kay, Euan R

    2015-01-01

    Existing methods for the covalent functionalization of nanoparticles rely on kinetically controlled reactions, and largely lack the sophistication of the preeminent oligonucleotide-based noncovalent strategies. Here we report the application of dynamic covalent chemistry for the reversible modification of nanoparticle (NP) surface functionality, combining the benefits of non-biomolecular covalent chemistry with the favorable features of equilibrium processes. A homogeneous monolayer of nanoparticle-bound hydrazones can undergo quantitative dynamic covalent exchange. The pseudomolecular nature of the NP system allows for the in situ characterization of surface-bound species, and real-time tracking of the exchange reactions. Furthermore, dynamic covalent exchange offers a simple approach for reversibly switching—and subtly tuning—NP properties such as solvophilicity. PMID:25973468

  20. Amide proton exchange of a dynamic loop in cell extracts.

    PubMed

    Smith, Austin E; Sarkar, Mohona; Young, Gregory B; Pielak, Gary J

    2013-10-01

    Intrinsic rates of exchange are essential parameters for obtaining protein stabilities from amide (1) H exchange data. To understand the influence of the intracellular environment on stability, one must know the effect of the cytoplasm on these rates. We probed exchange rates in buffer and in Escherichia coli lysates for the dynamic loop in the small globular protein chymotrypsin inhibitor 2 using a modified form of the nuclear magnetic resonance experiment, SOLEXSY. No significant changes were observed, even in 100 g dry weight L(-1) lysate. Our results suggest that intrinsic rates from studies conducted in buffers are applicable to studies conducted under cellular conditions.

  1. BOREAS TE-4 Gas Exchange Data from Boreal Tree Species

    NASA Technical Reports Server (NTRS)

    Hall, Forrest G. (Editor); Curd, Shelaine (Editor); Collatz, G. James; Berry, Joseph A.; Gamon, John; Fredeen, Art; Fu, Wei

    2000-01-01

    The BOREAS TE-4 team collected steady-state gas exchange and reflectance data from several species in the BOREAS SSA during 1994 and in the NSA during 1996. Measurements of light, CO2, temperature, and humidity response curves were made by the BOREAS TE-4 team during the summers of 1994 and 1996 using intact attached leaves of boreal forest species located in the BOREAS SSA and NSA. These measurements were conducted to calibrate models used to predict photosynthesis, stomatal conductance, and leaf respiration. The 1994 and 1996 data can be used to construct plots of response functions or for parameterizing models. Parameter values are suitable for application in SiB2 (Sellers et al., 1996) or the leaf model of Collatz et al. (1991), and programs can be obtained from the investigators. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  2. Glucans monomer-exchange dynamics as an open chemical network

    SciTech Connect

    Rao, Riccardo Esposito, Massimiliano; Lacoste, David

    2015-12-28

    We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them.

  3. Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.

    PubMed

    Orrillo, A Gastón; Escalante, Andrea M; Furlan, Ricardo L E

    2016-05-10

    Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks. PMID:26990904

  4. The Dynamics of Social Interaction in Telecollaborative Tandem Exchanges

    ERIC Educational Resources Information Center

    Janssen Sanchez, Brianna

    2015-01-01

    Using both quantitative and qualitative methods of inquiry, this dissertation study undertakes an exploration of the dynamics of the social interaction in discourse co-constructed by pairs of college students in telecollaborative tandem exchanges. Two groups of participants, Mexican learners of English as a foreign language and American learners…

  5. Combined Steady-State and Dynamic Heat Exchanger Experiment

    ERIC Educational Resources Information Center

    Luyben, William L.; Tuzla, Kemal; Bader, Paul N.

    2009-01-01

    This paper describes a heat-transfer experiment that combines steady-state analysis and dynamic control. A process-water stream is circulated through two tube-in-shell heat exchangers in series. In the first, the process water is heated by steam. In the second, it is cooled by cooling water. The equipment is pilot-plant size: heat-transfer areas…

  6. Dithioacetal Exchange: A New Reversible Reaction for Dynamic Combinatorial Chemistry.

    PubMed

    Orrillo, A Gastón; Escalante, Andrea M; Furlan, Ricardo L E

    2016-05-10

    Reversibility of dithioacetal bond formation is reported under acidic mild conditions. Its utility for dynamic combinatorial chemistry was explored by combining it with orthogonal disulfide exchange. In such a setup, thiols are positioned at the intersection of both chemistries, constituting a connecting node between temporally separated networks.

  7. Flight Dynamic Model Exchange using XML

    NASA Technical Reports Server (NTRS)

    Jackson, E. Bruce; Hildreth, Bruce L.

    2002-01-01

    The AIAA Modeling and Simulation Technical Committee has worked for several years to develop a standard by which the information needed to develop physics-based models of aircraft can be specified. The purpose of this standard is to provide a well-defined set of information, definitions, data tables and axis systems so that cooperating organizations can transfer a model from one simulation facility to another with maximum efficiency. This paper proposes using an application of the eXtensible Markup Language (XML) to implement the AIAA simulation standard. The motivation and justification for using a standard such as XML is discussed. Necessary data elements to be supported are outlined. An example of an aerodynamic model as an XML file is given. This example includes definition of independent and dependent variables for function tables, definition of key variables used to define the model, and axis systems used. The final steps necessary for implementation of the standard are presented. Software to take an XML-defined model and import/export it to/from a given simulation facility is discussed, but not demonstrated. That would be the next step in final implementation of standards for physics-based aircraft dynamic models.

  8. Tuning the dynamic exchange interaction in ferromagnet/semiconductor heterostructures

    NASA Astrophysics Data System (ADS)

    Ou, Yu-Sheng; Chiu, Yi-Hsin; Harmon, N. J.; Odenthal, Patrick; Sheffield, Matthew; Chilcote, Michael; Kawakami, R. K.; Flatté, M. E.; Johnston-Halperin, E.

    2015-09-01

    We investigate the impact of tunnel barrier thickness on electron spin dynamics in Fe/MgO/GaAs heterostructures using spin-resolved optical pump-probe spectroscopy. Comparison of the Larmor frequency between thick and thin MgO barriers reveals a four-fold variation in exchange coupling strength, and investigation of the inhomogeneous dephasing time, T2*, argues that inhomogeneity in the local effective hyperfine field dominates free-carrier spin relaxation across the entire range of barrier thickness. These results provide additional evidence to support the theory of hyperfine-dominated spin relaxation in GaAs at low temperature and in the presence of an externally applied magnetic field. Further, this work lays the foundation for engineering both the exchange coupling and the free carrier spin dynamics in ferromagnet/semiconductor heterostructures, allowing for the exploration of dissipation and transport in the regime of dynamically-driven spin pumping.

  9. Laser spectroscopy and dynamics of transient species

    SciTech Connect

    Clouthier, D.J.

    1993-12-01

    The goal of this program is to study the vibrational and electronic spectra and excited state dynamics of a number of transient sulfur and oxygen species. A variety of supersonic jet techniques, as well as high resolution FT-IR and intracavity dye laser spectroscopy, have been applied to these studies.

  10. Dynamics of genome change among Legionella species.

    PubMed

    Joseph, Sandeep J; Cox, Daniel; Wolff, Bernard; Morrison, Shatavia S; Kozak-Muiznieks, Natalia A; Frace, Michael; Didelot, Xavier; Castillo-Ramirez, Santiago; Winchell, Jonas; Read, Timothy D; Dean, Deborah

    2016-01-01

    Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires' Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1-17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD-causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence. PMID:27633769

  11. Dynamics of genome change among Legionella species.

    PubMed

    Joseph, Sandeep J; Cox, Daniel; Wolff, Bernard; Morrison, Shatavia S; Kozak-Muiznieks, Natalia A; Frace, Michael; Didelot, Xavier; Castillo-Ramirez, Santiago; Winchell, Jonas; Read, Timothy D; Dean, Deborah

    2016-09-16

    Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires' Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1-17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD-causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence.

  12. Dynamics of genome change among Legionella species

    PubMed Central

    Joseph, Sandeep J.; Cox, Daniel; Wolff, Bernard; Morrison, Shatavia S.; Kozak-Muiznieks, Natalia A.; Frace, Michael; Didelot, Xavier; Castillo-Ramirez, Santiago; Winchell, Jonas; Read, Timothy D.; Dean, Deborah

    2016-01-01

    Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires’ Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1–17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD–causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence. PMID:27633769

  13. Dynamic exchange of myosin molecules between thick filaments.

    PubMed

    Saad, A D; Pardee, J D; Fischman, D A

    1986-12-01

    To examine thick filament assembly and myosin exchange, a fluorescence energy transfer assay has been established. Assembly-competent myosin molecules labeled with the sulfhydryl-specific fluorochromes 5-(2-[(iodoacetyl)-amino]ethyl)aminonaphthalene-1-sulfonic acids (IAEDANS) or 5-iodoacetamidofluorescein (IAF) were prepared. Using IAEDANS-labeled myosin as fluorescence donor and IAF-labeled myosin as acceptor, thick filament formation was followed by the decrease in donor fluorescence at 0.1 M KCl/10 mM potassium phosphate, pH 6.9. The critical concentration of myosin--i.e., that concentration that remained unassembled at equilibrium with fully formed filaments--was 40 nM. In FET and 125I-labeled myosin incorporation assays, extensive exchange of myosin between thick filaments was observed. The presence of a critical concentration and the measurements of extensive exchange suggest a dynamic equilibrium between fully polymerized myosin and a small pool of soluble myosin.

  14. Glucans monomer-exchange dynamics as an open chemical network.

    PubMed

    Rao, Riccardo; Lacoste, David; Esposito, Massimiliano

    2015-12-28

    We describe the oligosaccharides-exchange dynamics performed by the so-called D-enzymes on polysaccharides. To mimic physiological conditions, we treat this process as an open chemical network by assuming some of the polymer concentrations fixed (chemostatting). We show that three different long-time behaviors may ensue: equilibrium states, nonequilibrium steady states, and continuous growth states. We dynamically and thermodynamically characterize these states and emphasize the crucial role of conservation laws in identifying the chemostatting conditions inducing them. PMID:26723707

  15. Species Abundance Patterns in Complex Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Tokita, Kei

    2004-10-01

    An analytic theory of species abundance patterns (SAPs) in biological networks is presented. The theory is based on multispecies replicator dynamics equivalent to the Lotka-Volterra equation, with diverse interspecies interactions. Various SAPs observed in nature are derived from a single parameter. The abundance distribution is formed like a widely observed left-skewed lognormal distribution. As the model has a general form, the result can be applied to similar patterns in other complex biological networks, e.g., gene expression.

  16. G-register exchange dynamics in guanine quadruplexes

    PubMed Central

    Harkness, Robert W.; Mittermaier, Anthony K.

    2016-01-01

    G-quadruplexes (GQs) are 4-stranded DNA structures formed by tracts of stacked, Hoogsteen-hydrogen bonded guanosines. GQs are found in gene promoters and telomeres where they regulate gene transcription and telomere elongation. Though GQ structures are well-characterized, many aspects of their conformational dynamics are poorly understood. For example, when there are surplus guanosines in some of the tracts, they can slide with respect to one another, a process we term G-register (GR) exchange. These motions could in principle entropically stabilize the folded state, crucially benefitting GQs as their stabilities are closely tied to biological function. We have developed a method for characterizing GR exchange where each isomer in the wild-type conformational ensemble is trapped by mutation and thermal denaturation data for the set of trapped mutants and wild-type are analyzed simultaneously. This yields GR isomer populations as a function of temperature, quantifies conformational entropy and sheds light on correlated sliding motions of the G-tracts. We measured entropic stabilizations from GR exchange up to 14.3 ± 1.6 J mol−1 K−1, with melting temperature increases up to 7.3 ± 1.6°C. Furthermore, bioinformatic analysis suggests a majority of putative human GQ sequences are capable of GR exchange, pointing to the generality of this phenomenon. PMID:27060139

  17. DYNACLIPS (DYNAmic CLIPS): A dynamic knowledge exchange tool for intelligent agents

    NASA Technical Reports Server (NTRS)

    Cengeloglu, Yilmaz; Khajenoori, Soheil; Linton, Darrell

    1994-01-01

    In a dynamic environment, intelligent agents must be responsive to unanticipated conditions. When such conditions occur, an intelligent agent may have to stop a previously planned and scheduled course of actions and replan, reschedule, start new activities and initiate a new problem solving process to successfully respond to the new conditions. Problems occur when an intelligent agent does not have enough knowledge to properly respond to the new situation. DYNACLIPS is an implementation of a framework for dynamic knowledge exchange among intelligent agents. Each intelligent agent is a CLIPS shell and runs a separate process under SunOS operating system. Intelligent agents can exchange facts, rules, and CLIPS commands at run time. Knowledge exchange among intelligent agents at run times does not effect execution of either sender and receiver intelligent agent. Intelligent agents can keep the knowledge temporarily or permanently. In other words, knowledge exchange among intelligent agents would allow for a form of learning to be accomplished.

  18. TIREX: Replica-exchange molecular dynamics using TINKER

    NASA Astrophysics Data System (ADS)

    Penev, Evgeni S.; Lampoudi, Sotiria; Shea, Joan-Emma

    2009-10-01

    We present a driver program for performing replica-exchange molecular dynamics simulations with the TINKER package. Parallelization is based on the Message Passing Interface, with every replica assigned to a separate process. The algorithm is not communication intensive, which makes the program suitable for running even on loosely coupled cluster systems. Particular attention is paid to the practical aspects of analyzing the program output. Program summaryProgram title: TiReX Catalogue identifier: AEEK_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEEK_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 43 385 No. of bytes in distributed program, including test data, etc.: 502 262 Distribution format: tar.gz Programming language: Fortran 90/95 Computer: Most UNIX machines Operating system: Linux Has the code been vectorized or parallelized?: parallelized with MPI Classification: 16.13 External routines: TINKER version 4.2 or 5.0, built as a library Nature of problem: Replica-exchange molecular dynamics. Solution method: Each replica is assigned to a separate process; temperatures are swapped between replicas at regular time intervals. Running time: The sample run may take up to a few minutes.

  19. Dynamic Group Diffie-Hellman Key Exchange under standard assumptions

    SciTech Connect

    Bresson, Emmanuel; Chevassut, Olivier; Pointcheval, David

    2002-02-14

    Authenticated Diffie-Hellman key exchange allows two principals communicating over a public network, and each holding public-private keys, to agree on a shared secret value. In this paper we study the natural extension of this cryptographic problem to a group of principals. We begin from existing formal security models and refine them to incorporate major missing details (e.g., strong-corruption and concurrent sessions). Within this model we define the execution of a protocol for authenticated dynamic group Diffie-Hellman and show that it is provably secure under the decisional Diffie-Hellman assumption. Our security result holds in the standard model and thus provides better security guarantees than previously published results in the random oracle model.

  20. Leaf gas exchange traits of domestic and exotic tree species in Cambodia

    NASA Astrophysics Data System (ADS)

    Miyazawa, Y.; Tateishi, M.; Kumagai, T.; Otsuki, K.

    2009-12-01

    In forests under the management by community villagers, exotic tree species with rapid growth rate are introduced in wide range of Cambodia. To evaluate the influence of the introduction on the forest gas exchange and water budget, we investigated the leaf gas exchange traits of two domestic (Dipterocarpus obtusifolius and Shorea roxburghii) and exotic tree species (Acasia auriculiformis and Eucalyptus camadilansis). We sampled shoots of each species and measured the leaf gas exchange traits (photosynthetic rates under different CO2 concentrations, transpiration rate and stomatal conductance) (6 leaves x 3 trees x 4 species). We carried out this measurement at 2 months intervals for a year from the beginning of rainy season and compared the obtained traits among species. Light saturated rate of net photosynthesis was higher in E. camadilansis but did not differ among other species both in rainy and dry seasons. Seasonal patter in photosynthetic traits was not obvious. Each species changed stomatal conductance in response to changes in environmental conditions. The response was more sensitive than reported values. In this presentation, we show details about the basic information about the leaf-level gas exchange traits, which are required to run soil- vegetation - atmosphere transfer model.

  1. Contribution of non methane organic volatiles exchange to the carbon budget of isoprene and monoterpene emitting plant species

    NASA Astrophysics Data System (ADS)

    Dindorf, T.; Kuhn, U.; Ammann, C.; Neftel, A.; Tritsch, C.; Ciccioli, P.; Koppmann, R.; Kesselmeier, J.

    2003-04-01

    Compared to the aerosol fraction, most of the organic carbon present in the atmosphere is found in form of volatile or semivolatile compounds. Vegetation was identified being the major source of these organic volatiles, releasing carbon at the same order of magnitude as the global net biome productivity (NBP). To achieve an estimate of plants carbon exchange, including the emission and deposition of volatile organics, the exchange activity of the two isoprene and monoterpene emitting plant species Quercus robur and Fagus sylvatica was observed under field conditions during the ECHO campaign (Emission and CHemical Transformation of Biogenic Volatile Organic Compounds) in summer 2002 in Jülich, Germany. Primary productivity and VOC exchange was investigated on the branch level by means of a dynamic cuvette system. Organic volatiles were collected on adsorbent tubes and analysed later on by GC-FID and GC-MS for species composition and quantification. Short chain carbonyls were sampled on DNPH coated cartridges and analysed by HPLC-UV. For identification of a broader spectrum of volatile compounds, both methods were complemented by PTR-MS measurements for the isoprene emitting species. Isoprenoid and methanol emissions accounted for the majority of the VOC release, which was partly compensated by the deposition of other oxygenated organic compounds.

  2. Probing exchange kinetics and atomic resolution dynamics in high-molecular-weight complexes using dark-state exchange saturation transfer NMR spectroscopy.

    PubMed

    Fawzi, Nicolas L; Ying, Jinfa; Torchia, Dennis A; Clore, G Marius

    2012-07-19

    We present the protocol for the measurement and analysis of dark-state exchange saturation transfer (DEST), a novel solution NMR method for characterizing, at atomic resolution, the interaction between an NMR-'visible' free species and an NMR-'invisible' species transiently bound to a very high-molecular-weight (>1 MDa) macromolecular entity. The reduced rate of reorientational motion in the bound state that precludes characterization by traditional NMR methods permits the observation of DEST. (15)N-DEST profiles are measured on a sample comprising the dark state in exchange with an NMR-visible species; in addition, the difference (ΔR(2)) in (15)N transverse relaxation rates between this sample and a control sample comprising only the NMR-visible species is also obtained. The (15)N-DEST and ΔR(2) data for all residues are then fitted simultaneously to the McConnell equations for various exchange models describing the residue-specific dynamics in the bound state(s) and the interconversion rate constants. Although the length of the experiments depends strongly on sample conditions, approximately 1 week of NMR spectrometer time was sufficient for full characterization of samples of amyloid-β (Aβ) at concentrations of ~100 μM.

  3. Dynamics of Exchange at Gas-Zeolite Interfaces 1: Pure Component n-Butane and Isobutane

    SciTech Connect

    CHANDROSS,MICHAEL E.; WEBB III,EDMUND B.; GREST,GARY S.; MARTIN,MARCUS G.; THOMPSON,AIDAN P.; ROTH,M.W.

    2000-07-13

    The authors present the results of molecular dynamics simulations of n-butane and isobutane in silicalite. They begin with a comparison of the bulk adsorption and diffusion properties for two different parameterizations of the interaction potential between the hydrocarbon species, both of which have been shown to reproduce experimental gas-liquid coexistence curves. They examine diffusion as a function of the loading of the zeolite, as well as the temperature dependence of the diffusion constant at loading and for infinite dilution. They continue with simulations in which interfaces are formed between single component gases and the zeolite. After reaching equilibrium, they examine the dynamics of exchange between the bulk gas and the zeolite. Finally, they calculate the permeability of the zeolite for n-butane and isobutane as a function of pressure. Their simulations are performed for a number of different gas temperatures and pressures, covering a wide range of state points.

  4. MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.

    PubMed

    Smith, Daniel B; Okur, Asim; Brooks, Bernard

    2012-08-30

    Replica exchange methods have become popular tools to explore conformational space for small proteins. For larger biological systems, even with enhanced sampling methods, exploring the free energy landscape remains computationally challenging. This problem has led to the development of many improved replica exchange methods. Unfortunately, testing these methods remains expensive. We propose a Molecular Dynamics Meta-Simulator (MDMS) based on transition state theory to simulate a replica exchange simulation, eliminating the need to run explicit dynamics between exchange attempts. MDMS simulations allow for rapid testing of new replica exchange based methods, greatly reducing the amount of time needed for new method development.

  5. Social organization influences the exchange and species richness of medicinal plants in Amazonian homegardens

    PubMed Central

    2016-01-01

    Medicinal plants provide indigenous and peasant communities worldwide with means to meet their healthcare needs. Homegardens often act as medicine cabinets, providing easily accessible medicinal plants for household needs. Social structure and social exchanges have been proposed as factors influencing the species diversity that people maintain in their homegardens. Here, we assess the association between the exchange of medicinal knowledge and plant material and medicinal plant richness in homegardens. Using Tsimane’ Amazonian homegardens as a case study, we explore whether social organization shapes exchanges of medicinal plant knowledge and medicinal plant material. We also use network centrality measures to evaluate people’s location and performance in medicinal plant knowledge and plant material exchange networks. Our results suggest that social organization, specifically kinship and gender relations, influences medicinal plant exchange patterns significantly. Homegardens total and medicinal plant species richness are related to gardeners’ centrality in the networks, whereby people with greater centrality maintain greater plant richness. Thus, together with agroecological conditions, social relations among gardeners and the culturally specific social structure seem to be important determinants of plant richness in homegardens. Understanding which factors pattern general species diversity in tropical homegardens, and medicinal plant diversity in particular, can help policy makers, health providers, and local communities to understand better how to promote and preserve medicinal plants in situ. Biocultural approaches that are also gender sensitive offer a culturally appropriate means to reduce the global and local loss of both biological and cultural diversity. PMID:27668001

  6. Social organization influences the exchange and species richness of medicinal plants in Amazonian homegardens

    PubMed Central

    2016-01-01

    Medicinal plants provide indigenous and peasant communities worldwide with means to meet their healthcare needs. Homegardens often act as medicine cabinets, providing easily accessible medicinal plants for household needs. Social structure and social exchanges have been proposed as factors influencing the species diversity that people maintain in their homegardens. Here, we assess the association between the exchange of medicinal knowledge and plant material and medicinal plant richness in homegardens. Using Tsimane’ Amazonian homegardens as a case study, we explore whether social organization shapes exchanges of medicinal plant knowledge and medicinal plant material. We also use network centrality measures to evaluate people’s location and performance in medicinal plant knowledge and plant material exchange networks. Our results suggest that social organization, specifically kinship and gender relations, influences medicinal plant exchange patterns significantly. Homegardens total and medicinal plant species richness are related to gardeners’ centrality in the networks, whereby people with greater centrality maintain greater plant richness. Thus, together with agroecological conditions, social relations among gardeners and the culturally specific social structure seem to be important determinants of plant richness in homegardens. Understanding which factors pattern general species diversity in tropical homegardens, and medicinal plant diversity in particular, can help policy makers, health providers, and local communities to understand better how to promote and preserve medicinal plants in situ. Biocultural approaches that are also gender sensitive offer a culturally appropriate means to reduce the global and local loss of both biological and cultural diversity.

  7. Fluctuation Dynamics of Exchange Rates on Indian Financial Market

    NASA Astrophysics Data System (ADS)

    Sarkar, A.; Barat, P.

    Here we investigate the scaling behavior and the complexity of the average daily exchange rate returns of the Indian Rupee against four foreign currencies namely US Dollar, Euro, Great Britain Pound and Japanese Yen. Our analysis revealed that the average daily exchange rate return of the Indian Rupee against the US Dollar exhibits a persistent scaling behavior and follow Levy stable distribution. On the contrary the average daily exchange rate returns of the other three foreign currencies show randomness and follow Gaussian distribution. Moreover, it is seen that the complexity of the average daily exchange rate return of the Indian Rupee against US Dollar is less than the other three exchange rate returns.

  8. Leaf gas exchange characteristics differ among Sonoran Desert riparian tree species.

    PubMed

    Horton, J L; Kolb, T E; Hart, S C

    2001-03-01

    We investigated leaf gas exchange responses to leaf temperature, leaf-to-air vapor pressure deficit (VPD), and predawn and midday shoot water potential (psipd and psimd, respectively) of two native Sonoran Desert riparian tree species, Fremont cottonwood (Populus fremontii S. Wats.) and Goodding willow (Salix gooddingii Ball), and one exotic riparian tree species, saltcedar (Tamarix chinensis Lour. and related species). Measurements were made at two sites over 2 years that differed climatically. Because multiple linear regression models explained less than 29% of the variation in stomatal conductance (gs) and less than 48% of the variation in net photosynthetic rate (Pn) of all species, we used boundary-line analysis to compare gas exchange responses among species. Gas exchange rates were high in all species. The hyperbolic relationship between Pn and gs suggested that initial reductions in gs at high gs did not inhibit Pn. Reductions in gs of cottonwood and willow occurred at psimd values at or below previously reported xylem cavitation thresholds (-1.6 and -1.4 MPa, respectively), indicating tight stomatal regulation of water loss and a narrow cavitation safety margin. In contrast, reductions in gs of saltcedar occurred at psimd values well above the cavitation threshold (-7.0 MPa), but at much lower psimd values than in cottonwood and willow, suggesting a wider cavitation safety margin and less tight regulation of water loss in saltcedar. High VPD had a smaller effect on leaf gas exchange in willow than in cottonwood. In contrast, willow had a less negative psipd threshold for stomatal closure than cottonwood. Compared with cottonwood and willow, leaf gas exchange of saltcedar was more tolerant of high VPD and low psipd. These physiological characteristics of saltcedar explain its widespread success as an invader of riparian ecosystems containing native Fremont cottonwood and Goodding willow in the Sonoran Desert.

  9. Computational fluid dynamics modeling of proton exchange membrane fuel cells

    SciTech Connect

    UM,SUKKEE; WANG,C.Y.; CHEN,KEN S.

    2000-02-11

    A transient, multi-dimensional model has been developed to simulate proton exchange membrane (PEM) fuel cells. The model accounts simultaneously for electrochemical kinetics, current distribution, hydrodynamics and multi-component transport. A single set of conservation equations valid for flow channels, gas-diffusion electrodes, catalyst layers and the membrane region are developed and numerically solved using a finite-volume-based computational fluid dynamics (CFD) technique. The numerical model is validated against published experimental data with good agreement. Subsequently, the model is applied to explore hydrogen dilution effects in the anode feed. The predicted polarization cubes under hydrogen dilution conditions are found to be in qualitative agreement with recent experiments reported in the literature. The detailed two-dimensional electrochemical and flow/transport simulations further reveal that in the presence of hydrogen dilution in the fuel stream, hydrogen is depleted at the reaction surface resulting in substantial kinetic polarization and hence a lower current density that is limited by hydrogen transport from the fuel stream to the reaction site.

  10. Antipersistent dynamics in kinetic models of wealth exchange

    NASA Astrophysics Data System (ADS)

    Goswami, Sanchari; Chatterjee, Arnab; Sen, Parongama

    2011-11-01

    We investigate the detailed dynamics of gains and losses made by agents in some kinetic models of wealth exchange. An earlier work suggested that a walk in an abstract gain-loss space can be conceived for the agents. For models in which agents do not save, or save with uniform saving propensity, the walk has diffusive behavior. For the case in which the saving propensity λ is distributed randomly (0≤λ<1), the resultant walk showed a ballistic nature (except at a particular value of λ*≈0.47). Here we consider several other features of the walk with random λ. While some macroscopic properties of this walk are comparable to a biased random walk, at microscopic level, there are gross differences. The difference turns out to be due to an antipersistent tendency toward making a gain (loss) immediately after making a loss (gain). This correlation is in fact present in kinetic models without saving or with uniform saving as well, such that the corresponding walks are not identical to ordinary random walks. In the distributed saving case, antipersistence occurs with a simultaneous overall bias.

  11. Optimization of replica exchange molecular dynamics by fast mimicking.

    PubMed

    Hritz, Jozef; Oostenbrink, Chris

    2007-11-28

    We present an approach to mimic replica exchange molecular dynamics simulations (REMD) on a microsecond time scale within a few minutes rather than the years, which would be required for real REMD. The speed of mimicked REMD makes it a useful tool for "testing" the efficiency of different settings for REMD and then to select those settings, that give the highest efficiency. We present an optimization approach with the example of Hamiltonian REMD using soft-core interactions on two model systems, GTP and 8-Br-GTP. The optimization process using REMD mimicking is very fast. Optimization of Hamiltonian-REMD settings of GTP in explicit water took us less than one week. In our study we focus not only on finding the optimal distances between neighboring replicas, but also on finding the proper placement of the highest level of softness. In addition we suggest different REMD simulation settings at this softness level. We allow several replicas to be simulated at the same Hamiltonian simultaneously and reduce the frequency of switching attempts between them. This approach allows for more efficient conversions from one stable conformation to the other.

  12. Dynamics of double-diffusive lock-exchange gravity currents

    NASA Astrophysics Data System (ADS)

    Konopliv, Nathan; Meiburg, Eckart

    2015-11-01

    The dynamics of double-diffusive gravity currents exhibiting the fingering instability were examined using 2D simulations of a lock exchange initial configuration. Both the initial stability ratio and the diffusivity ratio were varied. It was found that although the spreading of the currents was governed by a balance of buoyancy and turbulent drag forces, currents with more intense fingering spread faster than those with less intense or no fingering. This was due to an increase in the buoyancy of the currents with stronger fingering, which had a stronger effect than the increased drag. The fingering also affected the thickness of the currents, with more fingering corresponding to thinner currents. The mechanism that caused the thinner currents was also responsible for the creation of secondary and tertiary currents after a long time in a simulation that had intense fingering. If no secondary or tertiary currents formed, the density of the current was governed by a balance of double-diffusive and diffusive fluxes. An energy budget analysis revealed that double diffusive currents released more potential energy, had more dissipation and converted a significant amount of internal energy into potential energy via the diffusion of heat and salinity.

  13. Three dimensional dynamics of a flexible Motorised Momentum Exchange Tether

    NASA Astrophysics Data System (ADS)

    Ismail, N. A.; Cartmell, M. P.

    2016-03-01

    This paper presents a new flexural model for the three dimensional dynamics of the Motorised Momentum Exchange Tether (MMET) concept. This study has uncovered the relationships between planar and nonplanar motions, and the effect of the coupling between these two parameters on pragmatic circular and elliptical orbits. The tether sub-spans are modelled as stiffened strings governed by partial differential equations of motion, with specific boundary conditions. The tether sub-spans are flexible and elastic, thereby allowing three dimensional displacements. The boundary conditions lead to a specific frequency equation and the eigenvalues from this provide the natural frequencies of the orbiting flexible motorised tether when static, accelerating in monotonic spin, and at terminal angular velocity. A rotation transformation matrix has been utilised to get the position vectors of the system's components in an assumed inertial frame. Spatio-temporal coordinates are transformed to modal coordinates before applying Lagrange's equations, and pre-selected linear modes are included to generate the equations of motion. The equations of motion contain inertial nonlinearities which are essentially of cubic order, and these show the potential for intricate intermodal coupling effects. A simulation of planar and non-planar motions has been undertaken and the differences in the modal responses, for both motions, and between the rigid body and flexible models are highlighted and discussed.

  14. Atmospheric dust accumulation on native and non-native species: effects on gas exchange parameters.

    PubMed

    González, Juan A; Prado, Fernando E; Piacentini, Ruben D

    2014-05-01

    Plants are continuously exposed to atmospheric particulate matter (dust), and their leaves are the main receptors of deposited dust. The objective of this study was to assess the effects of dust deposition on leaf gas exchange parameters of 17 native and non-native tree and shrub species growing in Gran San Miguel de Tucumán in northwestern Argentina. Maximum assimilation rate (), stomatal conductance (), transpiration rate (), internal CO concentration (), and instantaneous water-use efficiency (WUE) were measured in cleaned leaves (CL) and dusted leaves (DL) of different species on November 2010, July 2011, and September 2011. In almost all studied species, gas exchange parameters were significantly affected by dust deposition. Values for , , and of DL were significantly reduced in 11, 12, and 14 species compared with CL. Morphological leaf traits seem to be related to reduction. Indeed, L. and (Mart. ex DC.) Standl. species with pubescent leaves and thick ribs showed the highest reduction percentages. Contrarily, and WUE were increased in DL but were less responsive to dust deposition than other parameters. Increases of and WUE were significant in 5 and 11 species, respectively. Correlation analyses between /, /, and / pairs showed significant positive linear correlations in CL and DL of many studied species, including small and tall plants. These results suggest that leaf stomatal factors and shade-induced effect by accumulated dust are primarily responsible for the observed reductions in photosynthesis rate of DL.

  15. Temporal Dynamics of Social Exchange and the Development of Solidarity: "Testing the Waters" versus "Taking a Leap of Faith"

    ERIC Educational Resources Information Center

    Kuwabara, Ko; Sheldon, Oliver

    2012-01-01

    In their concerted efforts to unpack the microprocesses that transform repeated exchanges into an exchange relation, exchange theorists have paid little attention to how actors perceive changes and dynamics in exchanges over time. We help fill this gap by studying how temporal patterns of exchange affect the development of cohesion. Some exchange…

  16. Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: Antiparallel versus parallel association

    SciTech Connect

    Vitagliano, Luigi; Esposito, Luciana; Pedone, Carlo; De Simone, Alfonso

    2008-12-26

    Protein and peptide aggregation into amyloid plaques is associated with a large variety of neurodegenerative diseases. The definition of the molecular bases of these pathologies is hampered by the transient nature of pre-fibrillar small-oligomers that are considered the toxic species. The ability of the peptide GNNQQNY to form amyloid-like structures makes it a good model to investigate the complex processes involved into amyloid fiber formation. By employing full atomistic replica exchange molecular dynamics simulations, we constructed the free energy surface of small assemblies of GNNQQNY to gain novel insights into the fiber formation process. The calculations suggest that the peptide exhibits a remarkable tendency to form both parallel and antiparallel {beta}-sheets. The data show that GNNQQNY preference for parallel or antiparallel {beta}-sheets is governed by a subtle balance of factors including assemblies' size, sidechain-sidechain interactions and pH. The samplings analysis provides a rationale to the observed trends.

  17. Modeling metapopulation dynamics for single species of seabirds

    USGS Publications Warehouse

    Buckley, P.A.; Downer, R.; McCullough, D.R.; Barrett, R.H.

    1992-01-01

    Seabirds share many characteristics setting them apart from other birds. Importantly, they breed more or less obligatorily in local clusters of colonies that can move regularly from site to site, and they routinely exchange breeders. The properties of such metapopulations have only recently begun to be examined, often with models that are occupancy-based (using only colony presence or absence data) and deterministic (using single, empirically determined values for each of several population biology parameters). Some recent models are now frequency-based (using actual population sizes at each site), as well as stochastic (randomly varying critical parameters between biologically realistic limits), yielding better estimates of the behavior of future populations. Using two such models designed to quantify relative risks of population changes under different future scenarios (RAMAS/stage and RAMAS/space), we have examined probable future populations dynamics for three hypothetical seabirds -- an albatross, a cormorant, and a tern. With real parameters and ranges of values we alternatively modelled each species with and without density dependence, as well as with their numbers in a single, large colony, or in many smaller ones, distributed evenly or lognormally. We produced a series of species-typical lines for different population risks over the 50 years we simulated. We call these curves Instantaneous Threat Assessments (ITAs), and their shapes mirror the varying life history characteristics of our three species. We also demonstrated (by a process known as sensitivity analysis) that the most important parameters determining future population fates of all three species were correlation of mean growth rate among colonies; dispersal rate of present and future breeders; subadult survivorship; and the number of subpopulations (=colonies) - in roughly that descending order of importance. In addition, density dependence was found to markedly alter ITA line shape and position

  18. EXCHANGE

    SciTech Connect

    Boltz, J.C.

    1992-09-01

    EXCHANGE is published monthly by the Idaho National Engineering Laboratory (INEL), a multidisciplinary facility operated for the US Department of Energy (DOE). The purpose of EXCHANGE is to inform computer users about about recent changes and innovations in both the mainframe and personal computer environments and how these changes can affect work being performed at DOE facilities.

  19. Two competing species in super-diffusive dynamical regimes

    NASA Astrophysics Data System (ADS)

    La Cognata, A.; Valenti, D.; Spagnolo, B.; Dubkov, A. A.

    2010-09-01

    The dynamics of two competing species within the framework of the generalized Lotka-Volterra equations, in the presence of multiplicative α-stable Lévy noise sources and a random time dependent interaction parameter, is studied. The species dynamics is characterized by two different dynamical regimes, exclusion of one species and coexistence of both, depending on the values of the interaction parameter, which obeys a Langevin equation with a periodically fluctuating bistable potential and an additive α-stable Lévy noise. The stochastic resonance phenomenon is analyzed for noise sources asymmetrically distributed. Finally, the effects of statistical dependence between multiplicative noise and additive noise on the dynamics of the two species are studied.

  20. Genome sequencing reveals widespread virulence gene exchange among human Neisseria species.

    PubMed

    Marri, Pradeep Reddy; Paniscus, Mary; Weyand, Nathan J; Rendón, María A; Calton, Christine M; Hernández, Diana R; Higashi, Dustin L; Sodergren, Erica; Weinstock, George M; Rounsley, Steven D; So, Magdalene

    2010-07-28

    Commensal bacteria comprise a large part of the microbial world, playing important roles in human development, health and disease. However, little is known about the genomic content of commensals or how related they are to their pathogenic counterparts. The genus Neisseria, containing both commensal and pathogenic species, provides an excellent opportunity to study these issues. We undertook a comprehensive sequencing and analysis of human commensal and pathogenic Neisseria genomes. Commensals have an extensive repertoire of virulence alleles, a large fraction of which has been exchanged among Neisseria species. Commensals also have the genetic capacity to donate DNA to, and take up DNA from, other Neisseria. Our findings strongly suggest that commensal Neisseria serve as reservoirs of virulence alleles, and that they engage extensively in genetic exchange.

  1. Transitional steady states of exchange dynamics between finite quantum systems.

    PubMed

    Jeon, Euijin; Yi, Juyeon; Kim, Yong Woon

    2016-08-01

    We examine energy and particle exchange between finite-sized quantum systems and find a new form of nonequilibrium state. The exchange rate undergoes stepwise evolution in time, and its magnitude and sign dramatically change according to system size differences. The origin lies in interference effects contributed by multiply scattered waves at system boundaries. Although such characteristics are utterly different from those of true steady state for infinite systems, Onsager's reciprocal relation remains universally valid. PMID:27627275

  2. Transitional steady states of exchange dynamics between finite quantum systems

    NASA Astrophysics Data System (ADS)

    Jeon, Euijin; Yi, Juyeon; Kim, Yong Woon

    2016-08-01

    We examine energy and particle exchange between finite-sized quantum systems and find a new form of nonequilibrium state. The exchange rate undergoes stepwise evolution in time, and its magnitude and sign dramatically change according to system size differences. The origin lies in interference effects contributed by multiply scattered waves at system boundaries. Although such characteristics are utterly different from those of true steady state for infinite systems, Onsager's reciprocal relation remains universally valid.

  3. Nesting behaviour influences species-specific gas exchange across avian eggshells

    PubMed Central

    Portugal, Steven J.; Maurer, Golo; Thomas, Gavin H.; Hauber, Mark E.; Grim, Tomáš; Cassey, Phillip

    2014-01-01

    Carefully controlled gas exchange across the eggshell is essential for the development of the avian embryo. Water vapour conductance (GH2O) across the shell, typically measured as mass loss during incubation, has been demonstrated to optimally ensure the healthy development of the embryo while avoiding desiccation. Accordingly, eggs exposed to sub-optimal gas exchange have reduced hatching success. We tested the association between eggshell GH2O and putative life-history correlates of adult birds, ecological nest parameters and physical characteristics of the egg itself to investigate how variation in GH2O has evolved to maintain optimal water loss across a diverse set of nest environments. We measured gas exchange through eggshell fragments in 151 British breeding bird species and fitted phylogenetically controlled, general linear models to test the relationship between GH2O and potential predictor parameters of each species. Of our 17 life-history traits, only two were retained in the final model: wet-incubating parent and nest type. Eggs of species where the parent habitually returned to the nest with wet plumage had significantly higher GH2O than those of parents that returned to the nest with dry plumage. Eggs of species nesting in ground burrows, cliffs and arboreal cups had significantly higher GH2O than those of species nesting on the ground in open nests or cups, in tree cavities and in shallow arboreal nests. Phylogenetic signal (measured as Pagel's λ) was intermediate in magnitude, suggesting that differences observed in the GH2O are dependent upon a combination of shared ancestry and species-specific life history and ecological traits. Although these data are correlational by nature, they are consistent with the hypothesis that parents constrained to return to the nest with wet plumage will increase the humidity of the nest environment, and the eggs of these species have evolved a higher GH2O to overcome this constraint and still achieve optimal water

  4. Microscopic Approach to Species Coexistence Based on Evolutionary Game Dynamics

    NASA Astrophysics Data System (ADS)

    Grebogi, Celso; Lai, Ying-Cheng; Wang, Wen-Xu

    2014-12-01

    An outstanding problem in complex systems and mathematical biology is to explore and understand the fundamental mechanisms of species coexistence. Existing approaches are based on niche partitioning, dispersal, chaotic evolutionary dynamics, and more recently, evolutionary games. Here we briefly review a number of fundamental issues associated with the coexistence of mobile species under cyclic competitions in the framework of evolutionary games.

  5. Leaf gas exchange characteristics of three neotropical mangrove species in response to varying hydroperiod

    USGS Publications Warehouse

    Krauss, Ken W.; Twilley, Robert R.; Doyle, Thomas W.; Gardiner, Emile S.

    2006-01-01

    We determined how different hydroperiods affected leaf gas exchange characteristics of greenhouse-grown seedlings (2002) and saplings (2003) of the mangrove species Avicennia germinans (L.) Stearn., Laguncularia racemosa (L.) Gaertn. f., and Rhizophora mangle L. Hydroperiod treatments included no flooding (unflooded), intermittent flooding (intermittent), and permanent flooding (flooded). Plants in the intermittent treatment were measured under both flooded and drained states and compared separately. In the greenhouse study, plants of all species maintained different leaf areas in the contrasting hydroperiods during both years. Assimilation–light response curves indicated that the different hydroperiods had little effect on leaf gas exchange characteristics in either seedlings or saplings. However, short-term intermittent flooding for between 6 and 22 days caused a 20% reduction in maximum leaf-level carbon assimilation rate, a 51% lower light requirement to attain 50% of maximum assimilation, and a 38% higher demand from dark respiration. Although interspecific differences were evident for nearly all measured parameters in both years, there was little consistency in ranking of the interspecific responses. Species by hydroperiod interactions were significant only for sapling leaf area. In a field study, R. mangle saplings along the Shark River in the Everglades National Park either demonstrated no significant effect or slight enhancement of carbon assimilation and water-use efficiency while flooded. We obtained little evidence that contrasting hydroperiods affect leaf gas exchange characteristics of mangrove seedlings or saplings over long time intervals; however, intermittent flooding may cause short-term depressions in leaf gas exchange. The resilience of mangrove systems to flooding, as demonstrated in the permanently flooded treatments, will likely promote photosynthetic and morphological adjustment to slight hydroperiod shifts in many settings..

  6. Leaf gas exchange characteristics of three neotropical mangrove species in response to varying hydroperiod.

    PubMed

    Krauss, Ken W; Twilley, Robert R; Doyle, Thomas W; Gardiner, Emile S

    2006-07-01

    We determined how different hydroperiods affected leaf gas exchange characteristics of greenhouse-grown seedlings (2002) and saplings (2003) of the mangrove species Avicennia germinans (L.) Stearn., Laguncularia racemosa (L.) Gaertn. f., and Rhizophora mangle L. Hydroperiod treatments included no flooding (unflooded), intermittent flooding (intermittent), and permanent flooding (flooded). Plants in the intermittent treatment were measured under both flooded and drained states and compared separately. In the greenhouse study, plants of all species maintained different leaf areas in the contrasting hydroperiods during both years. Assimilation-light response curves indicated that the different hydroperiods had little effect on leaf gas exchange characteristics in either seedlings or saplings. However, short-term intermittent flooding for between 6 and 22 days caused a 20% reduction in maximum leaf-level carbon assimilation rate, a 51% lower light requirement to attain 50% of maximum assimilation, and a 38% higher demand from dark respiration. Although interspecific differences were evident for nearly all measured parameters in both years, there was little consistency in ranking of the interspecific responses. Species by hydroperiod interactions were significant only for sapling leaf area. In a field study, R. mangle saplings along the Shark River in the Everglades National Park either demonstrated no significant effect or slight enhancement of carbon assimilation and water-use efficiency while flooded. We obtained little evidence that contrasting hydroperiods affect leaf gas exchange characteristics of mangrove seedlings or saplings over long time intervals; however, intermittent flooding may cause short-term depressions in leaf gas exchange. The resilience of mangrove systems to flooding, as demonstrated in the permanently flooded treatments, will likely promote photosynthetic and morphological adjustment to slight hydroperiod shifts in many settings. PMID:16585041

  7. Widespread horizontal genomic exchange does not erode species barriers among sympatric ducks

    PubMed Central

    2012-01-01

    Background The study of speciation and maintenance of species barriers is at the core of evolutionary biology. During speciation the genome of one population becomes separated from other populations of the same species, which may lead to genomic incompatibility with time. This separation is complete when no fertile offspring is produced from inter-population matings, which is the basis of the biological species concept. Birds, in particular ducks, are recognised as a challenging and illustrative group of higher vertebrates for speciation studies. There are many sympatric and ecologically similar duck species, among which fertile hybrids occur relatively frequently in nature, yet these species remain distinct. Results We show that the degree of shared single nucleotide polymorphisms (SNPs) between five species of dabbling ducks (genus Anas) is an order of magnitude higher than that previously reported between any pair of eukaryotic species with comparable evolutionary distances. We demonstrate that hybridisation has led to sustained exchange of genetic material between duck species on an evolutionary time scale without disintegrating species boundaries. Even though behavioural, genetic and ecological factors uphold species boundaries in ducks, we detect opposing forces allowing for viable interspecific hybrids, with long-term evolutionary implications. Based on the superspecies concept we here introduce the novel term "supra-population" to explain the persistence of SNPs identical by descent within the studied ducks despite their history as distinct species dating back millions of years. Conclusions By reviewing evidence from speciation theory, palaeogeography and palaeontology we propose a fundamentally new model of speciation to accommodate our genetic findings in dabbling ducks. This model, we argue, may also shed light on longstanding unresolved general speciation and hybridisation patterns in higher organisms, e.g. in other bird groups with unusually high

  8. Global attractors and extinction dynamics of cyclically competing species.

    PubMed

    Rulands, Steffen; Zielinski, Alejandro; Frey, Erwin

    2013-05-01

    Transitions to absorbing states are of fundamental importance in nonequilibrium physics as well as ecology. In ecology, absorbing states correspond to the extinction of species. We here study the spatial population dynamics of three cyclically interacting species. The interaction scheme comprises both direct competition between species as in the cyclic Lotka-Volterra model, and separated selection and reproduction processes as in the May-Leonard model. We show that the dynamic processes leading to the transient maintenance of biodiversity are closely linked to attractors of the nonlinear dynamics for the overall species' concentrations. The characteristics of these global attractors change qualitatively at certain threshold values of the mobility and depend on the relative strength of the different types of competition between species. They give information about the scaling of extinction times with the system size and thereby the stability of biodiversity. We define an effective free energy as the negative logarithm of the probability to find the system in a specific global state before reaching one of the absorbing states. The global attractors then correspond to minima of this effective energy landscape and determine the most probable values for the species' global concentrations. As in equilibrium thermodynamics, qualitative changes in the effective free energy landscape indicate and characterize the underlying nonequilibrium phase transitions. We provide the complete phase diagrams for the population dynamics and give a comprehensive analysis of the spatio-temporal dynamics and routes to extinction in the respective phases. PMID:23767569

  9. Dynamics of Chain Exchange in Block Copolymer Micelles

    NASA Astrophysics Data System (ADS)

    Lodge, Timothy

    Block copolymer micelles are rarely at equilibrium. The primary reason is the large number of repeat units in the insoluble block, Ncore, which makes the thermodynamic penalty for extracting a single chain (``unimer exchange'') substantial. As a consequence, the critical micelle concentration (CMC) is rarely accessed experimentally; however, in the proximity of a critical micelle temperature (CMT), equilibration is possible. We have been using time-resolved small angle neutron scattering (TR-SANS) to obtain a detailed picture of the mechanisms and time scales for chain exchange, at or near equilibrium. Our model system is poly(styrene)-block-poly(ethylene-alt-propylene)) (PS-PEP), in the PEP-selective solvent squalane (C30H62) . Equivalent micelles with either normal (hPS) or perdeuterated (dPS) cores are initially mixed in a blend of isotopically substituted squalane, designed to contrast-match a 50:50 hPS:dPS core. Samples are then annealed at a target temperature, and chain exchange is revealed quantitatively by the temporal decay in scattered intensity. The rate of exchange as function of concentration, temperature, Ncore, Ncorona, and chain architecture (diblock versus triblock) will be discussed.

  10. Dynamics in a three species food-web system

    NASA Astrophysics Data System (ADS)

    Gupta, K.; Gakkhar, S.

    2016-04-01

    In this paper, the dynamics of a three species food-web system is discussed. The food-web comprises of one predator and two logistically growing competing species. The predator species is taking food from one of the competitors with Holling type II functional response. Another competitor is the amensal species for the predator of first species. The system is shown to be positive and bounded. The stability of various axial points, boundary points and interior point has been investigated. The persistence of the system has been studied. Numerical simulation has been performed to show the occurrence of Hopf bifurcation and stable limit cycle about the interior point. The presence of second competitor and its interaction with predator gives more complex dynamics than the simple prey-predator system. The existence of transcritical bifurcation has been established about two axial points. The existence of periodic attractor having period-2 solution has been shown, when amensal coefficient is chosen as bifurcation parameter.

  11. Using a spectral approach to compare dynamic and static head driven hyporheic exchange

    NASA Astrophysics Data System (ADS)

    Wörman, Anders; Morén, Ida; Riml, Joakim

    2016-04-01

    Hyporheic exchange is an important process controlling the transportation and fate of solutes in natural streams. The exchange is driven by the hydraulic head gradients over the stream bottom and occurs on a wide range of spatial scales. The hydraulic head gradient is either dominated by the static head, originating from water surface elevation differences or it is dominated by the dynamic head that is created when the velocity head of the stream is transformed to pressure variations along an uneven bed surface. This article uses a power spectral approach to compare the exchange due to the static and dynamic head occurring over a range of spatial scales in the Tullstorps Brook. Prediction of hyporheic exchange is restrained by the complications of performing measurements of high quality and quantity in the field. In this study bottom elevation and water depth was measured with a levelling instrument every 2.56 - 16.83 m along a 500 m long reach of the Tullstorps Brook. The velocity head was calculated at the same sections based on the measured cross section area of the stream and the average discharge during the day when the measurements were done. Parallel to the head investigations a Rhodamine WT tracer test was performed in the reach and the parameters controlling hyporheic exchange was estimated through inverse modelling. These tracer test parameters were compared with theoretical parameters obtained from a spectral model. Hyporheic exchange is often modelled by assuming the head variations to be harmonic with a certain wavelength and amplitude. In the reality the head variation cannot be represented by a single harmonic function, but the representation of head geometry can be improved by superimposing a large number of harmonic functions. Here, to be able to include the whole range of harmonics, we used a power spectral approach to analyse the hydraulic head measurements from the field. The Fourier power spectrum of the data was calculated for the water

  12. Species Turnover through Time: Colonization and Extinction Dynamics across Metacommunities.

    PubMed

    Nuvoloni, Felipe Micali; Feres, Reinaldo José Fazzio; Gilbert, Benjamin

    2016-06-01

    Island biogeography and metacommunity theory often use equilibrium assumptions to predict local diversity, yet nonequilibrium dynamics are common in nature. In nonequilibrium communities, local diversity fluctuates through time as the relative importance of colonization and extinction change. Here, we test the prevalence and causes of nonequilibrium dynamics in metacommunities of mites associated with rubber trees distributed over large spatial (>1,000 km) and temporal (>30-60 generations) scales in Brazil. We measured colonization and extinction rates to test species turnover and nonequilibrium dynamics over a growing season. Mite metacommunities exhibited nonequilibrium dynamics for most months of the year, and these dynamics tracked climatic conditions. Monthly shifts in temperature of more than 1°C resulted in nonequilibrium dynamics, as did mean temperatures outside of two critical ranges. Nonequilibrium dynamics were caused by a change in colonization with temperature change and changes in both colonization and extinction with absolute temperature. Species turnover showed different trends; high relative humidity increased both colonization and extinction rates, increasing turnover but not nonequilibrium dynamics. Our study illustrates that testing nonequilibrium dynamics can provide new insights into the drivers of colonization, extinction, and diversity fluctuations in metacommunities. PMID:27172597

  13. INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Solvable Catalyzed Birth-Death-Exchange Competition Model of Three Species

    NASA Astrophysics Data System (ADS)

    Wang, Hai-Feng; Lin, Zhen-Quan; Gao, Yan; Zhang, Heng

    2009-10-01

    A competition model of three species in exchange-driven aggregation growth is proposed. In the model, three distinct aggregates grow by exchange of monomers and in parallel, birth of species A is catalyzed by species B and death of species A is catalyzed by species C. The rates for both catalysis processes are proportional to kjν and kjω respectively, where ν(Ω) is a parameter reflecting the dependence of the catalysis reaction rate of birth (death) on the catalyst aggregate's size. The kinetic evolution behaviors of the three species are investigated by the rate equation approach based on the mean-field theory. The form of the aggregate size distribution of A-species ak(t) is found to be dependent crucially on the two catalysis rate kernel parameters. The results show that (i) in case of μ <= 0, the form of ak(t) mainly depends on the competition between self-exchange of species A and species-C-catalyzed death of species A; (ii) in case of ν > 0, the form of ak(t) mainly depends on the competition between species-B-catalyzed birth of species A and species-C-catalyzed death of species A.

  14. Richards-like two species population dynamics model.

    PubMed

    Ribeiro, Fabiano; Cabella, Brenno Caetano Troca; Martinez, Alexandre Souto

    2014-12-01

    The two-species population dynamics model is the simplest paradigm of inter- and intra-species interaction. Here, we present a generalized Lotka-Volterra model with intraspecific competition, which retrieves as particular cases, some well-known models. The generalization parameter is related to the species habitat dimensionality and their interaction range. Contrary to standard models, the species coupling parameters are general, not restricted to non-negative values. Therefore, they may represent different ecological regimes, which are derived from the asymptotic solution stability analysis and are represented in a phase diagram. In this diagram, we have identified a forbidden region in the mutualism regime, and a survival/extinction transition with dependence on initial conditions for the competition regime. Also, we shed light on two types of predation and competition: weak, if there are species coexistence, or strong, if at least one species is extinguished.

  15. Richards-like two species population dynamics model.

    PubMed

    Ribeiro, Fabiano; Cabella, Brenno Caetano Troca; Martinez, Alexandre Souto

    2014-12-01

    The two-species population dynamics model is the simplest paradigm of inter- and intra-species interaction. Here, we present a generalized Lotka-Volterra model with intraspecific competition, which retrieves as particular cases, some well-known models. The generalization parameter is related to the species habitat dimensionality and their interaction range. Contrary to standard models, the species coupling parameters are general, not restricted to non-negative values. Therefore, they may represent different ecological regimes, which are derived from the asymptotic solution stability analysis and are represented in a phase diagram. In this diagram, we have identified a forbidden region in the mutualism regime, and a survival/extinction transition with dependence on initial conditions for the competition regime. Also, we shed light on two types of predation and competition: weak, if there are species coexistence, or strong, if at least one species is extinguished. PMID:25112794

  16. Dynamic modeling of tube-support interaction in heat exchangers

    NASA Astrophysics Data System (ADS)

    Azizian, Reza

    Flow-induced forces in heat exchangers can cause excessive tube vibration and interaction with their supports. Long term interaction may develop fretting-wear and consequently lead to tube failures. An accurate prediction of the tube-support interaction behavior is important to quantify tube fretting-wear. Therefore, a detailed study of the related friction and impact forces is required for formulating a precise wear model. This study aimed to develop a friction model for accurate representations of various states of the friction process, including elastic, plastic and partial slipping states. In addition, the tube-support impact model is verified both numerically and experimentally. A hybrid spring-damper rate dependent friction model was developed to precisely simulate the friction process from zero velocity to the gross slip state. This was achieved by considering various physical phenomena during the friction process including the Stribeck effect, varying break-away force, bristle elastic, plastic and partial-slipping behaviors. The slipping time in the velocity-limited friction model was compared to the LuGre friction model. The inability of the velocity limited friction model to detect the sticking region was explained by the dependency of a limiting velocity criterion on the varying break-away force and the Stribeck effect. This confirmed the importance of having an adaptive limiting velocity for the velocity limited friction model. In addition, the stress distribution within the contact region was studied in detail to demarcate different regions within a contact area during the friction process. This analysis attributed a physical meaning to each component of the new hybrid friction model. The ability of the hybrid model to accurately reproduce stick-slip behavior was examined using the Ozaki and Hashiguchi friction model and the Baumberger et al. experimental tests. The result showed better estimation of the stick-slip behavior, both qualitatively and

  17. Global attractors and extinction dynamics of cyclically competing species

    NASA Astrophysics Data System (ADS)

    Rulands, Steffen; Zielinski, Alejandro; Frey, Erwin

    2013-05-01

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

  18. Benchmarking novel approaches for modelling species range dynamics.

    PubMed

    Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H; Moore, Kara A; Zimmermann, Niklaus E

    2016-08-01

    Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species' range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species' response to climate change but also emphasize several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches

  19. Dynamical exchange-correlation potentials for the electron liquid

    NASA Astrophysics Data System (ADS)

    Qian, Zhixin; Vignale, Giovanni

    2002-03-01

    The imaginary parts of the exchange-correlation kernels f_xc^L,T(q=0, ω) in the linear density-density and transverse current-current response functions of a homogeneous electron liquid are calculated exactly at low frequency, to leading order in the Coulomb interaction. Combining these new results with the previously known high-frequency behaviors of Im f_xc^L,T(q=0, ω) and with the compressibility and the third frequency moment sum rules, we construct simple interpolation for Im f_xc^L,T(q=0, ω) in 3- and 2- dimensions. A novel feature of our interpolation formulas is that they explicitly take into account the two-plasmon component of the excitation spectrum: our longitudinal spectrum Im f_xc^L(q=0, ω) is thus intermediate between the Gross-Kohn interpolation, which ignores the two-plasmon contribution, and a recent approximate calculation by Nifosi, Conti, and Tosi, which probably overestimates it. Numerical results for both the real and imaginary parts of the exchange-correlation kernels at typical electron densities are presented, and compared with those obtained from previous approximations.

  20. Cluster fusion-fission dynamics in the Singapore stock exchange

    NASA Astrophysics Data System (ADS)

    Teh, Boon Kin; Cheong, Siew Ann

    2015-10-01

    In this paper, we investigate how the cross-correlations between stocks in the Singapore stock exchange (SGX) evolve over 2008 and 2009 within overlapping one-month time windows. In particular, we examine how these cross-correlations change before, during, and after the Sep-Oct 2008 Lehman Brothers Crisis. To do this, we extend the complete-linkage hierarchical clustering algorithm, to obtain robust clusters of stocks with stronger intracluster correlations, and weaker intercluster correlations. After we identify the robust clusters in all time windows, we visualize how these change in the form of a fusion-fission diagram. Such a diagram depicts graphically how the cluster sizes evolve, the exchange of stocks between clusters, as well as how strongly the clusters mix. From the fusion-fission diagram, we see a giant cluster growing and disintegrating in the SGX, up till the Lehman Brothers Crisis in September 2008 and the market crashes of October 2008. After the Lehman Brothers Crisis, clusters in the SGX remain small for few months before giant clusters emerge once again. In the aftermath of the crisis, we also find strong mixing of component stocks between clusters. As a result, the correlation between initially strongly-correlated pairs of stocks decay exponentially with average life time of about a month. These observations impact strongly how portfolios and trading strategies should be formulated.

  1. Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry.

    PubMed

    Xiao, Yiming; Konermann, Lars

    2015-08-01

    Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N(2) bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N(2) bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N(2) sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, "semi-unfolded" ↔ "native" ↔ "globally unfolded" → "aggregated". This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS. PMID:25761782

  2. Protein structural dynamics at the gas/water interface examined by hydrogen exchange mass spectrometry

    PubMed Central

    Xiao, Yiming; Konermann, Lars

    2015-01-01

    Gas/water interfaces (such as air bubbles or foam) are detrimental to the stability of proteins, often causing aggregation. This represents a potential problem for industrial processes, for example, the production and handling of protein drugs. Proteins possess surfactant-like properties, resulting in a high affinity for gas/water interfaces. The tendency of previously buried nonpolar residues to maximize contact with the gas phase can cause significant structural distortion. Most earlier studies in this area employed spectroscopic tools that could only provide limited information. Here we use hydrogen/deuterium exchange (HDX) mass spectrometry (MS) for probing the conformational dynamics of the model protein myoglobin (Mb) in the presence of N2 bubbles. HDX/MS relies on the principle that unfolded and/or highly dynamic regions undergo faster deuteration than tightly folded segments. In bubble-free solution Mb displays EX2 behavior, reflecting the occurrence of short-lived excursions to partially unfolded conformers. A dramatically different behavior is seen in the presence of N2 bubbles; EX2 dynamics still take place, but in addition the protein shows EX1 behavior. The latter results from interconversion of the native state with conformers that are globally unfolded and long-lived. These unfolded species likely correspond to Mb that is adsorbed to the surface of gas bubbles. N2 sparging also induces aggregation. To explain the observed behavior we propose a simple model, that is, “semi-unfolded” ↔ “native” ↔ “globally unfolded” → “aggregated”. This model quantitatively reproduces the experimentally observed kinetics. To the best of our knowledge, the current study marks the first exploration of surface denaturation phenomena by HDX/MS. PMID:25761782

  3. Respiratory dynamics of discontinuous gas exchange in the tracheal system of the desert locust, Schistocerca gregaria.

    PubMed

    Groenewald, Berlizé; Hetz, Stefan K; Chown, Steven L; Terblanche, John S

    2012-07-01

    Gas exchange dynamics in insects is of fundamental importance to understanding evolved variation in breathing patterns, such as discontinuous gas exchange cycles (DGCs). Most insects do not rely solely on diffusion for the exchange of respiratory gases but may also make use of respiratory movements (active ventilation) to supplement gas exchange at rest. However, their temporal dynamics have not been widely investigated. Here, intratracheal pressure, V(CO2) and body movements of the desert locust Schistocerca gregaria were measured simultaneously during the DGC and revealed several important aspects of gas exchange dynamics. First, S. gregaria employs two different ventilatory strategies, one involving dorso-ventral contractions and the other longitudinal telescoping movements. Second, although a true spiracular closed (C)-phase of the DGC could be identified by means of subatmospheric intratracheal pressure recordings, some CO(2) continued to be released. Third, strong pumping actions do not necessarily lead to CO(2) release and could be used to ensure mixing of gases in the closed tracheal system, or enhance water vapour reabsorption into the haemolymph from fluid-filled tracheole tips by increasing the hydrostatic pressure or forcing fluid into the haemocoel. Finally, this work showed that the C-phase of the DGC can occur at any pressure. These results provide further insights into the mechanistic basis of insect gas exchange. PMID:22675191

  4. Coupled acoustic-gravity field for dynamic evaluation of ion exchange with a single resin bead.

    PubMed

    Kanazaki, Takahiro; Hirawa, Shungo; Harada, Makoto; Okada, Tetsuo

    2010-06-01

    A coupled acoustic-gravity field is efficient for entrapping a particle at the position determined by its acoustic properties rather than its size. This field has been applied to the dynamic observation of ion-exchange reactions occurring in a single resin bead. The replacement of counterions in an ion-exchange resin induces changes in its acoustic properties, such as density and compressibility. Therefore, we can visually trace the advancement of an ion-exchange reaction as a time change in the levitation position of a resin bead entrapped in the field. Cation-exchange reactions occurring in resin beads with diameters of 40-120 microm are typically completed within 100-200 s. Ion-exchange equilibrium or kinetics is often evaluated with off-line chemical analyses, which require a batch amount of ion exchangers. Measurements with a single resin particle allow us to evaluate ion-exchange dynamics and kinetics of ions including those that are difficult to measure by usual off-line analyses. The diffusion properties of ions in resins have been successfully evaluated from the time change in the levitation positions of resin beads. PMID:20462180

  5. Dynamics of the force exchanged between membrane inclusions.

    PubMed

    Fournier, Jean-Baptiste

    2014-03-28

    We study the dynamical response of a fluid membrane to the sudden conformation change of active inclusions linearly coupled to the membrane curvature. The mutual force between two inclusions triggered simultaneously is shown to exhibit a transient maximum much larger than the equilibrium force. Even in the presence of tension, this dynamical interaction is long range over distances much larger than the correlation length. We derive the scaling laws describing these phenomena analytically, and we stress the importance of the damping due to intermonolayer friction. PMID:24724681

  6. Simultaneous Disulfide and Boronic Acid Ester Exchange in Dynamic Combinatorial Libraries.

    PubMed

    Diemer, Sanna L; Kristensen, Morten; Rasmussen, Brian; Beeren, Sophie R; Pittelkow, Michael

    2015-09-10

    Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinatorial libraries (DCLs) ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate conditions. We describe the detailed studies necessary to establish suitable reaction conditions and highlight the analytical techniques appropriate to study this type of system.

  7. Theoretical investigation on the mechanism and dynamics of oxo exchange of neptunyl(VI) hydroxide in aqueous solution.

    PubMed

    Yang, Xia; Chai, Zhifang; Wang, Dongqi

    2015-03-21

    Four types of reaction mechanisms for the oxo ligand exchange of monomeric and dimeric neptunyl(VI) hydroxide in aqueous solution were explored computationally using density functional theory (DFT) and ab initio classical molecular dynamics. The obtained results were compared with previous studies on the oxo exchange of uranyl hydroxide, as well as with experiments. It is found that the stable T-shaped [NpO3(OH)3](3-) intermediate is a key species for oxo exchange in the proton transfer in mononuclear Path I and binuclear Path IV, similar to the case of uranyl(VI) hydroxide. Path I is thought to be the preferred oxo exchange mechanism for neptunyl(VI) hydroxide in our calculations, due to the lower activation energy (22.7 and 13.1 kcal mol(-1) for ΔG(‡) and ΔH(‡), respectively) of the overall reaction. Path II via a cis-neptunyl structure assisted by a water molecule might be a competitive channel against Path I with a mononuclear mechanism, owing to a rapid dynamical process occurring in Path II. In Path IV with the binuclear mechanism, oxo exchange is accomplished via the interaction between [NpO2(OH)4](2-) and T-shaped [NpO3(OH)3](3-) with a low activation energy for the rate-determining step, however, the overall energy required to fulfill the reaction is slightly higher than that in mononuclear Path I, suggesting a possible binuclear process in the higher energy region. The chemical bonding evolution along the reaction pathways was discussed by using topological methodologies of the electron localization function (ELF).

  8. Dynamics of a lattice gas system of three species

    NASA Astrophysics Data System (ADS)

    Wang, Yuanshi; Wu, Hong; Liang, Junhao

    2016-10-01

    This paper considers a mutualism system of three species in which each species provides resource for the next one in a one-directional loop, while there exists spatial competition among them. The system is characterized by a lattice gas model and the cases of obligate mutualisms, obligate-facultative mutualisms and facultative mutualisms are considered. Using dynamical systems theory, it is shown that (i) the mutualisms can lead to coexistence of species; (ii) A weak mutualism or an extremely strong mutualism will result in extinction of species, while even the superior facultative species will be driven into extinction by its over-strong mutualism on the next one; (iii) Initial population density plays a role in the coexistence of species. It is also shown that when there exists weak mutualism, an obligate species can survive by providing more benefit to the next one, and the inferior facultative species will not be driven into extinction if it can strengthen its mutualism on the next species. Moreover, Hopf bifurcation, saddle-node bifurcation and bifurcation of heteroclinic cycles are shown in the system. Projection method is extended to exhibit bistability in the three-dimensional model: when saddle-node bifurcation occurs, stable manifold of the saddle-node point divides intR+3 into two basins of attraction of two equilibria. Furthermore, Lyapunov method is applied to exhibit unstability of heteroclinic cycles. Numerical simulations confirm and extend our results.

  9. Dynamics of compressible air flow in ducts with heat exchange

    NASA Astrophysics Data System (ADS)

    Abdulhadi, M.

    1986-12-01

    An investigation into the effect of heat addition on subsonic flow of an air stream in a constant-area duct preceded by a convergent nozzle is carried out. A nozzle flow apparatus with a heat exchanger encasing the constant-area duct has been built for this purpose. Hot water is provided from an electric boiler where the flow rate and the in-flow hot water temperature could be controlled. It is confirmed experimentally, as predicted analytically, that heat transfer to the gas decreases its local static pressure along the duct axis, and that this decrease is associated with an increase in Mach number toward M = 1 at the exit (thermal choking). In the case of subsonic flow, the additional entropy generated by the heat interaction exceeding the amount that produces thermal choking can only be accommodated by moving to a new Rayleigh line, at a decreased flow rate which lowers the inlet Mach number. The good correlation between the experimental results and the analytical derivations illustrates that the experimental arrangement has potential for further experiments and investigations.

  10. Aphid Species and Population Dynamics Associated with Strawberry.

    PubMed

    Bernardi, D; Araujo, E S; Zawadneak, M A C; Botton, M; Mogor, A F; Garcia, M S

    2013-12-01

    Aphids are among the major pests associated with strawberries in Southern Brasil. In this study, we identified the main species that occur in strawberry fields in the states of Paraná and Rio Grande do Sul, Brasil. We also compared the effectiveness of different sampling methods and studied the population dynamics of aphid species during two strawberry crop cycles in the municipality of Pinhais, state of Paraná, Brasil. Chaetosiphon fragaefolii (Cockerell) and Aphis forbesi Weed were the main species associated with strawberry. The method of hit plant and the Möericke trap showed equal effectiveness to capture wingless and winged insects. The peak population of aphids in the state of Paraná occurred from September to November. This information can help producers to implement strategies to monitor and control the major aphid species that occur in strawberry culture. PMID:27193281

  11. Time Dependency of Psychotherapeutic Exchanges: The Contribution of the Theory of Dynamic Systems in Analyzing Process

    PubMed Central

    Salvatore, Sergio; Tschacher, Wolfgang

    2012-01-01

    This paper provides a general framework for the use of Theory of Dynamic Systems (TDS) in the field of psychotherapy research. Psychotherapy is inherently dynamic, namely a function of time. Consequently, the improvement of construct validity and clinical relevance of psychotherapy process research require the development of models of investigation allowing dynamic mappings of clinical exchange. Thus, TDS becomes a significant theoretical and methodological reference. The paper focuses two topics. First, the main concepts of TDS are briefly introduced together with a basic typology of approaches developed within this domain. Second, we propose a repertoire of investigation strategies that can be used to capture the dynamic nature of clinical exchange. In this way we intend to highlight the feasibility and utility of strategies of analysis informed by TDS. PMID:22848205

  12. Leaf gas exchange performance and the lethal water potential of five European species during drought.

    PubMed

    Li, Shan; Feifel, Marion; Karimi, Zohreh; Schuldt, Bernhard; Choat, Brendan; Jansen, Steven

    2016-02-01

    Establishing physiological thresholds to drought-induced mortality in a range of plant species is crucial in understanding how plants respond to severe drought. Here, five common European tree species were selected (Acer campestre L., Acer pseudoplatanus L., Carpinus betulus L., Corylus avellana L. and Fraxinus excelsior L.) to study their hydraulic thresholds to mortality. Photosynthetic parameters during desiccation and the recovery of leaf gas exchange after rewatering were measured. Stem vulnerability curves and leaf pressure-volume curves were investigated to understand the hydraulic coordination of stem and leaf tissue traits. Stem and root samples from well-watered and severely drought-stressed plants of two species were observed using transmission electron microscopy to visualize mortality of cambial cells. The lethal water potential (ψlethal) correlated with stem P99 (i.e., the xylem water potential at 99% loss of hydraulic conductivity, PLC). However, several plants that were stressed beyond the water potential at 100% PLC showed complete recovery during the next spring, which suggests that the ψlethal values were underestimated. Moreover, we observed a 1 : 1 relationship between the xylem water potential at the onset of embolism and stomatal closure, confirming hydraulic coordination between leaf and stem tissues. Finally, ultrastructural changes in the cytoplasm of cambium tissue and mortality of cambial cells are proposed to provide an alternative approach to investigate the point of no return associated with plant death.

  13. Leaf gas exchange performance and the lethal water potential of five European species during drought.

    PubMed

    Li, Shan; Feifel, Marion; Karimi, Zohreh; Schuldt, Bernhard; Choat, Brendan; Jansen, Steven

    2016-02-01

    Establishing physiological thresholds to drought-induced mortality in a range of plant species is crucial in understanding how plants respond to severe drought. Here, five common European tree species were selected (Acer campestre L., Acer pseudoplatanus L., Carpinus betulus L., Corylus avellana L. and Fraxinus excelsior L.) to study their hydraulic thresholds to mortality. Photosynthetic parameters during desiccation and the recovery of leaf gas exchange after rewatering were measured. Stem vulnerability curves and leaf pressure-volume curves were investigated to understand the hydraulic coordination of stem and leaf tissue traits. Stem and root samples from well-watered and severely drought-stressed plants of two species were observed using transmission electron microscopy to visualize mortality of cambial cells. The lethal water potential (ψlethal) correlated with stem P99 (i.e., the xylem water potential at 99% loss of hydraulic conductivity, PLC). However, several plants that were stressed beyond the water potential at 100% PLC showed complete recovery during the next spring, which suggests that the ψlethal values were underestimated. Moreover, we observed a 1 : 1 relationship between the xylem water potential at the onset of embolism and stomatal closure, confirming hydraulic coordination between leaf and stem tissues. Finally, ultrastructural changes in the cytoplasm of cambium tissue and mortality of cambial cells are proposed to provide an alternative approach to investigate the point of no return associated with plant death. PMID:26614785

  14. Benchmarking novel approaches for modelling species range dynamics

    PubMed Central

    Zurell, Damaris; Thuiller, Wilfried; Pagel, Jörn; Cabral, Juliano S; Münkemüller, Tamara; Gravel, Dominique; Dullinger, Stefan; Normand, Signe; Schiffers, Katja H.; Moore, Kara A.; Zimmermann, Niklaus E.

    2016-01-01

    Increasing biodiversity loss due to climate change is one of the most vital challenges of the 21st century. To anticipate and mitigate biodiversity loss, models are needed that reliably project species’ range dynamics and extinction risks. Recently, several new approaches to model range dynamics have been developed to supplement correlative species distribution models (SDMs), but applications clearly lag behind model development. Indeed, no comparative analysis has been performed to evaluate their performance. Here, we build on process-based, simulated data for benchmarking five range (dynamic) models of varying complexity including classical SDMs, SDMs coupled with simple dispersal or more complex population dynamic models (SDM hybrids), and a hierarchical Bayesian process-based dynamic range model (DRM). We specifically test the effects of demographic and community processes on model predictive performance. Under current climate, DRMs performed best, although only marginally. Under climate change, predictive performance varied considerably, with no clear winners. Yet, all range dynamic models improved predictions under climate change substantially compared to purely correlative SDMs, and the population dynamic models also predicted reasonable extinction risks for most scenarios. When benchmarking data were simulated with more complex demographic and community processes, simple SDM hybrids including only dispersal often proved most reliable. Finally, we found that structural decisions during model building can have great impact on model accuracy, but prior system knowledge on important processes can reduce these uncertainties considerably. Our results reassure the clear merit in using dynamic approaches for modelling species’ response to climate change but also emphasise several needs for further model and data improvement. We propose and discuss perspectives for improving range projections through combination of multiple models and for making these approaches

  15. The dynamics of sorption of sulfuric acid by weakly basic polyacrylic anion exchangers

    NASA Astrophysics Data System (ADS)

    Mamchenko, A. V.; Kushnir, T. V.

    2009-05-01

    The nonequilibrium dynamics of sorption of sulfuric acid by free base forms of Amberlite IRA-67 and Lewatite VP.OC.1072 weakly basic anion exchangers is studied. It is established that, in hydrodynamic regimes of filtration, which are typical of OH filters of the first stage of water-desalting plants, the limiting stage of sorption kinetics is inside diffusion. It is concluded that the process is correctly described by an asymptotic solution to the inside-diffusion model of sorption dynamics.

  16. NASA geometry data exchange specification for computational fluid dynamics (NASA IGES)

    NASA Technical Reports Server (NTRS)

    Blake, Matthew W.; Kerr, Patricia A.; Thorp, Scott A.; Jou, Jin J.

    1994-01-01

    This document specifies a subset of an existing product data exchange specification that is widely used in industry and government. The existing document is called the Initial Graphics Exchange Specification. This document, a subset of IGES, is intended for engineers analyzing product performance using tools such as computational fluid dynamics (CFD) software. This document specifies how to define mathematically and exchange the geometric model of an object. The geometry is represented utilizing nonuniform rational B-splines (NURBS) curves and surfaces. Only surface models are represented; no solid model representation is included. This specification does not include most of the other types of product information available in IGES (e.g., no material properties or surface finish properties) and does not provide all the specific file format details of IGES. The data exchange protocol specified in this document is fully conforming to the American National Standard (ANSI) IGES 5.2.

  17. Acidity and hydrogen exchange dynamics of iron(II)-bound nitroxyl in aqueous solution.

    PubMed

    Gao, Yin; Toubaei, Abouzar; Kong, Xianqi; Wu, Gang

    2014-10-20

    Nitroxyl-iron(II) (HNO-Fe(II)) complexes are often unstable in aqueous solution, thus making them very difficult to study. Consequently, many fundamental chemical properties of Fe(II)-bound HNO have remained unknown. Using a comprehensive multinuclear ((1)H, (15)N, (17)O) NMR approach, the acidity of the Fe(II)-bound HNO in [Fe(CN)5(HNO)](3-) was investigated and its pK(a) value was determined to be greater than 11. Additionally, HNO undergoes rapid hydrogen exchange with water in aqueous solution and this exchange process is catalyzed by both acid and base. The hydrogen exchange dynamics for the Fe(II)-bound HNO have been characterized and the obtained benchmark values, when combined with the literature data on proteins, reveal that the rate of hydrogen exchange for the Fe(II)-bound HNO in the interior of globin proteins is reduced by a factor of 10(6). PMID:25205463

  18. Determining habitat quality for species that demonstrate dynamic habitat selection

    USGS Publications Warehouse

    Beerens, James; Frederick, Peter C; Noonburg, Erik G; Gawlik, Dale E.

    2015-01-01

    Determining habitat quality for wildlife populations requires relating a species' habitat to its survival and reproduction. Within a season, species occurrence and density can be disconnected from measures of habitat quality when resources are highly seasonal, unpredictable over time, and patchy. Here we establish an explicit link among dynamic selection of changing resources, spatio-temporal species distributions, and fitness for predictive abundance and occurrence models that are used for short-term water management and long-term restoration planning. We used the wading bird distribution and evaluation models (WADEM) that estimate (1) daily changes in selection across resource gradients, (2) landscape abundance of flocks and individuals, (3) conspecific foraging aggregation, and (4) resource unit occurrence (at fixed 400 m cells) to quantify habitat quality and its consequences on reproduction for wetland indicator species. We linked maximum annual numbers of nests detected across the study area and nesting success of Great Egrets (Ardea alba), White Ibises (Eudocimus albus), and Wood Storks (Mycteria americana) over a 20-year period to estimated daily dynamics of food resources produced by WADEM over a 7490 km2 area. For all species, increases in predicted species abundance in March and high abundance in April were strongly linked to breeding responses. Great Egret nesting effort and success were higher when birds also showed greater conspecific foraging aggregation. Synthesis and applications: This study provides the first empirical evidence that dynamic habitat selection processes and distributions of wading birds over environmental gradients are linked with reproductive measures over periods of decades. Further, predictor variables at a variety of temporal (daily-multiannual) resolutions and spatial (400 m to regional) scales effectively explained variation in ecological processes that change habitat quality. The process used here allows managers to develop

  19. Determining habitat quality for species that demonstrate dynamic habitat selection.

    PubMed

    Beerens, James M; Frederick, Peter C; Noonburg, Erik G; Gawlik, Dale E

    2015-12-01

    Determining habitat quality for wildlife populations requires relating a species' habitat to its survival and reproduction. Within a season, species occurrence and density can be disconnected from measures of habitat quality when resources are highly seasonal, unpredictable over time, and patchy. Here we establish an explicit link among dynamic selection of changing resources, spatio-temporal species distributions, and fitness for predictive abundance and occurrence models that are used for short-term water management and long-term restoration planning. We used the wading bird distribution and evaluation models (WADEM) that estimate (1) daily changes in selection across resource gradients, (2) landscape abundance of flocks and individuals, (3) conspecific foraging aggregation, and (4) resource unit occurrence (at fixed 400 m cells) to quantify habitat quality and its consequences on reproduction for wetland indicator species. We linked maximum annual numbers of nests detected across the study area and nesting success of Great Egrets (Ardea alba), White Ibises (Eudocimus albus), and Wood Storks (Mycteria americana) over a 20-year period to estimated daily dynamics of food resources produced by WADEM over a 7490 km(2) area. For all species, increases in predicted species abundance in March and high abundance in April were strongly linked to breeding responses. Great Egret nesting effort and success were higher when birds also showed greater conspecific foraging aggregation. Synthesis and applications: This study provides the first empirical evidence that dynamic habitat selection processes and distributions of wading birds over environmental gradients are linked with reproductive measures over periods of decades. Further, predictor variables at a variety of temporal (daily-multiannual) resolutions and spatial (400 m to regional) scales effectively explained variation in ecological processes that change habitat quality. The process used here allows managers to

  20. Dynamic exchanges between DOM and POM pools in coastal and inland aquatic ecosystems: A review.

    PubMed

    He, Wei; Chen, Meilian; Schlautman, Mark A; Hur, Jin

    2016-05-01

    Dynamic exchanges between dissolved organic matter (DOM) and particulate organic matter (POM) plays a critical role in organic carbon cycling in coastal and inland aquatic ecosystems, interactions with aquatic organisms, mobility and bioavailability of pollutants, among many other ecological and geochemical phenomena. Although DOM-POM exchange processes have been widely studied from different aspects, little to no effort has been made to date to provide a comprehensive, mechanistic, and micro-spatial schema for understanding various exchange processes occurring in different aquatic ecosystems in a unified way. The phenomena occurring between DOM and POM were explained here with the homogeneous and heterogeneous mechanisms. In the homogeneous mechanism, the participating components are only organic matter (OM) constituents themselves with aggregation and dissolution involved, whereas OM is associated with other components such as minerals and particulate colloids in the heterogeneous counterpart. Besides the generally concerned processes of aggregation/dissolution and adsorption/desorption, other ecological factors such as sunlight and organisms can also participate in DOM-POM exchanges through altering the chemical nature of OM. Despite the limitation of current analytical technologies, many unknown and/or unquantified processes need to be identified to unravel the complicated exchanges of OM between its dissolved and particulate states. Based on the review of several previous mathematical models, we proposed a unified conceptual model to describe all major dynamic exchange mechanisms on the basis of exergy theory. More knowledge of dynamic DOM-POM exchanges is warranted to overcome the potential problems arising from a simple division of OM into dissolved versus particulate states and to further develop more sophisticated mathematic models.

  1. Slow process in confined polymer melts: Layer exchange dynamics at a polymer solid interface

    NASA Astrophysics Data System (ADS)

    Yelash, L.; Virnau, P.; Binder, K.; Paul, W.

    2010-11-01

    Employing Molecular Dynamics simulations of a chemically realistic model of 1,4-polybutadiene between graphite walls we show that the mass exchange between layers close to the walls is a slow process already in the melt state. For the glass transition of confined polymers this process competes with the slowing down due to packing effects and intramolecular rotation barriers.

  2. Effect of experimental wood addition on hyporheic exchange and thermal dynamics in a losing meadow stream

    NASA Astrophysics Data System (ADS)

    Sawyer, Audrey H.; Cardenas, M. Bayani

    2012-10-01

    Stream restoration structures such as large wood can enhance shallow river-groundwater exchange, or hyporheic exchange, and alter temperature dynamics in restored reaches. We added and then removed channel-spanning logs in a second-order mountain meadow stream to test short-term impacts on hyporheic exchange, streambed temperatures, and surface water temperatures. Based on vertical seepage measurements and numerical simulations of hyporheic fluid and heat flow, large wood addition increased hyporheic exchange and altered streambed temperatures. In this losing stream, meter-scale hyporheic exchange cells formed beneath large wood. Upwelling pore water downstream of logs stabilized diel temperature cycles across <8% of the streambed, creating localized but potentially valuable thermal refuge. Exchange rates were <0.1% of channel discharge—too small to impact the range of diel temperature signals in surface water. However, the lag between downstream and upstream diel temperature signals was slightly greater with large wood, which may indicate that surface storage zones rather than hyporheic storage zones increased thermal retardation. Losing conditions limited the spatial extent and rates of hyporheic exchange near large wood. Impacts of large wood reintroduction on hyporheic exchange depend on ambient groundwater discharge or recharge, streambed permeability, channel Froude number, large wood blockage ratio, and large wood spacing. In many streams, large wood reintroduction may increase hyporheic habitat volume and complexity but may not increase exchange rates enough to alter surface water temperature or chemistry. Surface storage zones such as eddies and pools can still influence heat and solute retention in the channel.

  3. Environmental colour affects aspects of single-species population dynamics.

    PubMed

    Petchey, O L

    2000-04-22

    Single-species populations of ciliates (Colpidium and Paramecium) experienced constant temperature or white or reddened temperature fluctuations in aquatic microcosms in order to test three hypotheses about how environmental colour influences population dynamics. (i) Models predict that the colour of population dynamics is tinged by the colour of the environmental variability. However, environmental colour had no effect on the colour of population dynamics. All population dynamics in this experiment were reddened, regardless of environmental colour. (ii) Models predict that populations will track reddened environmental variability more closely than white environmental variability and that populations with a higher intrinsic growth rate (r) will track environmental variability more closely than populations with a low r. The experimental populations behaved as predicted. (iii) Models predict that population variability is determined by interaction between r and the environmental variability. The experimental populations behaved as predicted. These results show that (i) reddened population dynamics may need no special explanation, such as reddened environments, spatial subdivision or interspecific interactions, and (ii) and (iii) that population dynamics are sensitive to environmental colour, in agreement with population models. Correct specification of the colour of the environmental variability in models is required for accurate predictions. Further work is needed to study the effects of environmental colour on communities and ecosystems.

  4. Environmental variation, vegetation distribution, carbon dynamics and water/energy exchange at high latitudes

    USGS Publications Warehouse

    McGuire, A.D.; Wirth, C.; Apps, M.; Beringer, J.; Clein, J.; Epstein, H.; Kicklighter, D.W.; Bhatti, J.; Chapin, F. S.; De Groot, B.; Efremov, D.; Eugster, W.; Fukuda, M.; Gower, T.; Hinzman, L.; Huntley, B.; Jia, G.J.; Kasischke, E.; Melillo, J.; Romanovsky, V.; Shvidenko, A.; Vaganov, E.; Walker, D.

    2002-01-01

    The responses of high latitude ecosystems to global change involve complex interactions among environmental variables, vegetation distribution, carbon dynamics, and water and energy exchange. These responses may have important consequences for the earth system. In this study, we evaluated how vegetation distribution, carbon stocks and turnover, and water and energy exchange are related to environmental variation spanned by the network of the IGBP high latitude transects. While the most notable feature of the high latitude transects is that they generally span temperature gradients from southern to northern latitudes, there are substantial differences in temperature among the transects. Also, along each transect temperature co-varies with precipitation and photosynthetically active radiation, which are also variable among the transects. Both climate and disturbance interact to influence latitudinal patterns of vegetation and soil carbon storage among the transects, and vegetation distribution appears to interact with climate to determine exchanges of heat and moisture in high latitudes. Despite limitations imposed by the data we assembled, the analyses in this study have taken an important step toward clarifying the complexity of interactions among environmental variables, vegetation distribution, carbon stocks and turnover, and water and energy exchange in high latitude regions. This study reveals the need to conduct coordinated global change studies in high latitudes to further elucidate how interactions among climate, disturbance, and vegetation distribution influence carbon dynamics and water and energy exchange in high latitudes.

  5. Dynamic UltraFast 2D EXchange SpectroscopY (UF-EXSY) of hyperpolarized substrates

    PubMed Central

    Swisher, Christine Leon; Koelsch, Bertram; Sukumar, Subramianam; Sriram, Renuka; Santos, Romelyn Delos; Wang, Zhen Jane; Kurhanewicz, John; Vigneron, Daniel; Larson, Peder

    2015-01-01

    In this work, we present a new ultrafast method for acquiring dynamic 2D EXchange SpectroscopY (EXSY) within a single acquisition. This technique reconstructs two-dimensional EXSY spectra from one-dimensional spectra based on the phase accrual during echo times. The Ultrafast-EXSY acquisition overcomes long acquisition times typically needed to acquire 2D NMR data by utilizing sparsity and phase dependence to dramatically undersample in the indirect time dimension. This allows for the acquisition of the 2D spectrum within a single shot. We have validated this method in simulations and hyperpolarized enzyme assay experiments separating the dehydration of pyruvate and lactate-to-pyruvate conversion. In a renal cell carcinoma cell (RCC) line, bidirectional exchange was observed. This new technique revealed decreased conversion of lactate-to-pyruvate with high expression of monocarboxylate transporter 4 (MCT4), known to correlate with aggressive cancer phenotypes. We also showed feasibility of this technique in vivo in a RCC model where bidirectional exchange was observed for pyruvate–lactate, pyruvate–alanine, and pyruvate–hydrate and were resolved in time. Broadly, the technique is well suited to investigate the dynamics of multiple exchange pathways and applicable to hyperpolarized substrates where chemical exchange has shown great promise across a range of disciplines. PMID:26117655

  6. Improving the replica-exchange molecular-dynamics method for efficient sampling in the temperature space.

    PubMed

    Chen, Changjun; Xiao, Yi; Huang, Yanzhao

    2015-05-01

    Replica-exchange molecular dynamics (REMD) is a popular sampling method in the molecular simulation. By frequently exchanging the replicas at different temperatures, the molecule can jump out of the minima and sample efficiently in the conformational space. Although REMD has been shown to be practical in a lot of applications, it does have a critical limitation. All the replicas at all the temperatures must be simulated for a period between the replica-exchange steps. This may be problematic for the reaction with high free energy barriers. In that case, too many replicas are required in the simulation. To reduce the calculation quantity and improve its performance, in this paper we propose a modified REMD method. During the simulation, each replica at each temperature can stay in either the active or inactive state and only switch between the states at the exchange step. In the active state, the replica moves freely in the canonical ensemble by the normal molecular dynamics, and in the inactive state, the replica is frozen temporarily until the next exchange step. The number of the replicas in the active states (active replicas) depends on the number of CPUs in the computer. Using the additional inactive replicas, one can perform an REMD simulation in a wider temperature space. The practical applications show that the modified REMD method is reliable. With the same number of active replicas, this REMD method can produce a more reasonable free energy surface around the free energy minima than the standard REMD method. PMID:26066200

  7. Dynamic UltraFast 2D EXchange SpectroscopY (UF-EXSY) of hyperpolarized substrates

    NASA Astrophysics Data System (ADS)

    Leon Swisher, Christine; Koelsch, Bertram; Sukumar, Subramianam; Sriram, Renuka; Santos, Romelyn Delos; Wang, Zhen Jane; Kurhanewicz, John; Vigneron, Daniel; Larson, Peder

    2015-08-01

    In this work, we present a new ultrafast method for acquiring dynamic 2D EXchange SpectroscopY (EXSY) within a single acquisition. This technique reconstructs two-dimensional EXSY spectra from one-dimensional spectra based on the phase accrual during echo times. The Ultrafast-EXSY acquisition overcomes long acquisition times typically needed to acquire 2D NMR data by utilizing sparsity and phase dependence to dramatically undersample in the indirect time dimension. This allows for the acquisition of the 2D spectrum within a single shot. We have validated this method in simulations and hyperpolarized enzyme assay experiments separating the dehydration of pyruvate and lactate-to-pyruvate conversion. In a renal cell carcinoma cell (RCC) line, bidirectional exchange was observed. This new technique revealed decreased conversion of lactate-to-pyruvate with high expression of monocarboxylate transporter 4 (MCT4), known to correlate with aggressive cancer phenotypes. We also showed feasibility of this technique in vivo in a RCC model where bidirectional exchange was observed for pyruvate-lactate, pyruvate-alanine, and pyruvate-hydrate and were resolved in time. Broadly, the technique is well suited to investigate the dynamics of multiple exchange pathways and applicable to hyperpolarized substrates where chemical exchange has shown great promise across a range of disciplines.

  8. Dynamics of Aeromonas species isolated from wastewater treatment system.

    PubMed

    Martone-Rocha, S; Piveli, R P; Matté, G R; Dória, M C; Dropa, M; Morita, M; Peternella, F A; Matté, M H

    2010-12-01

    Aeromonas are widely distributed in the aquatic environment, and are considered to be emerging organisms that can produce a series of virulence factors. The present study was carried out in a sanitary sewage stabilization pond treatment system, located in Lins, State of São Paulo, Brazil. Most probable number was applied for estimation of the genus Aeromonas. Colony isolation was carried out on blood agar ampicillin and confirmed by biochemical characterization. Aeromonas species were isolated in 72.4% of influent samples, and in 55.2 and 48.3% of effluent from anaerobic and facultative lagoons, respectively. Thirteen Aeromonas species were isolated, representing most of the recognized species of these organisms. Even though it was possible to observe a tendency of decrease, total elimination of these organisms from the studied system was not achieved. Understanding of the pathogenic organism's dynamics in wastewater treatment systems with a reuse potential is especially important because of the risk it represents. PMID:20705981

  9. On the use of a weak-coupling thermostat in replica-exchange molecular dynamics simulations.

    PubMed

    Lin, Zhixiong; van Gunsteren, Wilfred F

    2015-07-21

    In a molecular dynamics (MD) simulation, various thermostat algorithms, including Langevin dynamics (LD), Nosé-Hoover (NH), and weak-coupling (WC) thermostats, can be used to keep the simulation temperature constant. A canonical ensemble is generated by the use of LD and NH, while the nature of the ensemble produced by WC has not yet been identified. A few years ago, it was shown that when using a WC thermostat with particular values of the temperature coupling time for liquid water at ambient temperature and pressure, the distribution of the potential energy is less wide than the canonical one. This led to an artifact in temperature replica-exchange molecular dynamics (T-REMD) simulations in which the potential energy distributions appear not to be equal to the ones of standard MD simulations. In this paper, we re-investigate this problem. We show that this artifact is probably due to the ensemble generated by WC being incompatible with the T-REMD replica-exchange criterion, which assumes a canonical configurational ensemble. We also show, however, that this artifact can be reduced or even eliminated by particular choices of the temperature coupling time of WC and the replica-exchange time period of T-REMD, i.e., when the temperature coupling time is chosen very close to the MD time step or when the exchange time period is chosen large enough. An attempt to develop a T-REMD replica-exchange criterion which is likely to be more compatible with the WC configurational ensemble is reported. Furthermore, an exchange criterion which is compatible with a microcanonical ensemble is used in total energy REMD simulations.

  10. Competition between abstraction and exchange channels in H + HCN reaction: Full-dimensional quantum dynamics

    SciTech Connect

    Jiang, Bin; Guo, Hua

    2013-12-14

    Dynamics of the title reaction is investigated on an ab initio based potential energy surface using a full-dimensional quantum wave packet method within the centrifugal sudden approximation. It is shown that the reaction between H and HCN leads to both the hydrogen exchange and hydrogen abstraction channels. The exchange channel has a lower threshold and larger cross section than the abstraction channel. It also has more oscillations due apparently to quantum resonances. Both channels are affected by long-lived resonances supported by potential wells. Comparison with experimental cross sections indicates underestimation of the abstraction barrier height.

  11. Competition between abstraction and exchange channels in H + HCN reaction: Full-dimensional quantum dynamics

    NASA Astrophysics Data System (ADS)

    Jiang, Bin; Guo, Hua

    2013-12-01

    Dynamics of the title reaction is investigated on an ab initio based potential energy surface using a full-dimensional quantum wave packet method within the centrifugal sudden approximation. It is shown that the reaction between H and HCN leads to both the hydrogen exchange and hydrogen abstraction channels. The exchange channel has a lower threshold and larger cross section than the abstraction channel. It also has more oscillations due apparently to quantum resonances. Both channels are affected by long-lived resonances supported by potential wells. Comparison with experimental cross sections indicates underestimation of the abstraction barrier height.

  12. Use of chemical species as dynamic membranes with crossflow microfiltration

    SciTech Connect

    Al-Malack, M.H.; Anderson, G.K.

    1998-12-01

    The feasibility of utilizing the phenomenon of dynamic membrane formation with crossflow microfiltration in treating domestic wastewater was investigated. The primary membrane, used throughout the investigation, was made of woven polyester. Different chemical species, such as CaCO{sub 3}, FeCl{sub 3}, and NaAlO{sub 2}, were used in forming dynamic membranes on top of the primary membrane. Secondary effluent from a domestic activated sludge wastewater treatment plant was treated. A calcium carbonate dynamic membrane produced a stabilized permeate flux of 90 L/m{sup 2} {center_dot} h, with a permeate turbidity of 0.21 Nephelometric Turbidity Unit (NTU), at optimum conditions. Ferric chloride produced optimum results when it was mixed with tap water. A permeate flux and turbidity of 70 L/m{sup 2} {center_dot} h and 0.16 NTU, respectively, were obtained. Sodium aluminate produced a stabilized permeate flux of 77 L/m{sup 2} {center_dot} h when it was mixed with tap water during the formation of the dynamic membrane. The permeate turbidity was 0.16 NTU. The fouling mechanism of the three dynamic membranes was investigated, and empirical models were produced.

  13. Modeling species occurrence dynamics with multiple states and imperfect detection

    USGS Publications Warehouse

    MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

    2009-01-01

    Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture-recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics. ?? 2009 by the Ecological Society of America.

  14. Dynamic models for problems of species occurrence with multiple states

    USGS Publications Warehouse

    MacKenzie, D.I.; Nichols, J.D.; Seamans, M.E.; Gutierrez, R.J.

    2009-01-01

    Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture?recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics.

  15. Modeling species occurrence dynamics with multiple states and imperfect detection.

    PubMed

    MacKenzie, Darryl I; Nichols, James D; Seamans, Mark E; Gutiérrez, R J

    2009-03-01

    Recent extensions of occupancy modeling have focused not only on the distribution of species over space, but also on additional state variables (e.g., reproducing or not, with or without disease organisms, relative abundance categories) that provide extra information about occupied sites. These biologist-driven extensions are characterized by ambiguity in both species presence and correct state classification, caused by imperfect detection. We first show the relationships between independently published approaches to the modeling of multistate occupancy. We then extend the pattern-based modeling to the case of sampling over multiple seasons or years in order to estimate state transition probabilities associated with system dynamics. The methodology and its potential for addressing relevant ecological questions are demonstrated using both maximum likelihood (occupancy and successful reproduction dynamics of California Spotted Owl) and Markov chain Monte Carlo estimation approaches (changes in relative abundance of green frogs in Maryland). Just as multistate capture-recapture modeling has revolutionized the study of individual marked animals, we believe that multistate occupancy modeling will dramatically increase our ability to address interesting questions about ecological processes underlying population-level dynamics. PMID:19341151

  16. Removal Dynamics of Immunoglobulin and Fibrinogen by Conventional Plasma Exchange, Selective Plasma Exchange, and a Combination of the Two.

    PubMed

    Miyamoto, Satoko; Ohkubo, Atsushi; Seshima, Hiroshi; Maeda, Takuma; Itagaki, Ayako; Kurashima, Naoki; Iimori, Soichiro; Naito, Shotaro; Sohara, Eisei; Rai, Tatemitsu; Uchida, Shinichi; Okado, Tomokazu

    2016-08-01

    While plasma exchange (PE) can eliminate plasma proteins, including all immunoglobulin (Ig) and coagulation factors, selective plasma exchange (SePE) can retain fibrinogen (Fbg). Here, we investigated the removal dynamics of Ig and Fbg in 53 patients with immunological disorders by PE, SePE, and a combination of the two. When the mean processed plasma volume (PPV) was 0.9 plasma volume (PV), the mean percent reductions of Ig and Fbg by PE were both approximately 62%-65%. When the mean PPV was 1.1 PV, the mean percent reductions by SePE were 53.1% for IgG, 30.1% for IgA, 3.6% for IgM, and 19.0% for Fbg, respectively. In the three plasmapheresis sessions performed on alternate days, we classified treatments into three categories: PE group (PE-PE-PE, N = 2), SePE group (SePE-SePE-SePE, N = 14), and PE/SePE group (PE-SePE-SePE, N = 4). The mean percent reductions of IgG, IgA, IgM, and Fbg were 82.0%, 80.4%, 87.3%, and 80.9%, respectively, for the PE group; 76.4%, 57.7%, 43.3%, and 35.9%, respectively, for the PE/SePE group; and 75.4%, 50.6%, 3.2%, and 29.3%, respectively, for the SePE group. Plasmapheresis modalities can be combined according to clinical conditions, for instance, to achieve both the unspecific removal of pathogens by PE and retention of coagulation factors, such as Fbg, by SePE. PMID:27523073

  17. Energy exchange analysis in droplet dynamics via the Navier–Stokes–Cahn–Hilliard model

    NASA Astrophysics Data System (ADS)

    Espath, L. F. R.; Sarmiento, A. F.; Vignal, P.; Varga, B. O. N.; Cortes, A. M. A.; Dalcin, L.; Calo, V. M.

    2016-06-01

    We develop the energy budget equation of the coupled Navier-Stokes-Cahn-Hilliard (NSCH) system. We use the NSCH equations to model the dynamics of liquid droplets in a liquid continuum. Buoyancy effects are accounted for through the Boussinesq assumption. We physically interpret each quantity involved in the energy exchange to further insight into the model. Highly resolved simulations involving density-driven flows and merging of droplets allow us to analyze these energy budgets. In particular, we focus on the energy exchanges when droplets merge, and describe flow features relevant to this phenomenon. By comparing our numerical simulations to analytical predictions and experimental results available in the literature, we conclude that modeling droplet dynamics within the framework of NSCH equations is a sensible approach worth further research.

  18. Exact-exchange time-dependent density-functional theory for static and dynamic polarizabilities

    SciTech Connect

    Hirata, So; Ivanov, Stanislav; Bartlett, Rodney J.; Grabowski, Ireneusz

    2005-03-01

    Time-dependent density-functional theory (TDDFT) employing the exact-exchange functional has been formulated on the basis of the optimized-effective-potential (OEP) method of Talman and Shadwick for second-order molecular properties and implemented into a Gaussian-basis-set, trial-vector algorithm. The only approximation involved, apart from the lack of correlation effects and the use of Gaussian-type basis functions, was the consistent use of the adiabatic approximation in the exchange kernel and in the linear response function. The static and dynamic polarizabilities and their anisotropy predicted by the TDDFT with exact exchange (TDOEP) agree accurately with the corresponding values from time-dependent Hartree-Fock theory, the exact-exchange counterpart in the wave function theory. The TDOEP is free from the nonphysical asymptotic decay of the exchange potential of most conventional density functionals or from any other manifestations of the incomplete cancellation of the self-interaction energy. The systematic overestimation of the absolute values and dispersion of polarizabilities that plagues most conventional TDDFT cannot be seen in the TDOEP.

  19. Gas exchange in Paulownia species growing under different soil moisture conditions in the field.

    PubMed

    Llano-Sotelo, J M; Alcaraz-Melendez, L; Castellanos Villegas, A E

    2010-07-01

    In order to evaluate their responses to drought, we determined the photosynthetic activity water potential, stomatal conductance, transpiration, water use efficiency photosynthetic photon flux density and leaf temperature of Paulownia imperialis, P. fortunei and P. elongata in three different soil moisture conditions in the field. Our results showed that P. imperialis had greater photosynthesis (8.86 micromol CO2 m(-2) s(-1)) and instantaneous water use efficiency (0.79 micromol CO2 mmol H2O(-1)) than either P. elongata (8.20 micromol CO2 m(-2) s(-1) and 0.71 micromol CO2 mmol H2O(-1)) or P. fortunei (3.26 micromol CO2 m(-2) s(-1) and 0.07 micromol CO2 mmol H2O(-1)). The rapid growth of Paulownia did not appear to be correlated with photosynthetic rates. Paulownia fortunei showed more transpiration (48.78 mmol H2O m(-2) s(-1)) and stomatal conductance (840 mmol m(-2) s(-1)) than P. imperialis (20 mmol H2O m(-2) s(-1) and 540 mmol m(-2) s(-1)) and P. elongata (20 mmol H2O m(-2) s(-1) and 410 mmol m(-2) s(-1)), which allowed these two Paulownia species to increase their tolerance to low soil moisture, and maintain higher water use efficiency under these conditions. According to our physiological gas exchange field tests, Paulownia imperialis does appear to be capable of successful growth in semiarid zones. PMID:21186726

  20. Combining Ballast Water Exchange and Treatment To Maximize Prevention of Species Introductions to Freshwater Ecosystems.

    PubMed

    Briski, Elizabeta; Gollasch, Stephan; David, Matej; Linley, R Dallas; Casas-Monroy, Oscar; Rajakaruna, Harshana; Bailey, Sarah A

    2015-08-18

    The most effective way to manage species transfers is to prevent their introduction via vector regulation. Soon, international ships will be required to meet numeric ballast discharge standards using ballast water treatment (BWT) systems, and ballast water exchange (BWE), currently required by several countries, will be phased out. However, there are concerns that BWT systems may not function reliably in fresh and/or turbid water. A land-based evaluation of simulated "BWE plus BWT" versus "BWT alone" demonstrated potential benefits of combining BWE with BWT for protection of freshwater ecosystems. We conducted ship-based testing to compare the efficacy of "BWE plus BWT" versus "BWT alone" on voyages starting with freshwater ballast. We tested the hypotheses that there is an additional effect of "BWE plus BWT" compared to "BWT alone" on the reduction of plankton, and that taxa remaining after "BWE plus BWT" will be marine (low risk for establishment at freshwater recipient ports). Our study found that BWE has significant additional effect on the reduction of plankton, and this effect increases with initial abundance. As per expectations, "BWT alone" tanks contained higher risk freshwater or euryhaline taxa at discharge, while "BWE plus BWT" tanks contained mostly lower risk marine taxa unlikely to survive in recipient freshwater ecosystems.

  1. Temperatures of individual ion species and heating due to charge exchange in the ionosphere of Venus

    NASA Technical Reports Server (NTRS)

    Kim, Jhoon; Nagy, Andrew F.; Cravens, Thomas E.; Shinagawa, Hiroyuki

    1990-01-01

    The coupled electron and multispecies ion energy equations were solved for daytime conditions in the Venus ionosphere. The heating rates due to charge exchange between hot oxygen atoms and thermal oxygen ions were calculated and incorporated into the energy equations. The combination of the traditional EUV heating and this hot oxygen energy source leads to calculated electron and individual ion temperatures significantly lower than the measured values during solar cycle maximum conditions. Calculations were also carried out for solar cycle minimum conditions, which led to considerably lower temperatures; no data are available which would allow direct comparisons of these results with measurements. In order to obtain calculated temperature values consistent with the observed ones, for solar cycle maximum conditions, topside heat inflows into the ion and electron gases have to be introduced or the thermal conductivity must be reduced by considering the effect of steady and fluctuating magnetic fields, as was done in previous studies. The addition of hot oxygen heating leads to minor increases in the calculated ion temperatures except for the case of reduced thermal conductivities. Separate temperatures were calculated for each ion species for a number of different conditions and in general the differences were found to be relatively small.

  2. MuSTAR MD: multi-scale sampling using temperature accelerated and replica exchange molecular dynamics.

    PubMed

    Yamamori, Yu; Kitao, Akio

    2013-10-14

    A new and efficient conformational sampling method, MuSTAR MD (Multi-scale Sampling using Temperature Accelerated and Replica exchange Molecular Dynamics), is proposed to calculate the free energy landscape on a space spanned by a set of collective variables. This method is an extension of temperature accelerated molecular dynamics and can also be considered as a variation of replica-exchange umbrella sampling. In the MuSTAR MD, each replica contains an all-atom fine-grained model, at least one coarse-grained model, and a model defined by the collective variables that interacts with the other models in the same replica through coupling energy terms. The coarse-grained model is introduced to drive efficient sampling of large conformational space and the fine-grained model can serve to conduct more accurate conformational sampling. The collective variable model serves not only to mediate the coarse- and fine-grained models, but also to enhance sampling efficiency by temperature acceleration. We have applied this method to Ala-dipeptide and examined the sampling efficiency of MuSTAR MD in the free energy landscape calculation compared to that for replica exchange molecular dynamics, replica exchange umbrella sampling, temperature accelerated molecular dynamics, and conventional MD. The results clearly indicate the advantage of sampling a relatively high energy conformational space, which is not sufficiently sampled with other methods. This feature is important in the investigation of transition pathways that go across energy barriers. MuSTAR MD was also applied to Met-enkephalin as a test case in which two Gō-like models were employed as the coarse-grained model.

  3. Water exchange dynamics around H₃O⁺ and OH⁻ ions

    SciTech Connect

    Roy, Santanu; Dang, Liem X.

    2015-05-01

    Proton transfer in water and other solvents is a complicated process and an active research area. Conformational changes of water hydrating a proton can have a significant influence on proton dynamics. A hydrated proton leads to H₃O⁺ that forms three hydrogen bonds with neighboring water molecules. In this letter, we report the first computer simulation of the dynamics of water exchanging between the first and second solvation shells of H₃O⁺. Employing different rate theories for chemical reactions such as the transition state theory, the Grote-Hynes theory, the reactive flux method, and the Impey-Madden-McDonald method, we calculate the solvent exchange rates from molecular dynamics simulations that account for explicit polarization effects. In addition, we also study water exchanges around OH⁻ and find that the corresponding time scale (~50 picoseconds [ps]) is much smaller than that for H₃O⁺ (~100 ps). Results from all the rate theories are computed and compared. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. The calculations were carried out using computer resources provided by the Office of Basic Energy Sciences.

  4. A molecular dynamics study of bond exchange reactions in covalent adaptable networks.

    PubMed

    Yang, Hua; Yu, Kai; Mu, Xiaoming; Shi, Xinghua; Wei, Yujie; Guo, Yafang; Qi, H Jerry

    2015-08-21

    Covalent adaptable networks are polymers that can alter the arrangement of network connections by bond exchange reactions where an active unit attaches to an existing bond then kicks off its pre-existing peer to form a new bond. When the polymer is stretched, bond exchange reactions lead to stress relaxation and plastic deformation, or the so-called reforming. In addition, two pieces of polymers can be rejoined together without introducing additional monomers or chemicals on the interface, enabling welding and reprocessing. Although covalent adaptable networks have been researched extensively in the past, knowledge about the macromolecular level network alternations is limited. In this study, molecular dynamics simulations are used to investigate the macromolecular details of bond exchange reactions in a recently reported epoxy system. An algorithm for bond exchange reactions is first developed and applied to study a crosslinking network formed by epoxy resin DGEBA with the crosslinking agent tricarballylic acid. The trace of the active units is tracked to show the migration of these units within the network. Network properties, such as the distance between two neighboring crosslink sites, the chain angle, and the initial modulus, are examined after each iteration of the bond exchange reactions to provide detailed information about how material behaviors and macromolecular structure evolve. Stress relaxation simulations are also conducted. It is found that even though bond exchange reactions change the macroscopic shape of the network, microscopic network characteristic features, such as the distance between two neighboring crosslink sites and the chain angle, relax back to the unstretched isotropic state. Comparison with a recent scaling theory also shows good agreement.

  5. Dynamic screening in a two-species asymmetric exclusion process.

    PubMed

    Kim, Kyung Hyuk; den Nijs, Marcel

    2007-08-01

    The dynamic scaling properties of the one-dimensional Burgers equation are expected to change with the inclusion of additional conserved degrees of freedom. We study this by means of one-dimensional (1D) driven lattice gas models that conserve both mass and momentum. The most elementary version of this is the Arndt-Heinzel-Rittenberg (AHR) process, which is usually presented as a two-species diffusion process, with particles of opposite charge hopping in opposite directions and with a variable passing probability. From the hydrodynamics perspective this can be viewed as two coupled Burgers equations, with the number of positive and negative momentum quanta individually conserved. We determine the dynamic scaling dimension of the AHR process from the time evolution of the two-point correlation functions, and find numerically that the dynamic critical exponent is consistent with simple Kardar-Parisi-Zhang- (KPZ) type scaling. We establish that this is the result of perfect screening of fluctuations in the stationary state. The two-point correlations decay exponentially in our simulations and in such a manner that in terms of quasiparticles, fluctuations fully screen each other at coarse grained length scales. We prove this screening rigorously using the analytic matrix product structure of the stationary state. The proof suggests the existence of a topological invariant. The process remains in the KPZ universality class but only in the sense of a factorization, as (KPZ)2. The two Burgers equations decouple at large length scales due to the perfect screening.

  6. Dynamic screening in a two-species asymmetric exclusion process

    NASA Astrophysics Data System (ADS)

    Kim, Kyung Hyuk; den Nijs, Marcel

    2007-08-01

    The dynamic scaling properties of the one-dimensional Burgers equation are expected to change with the inclusion of additional conserved degrees of freedom. We study this by means of one-dimensional (1D) driven lattice gas models that conserve both mass and momentum. The most elementary version of this is the Arndt-Heinzel-Rittenberg (AHR) process, which is usually presented as a two-species diffusion process, with particles of opposite charge hopping in opposite directions and with a variable passing probability. From the hydrodynamics perspective this can be viewed as two coupled Burgers equations, with the number of positive and negative momentum quanta individually conserved. We determine the dynamic scaling dimension of the AHR process from the time evolution of the two-point correlation functions, and find numerically that the dynamic critical exponent is consistent with simple Kardar-Parisi-Zhang- (KPZ) type scaling. We establish that this is the result of perfect screening of fluctuations in the stationary state. The two-point correlations decay exponentially in our simulations and in such a manner that in terms of quasiparticles, fluctuations fully screen each other at coarse grained length scales. We prove this screening rigorously using the analytic matrix product structure of the stationary state. The proof suggests the existence of a topological invariant. The process remains in the KPZ universality class but only in the sense of a factorization, as (KPZ)2 . The two Burgers equations decouple at large length scales due to the perfect screening.

  7. Quantitative chemical exchange saturation transfer with hyperpolarized nuclei (qHyper-CEST): Sensing xenon-host exchange dynamics and binding affinities by NMR

    SciTech Connect

    Kunth, M. Witte, C.; Schröder, L.

    2014-11-21

    The reversible binding of xenon to host molecules has found numerous applications in nuclear magnetic resonance studies. Quantitative characterization of the Xe exchange dynamics is important to understand and optimize the physico-chemical behavior of such Xe hosts, but is often challenging to achieve at low host concentrations. We have investigated a sensitive quantification technique based on chemical exchange saturation transfer with hyperpolarized nuclei, qHyper-CEST. Using simulated signals we demonstrated that qHyper-CEST yielded accurate and precise results and was robust in the presence of large amounts of noise (10%). This is of particular importance for samples with completely unknown exchange rates. Using these findings we experimentally determined the following exchange parameters for the Xe host cryptophane-A monoacid in dimethyl sulfoxide in one type of experiment: the ratio of bound and free Xe, the Xe exchange rate, the resonance frequencies of free and bound Xe, the Xe host occupancy, and the Xe binding constant. Taken together, qHyper-CEST facilitates sensitive quantification of the Xe exchange dynamics and binding to hydrophobic cavities and has the potential to analyze many different host systems or binding sites. This makes qHyper-CEST an indispensable tool for the efficient design of highly specific biosensors.

  8. Electron-Nuclear Dynamics of collision processes: Charge exchange and energy loss

    NASA Astrophysics Data System (ADS)

    Cabrera-Trujillo, Remigio; Sabin, John R.; Öhrn, Yngve; Deumens, Erik

    2004-03-01

    We present the Electron-Nuclear Dynamics (END) method for the study of time-dependent scattering processes. The END is a general approach for treating time-dependent problems which includes the dynamics of electrons and nuclei simultaneously by considering the full electron-nuclear coupling in the system and thus eliminates the necessity of constructing potential-energy surfaces. The theory approximates the time dependent Schrödinger equation starting from the time dependent variational principle by deriving a Hamiltonian dynamical system for time dependent nuclear and electronic wave function parameters. The wave function is described in a coherent state manifold, which leads to a system of Hamilton's equations of motion. Emphasis is put on electron exchange, differential cross section and energy loss (stopping cross section) of collision of ions, atoms and molecules involving H, He, C, N, O, and Ne atoms. We compare our results to available experimental data.

  9. Simulating the frontal instability of lock-exchange density currents with dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Li, Yanggui; Geng, Xingguo; Wang, Heping; Zhuang, Xin; Ouyang, Jie

    2016-06-01

    The frontal instability of lock-exchange density currents is numerically investigated using dissipative particle dynamics (DPD) at the mesoscopic particle level. For modeling two-phase flow, the “color” repulsion model is adopted to describe binary fluids according to Rothman-Keller method. The present DPD simulation can reproduce the flow phenomena of lock-exchange density currents, including the lobe-and-cleft instability that appears at the head, as well as the formation of coherent billow structures at the interface behind the head due to the growth of Kelvin-Helmholtz instability. Furthermore, through the DPD simulation, some small-scale characteristics can be observed, which are difficult to be captured in macroscopic simulation and experiment.

  10. High-resolution determination of 147Pm in urine using dynamic ion-exchange chromatography.

    PubMed

    Elchuk, S; Lucy, C A; Burns, K I

    1992-10-15

    A procedure has been developed for measuring 147Pm in bioassay samples, based on the separation and preconcentration of 147Pm from the urine matrix by adsorption onto a conventional cation-exchange column with final separation and purification by HPLC using dynamic ion-exchange chromatography. The concentration of 147Pm is determined by collecting the appropriate HPLC fraction and measuring the 147Pm by liquid scintillation counting. The limit of detection is 0.1 Bq (3 fg) 147Pm based on a 500-mL sample of urine and a counting time of 30 min with a background of 100 cpm. Ten samples can be processed in 1.5-2 days.

  11. Ultrafast Study of Dynamic interfacial Exchange Coupling in Ferromagnet/Oxide/Semiconductor Heterostructures

    NASA Astrophysics Data System (ADS)

    Ou, Yu-Sheng; Chiu, Yi-Hsin; Harmon, Nicholas; Odenthal, Patrick; Sheffield, Matthew; Chilcote, Michael; Kawakami, Roland; Flatté, Michael; Johnston-Halperin, Ezekiel

    Time-resolved Kerr/Faraday rotation (TRKR/TRFR) is employed to study GaAs spin dynamics in the regime of strong and dynamic exchange coupling to an adjacent MgO/Fe layer. This study reveals a dramatic, resonant suppression in the inhomogeneous spin lifetime (T2*) in the GaAs layer. Further investigation of the magnetization dynamics of the neighboring Fe layer, also using TRKR/TRFR, reveals not only the expected Kittel-dispersion but also additional lower frequency modes with very short lifetime (65 ps) that are not easily observed with conventional ferromagnetic resonance (FMR) techniques. These results suggest the intriguing possibility of resonant dynamic spin transfer between the GaAs and Fe spin systems. We discuss the potential for this work to establish GaAs spin dynamics as an efficient detector of spin dissipation and transport in the regime of dynamically-driven spin injection in ferromagnet/semiconductor heterostructures. Center for Emergent Materials; U.S. Department of Energy.

  12. Dynamic Regulation of Histone Modifications in Xenopus Oocytes through Histone Exchange

    PubMed Central

    Stewart, M. David; Sommerville, John; Wong, Jiemin

    2006-01-01

    Histone H3 lysine 9 (H3K9) methylation has broad roles in transcriptional repression, gene silencing, maintenance of heterochromatin, and epigenetic inheritance of heterochromatin. Using Xenopus laevis oocytes, we have previously shown that targeting G9a, an H3K9 histone methyltransferase, to chromatin increases H3K9 methylation and consequently represses transcription. Here we report that treatment with trichostatin A induces histone acetylation and is sufficient to activate transcription repressed by G9a, and this activation is accompanied by a reduction in dimethyl H3K9 (H3K9me2). We tested the possibility that the reduction in H3K9me2 was due to the replacement of methylated H3 with unmethylated H3.3. Surprisingly, we found that both free H3 and H3.3 are continually exchanged with chromatin-associated histones. This dynamic exchange of chromatin-associated H3 with free H3/H3.3 was not affected by alterations in transcriptional activity, elongation, acetylation, H3K9 methylation, or DNA replication. In support of this continual histone exchange model, we show that maintenance of H3K9 methylation at a specific site requires the continual presence of an H3K9 histone methyltransferase. Upon dissociation of the methyltransferase, H3K9 methylation decreases. Taken together, our data suggest that chromatin-associated and non-chromatin-associated histones are continually exchanged in the Xenopus oocyte, creating a highly dynamic chromatin environment. PMID:16943430

  13. Comparative Population Dynamics of Two Closely Related Species Differing in Ploidy Level

    PubMed Central

    Černá, Lucie; Münzbergová, Zuzana

    2013-01-01

    Background Many studies compare the population dynamics of single species within multiple habitat types, while much less is known about the differences in population dynamics in closely related species in the same habitat. Additionally, comparisons of the effect of habitat types and species are largely missing. Methodology and Principal Findings We estimated the importance of the habitat type and species for population dynamics of plants. Specifically, we compared the dynamics of two closely related species, the allotetraploid species Anthericum liliago and the diploid species Anthericum ramosum, occurring in the same habitat type. We also compared the dynamics of A. ramosum in two contrasting habitats. We examined three populations per species and habitat type. The results showed that single life history traits as well as the mean population dynamics of A. liliago and A. ramosum from the same habitat type were more similar than the population dynamics of A. ramosum from the two contrasting habitats. Conclusions Our findings suggest that when transferring knowledge regarding population dynamics between populations, we need to take habitat conditions into account, as these conditions appear to be more important than the species involved (ploidy level). However, the two species differ significantly in their overall population growth rates, indicating that the ploidy level has an effect on species performance. In contrast to what has been suggested by previous studies, we observed a higher population growth rate in the diploid species. This is in agreement with the wider range of habitats occupied by the diploid species. PMID:24116057

  14. Fast-growing species and sustainability (productivity and site dynamics of three fast-growing species)

    SciTech Connect

    Reddy, A.N.; Sugur, G.V.

    1992-12-31

    Growth of three fast-growing species, raised in a high rainfall zone (2000-2500 mm per annum) has been compared, and the associated site dynamics studies in the Western Ghat area of Karnataka State. Two fast-growing exotics, Acacia auriculiformis and Castuarina equisitifolia, were planted on degraded, open sites at high planting densities (5000 plants ha{sup {minus}1}), and one native fast-growing species. Dendrocalamus strictus, was planted on a good site under seasonal irrigation and wider spacing (500 plants ha{sup {minus}1}). These were studies at the age of 5 years for their comparative productivity, quantity of litter fall and changes in nutrient and microbial status. Among these species, A. auriculiformis recorded the highest total productivity closely followed by D. strictus. However, the MAI after 5 years indicated a higher productivity for D. strictus, when culm production attained harvestable size. C. equisitifolia was a close third. It was also found that D. strictus produced higher biomass at lower planting densities, under better sites and management. The litter fall and changes in nutrient status indicated the highest efficiency in A. auriculiformis, followed by C. equisitifolia. It was concluded that the higher planting density was the major contributing factor; the values were comparatively low for D. strictus mainly owing to a lower stocking density of plants.

  15. The Dynamic Hyporheic Zone: Variability of Groundwater-Surface Water Exchange at Multiple Temporal Scales

    NASA Astrophysics Data System (ADS)

    Binley, A. M.; Dudley-Southern, M. J.

    2014-12-01

    The pathways of exchange of surface water and groundwater can have a significant influence on the delivery of nutrient-rich groundwater to streams. Many studies have revealed how the spatial variability of physical properties (sediment permeability, bedform structures, etc.) at the interface of groundwater and surface water can impact on flow pathways and residence times of hyporheic exchange flow. Here we explore the temporal variability of flow pathways at this interface. We focus on observations made on a study reach of the River Leith, UK but also provide evidence of dynamic exchanges at a number of other study sites. Under baseflow conditions, the study reach of the River Leith shows a predominance of upwelling of groundwater to the river, and in some sections of the reach a significant groundwater discharge zone in evident. However, from observations of piezometric heads made over a two year study period, repeated reversal of flow direction was observed during storm events. By deploying novel miniature electrode sensors in the river bed we were able to monitor the migration of surface water during these events. Penetration of river water to depths of 30cm was observed during monitored events, which support the reported reversal of hydraulic gradients. We, therefore, observed event-driven hyporheic exchange flow. The duration and frequency of such events may have significant impact on the biogeochemistry of shallow river bed sediments within this reach. Furthermore, temporal variability of exchange is not limited to such events: changes in regional groundwater flow pathways over longer time scales may have a significant impact on the location of localised upwelling; at much shorter timescales we see evidence of diurnal fluctuations in hydraulic heads due to evapotranspiration processes. We report on similar observations at companion study sites and discuss implications on the management of water quality in these groundwater fed systems.

  16. Variation of gas exchange within native plant species of Switzerland and relationships with ozone injury: an open-top experiment.

    PubMed

    Zhang, J; Ferdinand, J A; Vanderheyden, D J; Skelly, J M; Innes, J L

    2001-01-01

    Gas exchange and ozone-induced foliar injury were intensively measured during a 6-day period in mid-August 1998 on leaves of Acer pseudoplatanus, Betula pendula, Corylus avellana, Fagus sylvatica, Fraxinus excelsior, Morus nigra, Prunus avium, Prunus serotina, Rhamnus cathartica, and Viburnum lantana at a forest nursery site in Canton Ticino, Switzerland. Plants were grown in four open plots (AA), four open-top chambers receiving carbon-filtered (CF) air, and four receiving non-filtered (NF) air. Significant variation in gas exchange (F > 12.7, P < 0.001) was detected among species with average net photosynthesis and average stomatal conductance differing by a factor of two. Species also varied significantly in foliar injury for those leaves for which we measured gas exchange (F = 39.6, P < 0.001). Fraxinus excelsior, M. nigra, P. avium, P. serotina, R. cathartica, and V. lantana showed more injury than A. pseudoplatanus, B. pendula, C. avellana, and Fagus sylvatica. Plants grown in CF chambers had significantly higher net photosynthesis (A) and stomatal conductance to water vapor (gwv), and lower foliar injury than plants grown in NF chambers and AA plots; interactions between species and ozone treatments were significant for all variables (F > or = 2.2, P < 0.05) except gwv (F = 0.7, P > 0.1). Although A and gwv decreased and foliar injury increased with leaf age, the magnitude of these changes was lower for plants grown in CF chambers than for plants grown in NF chambers and AA plots. Neither ozone uptake threshold (r = 0.26, P > 0.20) nor whole-plant injury (r = -0.15, P > 0.41) was significantly correlated with stomatal conductance across these species. It appears that the relationships between stomatal conductance and foliar injury are species-specific and interactions between physiology and environments and leaf biochemical processes must be considered in determining species sensitivity to ambient ozone exposures. PMID:11383335

  17. Exchange and redistribution dynamics of the cytoskeleton of the active zone molecule bassoon.

    PubMed

    Tsuriel, Shlomo; Fisher, Arava; Wittenmayer, Nina; Dresbach, Thomas; Garner, Craig C; Ziv, Noam E

    2009-01-14

    Presynaptic sites typically appear as varicosities (boutons) distributed along axons. Ultrastructurally, presynaptic boutons lack obvious physical barriers that separate them from the axon proper, yet activity-related and constitutive dynamics continuously promote the "reshuffling" of presynaptic components and even their dispersal into flanking axonal segments. How presynaptic sites manage to maintain their organization and individual characteristics over long durations is thus unclear. Conceivably, presynaptic tenacity might depend on the active zone (AZ), an electron-dense specialization of the presynaptic membrane, and particularly on the cytoskeletal matrix associated with the AZ (CAZ) that could act as a relatively stable "core scaffold" that conserves and dictates presynaptic organization. At present, however, little is known on the molecular dynamics of CAZ molecules, and thus, the factual basis for this hypothesis remains unclear. To examine the stability of the CAZ, we studied the molecular dynamics of the major CAZ molecule Bassoon in cultured hippocampal neurons. Fluorescence recovery after photobleaching and photoactivation experiments revealed that exchange rates of green fluorescent protein and photoactivatable green fluorescent protein-tagged Bassoon at individual presynaptic sites are very low (tau > 8 h). Exchange rates varied between boutons and were only slightly accelerated by stimulation. Interestingly, photoactivation experiments revealed that Bassoon lost from one synapse was occasionally assimilated into neighboring presynaptic sites. Our findings indicate that Bassoon is engaged in relatively stable associations within the CAZ and thus support the notion that the CAZ or some of its components might constitute a relatively stable presynaptic core scaffold.

  18. Electron-Nuclear Dynamics of atomic and molecular collisions: Charge exchange and energy loss

    NASA Astrophysics Data System (ADS)

    Cabrera-Trujillo, Remigio; Sabin, John R.; Ohrn, Yngve; Deumens, Erik

    2004-05-01

    Processes like electron exchange (capture and loss), bond breaking, and chemical reactions are difficult to visualize and treat in a time-independent approach. In this work, we present the Electron-Nuclear Dynamics (END) method for the study of time-dependent scattering processes. The END is a general approach for treating time-dependent problems which includes the dynamics of electrons and nuclei simultaneously by considering the full electron-nuclear coupling in the system and thus eliminates the necessity of constructing potential-energy surfaces. The theory approximates the time dependent Schrödinger equation starting from the time dependent variational principle (TDVP) by deriving a Hamiltonian dynamical system for time dependent nuclear and electronic wave function parameters. The wave function is described in a coherent state manifold, which leads to a system of Hamilton's equations of motion. The resulting system of coupled, first order, ordinary differential equations approximates the Schrödinger equation. A detailed analysis of the END equations is given for the case of a single-determinantal state for the electrons and a classical treatment of the nuclei. Emphasis is put on electron exchange, differential cross section and energy loss (stopping cross section) of collision of ions, atoms and molecules involving H, He, C, N, O, and Ne atoms. We compare our results to available experimental data.

  19. Probing protein dynamics and function under native and mildly denaturing conditions with hydrogen exchange and mass spectrometry

    NASA Astrophysics Data System (ADS)

    Kaltashov, Igor A.

    2005-02-01

    A combination of hydrogen exchange and mass spectrometry emerged in recent years as a powerful experimental tool capable of probing both structural and dynamic features of proteins. Although its concept is very simple, the interpretation of experimental data is not always straightforward, as a combination of chemical reactions (isotope exchange) and dynamic processes within protein molecules give rise to convoluted exchange patterns. This paper provides a historical background of this technique, candid assessment of its current state and limitations and a discussion of promising recent developments that can result in tremendous improvements and a dramatic expansion of the scope of its applications.

  20. Dynamic XML-based exchange of relational data: application to the Human Brain Project.

    PubMed

    Tang, Zhengming; Kadiyska, Yana; Li, Hao; Suciu, Dan; Brinkley, James F

    2003-01-01

    This paper discusses an approach to exporting relational data in XML format for data exchange over the web. We describe the first real-world application of SilkRoute, a middleware program that dynamically converts existing relational data to a user-defined XML DTD. The application, called XBrain, wraps SilkRoute in a Java Server Pages framework, thus permitting a web-based XQuery interface to a legacy relational database. The application is demonstrated as a query interface to the University of Washington Brain Project's Language Map Experiment Management System, which is used to manage data about language organization in the brain.

  1. Numerical simulation of gas dynamics and heat exchange tasks in fuel assemblies of the nuclear reactors

    SciTech Connect

    Zhuchenko, S. V.

    2014-11-12

    This report presents a PC-based program for solution gas dynamics and heat exchange mathematical tasks in fuel assemblies of the fast-neutron nuclear reactors. A fuel assembly consisting of bulk heat-generating elements, which are integrated together by the system of supply and pressure manifolds, is examined. Spherical heat-generating microelements, which contain nuclear fuel, are pulled into the heat-generating elements. Gaseous coolant proceed from supply manifolds to heat-generating elements, where it withdraws the nuclear reaction heat and assembles in pressure manifolds.

  2. Dynamics of nitrate limitation on gaseous nitrogen exchanges from pristine peatlands

    NASA Astrophysics Data System (ADS)

    Roobroeck, D.; Brüggemann, N.; Butterbach-Bahl, K.; Boeckx, P.

    2009-04-01

    The cycling of gaseous nitrogen species in peatland ecosystems and the functioning of driving forces on microbial denitrification rates are poorly accounted. Physico-chemical soil conditions and biotic interactions1 control the availability of nitrate for respiratory denitrification resulting in high spatial variability of gaseous nitrogen exchange rates in nutrient poor peat soils and complicating impact assessment of eutrophication. The responses of nitrous oxide (N2O) and dinitrogen (N2) fluxes to nitrate addition were compared between distinct contrasts in plant growth at a pristine, hummocky peatland. Allowing to determine the dynamics of nitrate limitation on gaseous nitrogen exchanges in accordance to covariance in soil anaerobiosis and resource competition. Two quantification techniques were applied parallel to soil core incubations in order to determine N2O and N2 fluxes. Helium atmosphere incubation was used for direct quantification of net N2O and N2 fluxes. Reducing the background N2 concentration in the soil atmosphere to approx. 20 ppm enabled highly sensitive measurement of N2 fluxes. On the other hand a 15N-N2O tracer technique was explored as a tool to demonstrate and quantify gross consumption rates of atmospheric N2O to N2 and recycling of gaseous N-losses by microbial fixation. The headspace N2O pool was increased with 0.03 ppm 15•15N-N2O rendering an enrichment of ± 9.8 atom% 15•15N-N2O. Triplicate soil core samples were taken from two contrasting soil habitat in a hummocky, Carex dominated fen located in the Biebrza National Park, NE Poland (53 °07′N; 23 °10′E). The hummocks had a gravimetric soil water content of 76.6 ± 2.2% and high root abundance, dissimilar to 83.4 ± 1.0% and little root prevalence in the hollows. Singular nitrate addition, comparable to the atmospheric NOY -deposition, was applied two days in advance of flux measurement. Actual net gaseous nitrogen fluxes and responses to nitrate addition were apparently

  3. How many species in the Southern Ocean? Towards a dynamic inventory of the Antarctic marine species

    NASA Astrophysics Data System (ADS)

    De Broyer, Claude; Danis, Bruno; with 64 SCAR-MarBIN Taxonomic Editors

    2011-03-01

    The IPY sister-projects CAML and SCAR-MarBIN provided a timely opportunity, a strong collaborative framework and an appropriate momentum to attempt assessing the "Known, Unknown and Unknowable" of Antarctic marine biodiversity. To allow assessing the known biodiversity, SCAR-MarBIN "Register of Antarctic Marine Species (RAMS)" was compiled and published by a panel of 64 taxonomic experts. Thanks to this outstanding expertise mobilized for the first time, an accurate list of more than 8100 valid species was compiled and an up-to-date systematic classification comprising more than 16,800 taxon names was established. This taxonomic information is progressively and systematically completed by species occurrence data, provided by literature, taxonomic and biogeographic databases, new data from CAML and other cruises, and museum collections. RAMS primary role was to establish a benchmark of the present taxonomic knowledge of the Southern Ocean biodiversity, particularly important in the context of the growing realization of potential impacts of the global change on Antarctic ecosystems. This, in turn, allowed detecting gaps in knowledge, taxonomic treatment and coverage, and estimating the importance of the taxonomic impediment, as well as the needs for more complete and efficient taxonomic tools. A second, but not less important, role of RAMS was to contribute to the "taxonomic backbone" of the SCAR-MarBIN, OBIS and GBIF networks, to establish a dynamic information system on Antarctic marine biodiversity for the future. The unknown part of the Southern Ocean biodiversity was approached by pointing out what remains to be explored and described in terms of geographical locations and bathymetric zones, habitats, or size classes of organisms. The growing importance of cryptic species is stressed, as they are more and more often detected by molecular studies in several taxa. Relying on RAMS results and on some case studies of particular model groups, the question of the

  4. Improving dynamic performance of proton-exchange membrane fuel cell system using time delay control

    NASA Astrophysics Data System (ADS)

    Kim, Young-Bae

    Transient behaviour is a key parameter for the vehicular application of proton-exchange membrane (PEM) fuel cell. The goal of this presentation is to construct better control technology to increase the dynamic performance of a PEM fuel cell. The PEM fuel cell model comprises a compressor, an injection pump, a humidifier, a cooler, inlet and outlet manifolds, and a membrane-electrode assembly. The model includes the dynamic states of current, voltage, relative humidity, stoichiometry of air and hydrogen, cathode and anode pressures, cathode and anode mass flow rates, and power. Anode recirculation is also included with the injection pump, as well as anode purging, for preventing anode flooding. A steady-state, isothermal analytical fuel cell model is constructed to analyze the mass transfer and water transportation in the membrane. In order to prevent the starvation of air and flooding in a PEM fuel cell, time delay control is suggested to regulate the optimum stoichiometry of oxygen and hydrogen, even when there are dynamical fluctuations of the required PEM fuel cell power. To prove the dynamical performance improvement of the present method, feed-forward control and Linear Quadratic Gaussian (LQG) control with a state estimator are compared. Matlab/Simulink simulation is performed to validate the proposed methodology to increase the dynamic performance of a PEM fuel cell system.

  5. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization

    PubMed Central

    Barnes, Alexander B.; Mak-Jurkauskas, Melody L.; Matsuki, Yoh; Bajaj, Vikram S.; van der Wel, Patrick C. A.; DeRocher, Ronald; Bryant, Jeffrey; Sirigiri, Jagadishwar R.; Temkin, Richard J.; Lugtenburg, Johan; Herzfeld, Judith; Griffin, Robert G.

    2009-01-01

    We describe a cryogenic sample exchange system that dramatically improves the efficiency of magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments by reducing the time required to change samples and by improving long-term instrument stability. Changing samples in conventional cryogenic MAS DNP/NMR experiments involves warming the probe to room temperature, detaching all cryogenic, RF, and microwave connections, removing the probe from the magnet, replacing the sample, and reversing all the previous steps, with the entire cycle requiring a few hours. The sample exchange system described here — which relies on an eject pipe attached to the front of the MAS stator and a vacuum jacketed dewar with a bellowed hole — circumvents these procedures. To demonstrate the excellent sensitivity, resolution, and stability achieved with this quadruple resonance sample exchange probe, we have performed high precision distance measurements on the active site of the membrane protein bacteriorhodopsin. We also include a spectrum of the tripeptide N-f-MLF-OH at 100 K which shows 30 Hz linewidths. PMID:19356957

  6. A Model for Dynamic Simulation and Analysis of Tether Momentum Exchange

    NASA Technical Reports Server (NTRS)

    Canfield, Stephen; Johnson, David; Sorensen, Kirk; Welzyn, Ken; Rodgers, Stephen L. (Technical Monitor)

    2002-01-01

    Momentum-exchange/electrodynamic reboost (MXER) tether systems may enable high-energy missions to the Moon, Mars, and beyond by serving as an 'upper stage in space'. Existing rockets that use an MXER tether station could double their capability to launch communications satellites and help improve US competitiveness. A MXER tether station would boost spacecraft from low Earth orbit to a high-energy orbit quickly, like a high-thrust rocket. Then, using the same principles that make an electric motor work, it would slowly rebuild its orbital momentum by pushing against the Earth's magnetic field-without using any propellant. One of the significant challenges in developing a momentum-exchange/electrodynamic reboost tether systems is in the analysis and design of the capture mechanism and its effects on the overall dynamics of the system. This paper will present a model for a momentum-exchange tether system that can simulate and evaluate the performance and requirements of such a system.

  7. Redox dynamics in the Chesapeake Bay: The effect on sediment/water uranium exchange

    SciTech Connect

    Shaw, T.J.; Sholkovitz, E.R.; Klinkhammer, G. )

    1994-07-01

    The effect of seasonal variations in productivity and redox dynamics on the sediment/water exchange of uranium was investigated on a twelve cruise time series in the Chesapeake Bay. The deep waters of the bay undergo seasonal anoxia in response to high primary productivity and water column stratification from late spring to early fall. Dissolved oxygen was used to monitor sediment redox conditions. Dissolved [sup 238]U was measured in the water column and sediment porewaters to monitor water column/sediment exchange. Uranium incorporation in bay sediments results from two distinct processes: productivity-dependent scavenging from the water column and redox-dependent cycling of uranium between sediments and bottomwater. Uranium is removed from surface waters of the bay by scavenging with biodetritus during periods of high primary productivity. Bottomwater and sediment redox conditions determine whether this particle-bound uranium is buried or released to overlying water. Particulate uranium is released to bottomwaters and porewaters during the degradation of biodetritus and oxidation of authigenic uranium. Low oxygen in bottomwaters in the summer results in minimal exchange of uranium between the sediments and bottomwater, due to the stability of reduced U(IV). High bottomwater oxygen concentrations associated with bay turnover in the fall results in release of authigenic uranium by oxidation to the soluble (VI) form. Enrichment of uranium in fall bottomwater suggests that authigenic uranium is very labile when exposed to oxic environmental conditions. This process is enhanced by physical mixing when anoxic sediments are resuspended into the oxic bottomwaters.

  8. Search for Length Dependent Stable Structures of Polyglutamaine Proteins with Replica Exchange Molecular Dynamic

    NASA Astrophysics Data System (ADS)

    Kluber, Alexander; Hayre, Robert; Cox, Daniel

    2012-02-01

    Motivated by the need to find beta-structure aggregation nuclei for the polyQ diseases such as Huntington's, we have undertaken a search for length dependent structure in model polyglutamine proteins. We use the Onufriev-Bashford-Case (OBC) generalized Born implicit solvent GPU based AMBER11 molecular dynamics with the parm96 force field coupled with a replica exchange method to characterize monomeric strands of polyglutamine as a function of chain length and temperature. This force field and solvation method has been shown among other methods to accurately reproduce folded metastability in certain small peptides, and to yield accurately de novo folded structures in a millisecond time-scale protein. Using GPU molecular dynamics we can sample out into the microsecond range. Additionally, explicit solvent runs will be used to verify results from the implicit solvent runs. We will assess order using measures of secondary structure and hydrogen bond content.

  9. Dynamics of oxygen sorption from water by copper-containing fibrous porous redox ion-exchangers

    SciTech Connect

    Ul'eva, L.S.; Burinskii, S.V.; Grebennikov, S.F.

    1985-08-10

    A most important field of practical application of oxidation-reduction (redox) polymers is the sorption of dissolved oxygen from water in order to prevent corrosion of power equipment. Copper-containing redox polymers, which have fairly high capacity and good swelling characteristics were used. Values of the dynamic exchange capacity (DEC) for copper ions, the redox capacity (ROC) for the reducing metal, and the dynamic reduction capacity for oxygen are given. It can be seen from these data that fibrous porous reactive materials (FPRM) in which the mass fiber content is 60% have somewhat better characteristics. The authors conclude that despite the fibrous porous material's considerably lower coefficient of internal diffusion, it is superior to granular EI-21 in the length of the masstransfer zone and in the coefficient of utilization of capacity, in consequence of the low linear density of the fibers. Their mass transfer zone is shorter by a factor of about 5.

  10. Adaptive Partitioning QM/MM Dynamics Simulations for Substrate Uptake, Product Release, and Solvent Exchange.

    PubMed

    Duster, A; Garza, C; Lin, H

    2016-01-01

    Combined quantum mechanics/molecular mechanics (QM/MM) plays an important role in multiscale simulations of biological systems including enzymes. The adaptive-partitioning (AP) schemes surpass the conventional QM/MM methods in that they allow the on-the-fly, smooth exchange of particles between QM and MM subsystems in molecular dynamics simulations, leading to a seamless and dynamic integration of the QM and MM realms. Originally developed for simulating ion solvation in bulk solutions, the AP schemes have recently been extended to the treatment of proteins, fostering applications in the simulations of enzymes. The present contribution provides a detailed account of the AP schemes. We delineate the background of the algorithms and their parallel implementation, as well as offer practical advice and examples for their applications in the simulations of biological systems. PMID:27498644

  11. Direct exchange of vitamin B12 is demonstrated by modelling the growth dynamics of algal–bacterial cocultures

    PubMed Central

    Grant, Matthew AA; Kazamia, Elena; Cicuta, Pietro; Smith, Alison G

    2014-01-01

    The growth dynamics of populations of interacting species in the aquatic environment is of great importance, both for understanding natural ecosystems and in efforts to cultivate these organisms for industrial purposes. Here we consider a simple two-species system wherein the bacterium Mesorhizobium loti supplies vitamin B12 (cobalamin) to the freshwater green alga Lobomonas rostrata, which requires this organic micronutrient for growth. In return, the bacterium receives photosynthate from the alga. Mathematical models are developed that describe minimally the interdependence between the two organisms, and that fit the experimental observations of the consortium. These models enable us to distinguish between different mechanisms of nutrient exchange between the organisms, and provide strong evidence that, rather than undergoing simple lysis and release of nutrients into the medium, M. loti regulates the levels of cobalamin it produces, resulting in a true mutualism with L. rostrata. Over half of all microalgae are dependent on an exogenous source of cobalamin for growth, and this vitamin is synthesised only by bacteria; it is very likely that similar symbiotic interactions underpin algal productivity more generally. PMID:24522262

  12. Network impact on persistence in a finite population dynamic diffusion model: application to an emergent seed exchange network.

    PubMed

    Barbillon, Pierre; Thomas, Mathieu; Goldringer, Isabelle; Hospital, Frédéric; Robin, Stéphane

    2015-01-21

    Dynamic extinction colonisation models (also called contact processes) are widely studied in epidemiology and in metapopulation theory. Contacts are usually assumed to be possible only through a network of connected patches. This network accounts for a spatial landscape or a social organization of interactions. Thanks to social network literature, heterogeneous networks of contacts can be considered. A major issue is to assess the influence of the network in the dynamic model. Most work with this common purpose uses deterministic models or an approximation of a stochastic Extinction-Colonisation model (sEC) which are relevant only for large networks. When working with a limited size network, the induced stochasticity is essential and has to be taken into account in the conclusions. Here, a rigorous framework is proposed for limited size networks and the limitations of the deterministic approximation are exhibited. This framework allows exact computations when the number of patches is small. Otherwise, simulations are used and enhanced by adapted simulation techniques when necessary. A sensitivity analysis was conducted to compare four main topologies of networks in contrasting settings to determine the role of the network. A challenging case was studied in this context: seed exchange of crop species in the Réseau Semences Paysannes (RSP), an emergent French farmers׳ organisation. A stochastic Extinction-Colonisation model was used to characterize the consequences of substantial changes in terms of RSP׳s social organization on the ability of the system to maintain crop varieties.

  13. Environmental variability uncovers disruptive effects of species' interactions on population dynamics

    PubMed Central

    Gudmundson, Sara; Eklöf, Anna; Wennergren, Uno

    2015-01-01

    How species respond to changes in environmental variability has been shown for single species, but the question remains whether these results are transferable to species when incorporated in ecological communities. Here, we address this issue by analysing the same species exposed to a range of environmental variabilities when (i) isolated or (ii) embedded in a food web. We find that all species in food webs exposed to temporally uncorrelated environments (white noise) show the same type of dynamics as isolated species, whereas species in food webs exposed to positively autocorrelated environments (red noise) can respond completely differently compared with isolated species. This is owing to species following their equilibrium densities in a positively autocorrelated environment that in turn enables species–species interactions to come into play. Our results give new insights into species' response to environmental variation. They especially highlight the importance of considering both species' interactions and environmental autocorrelation when studying population dynamics in a fluctuating environment. PMID:26224705

  14. Modeling the dynamic operation of a small fin plate heat exchanger - parametric analysis

    NASA Astrophysics Data System (ADS)

    Motyliński, Konrad; Kupecki, Jakub

    2015-09-01

    Given its high efficiency, low emissions and multiple fuelling options, the solid oxide fuel cells (SOFC) offer a promising alternative for stationary power generators, especially while engaged in micro-combined heat and power (μ-CHP) units. Despite the fact that the fuel cells are a key component in such power systems, other auxiliaries of the system can play a critical role and therefore require a significant attention. Since SOFC uses a ceramic material as an electrolyte, the high operating temperature (typically of the order of 700-900 °C) is required to achieve sufficient performance. For that reason both the fuel and the oxidant have to be preheated before entering the SOFC stack. Hot gases exiting the fuel cell stack transport substantial amount of energy which has to be partly recovered for preheating streams entering the stack and for heating purposes. Effective thermal integration of the μ-CHP can be achieved only when proper technical measures are used. The ability of efficiently preheating the streams of oxidant and fuel relies on heat exchangers which are present in all possible configurations of power system with solid oxide fuel cells. In this work a compact, fin plate heat exchanger operating in the high temperature regime was under consideration. Dynamic model was proposed for investigation of its performance under the transitional states of the fuel cell system. Heat exchanger was simulated using commercial modeling software. The model includes key geometrical and functional parameters. The working conditions of the power unit with SOFC vary due to the several factors, such as load changes, heating and cooling procedures of the stack and others. These issues affect parameters of the incoming streams to the heat exchanger. The mathematical model of the heat exchanger is based on a set of equations which are simultaneously solved in the iterative process. It enables to define conditions in the outlets of both the hot and the cold sides

  15. Patchiness of ion-exchanged mica revealed by DNA binding dynamics at short length scales.

    PubMed

    Billingsley, D J; Lee, A J; Johansson, N A B; Walton, A; Stanger, L; Crampton, N; Bonass, W A; Thomson, N H

    2014-01-17

    The binding of double-stranded (ds) DNA to mica can be controlled through ion-exchanging the mica with divalent cations. Measurements of the end-to-end distance of linear DNA molecules discriminate whether the binding mechanism occurs through 2D surface equilibration or kinetic trapping. A range of linear dsDNA fragments have been used to investigate length dependences of binding. Mica, ion-exchanged with Ni(II) usually gives rise to kinetically trapped DNA molecules, however, short linear fragments (<800 bp) are seen to deviate from the expected behaviour. This indicates that ion-exchanged mica is heterogeneous, and contains patches or domains, separating different ionic species. These results correlate with imaging of dsDNA under aqueous buffer on Ni(II)-mica and indicate that binding domains are of the order of 100 nm in diameter. Shorter DNA fragments behave intermediate to the two extreme cases of 2D equilibration and kinetic trapping. Increasing the incubation time of Ni(II) on mica, from minutes to hours, brings the conformations of the shorter DNA fragments closer to the theoretical value for kinetic trapping, indicating that long timescale kinetics play a role in ion-exchange. X-ray photoelectron spectroscopy (XPS) was used to confirm that the relative abundance of Ni(II) ions on the mica surface increases with time. These findings can be used to enhance spatial control of binding of DNA to inorganic surfaces with a view to patterning high densities arrays.

  16. Dynamics of intramolecular spin exchange interaction of a nitronyl nitroxide diradical in solution and on surfaces.

    PubMed

    Lloveras, V; Badetti, E; Veciana, J; Vidal-Gancedo, J

    2016-03-01

    In this paper we report the study of the dynamics of a thermally modulated intramolecular spin exchange interaction of a novel diradical nitronyl nitroxide-substituted disulfide in solution and when it is grafted on a gold surface. The structure of this diradical was designed to have flexible chains leading to intramolecular collisions and hence spin exchange interaction, and with an appropriate binding group to be grafted on the gold surface to study its behavior on the surface. In solution, this diradical shows a strong spin exchange interaction between both radicals which is modulated by temperature, but also gold nanoparticles (AuNPs) functionalized with this diradical permit investigation of such a phenomenon in surface-grafted radicals. The spin-labelled AuNP synthesis was optimized to obtain high coverage of spin labels to lead to high spin exchange interaction. The obtained AuNPs were studied by Electron Paramagnetic Resonance (EPR), UV-Vis, and IR spectroscopies, HR-TEM microscopy, Cyclic Voltammetry (CV), Energy Dispersive X-ray analysis (EDX) and Thermogravimetric Analysis (TGA). This inorganic-organic hybrid material also showed dipolar interactions between its radicals which were confirmed by the appearance in the EPR spectra of an |Δms| = 2 transition at half-field. This signal gives direct evidence of the presence of a high-spin state and permitted us to study the nature of the magnetic coupling between the spins which was found to be antiferromagnetic. Self-Assembled Monolayers (SAMs) of these radicals on the Au (111) substrate were also prepared and studied by contact angle, X-Ray Photoelectron Spectroscopy (XPS), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), Cyclic Voltammetry and EPR. The magnetic as well as the electrochemical properties of the hybrid surfaces were studied and compared with the properties of this diradical in solution. Analogies between the properties of AuNPs with high coverage of radicals and those of SAM were

  17. A canonical replica exchange molecular dynamics implementation with normal pressure in each replica

    NASA Astrophysics Data System (ADS)

    Peter, Emanuel K.; Pivkin, Igor V.; Shea, Joan-Emma

    2016-07-01

    In this paper, we present a new canonical replica exchange molecular dynamics (REMD) simulation method with normal pressure for all replicas (REMD-NV(p) T). This method is suitable for systems for which conventional constant NPT-setups are difficult to implement. In this implementation, each replica has an individual volume, with normal pressure maintained for each replica in the simulation. We derive a novel exchange term and validate this method on the structural properties of SPC/E water and dialanine (Ala2) in the bulk and in the presence of a graphene layer. Compared to conventional constant NPT-REMD and NVT-REMD simulations, we find that the structural properties of our new method are in good agreement with simulations in the NPT-ensemble at all temperatures. The structural properties of the systems considered are affected by high pressures at elevated temperatures in the constant NVT-ensemble, an effect that our method corrects for. Unprojected distributions reveal that essential motions of the peptide are affected by the presence of the barostat in the NPT implementation but that the dynamical eigenmodes of the NV(p)T method are in close quantitative agreement with the NVT-ensemble.

  18. A canonical replica exchange molecular dynamics implementation with normal pressure in each replica.

    PubMed

    Peter, Emanuel K; Pivkin, Igor V; Shea, Joan-Emma

    2016-07-28

    In this paper, we present a new canonical replica exchange molecular dynamics (REMD) simulation method with normal pressure for all replicas (REMD-NV(p) T). This method is suitable for systems for which conventional constant NPT-setups are difficult to implement. In this implementation, each replica has an individual volume, with normal pressure maintained for each replica in the simulation. We derive a novel exchange term and validate this method on the structural properties of SPC/E water and dialanine (Ala2) in the bulk and in the presence of a graphene layer. Compared to conventional constant NPT-REMD and NVT-REMD simulations, we find that the structural properties of our new method are in good agreement with simulations in the NPT-ensemble at all temperatures. The structural properties of the systems considered are affected by high pressures at elevated temperatures in the constant NVT-ensemble, an effect that our method corrects for. Unprojected distributions reveal that essential motions of the peptide are affected by the presence of the barostat in the NPT implementation but that the dynamical eigenmodes of the NV(p)T method are in close quantitative agreement with the NVT-ensemble. PMID:27475393

  19. Dynamics of suspended sediment exchange and transport in a degraded mangrove creek in Kenya.

    PubMed

    Kitheka, Johnson U; Ongwenyi, George S; Mavuti, Kenneth M

    2002-12-01

    This study focuses on sediment exchange dynamics in Mwache Creek, a shallow tidal mangrove wetland in Kenya. The surface area of the creek is 17 km2 at high water spring. The creek experiences semidiurnal tides with tidal ranges of 3.2 m and 1.4 m during spring and neap tides, respectively. The creek is ebb dominant in the frontwater zone main channel and is flood dominant in the backwater zone main channel. During rainy season, the creek receives freshwater and terrigenous sediments from the seasonal Mwache River. Heavy supply of terrigenous sediments during the El Niño of 1997-1998 led to the huge deposition of sediments (10(60 tonnes) in the wetland that caused massive destruction of the mangrove forest in the upper region. In this study, sea level, tidal discharges, tidal current velocities, salinity, total suspended sediment concentrations (TSSC) and particulate organic sediment concentrations (POSC) measured in stations established within the main channel and also within the mangrove forests, were used to determine the dynamics of sediment exchange between the frontwater and backwater zones of the main channel including also the exchange with mangrove forests. The results showed that during wet seasons, the high suspended sediment concentration associated with river discharge and tidal resuspension of fine channel-bed sediment accounts for the inflow of highly turbid water into the degraded mangrove forest. Despite the degradation of the mangrove forest, sediment outflow from the mangrove forest was considerably less than the inflow. This caused a net trapping of sediment in the wetland. The net import of the sediment dominated in spring tide during both wet and dry season and during neap tide in the wet season. However, as compared to heavily vegetated mangrove wetlands, the generally degraded Mwache Creek mangrove wetland sediment trapping efficiency is low as the average is about 30% for the highly degraded backwater zone mangrove forest and 65% in the

  20. Insights into the folding pathway of the Engrailed Homeodomain protein using replica exchange molecular dynamics simulations.

    PubMed

    Koulgi, Shruti; Sonavane, Uddhavesh; Joshi, Rajendra

    2010-11-01

    Protein folding studies were carried out by performing microsecond time scale simulations on the ultrafast/fast folding protein Engrailed Homeodomain (EnHD) from Drosophila melanogaster. It is a three-helix bundle protein consisting of 54 residues (PDB ID: 1ENH). The positions of the helices are 8-20 (Helix I), 26-36 (Helix II) and 40-53 (Helix III). The second and third helices together form a Helix-Turn-Helix (HTH) motif which belongs to the family of DNA binding proteins. The molecular dynamics (MD) simulations were performed using replica exchange molecular dynamics (REMD). REMD is a method that involves simulating a protein at different temperatures and performing exchanges at regular time intervals. These exchanges were accepted or rejected based on the Metropolis criterion. REMD was performed using the AMBER FF03 force field with the generalised Born solvation model for the temperature range 286-373 K involving 30 replicas. The extended conformation of the protein was used as the starting structure. A simulation of 600 ns per replica was performed resulting in an overall simulation time of 18 μs. The protein was seen to fold close to the native state with backbone root mean square deviation (RMSD) of 3.16 Å. In this low RMSD structure, the Helix I was partially formed with a backbone RMSD of 3.37 Å while HTH motif had an RMSD of 1.81 Å. Analysis suggests that EnHD folds to its native structure via an intermediate in which the HTH motif is formed. The secondary structure development occurs first followed by tertiary packing. The results were in good agreement with the experimental findings.

  1. Gas exchange, leaf structure and nitrogen in contrasting successional tree species growing in open and understory sites during a drought.

    PubMed

    Abrams, M D; Mostoller, S A

    1995-06-01

    Seasonal ecophysiology, leaf structure and nitrogen were measured in saplings of early (Populus grandidentata Michx. and Prunus serotina J.F. Ehrh.), middle (Fraxinus americana L. and Carya tomentosa Nutt.) and late (Acer rubrum L. and Cornus florida L.) successional tree species during severe drought on adjacent open and understory sites in central Pennsylvania, USA. Area-based net photosynthesis (A) and leaf conductance to water vapor diffusion (g(wv)) varied by site and species and were highest in open growing plants and early successional species at both the open and understory sites. In response to the period of maximum drought, both sunfleck and sun leaves of the early successional species exhibited smaller decreases in A than leaves of the other species. Shaded understory leaves of all species were more susceptible to drought than sun leaves and had negative midday A values during the middle and later growing season. Shaded understory leaves also displayed a reduced photosynthetic light response during the peak drought period. Sun leaves were thicker and had a greater mass per area (LMA) and nitrogen (N) content than shaded leaves, and early and middle successional species had higher N contents and concentrations than late successional species. In both sunfleck and sun leaves, seasonal A was positively related to predawn leaf Psi, g(wv), LMA and N, and was negatively related to vapor pressure deficit, midday leaf Psi and internal CO(2). Although a significant amount of plasticity occurred in all species for most gas exchange and leaf structural parameters, middle successional species exhibited the largest degree of phenotypic plasticity between open and understory plants. PMID:14965944

  2. The long-run dynamic relationship between exchange rate and its attention index: Based on DCCA and TOP method

    NASA Astrophysics Data System (ADS)

    Wang, Xuan; Guo, Kun; Lu, Xiaolin

    2016-07-01

    The behavior information of financial market plays a more and more important role in modern economic system. The behavior information reflected in INTERNET search data has already been used in short-term prediction for exchange rate, stock market return, house price and so on. However, the long-run relationship between behavior information and financial market fluctuation has not been studied systematically. Further, most traditional statistic methods and econometric models could not catch the dynamic and non-linear relationship. An attention index of CNY/USD exchange rate is constructed based on search data from 360 search engine of China in this paper. Then the DCCA and Thermal Optimal Path methods are used to explore the long-run dynamic relationship between CNY/USD exchange rate and the corresponding attention index. The results show that the significant interdependency exists and the change of exchange rate is 1-2 days lag behind the attention index.

  3. Dynamic Patterns, Parameters, and Climatic Response of CO2 Exchange of Agricultural Crops: Monocotyledons VS. Dicotyledons

    NASA Astrophysics Data System (ADS)

    Gilmanov, T. G.; Wylie, B. K.; Howard, D. M.

    2012-12-01

    Net CO2 exchange data from long-term flux tower measurements in monocotyledonous (wheat, maize) and dicotyledonous (soybeans, alfalfa, peas, peanuts) crops were partitioned into photosynthesis (P) and respiration (R) using the light-soil temperature-VPD response method. Analysis of the resulting time series of P and R revealed patterns of temporal and phenological dynamics in these plant groups. We established differences in ranges and dynamic patterns of P and R as well as CO2 exchange parameters (quantum yield, photosynthetic capacity, respiration rate, light-use efficiency, curvature of the VPD response). Weekly P and R data combined with remotely sensed 7-day eMODIS NDVI allow identification of the quasi-linear relationships between P, R, and NDVI, as well as estimation of parameters of NDVI response (start of the growing season, duration of the linearity period, slope of NDVI response). While the linear-like patterns occur early in the season, later the flux response to NDVI becomes less pronounced, and for the whole season the flux-NDVI relationship assumes a hysteresis-like pattern. Introduction of VPD and soil moisture limitation as well as phenological controls (growing degree days) leads to more flexible models for P and R in relation to NDVI and on-site drivers. These models allow mapping of the cropland CO2 exchange at regional and larger scales (e.g., the Great Plains). Significant relationships of the crop GPP to the seasonally integrated NDVI were also established, providing an opportunity for mapping of crop productivity using geographically distributed historic NDVI data. On the other hand, long time series (6 to 12 years and longer) of weekly P and R data lead to models of annual photosynthesis and respiration in response to climatic factors that may be used for prognostic purposes. We developed a model of maize GPP on the Great Plains in relation to the sum of temperatures above 5 °C and the hydrologic year precipitation. The model describes 75

  4. Assessing the Dynamics of Bittorrent Swarms Topologies Using the Peer Exchange Protocol

    NASA Astrophysics Data System (ADS)

    Fauzie, Mohamad Dikshie; Thamrin, Achmad Husni; van Meter, Rodney; Murai, Jun

    Bittorrent is one of the most popular and successful applications in the current Internet. However, we still have little knowledge about the topology of real Bittorrent swarms, how dynamic the topology is, and how it affects overall behavior. This paper describes an experimental study of the overlay topologies of real-world Bittorrent networks, focusing on the activity of the nodes of its P2P topology and especially their dynamic relationships. Peer Exchange Protocol (PEX) messages are analyzed to infer topologies and their properties, capturing the variations of their behavior. Our measurements, verified using the Kolmogorov-Smirnov goodness of fit test and the likelihood ratio test and confirmed via simulation, show that a power-law with exponential cutoff is a more plausible model than a pure power-law distribution. We also found that the average clustering coefficient is very low, supporting this observation. Bittorrent swarms are far more dynamic than has been recognized previously, potentially impacting attempts to optimize the performance of the system as well as the accuracy of simulations and analyses.

  5. Catalysis in a Cage: Condition-Dependent Speciation and Dynamics of Exchanged Cu Cations in SSZ-13 Zeolites.

    PubMed

    Paolucci, Christopher; Parekh, Atish A; Khurana, Ishant; Di Iorio, John R; Li, Hui; Albarracin Caballero, Jonatan D; Shih, Arthur J; Anggara, Trunojoyo; Delgass, W Nicholas; Miller, Jeffrey T; Ribeiro, Fabio H; Gounder, Rajamani; Schneider, William F

    2016-05-11

    The relationships among the macroscopic compositional parameters of a Cu-exchanged SSZ-13 zeolite catalyst, the types and numbers of Cu active sites, and activity for the selective catalytic reduction (SCR) of NOx with NH3 are established through experimental interrogation and computational analysis of materials across the catalyst composition space. Density functional theory, stochastic models, and experimental characterizations demonstrate that within the synthesis protocols applied here and across Si:Al ratios, the volumetric density of six-membered-rings (6MR) containing two Al (2Al sites) is consistent with a random Al siting in the SSZ-13 lattice subject to Löwenstein's rule. Further, exchanged Cu(II) ions first populate these 2Al sites before populating remaining unpaired, or 1Al, sites as Cu(II)OH. These sites are distinguished and enumerated ex situ through vibrational and X-ray absorption spectroscopies (XAS) and chemical titrations. In situ and operando XAS follow Cu oxidation state and coordination environment as a function of environmental conditions including low-temperature (473 K) SCR catalysis and are rationalized through first-principles thermodynamics and ab initio molecular dynamics. Experiment and theory together reveal that the Cu sites respond sensitively to exposure conditions, and in particular that Cu species are solvated and mobilized by NH3 under SCR conditions. While Cu sites are spectroscopically and chemically distinct away from these conditions, they exhibit similar turnover rates, apparent activation energies and apparent reaction orders at the SCR conditions, even on zeolite frameworks other than SSZ13. PMID:27070199

  6. Dynamic changes of the total pore area available for peritoneal exchange in children.

    PubMed

    Fischbach, M; Haraldsson, B

    2001-07-01

    The most important of the parameters that describe exchange across the peritoneal membrane is the total pore area over diffusion distance (A(0)/Deltax). It determines the rate of diffusion and mainly seems to reflect the number of capillaries available for exchange. In the present study, a simplified three-pore analysis was used to estimate A(0)/Deltax from peritoneal equilibration tests. Two groups of children (mean age, 9.5 yr) who were on chronic peritoneal dialysis underwent studies with peritoneal equilibration tests. In the first group of children, three levels of fill volumes were used in each patient. In the second group of patients, the effects of posture and dwell time were analyzed from four consecutive peritoneal dialysis samples obtained after 15, 30, 60, and 90 min. As the fill volume was raised from 800 to 1400 ml/m(2) BSA, the steady-state A(0)/Deltax increased significantly by 21%, i.e., from 19,900 +/- 1200 to 24,000 +/- 1450 cm(2)/cm per 1.73 m(2) (n = 8). A further increase to 2000 ml/m(2) did not result in any change of A(0)/Deltax. Moreover, steady-state A(0)/Deltax fell significantly when the patients were standing, 21,900 +/- 1400 compared with 29,400 +/- 1330 cm(2)/cm per 1.73m(2) (n = 6) obtained in the supine position. There was a transient (<30 min) increase in A(0)/Deltax initially during the dwell, probably reflecting vasodilation and recruitment of capillaries. It is concluded that factors such as the intraperitoneal fill volume, posture, and dwell time all dynamically affect the total pore area available for exchange.

  7. Erionite-Na upon heating: dehydration dynamics and exchangeable cations mobility.

    PubMed

    Ballirano, Paolo; Pacella, Alessandro

    2016-01-01

    Erionite is a fibrous zeolite significantly more tumorigenic than crocidolite asbestos upon inhalation. In recent years, several papers have been published aimed at characterizing from the crystal-chemical point of view erionite fibres. As their toxicity has been ascribed to Fe acquired within the human body, studies aimed at characterizing the iron topochemistry have also been published, suggesting a possible important role played by the ionic exchange properties and cations mobility of this zeolite on developing carcinogenicity. Here we report the analysis results of the thermal behaviour of erionite-Na, which has been found to deviate significantly from that of erionite-K. This result is in contrast with the current scientific view that differences in weighted ionic potential, Si/Al ratio and size of exchangeable cations result in significantly different thermal behaviours, all those parameters being nearly identical or very similar in both species. The different mobility of the extraframework cations observed in erionite samples with dissimilar chemistry is of particular interest within the frame of the hypothesis that their biological activity could depend, apart from surface interactions, also on bulk effects. PMID:26948139

  8. Erionite-Na upon heating: dehydration dynamics and exchangeable cations mobility

    NASA Astrophysics Data System (ADS)

    Ballirano, Paolo; Pacella, Alessandro

    2016-03-01

    Erionite is a fibrous zeolite significantly more tumorigenic than crocidolite asbestos upon inhalation. In recent years, several papers have been published aimed at characterizing from the crystal-chemical point of view erionite fibres. As their toxicity has been ascribed to Fe acquired within the human body, studies aimed at characterizing the iron topochemistry have also been published, suggesting a possible important role played by the ionic exchange properties and cations mobility of this zeolite on developing carcinogenicity. Here we report the analysis results of the thermal behaviour of erionite-Na, which has been found to deviate significantly from that of erionite-K. This result is in contrast with the current scientific view that differences in weighted ionic potential, Si/Al ratio and size of exchangeable cations result in significantly different thermal behaviours, all those parameters being nearly identical or very similar in both species. The different mobility of the extraframework cations observed in erionite samples with dissimilar chemistry is of particular interest within the frame of the hypothesis that their biological activity could depend, apart from surface interactions, also on bulk effects.

  9. Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

    SciTech Connect

    Kamberaj, Hiqmet

    2015-09-28

    In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4,  5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

  10. Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

    PubMed Central

    Wang, Kai; Yang, Yanzhi; Chodera, John D.; Shirts, Michael R.

    2014-01-01

    We present a method to identify small molecule ligand binding sites and orientations to a given protein crystal structure using GPU-accelerated Hamiltonian replica exchange molecular dynamics simulations. The Hamiltonians used vary from the physical end state of protein interacting with the ligand to a unphysical end state where the ligand does not interact with the protein. As replicas explore the space of Hamiltonians interpolating between these states the ligand can rapidly escape local minima and explore potential binding sites. Geometric restraints keep the ligands within the protein volume, and a potential energy pathway designed to increase phase space overlap between intermediates ensures good mixing. Because of the rigorous statistical mechanical nature of the Hamiltonian exchange framework, we can also extract binding free energy estimates at all putative binding sites, which agree well with free energies computed from occupation probabilities. We present results of this methodology on the T4 lysozyme L99A model system with four ligands, including one non-binder as a control. We find that our methodology identifies the crystallographic binding sites consistently and accurately for the small number of ligands considered here and gives free energies consistent with experiment. We are also able to analyze the contribution of individual binding sites on the overall binding affinity. Our methodology points to near term potential applications in early-stage drug discovery. PMID:24297454

  11. Fluid Analysis and Improved Structure of an ATEG Heat Exchanger Based on Computational Fluid Dynamics

    NASA Astrophysics Data System (ADS)

    Tang, Z. B.; Deng, Y. D.; Su, C. Q.; Yuan, X. H.

    2015-06-01

    In this study, a numerical model has been employed to analyze the internal flow field distribution in a heat exchanger applied for an automotive thermoelectric generator based on computational fluid dynamics. The model simulates the influence of factors relevant to the heat exchanger, including the automotive waste heat mass flow velocity, temperature, internal fins, and back pressure. The result is in good agreement with experimental test data. Sensitivity analysis of the inlet parameters shows that increase of the exhaust velocity, compared with the inlet temperature, makes little contribution (0.1 versus 0.19) to the heat transfer but results in a detrimental back pressure increase (0.69 versus 0.21). A configuration equipped with internal fins is proved to offer better thermal performance compared with that without fins. Finally, based on an attempt to improve the internal flow field, a more rational structure is obtained, offering a more homogeneous temperature distribution, higher average heat transfer coefficient, and lower back pressure.

  12. Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

    NASA Astrophysics Data System (ADS)

    Kamberaj, Hiqmet

    2015-09-01

    In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4, 5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

  13. Dynamics of energy exchange in model samples subjected to elastic and electromagnetic impacts

    NASA Astrophysics Data System (ADS)

    Avagimov, A. A.; Zeigarnik, V. A.; Okunev, V. I.

    2011-10-01

    The effects of elastic and electromagnetic (EM) fields are studied as an additional factor of energy exchange in the process of the deformation of a heterogeneous medium. The threshold value of initiating energy, Ktr( kp), relative to the current relaxation process is quantitatively estimated. It is shown that the estimated energy impacts below the threshold can initiate relaxation of local structural stresses and, thus, reduce the risk of a macrofracture. In a seismically active region, a similar scenario of initiation of dynamic development is considered in the local zones of potential sources of earthquakes. The possibility to determine the location, the time, and the intensity of the initiating EM impact is considered. From the experiments, the coefficient of electromechanical conversion is calculated.

  14. Replica exchange molecular dynamics of the thermodynamics of fibril growth of Alzheimer's Aβ42 peptide

    NASA Astrophysics Data System (ADS)

    Han, Ming; Hansmann, Ulrich H. E.

    2011-08-01

    The growth of amyloid fibrils is studied by replica exchange molecular dynamics in an implicit solvent. Our data indicate that extremely long simulation times (at least a few hundred ns) are necessary to study the thermodynamics of fibril elongation in detail. However some aspects of the aggregation process are already accessible on the time scales available in the present study. A peak in the specific heat indicates a docking temperature of Tdock ≈ 320 K. Irreversible locking requires lower temperatures with the locking temperature estimated as Tlock ≈ 280 K. In our simulation the fibril grows from both sides with the C-terminal of the incoming monomer attaching to the C-terminal of the peptides in the fibril forming a β-sheet on the fibril edge. Our simulation indicates that the C-terminal is crucial for aggregation.

  15. Molecular Dynamics Simulation Study on Energy Exchange Between Vibration Modes of a Square Graphene Nanoflake Oscillator.

    PubMed

    Lee, Eunae; Kang, Jeong Won; Kim, Ki-Sub; Kwon, Oh-Kuen

    2016-02-01

    Superlubricity in nanoscale graphene structures has been of interest for developing graphene-based nanoelectromechanical systems, as well as for the study of basic mechanical properties. Here, we investigated the translational and rotational motions of a square graphene nanoflake with retracting motions by performing classical molecular dynamics simulations. Our results show that the kinetic energy of the translational motion was exchanged into the kinetic energy of the rotational motion. Thus, square graphene nanoflake oscillators have very low quality factors in translational motions. We discuss that square graphene nanoflakes have great potential to be a core component in nanoelectromechanical systems by detecting their motions with ultrahigh sensitivity to facilitate the development of sensor, memory, and quantum computing.

  16. Molecular Dynamics Simulation Study on Energy Exchange Between Vibration Modes of a Square Graphene Nanoflake Oscillator.

    PubMed

    Lee, Eunae; Kang, Jeong Won; Kim, Ki-Sub; Kwon, Oh-Kuen

    2016-02-01

    Superlubricity in nanoscale graphene structures has been of interest for developing graphene-based nanoelectromechanical systems, as well as for the study of basic mechanical properties. Here, we investigated the translational and rotational motions of a square graphene nanoflake with retracting motions by performing classical molecular dynamics simulations. Our results show that the kinetic energy of the translational motion was exchanged into the kinetic energy of the rotational motion. Thus, square graphene nanoflake oscillators have very low quality factors in translational motions. We discuss that square graphene nanoflakes have great potential to be a core component in nanoelectromechanical systems by detecting their motions with ultrahigh sensitivity to facilitate the development of sensor, memory, and quantum computing. PMID:27433628

  17. Replica exchange molecular dynamics optimization of tensor network states for quantum many-body systems.

    PubMed

    Liu, Wenyuan; Wang, Chao; Li, Yanbin; Lao, Yuyang; Han, Yongjian; Guo, Guang-Can; Zhao, Yong-Hua; He, Lixin

    2015-03-01

    Tensor network states (TNS) methods combined with the Monte Carlo (MC) technique have been proven a powerful algorithm for simulating quantum many-body systems. However, because the ground state energy is a highly non-linear function of the tensors, it is easy to get stuck in local minima when optimizing the TNS of the simulated physical systems. To overcome this difficulty, we introduce a replica-exchange molecular dynamics optimization algorithm to obtain the TNS ground state, based on the MC sampling technique, by mapping the energy function of the TNS to that of a classical mechanical system. The method is expected to effectively avoid local minima. We make benchmark tests on a 1D Hubbard model based on matrix product states (MPS) and a Heisenberg J1-J2 model on square lattice based on string bond states (SBS). The results show that the optimization method is robust and efficient compared to the existing results.

  18. Radon exchange dynamics in a karst system investigated by radon continuous measurements in water: first results.

    PubMed

    Peano, G; Vigna, B; Villavecchia, E; Agnesod, G

    2011-05-01

    In 2008 the underground Karst Laboratory of Bossea Cave started research on radon exchange dynamics between bedrock, cave waters (main collector and percolations) and indoor underground atmosphere. Radon air concentrations, normally high, increase more and more during the collector's floods. An explanation of this is a radon-water solubilisation process more effective in flood events, because of a greater rock-water contact surface. Radon is then carried by water into the cave and released into the air. To verify this, continuous measurements of radon concentration are needed not only in the air, but also in the waters of the cave. So a new device for continuous radon monitoring in water was tested, connected to the AlphaGuard radon monitor. For the first 6 months of 2010, for different sections of the cave, the correlations between radon in the air, radon in the waters and the collector's stream flow fluctuations were presented and discussed. PMID:21586541

  19. Stomatal encryption by epicuticular waxes as a plastic trait modifying gas exchange in a Mediterranean evergreen species (Quercus coccifera L.).

    PubMed

    Roth-Nebelsick, Anita; Fernández, Victoria; Peguero-Pina, José Javier; Sancho-Knapik, Domingo; Gil-Pelegrín, Eustaquio

    2013-03-01

    The adaptive benefit of stomatal crypts remains a matter of controversy. This work studies the effect on gas exchange of cuticular rims that overarch the stomatal pore in the Mediterranean species Quercus coccifera L. growing under Mediterranean (lower relative humidities and high summer temperatures) or oceanic conditions (higher daily relative humidities and mild temperatures). After microscopic assessment of the leaf surfaces and stomatal architecture, the impact of the cuticular 'cup' on gas exchange was evaluated by employing three-dimensional finite element models. Here, we provide evidence for a high plasticity of the Q. coccifera cuticular cup, with much larger vents under oceanic conditions compared to small vents under Mediterranean conditions. This structure adds a substantial fixed resistance thereby strongly decreasing gas exchange under Mediterranean conditions. The cuticular cup, which also increases leaf internal humidity, might buffer the rapid changes in vapour pressure deficit (VPD) often observed under Mediterranean conditions. Since water loss of guard and adjacent epidermal cells regulates stomatal aperture, we suggest that this structure allows an efficient regulation of stomatal conductance and optimum use of resources under high VPD. This study provides evidence that plasticity of stomatal architecture can be an important structural component of hydraulic adaptation to different climate conditions. PMID:22897384

  20. Stomatal encryption by epicuticular waxes as a plastic trait modifying gas exchange in a Mediterranean evergreen species (Quercus coccifera L.).

    PubMed

    Roth-Nebelsick, Anita; Fernández, Victoria; Peguero-Pina, José Javier; Sancho-Knapik, Domingo; Gil-Pelegrín, Eustaquio

    2013-03-01

    The adaptive benefit of stomatal crypts remains a matter of controversy. This work studies the effect on gas exchange of cuticular rims that overarch the stomatal pore in the Mediterranean species Quercus coccifera L. growing under Mediterranean (lower relative humidities and high summer temperatures) or oceanic conditions (higher daily relative humidities and mild temperatures). After microscopic assessment of the leaf surfaces and stomatal architecture, the impact of the cuticular 'cup' on gas exchange was evaluated by employing three-dimensional finite element models. Here, we provide evidence for a high plasticity of the Q. coccifera cuticular cup, with much larger vents under oceanic conditions compared to small vents under Mediterranean conditions. This structure adds a substantial fixed resistance thereby strongly decreasing gas exchange under Mediterranean conditions. The cuticular cup, which also increases leaf internal humidity, might buffer the rapid changes in vapour pressure deficit (VPD) often observed under Mediterranean conditions. Since water loss of guard and adjacent epidermal cells regulates stomatal aperture, we suggest that this structure allows an efficient regulation of stomatal conductance and optimum use of resources under high VPD. This study provides evidence that plasticity of stomatal architecture can be an important structural component of hydraulic adaptation to different climate conditions.

  1. Physical Non-Contact Communication between Microscopic Aquatic Species: Novel Experimental Evidences for an Interspecies Information Exchange.

    PubMed

    Fels, Daniel

    2016-01-01

    Previous experiments on physical non-contact communication within same species gave rise to test for this type of communication also across the species border, which was the aim of the present study. It was found that autotrophic unicellular organisms (Euglena viridis), separated by cuvettes, affected the proliferation rate of heterotrophic unicellular organisms (Paramecium caudatum). Further, the heterotrophic unicellular organism affected also the proliferation rate of a multicellular heterotrophic organism (Rotatoria sp.) and vice versa. In the case when populations (of Euglena viridis and Paramecium caudatum) were shielded against electromagnetic fields in the optical spectrum from each other, no effects were measured. The results may support the notion that the organisation of ecosystems relies also on the exchange of electromagnetic fields from their constituting biosystems. PMID:27042178

  2. Physical Non-Contact Communication between Microscopic Aquatic Species: Novel Experimental Evidences for an Interspecies Information Exchange

    PubMed Central

    2016-01-01

    Previous experiments on physical non-contact communication within same species gave rise to test for this type of communication also across the species border, which was the aim of the present study. It was found that autotrophic unicellular organisms (Euglena viridis), separated by cuvettes, affected the proliferation rate of heterotrophic unicellular organisms (Paramecium caudatum). Further, the heterotrophic unicellular organism affected also the proliferation rate of a multicellular heterotrophic organism (Rotatoria sp.) and vice versa. In the case when populations (of Euglena viridis and Paramecium caudatum) were shielded against electromagnetic fields in the optical spectrum from each other, no effects were measured. The results may support the notion that the organisation of ecosystems relies also on the exchange of electromagnetic fields from their constituting biosystems. PMID:27042178

  3. Reactive oxygen species accelerate degradation of anion exchange membranes based on polyphenylene oxide in alkaline environments.

    PubMed

    Parrondo, Javier; Wang, Zhongyang; Jung, Min-Suk J; Ramani, Vijay

    2016-07-20

    Anion exchange membranes (AEM) based on polyphenylene oxide (PPO) suffered quaternary-ammonium-cation-site degradation in alkaline environments. Surprisingly, the degradation rate was considerably faster in the presence of molecular oxygen. We postulated that the AEM cation-site catalyzes the reduction of dioxygen by hydroxide ions to yield the superoxide anion radical and the highly reactive hydroxyl free radical. We substantiated our hypothesis by using a phosphorous-containing spin trap (5-diisopropoxy-phosphoryl-5-methyl-1-pyrroline-N-oxide) to detect the adducts for both free radicals in situ using (31)P-NMR spectroscopy. PMID:27381009

  4. Generation of Benzyne Species from Diphenylphosphoryl Derivatives: Simultaneous Exchange of Three Functional Groups.

    PubMed

    Gorobets, Evgueni; Parvez, Masood; Derksen, Darren J; Keay, Brian A

    2016-06-13

    Interaction of (2-diphenylphosphoryl-3-iodo-4-methoxy-phenyl) methanol with NaH in DMF at ambient temperature results in the generation of benzyne intermediates that can be trapped by furan or DMF. Trapping with DMF forms 3-(dimethylaminomethyl)-2-hydroxy-6-methoxybenzaldehyde demonstrating the simultaneous exchange of three functionalities in a single step. The presence of the alkoxy substituent adjacent to iodine is critical for high regioselectivity addition of DMF. The corresponding bromide or triflate can be used in place of the iodide with equal efficiency. This methodology was used to synthesize the reported structure of gigasol and leading to a structural reassignment of this biscoumarin natural product.

  5. Linking nonstructural carbohydrate dynamics to gas exchange and leaf hydraulic behavior in Pinus edulis and Juniperus monosperma.

    PubMed

    Woodruff, David R; Meinzer, Frederick C; Marias, Danielle E; Sevanto, Sanna; Jenkins, Michael W; McDowell, Nate G

    2015-04-01

    Leaf hydraulics, gas exchange and carbon storage in Pinus edulis and Juniperus monosperma, two tree species on opposite ends of the isohydry-anisohydry spectrum, were analyzed to examine relationships between hydraulic function and carbohydrate dynamics. Leaf hydraulic vulnerability, leaf water potential (Ψl ), leaf hydraulic conductance (Kleaf ), photosynthesis (A), stomatal conductance (gs) and nonstructural carbohydrate (NSC) content were analyzed throughout the growing season. Leaf hydraulic vulnerability was significantly lower in the relatively anisohydric J. monosperma than in the more isohydric P. edulis. In P. edulis, Ψl dropped and stayed below 50% loss of leaf hydraulic conductance (P₅₀) early in the day during May, August and around midday in September, leading to sustained reductions in Kleaf . In J. monosperma, Ψl dropped below P₅₀ only during August, resulting in the maintenance of Kleaf during much of the growing season. Mean A and gs during September were significantly lower in P. edulis than in J. monosperma. Foliar total NSC was two to three times greater in J. monosperma than in P. edulis in June, August and September. Consistently lower levels of total NSC in P. edulis suggest that its isohydric strategy pushes it towards the exhaustion of carbon reserves during much of the growing season.

  6. Weak coordination among petiole, leaf, vein, and gas-exchange traits across Australian angiosperm species and its possible implications.

    PubMed

    Gleason, Sean M; Blackman, Chris J; Chang, Yvonne; Cook, Alicia M; Laws, Claire A; Westoby, Mark

    2016-01-01

    Close coordination between leaf gas exchange and maximal hydraulic supply has been reported across diverse plant life forms. However, it has also been suggested that this relationship may become weak or break down completely within the angiosperms. We examined coordination between hydraulic, leaf vein, and gas-exchange traits across a diverse group of 35 evergreen Australian angiosperms, spanning a large range in leaf structure and habitat. Leaf-specific conductance was calculated from petiole vessel anatomy and was also measured directly using the rehydration technique. Leaf vein density (thought to be a determinant of gas exchange rate), maximal stomatal conductance, and net CO 2 assimilation rate were also measured for most species (n = 19-35). Vein density was not correlated with leaf-specific conductance (either calculated or measured), stomatal conductance, nor maximal net CO 2 assimilation, with r (2) values ranging from 0.00 to 0.11, P values from 0.909 to 0.102, and n values from 19 to 35 in all cases. Leaf-specific conductance calculated from petiole anatomy was weakly correlated with maximal stomatal conductance (r (2) = 0.16; P = 0.022; n = 32), whereas the direct measurement of leaf-specific conductance was weakly correlated with net maximal CO 2 assimilation (r (2) = 0.21; P = 0.005; n = 35). Calculated leaf-specific conductance, xylem ultrastructure, and leaf vein density do not appear to be reliable proxy traits for assessing differences in rates of gas exchange or growth across diverse sets of evergreen angiosperms.

  7. Weak coordination among petiole, leaf, vein, and gas-exchange traits across Australian angiosperm species and its possible implications.

    PubMed

    Gleason, Sean M; Blackman, Chris J; Chang, Yvonne; Cook, Alicia M; Laws, Claire A; Westoby, Mark

    2016-01-01

    Close coordination between leaf gas exchange and maximal hydraulic supply has been reported across diverse plant life forms. However, it has also been suggested that this relationship may become weak or break down completely within the angiosperms. We examined coordination between hydraulic, leaf vein, and gas-exchange traits across a diverse group of 35 evergreen Australian angiosperms, spanning a large range in leaf structure and habitat. Leaf-specific conductance was calculated from petiole vessel anatomy and was also measured directly using the rehydration technique. Leaf vein density (thought to be a determinant of gas exchange rate), maximal stomatal conductance, and net CO 2 assimilation rate were also measured for most species (n = 19-35). Vein density was not correlated with leaf-specific conductance (either calculated or measured), stomatal conductance, nor maximal net CO 2 assimilation, with r (2) values ranging from 0.00 to 0.11, P values from 0.909 to 0.102, and n values from 19 to 35 in all cases. Leaf-specific conductance calculated from petiole anatomy was weakly correlated with maximal stomatal conductance (r (2) = 0.16; P = 0.022; n = 32), whereas the direct measurement of leaf-specific conductance was weakly correlated with net maximal CO 2 assimilation (r (2) = 0.21; P = 0.005; n = 35). Calculated leaf-specific conductance, xylem ultrastructure, and leaf vein density do not appear to be reliable proxy traits for assessing differences in rates of gas exchange or growth across diverse sets of evergreen angiosperms. PMID:26811791

  8. Heat Exchange Processes and Thermal Dynamics of a Glacier-Fed Stream

    NASA Astrophysics Data System (ADS)

    Khamis, K.; Hannah, D. M.; Brown, L. E.; Milner, A. M.

    2012-12-01

    Glacier-fed river thermal regimes vary markedly in space and time. However, knowledge is limited of fundamental processes controlling alpine stream temperature dynamics. The few studies have not sufficiently characterised above-stream micro-climate and have been limited to single melt seasons. To address the research gap, this study quantified heat exchanges at the water surface and bed of a glacier fed stream over two summers to improve understanding of factors and processes driving thermal dynamics. An automatic weather station and river gauge were set up on a stream 1.5 km from the Taillon Glacier, French Pyrénées. Hydro-meteorological observations were recorded at 15-min intervals between 16 June-2 September 2010 and 2011. Energy balance components were measured [net radiation (Q*); bed heat flux (Qbhf)] or estimated based on site-specific data [sensible heat transfer (Qh); latent heat (Qe); fluid friction (Qf)]. During 2010, snowline altitude was lower and glacier ablation occurred in late season. During 2010, the mean snowline altitude was lower and ablation of glacier ice occurred later in the season Mean water temperature was lower (-0.8°C), precipitation greater (+87mm) and daily discharge variation lower (-0.03 m3s-1) than 2011. The net heat budget was strongly positive in both summers, with the majority of energy exchanged at the air-water interface. Averaged over the seasons, Q* was the largest heat source (~80% of total flux); Qh (~13%) and Qf (~3%) were also sources. Qe displayed inter-annual variability; during 2010 (2011) it contributed 5.2% (0.03%) of the total heat budget due to windier, drier conditions that offset early season condensation gains with late season evaporative losses. Energy exchanges at the channel - river bed interface comprised <1% of the heat budget; Qbhf was a sink (source) during 2010 (2011). Daily flux totals were used to characterize sub-seasonal dynamics. Declines in net radiation receipt and total energy available to

  9. Dynamics of two competing species in the presence of Lévy noise sources

    NASA Astrophysics Data System (ADS)

    La Cognata, A.; Valenti, D.; Dubkov, A. A.; Spagnolo, B.

    2010-07-01

    We consider a Lotka-Volterra system of two competing species subject to multiplicative α -stable Lévy noise. The interaction parameter between the species is a random process which obeys a stochastic differential equation with a generalized bistable potential in the presence both of a periodic driving term and an additive α -stable Lévy noise. We study the species dynamics, which is characterized by two different regimes, exclusion of one species and coexistence of both. We find quasiperiodic oscillations and stochastic resonance phenomenon in the dynamics of the competing species, analyzing the role of the Lévy noise sources.

  10. Temporal stability in forest productivity increases with tree diversity due to asynchrony in species dynamics.

    PubMed

    Morin, Xavier; Fahse, Lorenz; de Mazancourt, Claire; Scherer-Lorenzen, Michael; Bugmann, Harald

    2014-12-01

    Theory predicts a positive relationship between biodiversity and stability in ecosystem properties, while diversity is expected to have a negative impact on stability at the species level. We used virtual experiments based on a dynamic simulation model to test for the diversity-stability relationship and its underlying mechanisms in Central European forests. First our results show that variability in productivity between stands differing in species composition decreases as species richness and functional diversity increase. Second we show temporal stability increases with increasing diversity due to compensatory dynamics across species, supporting the biodiversity insurance hypothesis. We demonstrate that this pattern is mainly driven by the asynchrony of species responses to small disturbances rather than to environmental fluctuations, and is only weakly affected by the net biodiversity effect on productivity. Furthermore, our results suggest that compensatory dynamics between species may enhance ecosystem stability through an optimisation of canopy occupancy by coexisting species. PMID:25212251

  11. Influence of Hydration Level on Polymer and Water Dynamics in Alkaline Anion Exchange Fuel Cell Membranes

    NASA Astrophysics Data System (ADS)

    Tarver, Jacob; Kim, Jenny; Tyagi, Madhu; Soles, Christopher; Tsai, Tsung-Han; Coughlin, Bryan

    2015-03-01

    Triblock copolymers based on poly(chloromethylstyrene)-b-poly(ethylene)-b-poly(chloromethylstyrene) can be quaternized to different extents to yield anion exchange membranes for alkaline fuel cells. In the absence of moisture, these membranes demonstrate bilayer lamellar morphology. Upon high levels of hydration, however, in-situ small angle neutron scattering reveals the emergence of higher-order diffraction peaks. This phenomena has previously been observed in analogous diblock copolymer-based membranes and has been attributed to the induction of a multilayer lamellar morphology in which selective striping of water occurs in the center of the ion-rich domain. By conducting humidity-resolved quasielastic neutron scattering (QENS) measurements using deuterated water, we are able to isolate differences in the pico- to nanosecond timescale dynamics of the hydrogenated membrane upon hydration. QENS measurements in the presence of a hydrogenated water source subsequently permit deconvolution and isolation of the translational and rotational dynamics of water as a function of relative humidity, revealing spatial and temporal changes in polymer and water motion at high levels of hydration.

  12. Dynamics of ventilation, heart rate, and gas exchange: sinusoidal and impulse work loads in man.

    PubMed

    Bakker, H K; Struikenkamp, R S; De Vries, G A

    1980-02-01

    Dynamic characteristics of ventilation, heart rate, and gas exchange in response to sinusoidally varying work loads were analyzed in four male subjects, exercising in the upright position on a bicycle ergometer. Mean work-load and sinusoidal amplitude were about 1.5 and 0.9 W/kg, fat-free mass), respectively. Seven different frequencies were used, the periods ranging from 12 to 0.75 min. To further investigate the linearity of the variables under study, 10-s impulse loads were also applied to three of the four subjects. Harmonic analysis of the sine-wave data and comparison of the sine-wave fundamental responses with the impulse frequency responses showed that only O2 uptake behaves in a linear fashion. Ventilation and CO2 production showed quasi- to nonlinear behaviors, whereas the responses of heart rate and alveolar partial pressures were clearly dependent on the type of forcing used. By means of mathematical parameter identification techniques, it was found that the individual frequency responses of O2 uptake could be almost completely described by a four-parameter transfer function with parameter values showing second-order underdamped to critically damped dynamics.

  13. Dynamics of intramolecular spin exchange interaction of a nitronyl nitroxide diradical in solution and on surfaces

    NASA Astrophysics Data System (ADS)

    Lloveras, V.; Badetti, E.; Veciana, J.; Vidal-Gancedo, J.

    2016-02-01

    In this paper we report the study of the dynamics of a thermally modulated intramolecular spin exchange interaction of a novel diradical nitronyl nitroxide-substituted disulfide in solution and when it is grafted on a gold surface. The structure of this diradical was designed to have flexible chains leading to intramolecular collisions and hence spin exchange interaction, and with an appropriate binding group to be grafted on the gold surface to study its behavior on the surface. In solution, this diradical shows a strong spin exchange interaction between both radicals which is modulated by temperature, but also gold nanoparticles (AuNPs) functionalized with this diradical permit investigation of such a phenomenon in surface-grafted radicals. The spin-labelled AuNP synthesis was optimized to obtain high coverage of spin labels to lead to high spin exchange interaction. The obtained AuNPs were studied by Electron Paramagnetic Resonance (EPR), UV-Vis, and IR spectroscopies, HR-TEM microscopy, Cyclic Voltammetry (CV), Energy Dispersive X-ray analysis (EDX) and Thermogravimetric Analysis (TGA). This inorganic-organic hybrid material also showed dipolar interactions between its radicals which were confirmed by the appearance in the EPR spectra of an |Δms| = 2 transition at half-field. This signal gives direct evidence of the presence of a high-spin state and permitted us to study the nature of the magnetic coupling between the spins which was found to be antiferromagnetic. Self-Assembled Monolayers (SAMs) of these radicals on the Au (111) substrate were also prepared and studied by contact angle, X-Ray Photoelectron Spectroscopy (XPS), Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS), Cyclic Voltammetry and EPR. The magnetic as well as the electrochemical properties of the hybrid surfaces were studied and compared with the properties of this diradical in solution. Analogies between the properties of AuNPs with high coverage of radicals and those of SAM were

  14. Dynamic communities in multichannel data: An application to the foreign exchange market during the 2007-2008 credit crisis

    NASA Astrophysics Data System (ADS)

    Fenn, Daniel J.; Porter, Mason A.; McDonald, Mark; Williams, Stacy; Johnson, Neil F.; Jones, Nick S.

    2009-09-01

    We study the cluster dynamics of multichannel (multivariate) time series by representing their correlations as time-dependent networks and investigating the evolution of network communities. We employ a node-centric approach that allows us to track the effects of the community evolution on the functional roles of individual nodes without having to track entire communities. As an example, we consider a foreign exchange market network in which each node represents an exchange rate and each edge represents a time-dependent correlation between the rates. We study the period 2005-2008, which includes the recent credit and liquidity crisis. Using community detection, we find that exchange rates that are strongly attached to their community are persistently grouped with the same set of rates, whereas exchange rates that are important for the transfer of information tend to be positioned on the edges of communities. Our analysis successfully uncovers major trading changes that occurred in the market during the credit crisis.

  15. Developmental Changes in Photosynthetic Gas Exchange in the Polyol-Synthesizing Species, Apium graveolens L. (Celery).

    PubMed

    Fox, T C; Kennedy, R A; Loescher, W H

    1986-09-01

    Developmental changes in photosynthetic gas exchange were investigated in the mannitol synthesizing plant celery (Apium graveolens L. ;Giant Pascal'). Greenhouse-grown plants had unusually high photosynthetic rates for a C(3) plant, but consistent with field productivity data reported elsewhere for this plant. In most respects, celery exhibited typical C(3) photosynthetic characteristics; light saturation occurred at 600 micromoles photons per square meter per second, with a broad temperature optimum, peaking at 26 degrees C. At 2% O(2), photosynthesis was enhanced 15 to 25% compared to rates at 21% O(2). However, celery had low CO(2) compensation points, averaging 7 to 20 microliters per liter throughout the canopy. Conventional mechanisms for concentrating CO(2) were not detectable.

  16. Nutritional stress induces exchange of cell material and energetic coupling between bacterial species.

    PubMed

    Benomar, Saida; Ranava, David; Cárdenas, María Luz; Trably, Eric; Rafrafi, Yan; Ducret, Adrien; Hamelin, Jérôme; Lojou, Elisabeth; Steyer, Jean-Philippe; Giudici-Orticoni, Marie-Thérèse

    2015-02-23

    Knowledge of the behaviour of bacterial communities is crucial for understanding biogeochemical cycles and developing environmental biotechnology. Here we demonstrate the formation of an artificial consortium between two anaerobic bacteria, Clostridium acetobutylicum (Gram-positive) and Desulfovibrio vulgaris Hildenborough (Gram-negative, sulfate-reducing) in which physical interactions between the two partners induce emergent properties. Molecular and cellular approaches show that tight cell-cell interactions are associated with an exchange of molecules, including proteins, which allows the growth of one partner (D. vulgaris) in spite of the shortage of nutrients. This physical interaction induces changes in expression of two genes encoding enzymes at the pyruvate crossroads, with concomitant changes in the distribution of metabolic fluxes, and allows a substantial increase in hydrogen production without requiring genetic engineering. The stress induced by the shortage of nutrients of D. vulgaris appears to trigger the interaction.

  17. Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization.

    PubMed

    Chamachi, Neharika G; Chakrabarty, Suman

    2016-08-01

    The pathological forms of prions are known to be a result of misfolding, oligomerization, and aggregation of the cellular prion. While the mechanism of misfolding and aggregation in prions has been widely studied using both experimental and computational tools, the structural and energetic characterization of the dimer form have not garnered as much attention. On one hand dimerization can be the first step toward a nucleation-like pathway to aggregation, whereas on the other hand it may also increase the conformational stability preventing self-aggregation. In this work, we have used extensive all-atom replica exchange molecular dynamics simulations of both monomer and dimer forms of a mouse prion protein to understand the structural, dynamic, and thermodynamic stability of dimeric prion as compared to the monomeric form. We show that prion proteins can dimerize spontaneously being stabilized by hydrophobic interactions as well as intermolecular hydrogen bonding and salt bridge formation. We have computed the conformational free energy landscapes for both monomer and dimer forms to compare the thermodynamic stability and misfolding pathways. We observe large conformational heterogeneity among the various modes of interactions between the monomers and the strong intermolecular interactions may lead to as high as 20% β-content. The hydrophobic regions in helix-2, surrounding coil regions, terminal regions along with the natively present β-sheet region appear to actively participate in prion-prion intermolecular interactions. Dimerization seems to considerably suppress the inherent dynamic instability observed in monomeric prions, particularly because the regions of structural frustration constitute the dimer interface. Further, we demonstrate an interesting reversible coupling between the Q160-G131 interaction (which leads to inhibition of β-sheet extension) and the G131-V161 H-bond formation. PMID:27390876

  18. Amide hydrogen exchange and internal dynamics in the chemotactic protein CheY from Escherichia coli.

    PubMed

    Lacroix, E; Bruix, M; López-Hernández, E; Serrano, L; Rico, M

    1997-08-22

    The backbone internal dynamics of the wild-type 129 amino acid alpha/beta parallel protein CheY and its double mutant F14N/P110G are analysed here by the hydrogen-exchange method. The F14N mutation is known to stabilise the protein and to accelerate refolding while P110G is destabilising and accelerates unfolding. We first assigned and characterised the double mutant by nuclear magnetic resonance (NMR), to try and discover any possible conformational change induced by the two mutations. The main difference between the two proteins is a favourable N-capping interaction of the newly introduced Asn14 side-chain at the beginning of the first alpha-helix (alpha-helix A). Second, we have measured the exchange rates in the wild-type and mutant CheY. In the first case the observed protection factors are slightly dispersed around an average value. According to their distribution in the structure, protein stability is highest on one face of the central beta-sheet, in the surroundings of the main hydrophobic core formed by side-chains of residues in beta-strands I, II and III and helices A and E. The mutations in the double mutant protein affect two distinct subdomains differently (from beta-strand I to III and from alpha-helix C to the end). In the second subdomain the number of protected protons is reduced with respect to those in the wild-type. This differential behaviour can be explained by a selective decrease in stability of the second folding subdomain produced by the P110G mutation and the opposite effect in the first subdomain, produced by the F14N mutation. alpha-Helix A, which is involved together with beta-strands I and III in the folding nucleus of CheY, shows the largest protection factors in both proteins.

  19. Gas exchange responses of two Eucalyptus species to salinity and waterlogging.

    PubMed

    Van Der Moezel, P G; Watson, L E; Bell, D T

    1989-06-01

    The effects of salinity and waterlogging on stomatal conductance, net photosynthesis and transpiration of 3-month-old Eucalyptus camaldulensis Dehnh. and Eucalyptus lesouefii Maiden seedlings were studied under greenhouse conditions. Under non-saline conditions, waterlogging induced stomatal closure in both species. However, the stomata of E. camaldulensis reopened after five weeks, when adventitious roots were produced. Relative to that of controls, height growth of waterlogged seedlings was greater in E. camaldulensis than in E. lesouefii, as were rates of photosynthesis and transpiration. In a freely drained medium, high salinity reduced rates of seedling height growth and photosynthesis, relative to those in controls, less in E. lesouefii than in E. camaldulensis. In both species, height growth, stomatal conductance and photosynthetic rate were lowest under conditions of saline waterlogging.

  20. Molecular and functional comparisons of the vacuolar Na+/H+ exchangers originated from glycophytic and halophytic species.

    PubMed

    Li, Jin-yao; He, Xiao-wei; Xu, Li; Zhou, Jie; Wu, Ping; Shou, Hui-xia; Zhang, Fu-chun

    2008-02-01

    A novel vacuolar Na+/H+ exchanger, CgNHX1, was cloned from a halophytic species Chenopodium glaucum by using reverse transcriptase-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) technique. Sequence alignment and phylogenetic analysis of 22 NHX genes from GenBank as well as the new CgNHX1 gene indicate that NHX genes shared a great degree of similarity, regardless of their glycophytic or halophytic origin. Expression of the CgNHX1 gene was induced by NaCl and peaked at 400 mmol/L NaCl. Overexpression of NHX1 genes in rice enhanced their tolerance to salt stress. However, there is no significant difference in salt tolerance among the transgenic rice plants overexpressing the NHX1 genes from either glycophytic or halophytic species. The Na+ content of both the wild type (WT) and transgenic plants increased when exposed to 50 and 100 mmol/L NaCl, and the Na+ concentration in transgenic plants was marginally higher than that of WT. Our data demonstrate that the overexpression of the NHX1 gene from either glycophytic or halophytic species resulted in the enhanced tolerance to salt stress at a similar level, suggesting that NHX gene per se might not be the reason accounting for the difference in salt tolerance between glycophytes and halophytes. PMID:18257135

  1. Quantum dynamics of two-optical modes and a single mechanical mode optomechanical system: Selective energy exchange

    NASA Astrophysics Data System (ADS)

    Aggarwal, Neha; Bhattacherjee, Aranya B.

    2014-01-01

    We study the quantum dynamics of an optomechanical setup comprising two optical modes and one mechanical mode. We show that the same system can undergo a dynamical phase transition analogous to Dicke-Hepp-Lieb superradiant type phase transition. We found that the coupling between the momentum quadratures of the two optical fields gives rise to a new dynamical critical point. We show that selective energy exchange between any two modes is possible by coherent control of the coupling parameters. In addition we also demonstrate the occurrence of normal mode splitting (NMS) in the mechanical displacement spectrum.

  2. Helix bending in alamethicin: molecular dynamics simulations and amide hydrogen exchange in methanol.

    PubMed Central

    Gibbs, N; Sessions, R B; Williams, P B; Dempsey, C E

    1997-01-01

    Molecular dynamics simulations of alamethicin in methanol were carried out with either a regular alpha-helical conformation or the x-ray crystal structure as starting structures. The structures rapidly converged to a well-defined hydrogen-bonding pattern with mixed alpha-helical and 3(10)-helical hydrogen bonds, consistent with NMR structural characterization, and did not unfold throughout the 1-ns simulation, despite some sizable backbone fluctuations involving reversible breaking of helical hydrogen bonds. Bending of the helical structure around residues Aib10-Aib13 was associated with reversible flips of the peptide bonds involving G11 (Aib10-G11 or G11-L12 peptide bonds), yielding discrete structural states in which the Aib10 carbonyl or (rarely) the G11 carbonyl was oriented away from the peptide helix. These peptide bond reversals could be accommodated without greatly perturbing the adjacent helical structure, and intramolecular hydrogen bonding was generally maintained in bent states through the formation of new (non-alpha or 3[10]) hydrogen bonds with good geometries: G11 NH-V9 CO (inverse gamma turn), Aib13 NH-Aib8 CO (pi-helix) and, rarely, L12 NH- Q7 NH (pi-helix). These observations may reconcile potentially conflicting NMR structural information for alamethicin in methanol, in which evidence for conformational flexibility in the peptide sequence before P14 (G11-Aib13) contrasts with the stability of backbone amide NH groups to exchange with solvent. Similar reversible reorientation of the Thr11-Gly12 peptide bond of melittin is also observed in dynamics simulations in methanol (R. B. Sessions, N. Gibbs, and C. E. Dempsey, submitted). This phenomenon may have some role in the orientation of the peptide carbonyl in solvating the channel lumen in membrane ion channel states of these peptides. Images FIGURE 1 FIGURE 2 PMID:9168025

  3. Simulating carbon dioxide exchange rates of deciduous tree species: evidence for a general pattern in biochemical changes and water stress response

    PubMed Central

    Reynolds, Robert F.; Bauerle, William L.; Wang, Ying

    2009-01-01

    Background and Aims Deciduous trees have a seasonal carbon dioxide exchange pattern that is attributed to changes in leaf biochemical properties. However, it is not known if the pattern in leaf biochemical properties – maximum Rubisco carboxylation (Vcmax) and electron transport (Jmax) – differ between species. This study explored whether a general pattern of changes in Vcmax, Jmax, and a standardized soil moisture response accounted for carbon dioxide exchange of deciduous trees throughout the growing season. Methods The model MAESTRA was used to examine Vcmax and Jmax of leaves of five deciduous trees, Acer rubrum ‘Summer Red’, Betula nigra, Quercus nuttallii, Quercus phellos and Paulownia elongata, and their response to soil moisture. MAESTRA was parameterized using data from in situ measurements on organs. Linking the changes in biochemical properties of leaves to the whole tree, MAESTRA integrated the general pattern in Vcmax and Jmax from gas exchange parameters of leaves with a standardized soil moisture response to describe carbon dioxide exchange throughout the growing season. The model estimates were tested against measurements made on the five species under both irrigated and water-stressed conditions. Key Results Measurements and modelling demonstrate that the seasonal pattern of biochemical activity in leaves and soil moisture response can be parameterized with straightforward general relationships. Over the course of the season, differences in carbon exchange between measured and modelled values were within 6–12 % under well-watered conditions and 2–25 % under water stress conditions. Hence, a generalized seasonal pattern in the leaf-level physiological change of Vcmax and Jmax, and a standardized response to soil moisture was sufficient to parameterize carbon dioxide exchange for large-scale evaluations. Conclusions Simplification in parameterization of the seasonal pattern of leaf biochemical activity and soil moisture response of

  4. River temperature processes under contrasting riparian land cover: linking microclimate, heat exchange and water thermal dynamics

    NASA Astrophysics Data System (ADS)

    Hannah, D. M.; Kantola, K.; Malcolm, I.

    2012-12-01

    River temperature influences strongly growth and survival in salmonid fish, which are often the target of river management strategies. Temperature is controlled by transfers of heat and water to/ from the river system, with land and water management modifying exchanges and consequently thermal regime. In the UK, fisheries managers are promoting riparian forest planting as a climate change adaption measure to reduce water temperature extremes. However, scientific understanding lags behind management and policy needs. Specifically, there is an urgent requirement to determine planting strategies that maximise expected benefits of riparian forest in terms of reduction in maximum water temperature. Scientific knowledge is necessary to underpin conceptual and deterministic models to inform management. To address this research gap, this paper analyses high resolution (15 minute) hydrometeorological data collected over a calendar year in the western Scottish Highlands (Loch Ard) to understand the controls and processes determining river temperature dynamics under open moorland (control), semi-natural woodland and commercial forest. The research programme aims: (1) to characterise spatial and temporal variability in riparian microclimate and stream water temperature regime across forest treatments; (2) to identify the hydrological, climatological and site-specific factors affecting stream temperature; (3) to estimate the energy balance at sites representative of each forest treatment and, thus, yield physical process understanding about dominant heat exchanges driving thermal variability; and (4) to use 1-3 to predict stream temperature sensitivity under different forestry and hydroclimatological scenarios. Results indicated that inter-treatment differences in mean and maximum daily water column temperature were ordered open > semi-natural > commercial during summer, but semi-natural > commercial > open during winter. Minimum water temperature was ordered commercial > semi

  5. Assessment of the Draft AIAA S-119 Flight Dynamic Model Exchange Standard

    NASA Technical Reports Server (NTRS)

    Jackson, E. Bruce; Murri, Daniel G.; Hill, Melissa A.; Jessick, Matthew V.; Penn, John M.; Hasan, David A.; Crues, Edwin Z.; Falck, Robert D.; McCarthy, Thomas G.; Vuong, Nghia; Zimmerman, Curtis

    2011-01-01

    An assessment of a draft AIAA standard for flight dynamics model exchange, ANSI/AIAA S-119-2011, was conducted on behalf of NASA by a team from the NASA Engineering and Safety Center. The assessment included adding the capability of importing standard models into real-time simulation facilities at several NASA Centers as well as into analysis simulation tools. All participants were successful at importing two example models into their respective simulation frameworks by using existing software libraries or by writing new import tools. Deficiencies in the libraries and format documentation were identified and fixed; suggestions for improvements to the standard were provided to the AIAA. An innovative tool to generate C code directly from such a model was developed. Performance of the software libraries compared favorably with compiled code. As a result of this assessment, several NASA Centers can now import standard models directly into their simulations. NASA is considering adopting the now-published S-119 standard as an internal recommended practice.

  6. Custom-tailored adsorbers: A molecular dynamics study on optimal design of ion exchange chromatography material.

    PubMed

    Lang, Katharina M H; Kittelmann, Jörg; Pilgram, Florian; Osberghaus, Anna; Hubbuch, Jürgen

    2015-09-25

    The performance of functionalized materials, e.g., ion exchange resins, depends on multiple resin characteristics, such as type of ligand, ligand density, the pore accessibility for a molecule, and backbone characteristics. Therefore, the screening and identification process for optimal resin characteristics for separation is very time and material consuming. Previous studies on the influence of resin characteristics have focused on an experimental approach and to a lesser extent on the mechanistic understanding of the adsorption mechanism. In this in silico study, a previously developed molecular dynamics (MD) tool is used, which simulates any given biomolecule on resins with varying ligand densities. We describe a set of simulations and experiments with four proteins and six resins varying in ligand density, and show that simulations and experiments correlate well in a wide range of ligand density. With this new approach simulations can be used as pre-experimental screening for optimal adsorber characteristics, reducing the actual number of screening experiments, which results in a faster and more knowledge-based development of custom-tailored adsorbers.

  7. Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics.

    PubMed

    Jo, Sunhwan; Chipot, Christophe; Roux, Benoît

    2015-05-12

    The performance and accuracy of different simulation schemes for estimating the entropy inferred from free energy calculations are tested. The results obtained from replica-exchange molecular dynamics (REMD) simulations based on a simplified toy model are compared to exact numerically derived ones to assess accuracy and convergence. It is observed that the error in entropy estimation decreases by at least an order of magnitude and the quantities of interest converge much faster when the simulations are coupled via a temperature REMD algorithm and the trajectories from different temperatures are combined. Simulations with the infinite-swapping method and its variants show some improvement over the traditional nearest-neighbor REMD algorithms, but they are more computationally expensive. To test the methodologies further, the free energy profile for the reversible association of two methane molecules in explicit water was calculated and decomposed into its entropic and enthalpic contributions. Finally, a strategy based on umbrella sampling computations carried out via simultaneous temperature and Hamiltonian REMD simulations is shown to yield the most accurate entropy estimation. The entropy profile between the two methane molecules displays the characteristic signature of a hydrophobic interaction.

  8. Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

    SciTech Connect

    Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.

    2014-10-14

    In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW₁₂O₄₀³⁻, as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

  9. Replica exchange molecular dynamics simulations of an α/β-type small acid soluble protein (SASP).

    PubMed

    Ojeda-May, P; Pu, Jingzhi

    2013-12-31

    Small acid soluble proteins (SASPs) of α/β-type play a major role in the resistance of spore DNAs to external assaults. It has been found that α/β-type SASP exhibits intrinsic disorder on isolation, but it acquires a defined native state upon binding to DNA. This disorder to order transition is not yet understood. Other questions related to the role of the thermodynamics and structure of the individual protein in the complex formation remain elusive. Characterization of the unbound state of α/β-type SASP in experiments could be a challenging problem because of the heterogeneous nature of the ensemble. Here, computer simulations can help gain more insights into the unbound state of α/β-type SASP. In the present work, by using replica exchange molecular dynamics (REMD), we simulated an α/β-type SASP on isolation with an implicit solvent. We found that α/β-type SASP undergoes a continuous phase transition with a small free energy barrier, a common feature of intrinsically disordered proteins (IDPs). Additionally, we detected the presence of residual α-helical structures at local level and a high degree of plasticity in the chain which can contribute to the fast disorder to order transition by reducing the fly-casting mechanism.

  10. Elucidation of molecular dynamics of invasive species of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated rice fields are aggressively invaded by weedy rice in the U.S. and worldwide. Weedy rice results in loss of yield and seed contamination. The molecular dynamics of the evolutionary adaptive traits of weedy rice are not fully understood. To understand the molecular basis and identify the i...

  11. Is parasitoid acceptance of different host species dynamic?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Choice of host individuals by parasitoids is dynamic, varying with physiological state and experience. In particular, female parasitoids with high egg loads and low life expectancy are more willing to accept low quality hosts than females with low egg loads and high life expectancy. However, studi...

  12. Native and exotic plant species exhibit similar population dynamics during succession.

    PubMed

    Meiners, Scott J

    2007-05-01

    A growing body of literature has led to the debate in invasion biology whether exotic species perform within communities differently than native taxa due to inherent advantages. To address this issue, the population dynamics of native and exotic plant species were assessed from a 48-year record of permanent plot data from the Hutcheson Memorial Forest Center (New Jersey, USA) to determine rate of increase, lag time, maximum frequency, and the year of peak frequency. Overall, native and exotic species exhibited very similar population dynamics. Rates of increase and length of lag times were similar between native and exotic taxa but were strongly influenced by plant life form. Short-lived species were characterized by rapid population growth rates and short lag times. Growth rates decreased and lag times increased with species longevity. Overall, correlations between population metrics were the same in native and exotic taxa, suggesting similar trade-offs in life history patterns. The one difference observed was that, in native species, peak frequency was negatively associated with the year of peak frequency (i.e., early-successional species tended to become more abundant), while there was no relationship in exotic species. These analyses show that exotic species behave in essentially the same way as native taxa within dynamic communities. This suggests that abundant native and exotic plant species are exploiting the same range of ecological strategies resulting in similar roles within communities.

  13. Cooperation can emerge in prisoner's dilemma from a multi-species predator prey replicator dynamic.

    PubMed

    Paulson, Elisabeth; Griffin, Christopher

    2016-08-01

    In this paper we study a generalized variation of the replicator dynamic that involves several species and sub-species that may interact. We show how this dynamic comes about from a specific finite-population model, but also show that one must take into consideration the dynamic nature of the population sizes (and hence proportions) in order to make the model complete. We provide expressions for these population dynamics to produce a kind of multi-replicator dynamic. We then use this replicator dynamic to show that cooperation can emerge as a stable behavior when two species each play prisoner's dilemma as their intra-species game and a form of zero-sum predator prey game as their inter-species game. General necessary and sufficient conditions for cooperation to emerge as stable are provided for a number of game classes. We also showed an example using Hawk-Dove where both species can converge to stable (asymmetric) mixed strategies. PMID:27318117

  14. Coccolithophore Dynamics In Alfonso Basin: Seasonal Variation And Species Composition

    NASA Astrophysics Data System (ADS)

    Cortés, M. Y.; Urcádiz-Cázares, F. J.; Silverberg, N.; Aguirre-Bahena, F.; Bollmann, J.

    2007-05-01

    The production of organic and inorganic carbon by coccolithophores is considered to play a significant role in the global carbon cycle. Therefore, detailed knowledge of their vertical flux is needed. Here we present a time-series record of coccolithophore standing stock and vertical coccolith flux from Alfonso Basin, southwest coast of the Gulf of California. This location is of particular interest as it is very sensitive to changes in environmental conditions and these may be preserved in laminated underlying sediments. Coccolithophore standing stock and assemblage composition were obtained from plankton samples taken at 3- month intervals during 2002-2003. Furthermore, coccolith flux and species composition were determined in samples from a time-series sediment trap (sampling intervals 7-14 days) deployed at 350 m depth from January 2002 to October 2003. The coccolithophore standing stock and coccolith flux varied considerably between sampling periods but, in general, a seasonal pattern was apparent, with low fluxes in spring-summer and maximal values in autumn- winter. During 2002, fluxes ranged from 0.02x108 coccoliths m-2 d-1 in summer to 64.7x108 coccoliths m-2 d-1 in autumn. Values increased considerably during 2003: registering 52.4 x108 coccoliths m-2 d-1 in spring to the highest (128.8x108 coccoliths m-2 d-1) in late summer/autumn. The latter are related to hurricanes that occurred during the sampling period. In total 47 taxa were identified but only three species, Gephyrocapsa oceanica (43.6%), Emiliania huxleyi (28%) and Florisphera profunda (15.7%), constituted 88 percent of the total coccolith flux. This corresponds to the species composition observed in the water column. G. oceanica was always present and its flux pattern followed that of the total flux. The flux of E. huxleyi remained almost constant during the observed time period whereas F. profunda showed peak fluxes in autumn. Although the cosmopolitan species E. huxleyi has been considered the

  15. Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution

    NASA Astrophysics Data System (ADS)

    Wernet, Ph.; Kunnus, K.; Josefsson, I.; Rajkovic, I.; Quevedo, W.; Beye, M.; Schreck, S.; Grübel, S.; Scholz, M.; Nordlund, D.; Zhang, W.; Hartsock, R. W.; Schlotter, W. F.; Turner, J. J.; Kennedy, B.; Hennies, F.; de Groot, F. M. F.; Gaffney, K. J.; Techert, S.; Odelius, M.; Föhlisch, A.

    2015-04-01

    Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion. Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in charge and spin density at the metal site that need to be controlled to optimize complexes for photocatalytic hydrogen production and selective carbon-hydrogen bond activation. An understanding at the molecular level of how transition-metal complexes catalyse reactions, and in particular of the role of the short-lived and reactive intermediate states involved, will be critical for such optimization. However, suitable methods for detailed characterization of electronic excited states have been lacking. Here we show, with the use of X-ray laser-based femtosecond-resolution spectroscopy and advanced quantum chemical theory to probe the reaction dynamics of the benchmark transition-metal complex Fe(CO)5 in solution, that the photo-induced removal of CO generates the 16-electron Fe(CO)4 species, a homogeneous catalyst with an electron deficiency at the Fe centre, in a hitherto unreported excited singlet state that either converts to the triplet ground state or combines with a CO or solvent molecule to regenerate a penta-coordinated Fe species on a sub-picosecond timescale. This finding, which resolves the debate about the relative importance of different spin channels in the photochemistry of Fe(CO)5 (refs 4, 16,17,18,19 and 20), was made possible by the ability of femtosecond X-ray spectroscopy to probe frontier-orbital interactions with atom specificity. We expect the method to be broadly applicable in the chemical sciences, and to complement approaches that probe structural dynamics in ultrafast processes.

  16. Characterization of At- species in simple and biological media by high performance anion exchange chromatography coupled to gamma detector.

    PubMed

    Sabatié-Gogova, A; Champion, J; Huclier, S; Michel, N; Pottier, F; Galland, N; Asfari, Z; Chérel, M; Montavon, G

    2012-04-01

    Astatine is a rare radioelement belonging to the halogen group. Considering the trace amounts of astatine produced in cyclotrons, its chemistry cannot be evaluated by spectroscopic tools. Analytical tools, provided that they are coupled with a radioactive detection system, may be an alternative way to study its chemistry. In this research work, high performance anion exchange chromatography (HPAEC) coupled to a gamma detector (γ) was used to evaluate astatine species under reducing conditions. Also, to strengthen the reliability of the experiments, a quantitative analysis using a reactive transport model has been done. The results confirm the existence of one species bearing one negative charge in the pH range 2-7.5. With respect to the other halogens, its behavior indicates the existence of negative ion, astatide At(-). The methodology was successfully applied to the speciation of the astatine in human serum. Under fixed experimental conditions (pH 7.4-7.5 and redox potential of 250 mV) astatine exists mainly as astatide At(-) and does not interact with the major serum components. Also, the method might be useful for the in vitro stability assessment of (211)At-labeled molecules potentially applicable in nuclear medicine. PMID:22405318

  17. Characterization of At- species in simple and biological media by high performance anion exchange chromatography coupled to gamma detector.

    PubMed

    Sabatié-Gogova, A; Champion, J; Huclier, S; Michel, N; Pottier, F; Galland, N; Asfari, Z; Chérel, M; Montavon, G

    2012-04-01

    Astatine is a rare radioelement belonging to the halogen group. Considering the trace amounts of astatine produced in cyclotrons, its chemistry cannot be evaluated by spectroscopic tools. Analytical tools, provided that they are coupled with a radioactive detection system, may be an alternative way to study its chemistry. In this research work, high performance anion exchange chromatography (HPAEC) coupled to a gamma detector (γ) was used to evaluate astatine species under reducing conditions. Also, to strengthen the reliability of the experiments, a quantitative analysis using a reactive transport model has been done. The results confirm the existence of one species bearing one negative charge in the pH range 2-7.5. With respect to the other halogens, its behavior indicates the existence of negative ion, astatide At(-). The methodology was successfully applied to the speciation of the astatine in human serum. Under fixed experimental conditions (pH 7.4-7.5 and redox potential of 250 mV) astatine exists mainly as astatide At(-) and does not interact with the major serum components. Also, the method might be useful for the in vitro stability assessment of (211)At-labeled molecules potentially applicable in nuclear medicine.

  18. State-to-state quantum dynamics of O + O2 isotope exchange reactions reveals nonstatistical behavior at atmospheric conditions.

    PubMed

    Sun, Zhigang; Liu, Lan; Lin, Shi Ying; Schinke, Reinhard; Guo, Hua; Zhang, Dong H

    2010-01-12

    The O + O(2) exchange reaction is a prerequisite for the formation of ozone in Earth's atmosphere. We report here state-to-state differential and integral cross sections for several O + O(2) isotope-exchange reactions obtained by dynamically exact quantum scattering calculations at collision energies relevant to atmospheric conditions. These reactions are shown to be highly nonstatistical, evidenced by dominant forward scattering and deviation of the integral cross section from the statistical limit. Mechanistic analyses revealed that the nonstatistical channel is facilitated by short-lived osculating resonances. The theoretical results provided an in-depth interpretation of a recent molecular beam experiment of the exchange reaction and shed light on the initial step of ozone recombination.

  19. Fluence-dependent dynamics of the 5d6s exchange splitting in Gd metal after femtosecond laser excitation

    NASA Astrophysics Data System (ADS)

    Frietsch, Björn; Carley, Robert; Gleich, Markus; Teichmann, Martin; Bowlan, John; Weinelt, Martin

    2016-07-01

    We investigate the fluence-dependent dynamics of the exchange-split 5d6s valence bands of Gd metal after femtosecond, near-infrared (IR) laser excitation. Time- and angle-resolved photoelectron spectroscopy (tr-ARPES) with extreme ultraviolet (XUV) probe pulses is used to simultaneously map the transient binding energies of the minority and majority spin valence bands. The decay constant of the exchange splitting increases with fluence. This reflects the slower response of the occupied majority-spin component, which we attribute to Elliot–Yafet spin-flip scattering in accordance with the microscopic three-temperature model (M3TM). In contrast, the time constant of the partly unoccupied minority-spin band stays unaffected by a change in pump fluence. Here, we introduce as an alternative to superdiffusive spin transport exchange scattering, which is an ultrafast electronic mechanism explaining the observed dynamics. Exchange scattering can reduce the spin polarization in the partially unoccupied minority-spin band and thus its energetic position without effective demagnetization.

  20. Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with α and α+β Proteins

    PubMed Central

    Czaplewski, Cezary; Kalinowski, Sebastian; Liwo, Adam; Scheraga, Harold A.

    2009-01-01

    The replica exchange (RE) method is increasingly used to improve sampling in molecular dynamics (MD) simulations of biomolecular systems. Recently, we implemented the united-residue UNRES force field for mesoscopic MD. Initial results from UNRES MD simulations show that we are able to simulate folding events that take place in a microsecond or even a millisecond time scale. To speed up the search further, we applied the multiplexing replica exchange molecular dynamics (MREMD) method. The multiplexed variant (MREMD) of the RE method, developed by Rhee and Pande, differs from the original RE method in that several trajectories are run at a given temperature. Each set of trajectories run at a different temperature constitutes a layer. Exchanges are attempted not only within a single layer but also between layers. The code has been parallelized and scales up to 4000 processors. We present a comparison of canonical MD, REMD, and MREMD simulations of protein folding with the UNRES force-field. We demonstrate that the multiplexed procedure increases the power of replica exchange MD considerably and convergence of the thermodynamic quantities is achieved much faster. PMID:20161452

  1. Species diversity, structure and dynamics of two populations of an endangered species, Magnolia dealbata (Magnoliaceae).

    PubMed

    Sánchez-Velásquez, Lázaro R; Pineda-López, María del Rosario

    2006-09-01

    Little is known about the ecology and demography of the genus Magnolia. Magnolia dealbata Zucc. is an endangered species endemic to Mexico. Two contrasting populations of M. dealbata (one from the grasslands and other from a secondary cloud forest) were studied. We asked the following questions: (a) Are size structure (diameter at breast height, DBH) and infrutescence production significantly different between the two populations? (b) What are the populations' growth rates (lambda) based on an initial 1987 study? (c) Are the associated species diversity indices of these M. dealbata populations significantly different? The results show no significant differences between the population size structure (p=.094); the growth rates of the populations were 0.992 in grassland and 1.053 in secondary cloud forest. The number of infrutescences produced in year 2001 and DBH relationship were significantly linear (p<.001) in both populations, and there was no significant difference (p>.01) between their slopes. The diversity indices were not significantly different (p>.05), and only 54% of the species were common to both sites. Our study suggests that both populations are relatively stable and that the management history could impact more on the species composition than on the diversity indices. PMID:18494171

  2. Species diversity, structure and dynamics of two populations of an endangered species, Magnolia dealbata (Magnoliaceae).

    PubMed

    Sánchez-Velásquez, Lázaro R; Pineda-López, María del Rosario

    2006-09-01

    Little is known about the ecology and demography of the genus Magnolia. Magnolia dealbata Zucc. is an endangered species endemic to Mexico. Two contrasting populations of M. dealbata (one from the grasslands and other from a secondary cloud forest) were studied. We asked the following questions: (a) Are size structure (diameter at breast height, DBH) and infrutescence production significantly different between the two populations? (b) What are the populations' growth rates (lambda) based on an initial 1987 study? (c) Are the associated species diversity indices of these M. dealbata populations significantly different? The results show no significant differences between the population size structure (p=.094); the growth rates of the populations were 0.992 in grassland and 1.053 in secondary cloud forest. The number of infrutescences produced in year 2001 and DBH relationship were significantly linear (p<.001) in both populations, and there was no significant difference (p>.01) between their slopes. The diversity indices were not significantly different (p>.05), and only 54% of the species were common to both sites. Our study suggests that both populations are relatively stable and that the management history could impact more on the species composition than on the diversity indices.

  3. Reaction Engineering International and Pacific Northwest Laboratory staff exchange: Addressing computational fluid dynamics needs of the chemical process industry

    SciTech Connect

    Fort, J.A.

    1995-07-01

    Staff exchanges, such as the one described in this report, are intended to facilitate communications and collaboration among scientists and engineers at Department of Energy (DOE) laboratories, in US industry, and academia. Funding support for these exchanges is provided by the DOE, Office of Energy Research, Laboratory Technology Transfer Program. Funding levels for each exchange typically range from $20,000 to $40,000. The exchanges offer the opportunity for the laboratories to transfer technology and expertise to industry, gain a perspective to industry`s problems, and develop the basis for further cooperative efforts through Cooperative Research and Development Agreements (CRADAS) or other mechanisms. Information in this report on the staff exchange of the Pacific Northwest Laboratory (PNL) staff with Reaction Engineering International (REI) includes the significant accomplishments, significant problems, industry benefits realized, recommended follow-on work and potential benefit of that work. The objectives of this project were as follows: Work with REI to develop an understanding of the computational fluid dynamics (CFD) needs of the chemical process industry; assess the combined capabilities of the PNL and REI software analysis tools to address these needs; and establish a strategy for a future programmatically funded, joint effort to develop a new CFD tool for the chemical process industry.

  4. Tree species affect cation exchange capacity (CEC) and cation binding properties of organic matter in acid forest soils.

    PubMed

    Gruba, Piotr; Mulder, Jan

    2015-04-01

    Soil organic matter (SOM) in forest soil is of major importance for cation binding and acid buffering, but its characteristics may differ among soils under different tree species. We investigated acidity, cation exchange properties and Al bonding to SOM in stands of Scots pine, pedunculate oak, Norway spruce, European beech and common hornbeam in southern Poland. The content of total carbon (Ct) was by far the major contributor to total cation exchange capacity (CECt) even in loamy soils and a strong relationship between Ct and CECt was found. The slope of the regression of CECt to Ct increased in the order hornbeam≈oak

  5. Tree species affect cation exchange capacity (CEC) and cation binding properties of organic matter in acid forest soils.

    PubMed

    Gruba, Piotr; Mulder, Jan

    2015-04-01

    Soil organic matter (SOM) in forest soil is of major importance for cation binding and acid buffering, but its characteristics may differ among soils under different tree species. We investigated acidity, cation exchange properties and Al bonding to SOM in stands of Scots pine, pedunculate oak, Norway spruce, European beech and common hornbeam in southern Poland. The content of total carbon (Ct) was by far the major contributor to total cation exchange capacity (CECt) even in loamy soils and a strong relationship between Ct and CECt was found. The slope of the regression of CECt to Ct increased in the order hornbeam≈oak

  6. Biasing Potential Replica Exchange Multi-Site λ-Dynamics for Efficient Free Energy Calculations

    PubMed Central

    Armacost, Kira A.; Goh, Garrett B.; Brooks, Charles L.

    2016-01-01

    Traditional free energy calculation methods are well known for their drawbacks in scalability and speed in converging results particularly for calculations with large perturbations. In the present work, we report on the development of biasing potential replica exchange multi-site λ-dynamics (BP-REX MSλD), which is a free energy method that is capable of performing simultaneous alchemical free energy transformations, including perturbations between flexible moieties. BP-REX MSλD and the original MSλD are applied to a series of symmetrical 2,5-benzoquinone derivatives covering a diverse chemical space and range of conformational flexibility. Improved λ-space sampling is observed for the BP-REX MSλD simulations, yielding a 2–5-fold increase in the number of transitions between substituents compared to traditional MSλD. We also demonstrate the efficacy of varying the value of c, the parameter that controls the ruggedness of the landscape mediating the sampling of λ-states, based on the flexibility of the fragment. Finally, we developed a protocol for maximizing the transition frequency between fragments. This protocol reduces the “kinetic barrier” for alchemically transforming fragments by grouping and ordering based on volume. These findings are applied to a challenging test set involving a series of geldanamycin-based inhibitors of heat shock protein 90 (Hsp90). Even though the perturbations span volume changes by as large as 60 Å3, the values for the free energy change achieve an average unsigned error (AUE) of 1.5 kcal/mol relative to experimental Kd measurements with a reasonable correlation (R = 0.56). Our results suggest that the BP-REX MSλD algorithm is a highly efficient and scalable free energy method, which when utilized will enable routine calculations on the order of hundreds of compounds using only a few simulations. PMID:26579773

  7. Effect of the geometric phase on the dynamics of the hydrogen-exchange reaction.

    PubMed

    Juanes-Marcos, Juan Carlos; Althorpe, Stuart C; Wrede, Eckart

    2007-01-28

    A recent puzzle in nonadiabatic quantum dynamics is that geometric phase (GP) effects are present in the state-to-state opacity functions of the hydrogen-exchange reaction, but cancel out in the state-to-state integral cross sections (ICSs). Here the authors explain this result by using topology to separate the scattering amplitudes into contributions from Feynman paths that loop in opposite senses around the conical intersection. The clockwise-looping paths pass over one transition state (1-TS) and scatter into positive deflection angles; the counterclockwise-looping paths pass over two transition states (2-TS) and scatter into negative deflection angles. The interference between the 1-TS and 2-TS paths thus integrates to a very small value, which cancels the GP effects in the ICS. Quasiclassical trajectory (QCT) calculations reproduce the scattering of the 1-TS and 2-TS paths into positive and negative deflection angles and show that the 2-TS paths describe a direct insertion mechanism. The inserting atom follows a highly constrained "S-bend" path, which allows it to avoid both the other atoms and the conical intersection and forces the product diatom to scatter into high rotational states. By contrast, the quantum 2-TS paths scatter into a mainly statistical distribution of rotational states, so that the quantum 2-TS total ICS is roughly twice the QCT ICS at 2.3 eV total energy. This suggests that the S-bend constraint is relaxed by tunneling in the quantum system. These findings on H+H(2) suggest that similar cancellations or reductions in GP effects are likely in many other reactions.

  8. Dynamics of Inorganic Nutrients in Intertidal Sediments: Porewater, Exchangeable, and Intracellular Pools

    PubMed Central

    Garcia-Robledo, Emilio; Bohorquez, Julio; Corzo, Alfonso; Jimenez-Arias, Juan L.; Papaspyrou, Sokratis

    2016-01-01

    The study of inorganic nutrients dynamics in shallow sediments usually focuses on two main pools: porewater (PW) nutrients and exchangeable (EX) ammonium and phosphate. Recently, it has been found that microphytobenthos (MPB) and other microorganisms can accumulate large amounts of nutrients intracellularly (IC), highlighting the biogeochemical importance of this nutrient pool. Storing nutrients could support the growth of autotrophs when nutrients are not available, and could also provide alternative electron acceptors for dissimilatory processes such as nitrate reduction. Here, we studied the magnitude and relative importance of these three nutrient pools (PW, IC, and EX) and their relation to chlorophylls (used as a proxy for MPB abundance) and organic matter (OM) contents in an intertidal mudflat of Cadiz Bay (Spain). MPB was localized in the first 4 mm of the sediment and showed a clear seasonal pattern; highest chlorophylls content was found during autumn and lowest during spring-summer. The temporal and spatial distribution of nutrients pools and MPB were largely correlated. Ammonium was higher in the IC and EX fractions, representing on average 59 and 37% of the total ammonium pool, respectively. Similarly, phosphate in the IC and EX fractions accounted on average for 40 and 31% of the total phosphate pool, respectively. Nitrate in the PW was low, suggesting low nitrification activity and rapid consumption. Nitrate accumulated in the IC pool during periods of moderate MPB abundance, being up to 66% of the total nitrate pool, whereas it decreased when chlorophyll concentration peaked likely due to a high nitrogen demand. EX-Nitrate accounted for the largest fraction of total sediment nitrate, 66% on average. The distribution of EX-Nitrate was significantly correlated with chlorophyll and OM, which probably indicates a relation of this pool to an increased availability of sites for ionic adsorption. This EX-Nitrate pool could represent an alternative nitrate

  9. Dynamics of Inorganic Nutrients in Intertidal Sediments: Porewater, Exchangeable, and Intracellular Pools.

    PubMed

    Garcia-Robledo, Emilio; Bohorquez, Julio; Corzo, Alfonso; Jimenez-Arias, Juan L; Papaspyrou, Sokratis

    2016-01-01

    The study of inorganic nutrients dynamics in shallow sediments usually focuses on two main pools: porewater (PW) nutrients and exchangeable (EX) ammonium and phosphate. Recently, it has been found that microphytobenthos (MPB) and other microorganisms can accumulate large amounts of nutrients intracellularly (IC), highlighting the biogeochemical importance of this nutrient pool. Storing nutrients could support the growth of autotrophs when nutrients are not available, and could also provide alternative electron acceptors for dissimilatory processes such as nitrate reduction. Here, we studied the magnitude and relative importance of these three nutrient pools (PW, IC, and EX) and their relation to chlorophylls (used as a proxy for MPB abundance) and organic matter (OM) contents in an intertidal mudflat of Cadiz Bay (Spain). MPB was localized in the first 4 mm of the sediment and showed a clear seasonal pattern; highest chlorophylls content was found during autumn and lowest during spring-summer. The temporal and spatial distribution of nutrients pools and MPB were largely correlated. Ammonium was higher in the IC and EX fractions, representing on average 59 and 37% of the total ammonium pool, respectively. Similarly, phosphate in the IC and EX fractions accounted on average for 40 and 31% of the total phosphate pool, respectively. Nitrate in the PW was low, suggesting low nitrification activity and rapid consumption. Nitrate accumulated in the IC pool during periods of moderate MPB abundance, being up to 66% of the total nitrate pool, whereas it decreased when chlorophyll concentration peaked likely due to a high nitrogen demand. EX-Nitrate accounted for the largest fraction of total sediment nitrate, 66% on average. The distribution of EX-Nitrate was significantly correlated with chlorophyll and OM, which probably indicates a relation of this pool to an increased availability of sites for ionic adsorption. This EX-Nitrate pool could represent an alternative nitrate

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

    PubMed

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

    2016-10-01

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

  11. Long-term successional forest dynamics: species and community responses to climatic variability

    SciTech Connect

    Kardol, Paul; Todd Jr, Donald E; Hanson, Paul J; Mulholland, Patrick J

    2010-01-01

    Question: Are tree dynamics sensitive to climatic variability, and do tree species differ in their responses to climatic variability? Hence, is vulnerability of forest communities to climatic variability depending on stand composition? Location: Mixed young forest at Walker Branch Watershed near Oak Ridge, East-Tennessee, USA. Methods: Using a long-term data set (1967-2006), we analyzed temporal forest dynamics at the tree and species level, and we analyzed community dynamics for forest stands that different in their initial species composition (i.e., Chestnut Oak, Oak-Hickory, Pine, and Yellow poplar stands). Using summer drought and growing season temperature as defined climate drivers, we evaluated relationships between forest dynamics and climate across levels of organization. Results: Over the 4-decade studied period, forest communities underwent successional change and substantially increased their biomass. Variation in summer drought and growing season temperature contributed to temporal biomass dynamics for some tree species, but not for others. Stand-level responses to climatic variability were shown to be related to responses of specific component species; however, not for Pine stands. Pinus echinata, the dominant species in stands initially identified as Pine stands, decreased over time due to periodical outbreaks of the pine bark beetle (Dendroctonus frontalis). The outbreaks on Walker Branch could not be directly related to climatic conditions. Conclusions: Our results imply that vulnerability of developing forests to predicted climate conditions is stand-type dependent, and hence, is a function of species composition. Autogenic successional processes (or insect outbreaks) were found to prevail over climatic variability in determining long-term forest dynamics for stands dominated by sensitive species, emphasizing the importance of studying interactions between forest succession and climate change.

  12. Temporal and Spatial Dynamics of Tree Species Composition in Temperate Mountains of South Korea

    NASA Astrophysics Data System (ADS)

    Lee, Boknam; Park, Juhan; Cho, Sungsik; Ryu, Daun; Zaw Wynn, Khine; Park, Minji; Cho, Sunhee; Yoon, Jongguk; Park, Jongyoung; Kim, Hyun Seok

    2015-04-01

    Long term studies on vegetation dynamics are important to identify changes of ecosystem-level responses to climate change. To learn how tree species composition and stand structure change across temperate mountains, the temporal and spatial variations in tree species diversity and structure were investigated using the species composition and DBH size collected over the fourteen-year period across 134 sites in Jiri and Baekoon Mountains, South Korea. The overall temporal changes over fourteen years showed significant increase in stand density, species diversity and evenness according to the indices of Shannon-Weiner diversity, Bray-Curtis dissimilarity, and Pielou's evenness, contributing to the increase of basal area and biomass growth. The change of tree species composition could be categorized into five species communities, representing gradual increase or decrease, establishment, extinction, fluctuation of species population. However, in general, the change in species composition appeared to have consistent and directional patterns of increase in the annual rate of change in the mean species traits including species richness, pole growth rate, adult growth rate, and adult stature with five common dominant species (Quercus mongolica, Quercus variabilis, Quercus serrata, Carpinus laxiflora, and Styrax japonicus). The spatial patterns of species composition appeared to have a higher stand density and species diversity along with the low latitude and high slope ecosystem. The climate change was another main driver to vary the distribution of species abundance. Overall, both temporal and spatial changes of composition in tree species community was clear and further analysis to clarify the reasons for such fast and species-specific changes is underway especially to separate the effect of successional change and climate change. Keywords species composition; climate change; temporal and spatial variation ; forest structure; temperate forest

  13. Species with more volatile population dynamics are differentially impacted by weather.

    PubMed

    Harrison, Joshua G; Shapiro, Arthur M; Espeset, Anne E; Nice, Christopher C; Jahner, Joshua P; Forister, Matthew L

    2015-02-01

    Climatic variation has been invoked as an explanation of population dynamics for a variety of taxa. Much work investigating the link between climatic forcings and population fluctuation uses single-taxon case studies. Here, we conduct comparative analyses of a multi-decadal dataset describing population dynamics of 50 co-occurring butterfly species at 10 sites in Northern California. Specifically, we explore the potential commonality of response to weather among species that encompass a gradient of population dynamics via a hierarchical Bayesian modelling framework. Results of this analysis demonstrate that certain weather conditions impact volatile, or irruptive, species differently as compared with relatively stable species. Notably, precipitation-related variables, including indices of the El Niño Southern Oscillation, have a more pronounced impact on the most volatile species. We hypothesize that these variables influence vegetation resource availability, and thus indirectly influence population dynamics of volatile taxa. As one of the first studies to show a common influence of weather among taxa with similar population dynamics, the results presented here suggest new lines of research in the field of biotic-abiotic interactions.

  14. Development of gas exchange and ion regulation in two species of air-breathing fish, Betta splendens and Macropodus opercularis.

    PubMed

    Huang, Chun-Yen; Lin, Cheng-Huang; Lin, Hui-Chen

    2015-07-01

    Aquatic air-breathing anabantoids, a group of fish species characterized by the presence of a labyrinth organ and some gills, exhibit morphological variations. This study aimed to examine whether unequal gill growth begins during the early stages and described the sequence of the early gill developmental events in Betta splendens and Macropodus opercularis. To determine when the ion regulatory and gas exchange abilities first appear in the gills, mitochondria-rich cells (MRCs) and neuroepithelial cells (NECs) were examined in young B. splendens. To evaluate the relative importance of the gills and the labyrinth organ under different levels of oxygen uptake stress, the levels of carbonic anhydrase II (CAII) and Na(+)/K(+)-ATPase (NKA) protein expressions in 2 gills and the labyrinth organ were examined in M. opercularis. We found that the first 3 gills developed earlier than the 4th gill in both species, an indication that the morphological variation begins early in life. In B. splendens, the MRCs and NECs clearly appeared in the first 3 gills at 4 dph and were first found in the 4th gill until 11 dph. The oxygen-sensing ability of the gills was concordant with the ionoregulatory function. In M. opercularis, the hypoxic group had a significantly higher air-breathing frequency. CAII protein expression was higher in the labyrinth organ in the hypoxic group. The gills exhibited increased NKA protein expression in the hypoxic and restricted groups, respectively. Functional plasticity in CAII and NKA protein expressions was found between the gills and the labyrinth organ in adult M. opercularis.

  15. Development of gas exchange and ion regulation in two species of air-breathing fish, Betta splendens and Macropodus opercularis.

    PubMed

    Huang, Chun-Yen; Lin, Cheng-Huang; Lin, Hui-Chen

    2015-07-01

    Aquatic air-breathing anabantoids, a group of fish species characterized by the presence of a labyrinth organ and some gills, exhibit morphological variations. This study aimed to examine whether unequal gill growth begins during the early stages and described the sequence of the early gill developmental events in Betta splendens and Macropodus opercularis. To determine when the ion regulatory and gas exchange abilities first appear in the gills, mitochondria-rich cells (MRCs) and neuroepithelial cells (NECs) were examined in young B. splendens. To evaluate the relative importance of the gills and the labyrinth organ under different levels of oxygen uptake stress, the levels of carbonic anhydrase II (CAII) and Na(+)/K(+)-ATPase (NKA) protein expressions in 2 gills and the labyrinth organ were examined in M. opercularis. We found that the first 3 gills developed earlier than the 4th gill in both species, an indication that the morphological variation begins early in life. In B. splendens, the MRCs and NECs clearly appeared in the first 3 gills at 4 dph and were first found in the 4th gill until 11 dph. The oxygen-sensing ability of the gills was concordant with the ionoregulatory function. In M. opercularis, the hypoxic group had a significantly higher air-breathing frequency. CAII protein expression was higher in the labyrinth organ in the hypoxic group. The gills exhibited increased NKA protein expression in the hypoxic and restricted groups, respectively. Functional plasticity in CAII and NKA protein expressions was found between the gills and the labyrinth organ in adult M. opercularis. PMID:25783787

  16. Dynamic of Campylobacter Species Contamination Along a Poultry Slaughtering Chain

    PubMed Central

    Dib, Hussein; Mrad, Rachelle; Chami, Christelle; Jalkh, Rita

    2014-01-01

    The prevalence of Campylobacters was studied in a poultry farm and along the slaughtering chain. Fifteen swabs from a farm and 75 samples (swabs and rinsates) from its slaughterhouse were collected. All the faecal and cloacal farm swabs were contaminated by Campylobacter jejuni and C. coli against 50% for breast swabs. C. jejuni had a concentration of 6.26, 6.34 and 5.38 Log10 CFU/mL in faecal, cloacal and breast swabs respectively. Rinsates showed an almost constant concentration of Campylobacters (6 Log10 CFU/mL) with a predominance of the presumptive C. jejuni. C. lari was found in 22% of eviscerated samples. Faecal coliforms and E. coli, used as indicators, were detected in all samples (5.46 and 5.15 Log10 CFU/mL, respectively). Final chilling and chlorine (50 ppm) treatments decreased them to acceptable levels, unlike for Campylobacters. Further investigation of the dynamics of Campylobacters and their response to prevention and treatment measures is required. PMID:27800361

  17. Monitoring the Dynamics of Monomer Exchange Using Electrospray Mass Spectrometry: The Case of the Dimeric Glucosamine-6-Phosphate Synthase

    NASA Astrophysics Data System (ADS)

    Chevreux, Guillaume; Atmanene, Cédric; Lopez, Philippe; Ouazzani, Jamal; Van Dorsselaer, Alain; Badet, Bernard; Badet-Denisot, Marie-Ange; Sanglier-Cianférani, Sarah

    2011-03-01

    Escherichia coli glucosamine-6-phosphate synthase (GlmS) is a dimeric enzyme from the glutamine-dependent amidotransferases family, which catalyses the conversion of D-fructose-6-phosphate (Fru6P) and glutamine (Gln) into D-glucosamine-6-phosphate (GlcN6P) and glutamate, respectively. Extensive X-ray crystallography investigations have been reported, highlighting the importance of the dimeric association to form the sugar active site as well as significant conformational changes of the protein upon substrate and product binding. In the present work, an approach based on time-resolved noncovalent mass spectrometry has been developed to study the dynamics of GlmS subunit exchange. Using 14N versus 15N labeled proteins, the kinetics of GlmS subunit exchange was monitored with the wild-type enzyme in the presence of different substrates and products as well as with the protein bearing a key amino acid mutation specially designed to weaken the dimer interface. Determination of rate constants of subunit exchange revealed important modifications of the protein dynamics: while glutamine, glutamate, and K603A mutation accelerates subunit exchange, Fru6P and GlcN6P totally prevent it. These results are described in light of the available structural information, providing additional useful data for both the characterization of GlmS catalytic process and the design of new GlmS inhibitors. Finally, time-resolved noncovalent MS can be proposed as an additional biophysical technique for real-time monitoring of protein dynamics.

  18. Niche dynamics of alien species do not differ among sexual and apomictic flowering plants.

    PubMed

    Dellinger, Agnes S; Essl, Franz; Hojsgaard, Diego; Kirchheimer, Bernhard; Klatt, Simone; Dawson, Wayne; Pergl, Jan; Pyšek, Petr; van Kleunen, Mark; Weber, Ewald; Winter, Marten; Hörandl, Elvira; Dullinger, Stefan

    2016-02-01

    Biological invasions can be associated with shifts of the species' climatic niches but the incidence of such shifts is under debate. The reproductive system might be a key factor controlling such shifts because it influences a species' evolutionary flexibility. However, the link between reproductive systems and niche dynamics in plant invasions has been little studied so far. We compiled global occurrence data sets of 13 congeneric sexual and apomictic species pairs, and used principal components analysis (PCA) and kernel smoothers to compare changes in climatic niche optima, breadths and unfilling/expansion between native and alien ranges. Niche change metrics were compared between sexual and apomictic species. All 26 species showed changes in niche optima and/or breadth and 14 species significantly expanded their climatic niches. However, we found no effect of the reproductive system on niche dynamics. Instead, species with narrower native niches showed higher rates of niche expansion in the alien ranges. Our results suggest that niche shifts are frequent in plant invasions but evolutionary potential may not be of major importance for such shifts. Niche dynamics rather appear to be driven by changes of the realized niche without adaptive change of the fundamental climatic niche. PMID:26508329

  19. Niche dynamics of alien species do not differ among sexual and apomictic flowering plants.

    PubMed

    Dellinger, Agnes S; Essl, Franz; Hojsgaard, Diego; Kirchheimer, Bernhard; Klatt, Simone; Dawson, Wayne; Pergl, Jan; Pyšek, Petr; van Kleunen, Mark; Weber, Ewald; Winter, Marten; Hörandl, Elvira; Dullinger, Stefan

    2016-02-01

    Biological invasions can be associated with shifts of the species' climatic niches but the incidence of such shifts is under debate. The reproductive system might be a key factor controlling such shifts because it influences a species' evolutionary flexibility. However, the link between reproductive systems and niche dynamics in plant invasions has been little studied so far. We compiled global occurrence data sets of 13 congeneric sexual and apomictic species pairs, and used principal components analysis (PCA) and kernel smoothers to compare changes in climatic niche optima, breadths and unfilling/expansion between native and alien ranges. Niche change metrics were compared between sexual and apomictic species. All 26 species showed changes in niche optima and/or breadth and 14 species significantly expanded their climatic niches. However, we found no effect of the reproductive system on niche dynamics. Instead, species with narrower native niches showed higher rates of niche expansion in the alien ranges. Our results suggest that niche shifts are frequent in plant invasions but evolutionary potential may not be of major importance for such shifts. Niche dynamics rather appear to be driven by changes of the realized niche without adaptive change of the fundamental climatic niche.

  20. A CORBA-based object framework with patient identification translation and dynamic linking. Methods for exchanging patient data.

    PubMed

    Wang, C; Ohe, K

    1999-03-01

    Exchanging and integration of patient data across heterogeneous databases and institutional boundaries offers many problems. We focused on two issues: (1) how to identify identical patients between different systems and institutions while lacking universal patient identifiers; and (2) how to link patient data across heterogeneous databases and institutional boundaries. To solve these problems, we created a patient identification (ID) translation model and a dynamic linking method in the Common Object Request Broker Architecture (CORBA) environment. The algorithm for the patient ID translation is based on patient attribute matching plus computer-based human checking; the method for dynamic linking is temporal mapping. By implementing these methods into computer systems with help of the distributed object computing technology, we built a prototype of a CORBA-based object framework in which the patient ID translation and dynamic linking methods were embedded. Our experiments with a Web-based user interface using the object framework and dynamic linking-through the object framework were successful. These methods are important for exchanging and integrating patient data across heterogeneous databases and institutional boundaries.

  1. Dynamic NMR of Intramolecular Exchange Processes in EDTA Complexes of Sc[superscript 3+], Y[superscript 3+], and La[superscript 3+

    ERIC Educational Resources Information Center

    Ba, Yong; Han, Steven; Ni, Lily; Su, Tony; Garcia, Andres

    2006-01-01

    Dynamic NMR makes use of the effect of chemical exchanges on NMR spectra to study kinetics and thermodynamics. An advanced physical chemistry lab experiment was developed to study the intramolecular exchange processes of EDTA (the disodium salt of ethylenediaminetetraacetic acid) metal complexes. EDTA is an important chelating agent, used in…

  2. Dynamic communities in multichannel data: an application to the foreign exchange market during the 2007-2008 credit crisis.

    PubMed

    Fenn, Daniel J; Porter, Mason A; McDonald, Mark; Williams, Stacy; Johnson, Neil F; Jones, Nick S

    2009-09-01

    We study the cluster dynamics of multichannel (multivariate) time series by representing their correlations as time-dependent networks and investigating the evolution of network communities. We employ a node-centric approach that allows us to track the effects of the community evolution on the functional roles of individual nodes without having to track entire communities. As an example, we consider a foreign exchange market network in which each node represents an exchange rate and each edge represents a time-dependent correlation between the rates. We study the period 2005-2008, which includes the recent credit and liquidity crisis. Using community detection, we find that exchange rates that are strongly attached to their community are persistently grouped with the same set of rates, whereas exchange rates that are important for the transfer of information tend to be positioned on the edges of communities. Our analysis successfully uncovers major trading changes that occurred in the market during the credit crisis. PMID:19791999

  3. Modelling community dynamics based on species-level abundance models from detection/nondetection data

    USGS Publications Warehouse

    Yamaura, Yuichi; Royle, J. Andrew; Kuboi, Kouji; Tada, Tsuneo; Ikeno, Susumu; Makino, Shun'ichi

    2011-01-01

    1. In large-scale field surveys, a binary recording of each species' detection or nondetection has been increasingly adopted for its simplicity and low cost. Because of the importance of abundance in many studies, it is desirable to obtain inferences about abundance at species-, functional group-, and community-levels from such binary data. 2. We developed a novel hierarchical multi-species abundance model based on species-level detection/nondetection data. The model accounts for the existence of undetected species, and variability in abundance and detectability among species. Species-level detection/nondetection is linked to species- level abundance via a detection model that accommodates the expectation that probability of detection (at least one individuals is detected) increases with local abundance of the species. We applied this model to a 9-year dataset composed of the detection/nondetection of forest birds, at a single post-fire site (from 7 to 15 years after fire) in a montane area of central Japan. The model allocated undetected species into one of the predefined functional groups by assuming a prior distribution on individual group membership. 3. The results suggest that 15–20 species were missed in each year, and that species richness of communities and functional groups did not change with post-fire forest succession. Overall abundance of birds and abundance of functional groups tended to increase over time, although only in the winter, while decreases in detectabilities were observed in several species. 4. Synthesis and applications. Understanding and prediction of large-scale biodiversity dynamics partly hinge on how we can use data effectively. Our hierarchical model for detection/nondetection data estimates abundance in space/time at species-, functional group-, and community-levels while accounting for undetected individuals and species. It also permits comparison of multiple communities by many types of abundance-based diversity and similarity

  4. Spin dynamics induced by ultrafast heating with ferromagnetic/antiferromagnetic interfacial exchange in perpendicularly magnetized hard/soft bilayers

    SciTech Connect

    Ma, Q. L. E-mail: mizukami@wpi-aimr.tohoku.ac.jp; Miyazaki, T.; Mizukami, S. E-mail: mizukami@wpi-aimr.tohoku.ac.jp; Iihama, S.; Zhang, X. M.

    2015-11-30

    The laser-induced spin dynamics of FeCo in perpendicularly magnetized L1{sub 0}-MnGa/FeCo bilayers with ferromagnetic and antiferromagnetic interfacial exchange coupling (IEC) are examined using the time-resolved magneto-optical Kerr effect. We found a precessional phase reversal of the FeCo layer as the IEC changes from ferromagnetic to antiferromagnetic. Moreover, a precession-suspension window was observed when the magnetic field was applied in a certain direction for the bilayer with ferromagnetic IEC. Our observations reveal that the spin dynamics modulation is strongly dependent on the IEC type within the Landau-Lifshitz-Gilbert depiction. The IEC dependence of the precessional phase and amplitude suggests the interesting method for magnetization dynamics modulation.

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

    USGS Publications Warehouse

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

    2013-01-01

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

  6. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall,G.E.; Sears, T.J.

    2009-04-03

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. High-resolution spectroscopy, augmented by theoretical and computational methods, is used to investigate the structure and collision dynamics of chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry. Applications and methods development are equally important experimental components of this work.

  7. Dynamics of leaf gas exchange, chlorophyll fluorescence and stem diameter changes during freezing and thawing of Scots pine seedlings.

    PubMed

    Lindfors, Lauri; Hölttä, Teemu; Lintunen, Anna; Porcar-Castell, Albert; Nikinmaa, Eero; Juurola, Eija

    2015-12-01

    Boreal trees experience repeated freeze-thaw cycles annually. While freezing has been extensively studied in trees, the dynamic responses occurring during the freezing and thawing remain poorly understood. At freezing and thawing, rapid changes take place in the water relations of living cells in needles and in stem. While freezing is mostly limited to extracellular spaces, living cells dehydrate, shrink and their osmotic concentration increases. We studied how the freezing-thawing dynamics reflected on leaf gas exchange, chlorophyll fluorescence and xylem and living bark diameter changes of Scots pine (Pinus sylvestris L.) saplings in controlled experiments. Photosynthetic rate quickly declined following ice nucleation and extracellular freezing in xylem and needles, almost parallel to a rapid shrinking of xylem diameter, while that of living bark followed with a slightly longer delay. While xylem and living bark diameters responded well to decreasing temperature and water potential of ice, the relationship was less consistent in the case of increasing temperature. Xylem showed strong temporal swelling at thawing suggesting water movement from bark. After thawing xylem diameter recovered to a pre-freezing level but living bark remained shrunk. We found that freezing affected photosynthesis at multiple levels. The distinct dynamics of photosynthetic rate and stomatal conductance reveals that the decreased photosynthetic rate reflects impaired dark reactions rather than stomatal closure. Freezing also inhibited the capacity of the light reactions to dissipate excess energy as heat, via non-photochemical quenching, whereas photochemical quenching of excitation energy decreased gradually with temperature in agreement with the gas exchange data.

  8. Long-Term Competitive Dynamics of Two Cryptic Rotifer Species: Diapause and Fluctuating Conditions

    PubMed Central

    Gabaldón, Carmen; Carmona, María José; Montero-Pau, Javier; Serra, Manuel

    2015-01-01

    Life-history traits may have an important role in promoting species coexistence. However, the complexity of certain life cycles makes it difficult to draw conclusions about the conditions for coexistence or exclusion based on the study of short-term competitive dynamics. Brachionus plicatilis and B. manjavacasare two cryptic rotifer species co-occurring in many lakes on the Iberian Peninsula. They have a complex life cycle in which cyclical parthenogenesis occurs with diapausing stages being the result of sexual reproduction. B. plicatilis and B. manjavacasare identical in morphology and size, their biotic niches are broadly overlapping, and they have similar competitive abilities. However, the species differ in life-history traits involving sexual reproduction and diapause, and respond differently to salinity and temperature. As in the case of certain other species that are extremely similar in morphology, a fluctuating environment are considered to be important for their coexistence. We studied the long-term competitive dynamics of B. plicatilis and B. manjavacas under different salinity regimes (constant and fluctuating). Moreover, we focused on the dynamics of the diapausing egg bank to explore how the outcome of the entire life cycle of these rotifers can work to mediate stable coexistence. We demonstrated that these species do not coexist under constant-salinity environment, as the outcome of competition is affected by the level of salinity—at low salinity, B. plicatilis excluded B. manjavacas, and the opposite outcome occurred at high salinity. Competitive dynamics under fluctuating salinity showed that the dominance of one species over the other also tended to fluctuate. The duration of co-occurrence of these species was favoured by salinity fluctuation and perhaps by the existence of a diapausing egg bank. Stable coexistence was not found in our system, which suggests that other factors or other salinity fluctuation patterns might act as stabilizing

  9. Long-term competitive dynamics of two cryptic rotifer species: diapause and fluctuating conditions.

    PubMed

    Gabaldón, Carmen; Carmona, María José; Montero-Pau, Javier; Serra, Manuel

    2015-01-01

    Life-history traits may have an important role in promoting species coexistence. However, the complexity of certain life cycles makes it difficult to draw conclusions about the conditions for coexistence or exclusion based on the study of short-term competitive dynamics. Brachionus plicatilis and B. manjavacasare two cryptic rotifer species co-occurring in many lakes on the Iberian Peninsula. They have a complex life cycle in which cyclical parthenogenesis occurs with diapausing stages being the result of sexual reproduction. B. plicatilis and B. manjavacasare identical in morphology and size, their biotic niches are broadly overlapping, and they have similar competitive abilities. However, the species differ in life-history traits involving sexual reproduction and diapause, and respond differently to salinity and temperature. As in the case of certain other species that are extremely similar in morphology, a fluctuating environment are considered to be important for their coexistence. We studied the long-term competitive dynamics of B. plicatilis and B. manjavacas under different salinity regimes (constant and fluctuating). Moreover, we focused on the dynamics of the diapausing egg bank to explore how the outcome of the entire life cycle of these rotifers can work to mediate stable coexistence. We demonstrated that these species do not coexist under constant-salinity environment, as the outcome of competition is affected by the level of salinity-at low salinity, B. plicatilis excluded B. manjavacas, and the opposite outcome occurred at high salinity. Competitive dynamics under fluctuating salinity showed that the dominance of one species over the other also tended to fluctuate. The duration of co-occurrence of these species was favoured by salinity fluctuation and perhaps by the existence of a diapausing egg bank. Stable coexistence was not found in our system, which suggests that other factors or other salinity fluctuation patterns might act as stabilizing

  10. Spatial-temporal population dynamics across species range: from center to margin

    USGS Publications Warehouse

    Guo, Q.; Taper, M.L.; Schoenberger, M.; Brandl, J.

    2005-01-01

    Understanding the boundaries of species' ranges and the variations in population dynamics from the centre to margin of a species' range is critical. This study simulated spatial-temporal patterns of birth and death rates and migration across a species' range in different seasons. Our results demonstrated the importance of dispersal and migration in altering birth and death rates, balancing source and sink habitats, and governing expansion or contraction of species' ranges in changing environments. We also showed that the multiple equilibria of metapopulations across a species' range could be easily broken following climatic changes or physical disturbances either or local or regional. Although we refer to our models as describing the population dynamics across whole species' range, they should also apply to small-scale habitats (metapopulations) in which species abundance follows a humped pattern or to any ecosystem or landscape where strong central-marginal (C-M) environmental gradients exist. Conservation of both central and marginal populations would therefore be equally important considerations in making management decisions.

  11. Spatial-temporal population dynamics across species range: From centre to margin

    USGS Publications Warehouse

    Guo, Q.; Taper, M.; Schoenberger, M.; Brandle, J.

    2005-01-01

    Understanding the boundaries of species' ranges and the variations in population dynamics from the centre to margin of a species' range is critical. This study simulated spatial-temporal patterns of birth and death rates and migration across a species' range in different seasons. Our results demonstrated the importance of dispersal and migration in altering birth and death rates, balancing source and sink habitats, and governing expansion or contraction of species' ranges in changing environments. We also showed that the multiple equilibria of metapopulations across a species' range could be easily broken following climatic changes or physical disturbances either local or regional. Although we refer to our models as describing the population dynamics across whole species' range, they should also apply to small-scale habitats (metapopulations) in which species abundance follows a humped pattern or to any ecosystem or landscape where strong central-marginal (C-M) environmental gradients exist. Conservation of both central and marginal populations would therefore be equally important considerations in making management decisions.

  12. Model of Prey-Predator Dynamics with Reflexive Spatial Behaviour of Species Based on Optimal Migration.

    PubMed

    Sadovsky, Michael; Senashova, Mariya

    2016-04-01

    We consider the model of spatially distributed community consisting of two species with "predator-prey" interaction; each of the species occupies two stations. Transfer of individuals between the stations (migration) is not random, and migration stipulates the maximization of net reproduction of each species. The spatial distribution pattern is provided by discrete stations, and the dynamics runs in discrete time. For each time moment, firstly a redistribution of individuals between the stations is carried out to maximize the net reproduction, and then the reproduction takes place, with the upgraded abundances. Besides, three versions of the basic model are implemented where each species implements reflexive behaviour strategy to determine the optimal migration flow. It was found that reflexivity gives an advantage to the species realizing such strategy, for some specific sets of parameters. Nevertheless, the regular scanning of the parameters area shows that non-reflexive behaviour yields an advantage in the great majority of parameters combinations. PMID:27125654

  13. Species-Specific Dynamic Responses of Gut Bacteria to a Mammalian Glycan

    PubMed Central

    Raghavan, Varsha

    2015-01-01

    ABSTRACT The mammalian intestine provides nutrients to hundreds of bacterial species. Closely related species often harbor homologous nutrient utilization genes and cocolonize the gut, raising questions regarding the strategies mediating their stable coexistence. Here we reveal that related Bacteroides species that can utilize the mammalian glycan chondroitin sulfate (CS) have diverged in the manner in which they temporally regulate orthologous CS utilization genes. Whereas certain Bacteroides species display a transient surge in CS utilization transcripts upon exposure to CS, other species exhibit sustained activation of these genes. Remarkably, species-specific expression dynamics are retained even when the key players governing a particular response are replaced by those from a species with a dissimilar response. Bacteroides species exhibiting distinct expression behaviors in the presence of CS can be cocultured on CS. However, they vary in their responses to CS availability and to the composition of the bacterial community when CS is the sole carbon source. Our results indicate that diversity resulting from regulation of polysaccharide utilization genes may enable the coexistence of gut bacterial species using a given nutrient. IMPORTANCE Genes mediating a specific task are typically conserved in related microbes. For instance, gut Bacteroides species harbor orthologous nutrient breakdown genes and may face competition from one another for these nutrients. How, then, does the gut microbial composition maintain such remarkable stability over long durations? We establish that in the case of genes conferring the ability to utilize the nutrient chondroitin sulfate (CS), microbial species vary in how they temporally regulate these genes and exhibit subtle growth differences on the basis of CS availability and community composition. Similarly to how differential regulation of orthologous genes enables related species to access new environments, gut bacteria may

  14. Isobaric molecular dynamics version of the generalized replica exchange method (gREM): Liquid–vapor equilibrium

    SciTech Connect

    Malolepsza, Edyta; Secor, Maxim; Keyes, Tom

    2015-09-23

    A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed for simulating first-order phase transitions. The properties of the isobaric gREM ensemble are discussed and a study is presented of the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. As a result, phase diagrams, critical parameters, and a law of corresponding states are obtained.

  15. Isobaric Molecular Dynamics Version of the Generalized Replica Exchange Method (gREM): Liquid-Vapor Equilibrium.

    PubMed

    Małolepsza, Edyta; Secor, Maxim; Keyes, Tom

    2015-10-22

    A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed to simulate first-order phase transitions. The properties of the isobaric gREM ensemble are discussed, and a study is presented for the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. Phase diagrams, critical parameters, and a law of corresponding states are obtained. PMID:26398582

  16. Source-sink dynamics and the coexistence of species on a single resource

    USGS Publications Warehouse

    Loreau, M.; DeAngelis, D.L.

    1997-01-01

    We investigate the potential for coexistence of species that compete for a shared resource when the resource occurs in both a source area acting as a refuge and a sink area where it is used by the competing species. Our model shows that the mixing rate between the source and sink resource populations has a dramatic influence on the outcome of competition. When there is a strict sink–source dependence, so that resource renewal in the sink is entirely dependent on the source, only exploitation competition decides which species can survive at a very small mixing rate. Increasing the flow rate basically amounts to increasing the role played by interference competition. If interspecific interference is very small, compared with intraspecific interference, increasing the mixing rate allows coexistence of many species, indeed, unlimited coexistence if the species' resource exploitation efficiencies are similar enough. If interspecific interference is significant and there is a trade-off between the exploitation and interference competitive abilities of two species, it is possible to have one species replacing the other along a gradient of increasing mixing rate, with either coexistence or alternative single-species equilibria at intermediate values of the mixing rate. It is also possible to have one species always outcompeting the other, or alternative single-species stable equilibria at large mixing rates. When the strict sink–source dependence is relaxed by allowing the resource to have a partly independent renewal–loss dynamics in the sink area, the variety of possible outcomes along a gradient of mixing rate is further increased. These outcomes are often strongly sensitive to the parameters of resource dynamics and interspecific interference competition. The implications of these results for biological conservation can be profound; detailed knowledge of interspecific interactions appears to be necessary to determine the effect of any land management that alters

  17. Mesoscopic interactions and species coexistence in evolutionary game dynamics of cyclic competitions.

    PubMed

    Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

    2014-12-15

    Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species.

  18. Fish and Phytoplankton Exhibit Contrasting Temporal Species Abundance Patterns in a Dynamic North Temperate Lake

    PubMed Central

    Hansen, Gretchen J. A.; Carey, Cayelan C.

    2015-01-01

    Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of “core” (common occurrence and high abundance) and “occasional” (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions. PMID:25651399

  19. Fish and phytoplankton exhibit contrasting temporal species abundance patterns in a dynamic north temperate lake.

    PubMed

    Hansen, Gretchen J A; Carey, Cayelan C

    2015-01-01

    Temporal patterns of species abundance, although less well-studied than spatial patterns, provide valuable insight to the processes governing community assembly. We compared temporal abundance distributions of two communities, phytoplankton and fish, in a north temperate lake. We used both 17 years of observed relative abundance data as well as resampled data from Monte Carlo simulations to account for the possible effects of non-detection of rare species. Similar to what has been found in other communities, phytoplankton and fish species that appeared more frequently were generally more abundant than rare species. However, neither community exhibited two distinct groups of "core" (common occurrence and high abundance) and "occasional" (rare occurrence and low abundance) species. Both observed and resampled data show that the phytoplankton community was dominated by occasional species appearing in only one year that exhibited large variation in their abundances, while the fish community was dominated by core species occurring in all 17 years at high abundances. We hypothesize that the life-history traits that enable phytoplankton to persist in highly dynamic environments may result in communities dominated by occasional species capable of reaching high abundances when conditions allow. Conversely, longer turnover times and broad environmental tolerances of fish may result in communities dominated by core species structured primarily by competitive interactions. PMID:25651399

  20. Mesoscopic Interactions and Species Coexistence in Evolutionary Game Dynamics of Cyclic Competitions

    NASA Astrophysics Data System (ADS)

    Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

    2014-12-01

    Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species.

  1. Mesoscopic Interactions and Species Coexistence in Evolutionary Game Dynamics of Cyclic Competitions

    PubMed Central

    Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

    2014-01-01

    Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species. PMID:25501627

  2. Dynamic Models of Learning That Characterize Parent-Child Exchanges Predict Vocabulary Growth

    ERIC Educational Resources Information Center

    Ober, David R.; Beekman, John A.

    2016-01-01

    Cumulative vocabulary models for infants and toddlers were developed from models of learning that predict trajectories associated with low, average, and high vocabulary growth rates (14 to 46 months). It was hypothesized that models derived from rates of learning mirror the type of exchanges provided to infants and toddlers by parents and…

  3. Interactions among K+-Ca2+ Exchange, Sorption of m-Dinitrobenzene, and Smectite Quasicrystal Dynamics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The fate of organic compounds in soils and sediments is influenced by sorption of the compounds on surfaces of soil materials. We investigated the interaction among sorption of an organic compound, cation exchange reactions, and both the size and swelling of smectite quasicrystals. Two reference sme...

  4. High-resolution determination of {sup 147}Pm in urine using dynamic ion-exchange chromatography

    SciTech Connect

    Elchuk, S.; Lucy, C.A.; Burns, K.I.

    1992-10-15

    Ion exchange preconcentration followed by HPLC purification prior to scintillation counting was used to measure the concentration of {sup 147}Pm in urine. the detection limit for this method was found to be 0.1 Bq (3 fg) of {sup 147}Pm in 500 ml of urine.

  5. Inter-species competition-facilitation in stochastic riparian vegetation dynamics.

    PubMed

    Tealdi, Stefano; Camporeale, Carlo; Ridolfi, Luca

    2013-02-01

    Riparian vegetation is a highly dynamic community that lives on river banks and which depends to a great extent on the fluvial hydrology. The stochasticity of the discharge and erosion/deposition processes in fact play a key role in determining the distribution of vegetation along a riparian transect. These abiotic processes interact with biotic competition/facilitation mechanisms, such as plant competition for light, water, and nutrients. In this work, we focus on the dynamics of plants characterized by three components: (1) stochastic forcing due to river discharges, (2) competition for resources, and (3) inter-species facilitation due to the interplay between vegetation and fluid dynamics processes. A minimalist stochastic bio-hydrological model is proposed for the dynamics of the biomass of two vegetation species: one species is assumed dominant and slow-growing, the other is subdominant, but fast-growing. The stochastic model is solved analytically and the probability density function of the plant biomasses is obtained as a function of both the hydrologic and biologic parameters. The impact of the competition/facilitation processes on the distribution of vegetation species along the riparian transect is investigated and remarkable effects are observed. Finally, a good qualitative agreement is found between the model results and field data. PMID:23147231

  6. Tree species effects on decomposition and forest floor dynamics in a common garden.

    PubMed

    Hobbie, Sarah E; Reich, Peter B; Oleksyn, Jacek; Ogdahl, Megan; Zytkowiak, Roma; Hale, Cynthia; Karolewski, Piotr

    2006-09-01

    We studied the effects of tree species on leaf litter decomposition and forest floor dynamics in a common garden experiment of 14 tree species (Abies alba, Acer platanoides, Acer pseudoplatanus, Betula pendula, Carpinus betulus, Fagus sylvatica, Larix decidua, Picea abies, Pinus nigra, Pinus sylvestris, Pseudotsuga menziesii, Quercus robur, Quercus rubra, and Tilia cordata) in southwestern Poland. We used three simultaneous litter bag experiments to tease apart species effects on decomposition via leaf litter chemistry vs. effects on the decomposition environment. Decomposition rates of litter in its plot of origin were negatively correlated with litter lignin and positively correlated with mean annual soil temperature (MAT(soil)) across species. Likewise, decomposition of a common litter type across all plots was positively associated with MAT(soil), and decomposition of litter from all plots in a common plot was negatively related to litter lignin but positively related to litter Ca. Taken together, these results indicate that tree species influenced microbial decomposition primarily via differences in litter lignin (and secondarily, via differences in litter Ca), with high-lignin (and low-Ca) species decomposing most slowly, and by affecting MAT(soil), with warmer plots exhibiting more rapid decomposition. In addition to litter bag experiments, we examined forest floor dynamics in each plot by mass balance, since earthworms were a known component of these forest stands and their access to litter in litter bags was limited. Forest floor removal rates estimated from mass balance were positively related to leaf litter Ca (and unrelated to decay rates obtained using litter bags). Litter Ca, in turn, was positively related to the abundance of earthworms, particularly Lumbricus terrestris. Thus, while species influence microbially mediated decomposition primarily through differences in litter lignin, differences among species in litter Ca are most important in

  7. Temporal latitudinal-gradient dynamics and tropical instability of deep-sea species diversity

    USGS Publications Warehouse

    Yasuhara, Moriaki; Hunt, G.; Cronin, T. M.; Okahashi, H.

    2009-01-01

    A benthic microfaunal record from the equatorial Atlantic Ocean over the past four glacial-interglacial cycles was investigated to understand temporal dynamics of deep-sea latitudinal species diversity gradients (LSDGs). The results demonstrate unexpected instability and high amplitude fluctuations of species diversity in the tropical deep ocean that are correlated with orbital-scale oscillations in global climate: Species diversity is low during glacial and high during interglacial periods. This implies that climate severely influences deep-sea diversity, even at tropical latitudes, and that deep-sea LSDGs, while generally present for the last 36 million years, were weakened or absent during glacial periods. Temporally dynamic LSDGs and unstable tropical diversity require reconsideration of current ecological hypotheses about the generation and maintenance of biodiversity as they apply to the deep sea, and underscore the potential vulnerability and conservation importance of tropical deep-sea ecosystems.

  8. Herbivory affects salt marsh succession dynamics by suppressing the recovery of dominant species.

    PubMed

    Daleo, Pedro; Alberti, Juan; Pascual, Jesús; Canepuccia, Alejandro; Iribarne, Oscar

    2014-05-01

    Disturbance can generate heterogeneous environments and profoundly influence plant diversity by creating patches at different successional stages. Herbivores, in turn, can govern plant succession dynamics by determining the rate of species replacement, ultimately affecting plant community structure. In a south-western Atlantic salt marsh, we experimentally evaluated the role of herbivory in the recovery following disturbance of the plant community and assessed whether herbivory affects the relative importance of sexual and clonal reproduction on these dynamics. Our results show that herbivory strongly affects salt marsh secondary succession by suppressing seedlings and limiting clonal colonization of the dominant marsh grass, allowing subordinate species to dominate disturbed patches. These results demonstrate that herbivores can have an important role in salt marsh community structure and function, and can be a key force during succession dynamics.

  9. Membrane dynamics at the nuclear exchange junction during early mating (one to four hours) in the ciliate Tetrahymena thermophila.

    PubMed

    Cole, Eric S; Giddings, Thomas H; Ozzello, Courtney; Winey, Mark; O'Toole, Eileen; Orias, Judy; Hamilton, Eileen; Guerrier, Sabrice; Ballard, Anna; Aronstein, Tyler

    2015-02-01

    Using serial-section transmission electron microscopy and three-dimensional (3D) electron tomography, we characterized membrane dynamics that accompany the construction of a nuclear exchange junction between mating cells in the ciliate Tetrahymena thermophila. Our methods revealed a number of previously unknown features. (i) Membrane fusion is initiated by the extension of hundreds of 50-nm-diameter protrusions from the plasma membrane. These protrusions extend from both mating cells across the intercellular space to fuse with membrane of the mating partner. (ii) During this process, small membrane-bound vesicles or tubules are shed from the plasma membrane and into the extracellular space within the junction. The resultant vesicle-filled pockets within the extracellular space are referred to as junction lumens. (iii) As junction lumens fill with extracellular microvesicles and swell, the plasma membrane limiting these swellings undergoes another deformation, pinching off vesicle-filled vacuoles into the cytoplasm (reclamation). (iv) These structures (resembling multivesicular bodies) seem to associate with autophagosomes abundant near the exchange junction. We propose a model characterizing the membrane-remodeling events that establish cytoplasmic continuity between mating Tetrahymena cells. We also discuss the possible role of nonvesicular lipid transport in conditioning the exchange junction lipid environment. Finally, we raise the possibility of an intercellular signaling mechanism involving microvesicle shedding and uptake.

  10. Membrane Dynamics at the Nuclear Exchange Junction during Early Mating (One to Four Hours) in the Ciliate Tetrahymena thermophila

    PubMed Central

    Giddings, Thomas H.; Ozzello, Courtney; Winey, Mark; O'Toole, Eileen; Orias, Judy; Hamilton, Eileen; Guerrier, Sabrice; Ballard, Anna; Aronstein, Tyler

    2014-01-01

    Using serial-section transmission electron microscopy and three-dimensional (3D) electron tomography, we characterized membrane dynamics that accompany the construction of a nuclear exchange junction between mating cells in the ciliate Tetrahymena thermophila. Our methods revealed a number of previously unknown features. (i) Membrane fusion is initiated by the extension of hundreds of 50-nm-diameter protrusions from the plasma membrane. These protrusions extend from both mating cells across the intercellular space to fuse with membrane of the mating partner. (ii) During this process, small membrane-bound vesicles or tubules are shed from the plasma membrane and into the extracellular space within the junction. The resultant vesicle-filled pockets within the extracellular space are referred to as junction lumens. (iii) As junction lumens fill with extracellular microvesicles and swell, the plasma membrane limiting these swellings undergoes another deformation, pinching off vesicle-filled vacuoles into the cytoplasm (reclamation). (iv) These structures (resembling multivesicular bodies) seem to associate with autophagosomes abundant near the exchange junction. We propose a model characterizing the membrane-remodeling events that establish cytoplasmic continuity between mating Tetrahymena cells. We also discuss the possible role of nonvesicular lipid transport in conditioning the exchange junction lipid environment. Finally, we raise the possibility of an intercellular signaling mechanism involving microvesicle shedding and uptake. PMID:25107923

  11. Modelling static and dynamic behaviour of proton exchange membrane fuel cells on the basis of electro-chemical description

    NASA Astrophysics Data System (ADS)

    Ceraolo, M.; Miulli, C.; Pozio, A.

    A simplified dynamical model of a fuel cell of the proton exchange membrane (PEM) type, based on physical-chemical knowledge of the phenomena occurring inside the cell has been developed by the authors. The model has been implemented in the MATLAB/SIMULINK environment. Lab tests have been carried out at ENEA's laboratories; and a good agreement has been found between tests and simulations, both in static and dynamic conditions. In a previous study [M. Ceraolo, R. Giglioli, C. Miulli, A. Pozio, in: Proceedings of the 18th International Electric Fuel Cell and Hybrid Vehicle Symposium (EVS18), Berlin, 20-24 October 2001, p. 306] the basic ideas of the model, as well as its experimental validation have been published. In the present paper, the full implementation of the model is reported in detail. Moreover, a procedure for evaluating all the needed numerical parameters is presented.

  12. Species traits predict assemblage dynamics at ephemeral resource patches created by carrion.

    PubMed

    Barton, Philip S; Cunningham, Saul A; Macdonald, Ben C T; McIntyre, Sue; Lindenmayer, David B; Manning, Adrian D

    2013-01-01

    Carrion is an ephemeral and spatially patchy resource that supports a diverse subset of species linked to nutrient cycling and the decomposition process. A number of studies have separately documented changes in the diversity of plants, arthropods and vertebrates at individual carcasses, but there are few studies that have examined how functional traits of different groups of organisms underpin their responses to carrion patches. We used a carrion addition experiment to compare changes in composition and functional traits of insect and plant assemblages at carcasses compared with control sites. We found that significant changes in insect assemblage evenness and heterogeneity was associated with species' dispersal traits, and that plant assemblage responses to subsequent soil nitrogen changes was most apparent among graminoids and exotic species. Beetles at carcasses were twice as large as their counterparts at control sites during the first week of carrion decomposition, and also had higher wing loadings. Plants with high specific leaf area responded faster to the carcass addition, and twice as many species recolonised the centre of carcasses in exotic-dominated grassland compared with carcasses in native-dominated grassland. These results provide an example of how traits of opportunist species enable them to exploit patchy and dynamic resources. This increases our understanding of how carcasses can drive biodiversity dynamics, and has implications for the way carrion might be managed in ecosystems, such as appropriate consideration of spatial and temporal continuity in carrion resources to promote heterogeneity in nutrient cycling and species diversity within landscapes.

  13. Beam dynamics of a double-gap acceleration cell for ion implantation with multiple atomic species

    SciTech Connect

    Wadlinger, E.A.; Lysenko, W.P.; Rusnak, B.; Saadatmand, K.

    1997-02-01

    As a result of our work on ion implantation, we derived equations for the beam dynamics of a two-gap-resonator cavity for accelerating and bunching various ion species of varying energies with the cavity designed for one particular ion species of a given energy (the design-reference particle). A two gap structure is useful at low resonant frequencies where lumped circuit elements (inductors) can be used and the structure kept small. A single gap structure has the advantage that each gap can be independently phased to produce the desired beam dynamics behavior for various ion species and ion energies. However at low frequencies, single gap resonant structures can be large. We find that the two-gap structure, where the phase difference between gaps, for the design reference particle, is fixed at {pi} radians can give acceptable performance provided that the individual two gap cells in the entire accelerator are optimized for the ion species having the largest mass to charge ratio and having the maximum required output energy. Our equations show how to adjust the cavity phases and electric fields to obtain equivalent first-order accelerator performance for various ion species and energies. These equations allow for the effective evaluation of various accelerator concepts and can facilitate the tuning of a linac when changing energies and ion species. Extensive simulations have confirmed the efficacy of our equations. {copyright} {ital 1997 American Institute of Physics.}

  14. Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

    NASA Astrophysics Data System (ADS)

    De Simone, Alfonso; Derreumaux, Philippe

    2010-04-01

    The self-assembly of proteins and peptides into amyloid fibrils is connected to over 40 pathological conditions including neurodegenerative diseases and systemic amyloidosis. Diffusible, low molecular weight protein and peptide oligomers that form in the early steps of aggregation appear to be the harmful cytotoxic species in the molecular etiology of these diseases. So far, the structural characterization of these oligomers has remained elusive owing to their transient and dynamic features. We here address, by means of full atomistic replica exchange molecular dynamics simulations, the energy landscape of heptamers of the amyloidogenic peptide NHVTLSQ from the beta-2 microglobulin protein. The simulations totaling 5 μs show that low molecular weight oligomers in explicit solvent consist of β-barrels in equilibrium with amorphous states and fibril-like assemblies. The results, also accounting for the influence of the pH on the conformational properties, provide a strong evidence of the formation of transient β-barrel assemblies in the early aggregation steps of amyloid-forming systems. Our findings are discussed in terms of oligomers cytotoxicity.

  15. Genotypic variation in foundation species generates network structure that may drive community dynamics and evolution.

    PubMed

    Lau, Matthew K; Keith, Arthur R; Borrett, Stuart R; Shuster, Stephen M; Whitham, Thomas G

    2016-03-01

    Although genetics in a single species is known to impact whole communities, little is known about how genetic variation influences species interaction networks in complex ecosystems. Here, we examine the interactions in a community of arthropod species on replicated genotypes (clones) of a foundation tree species, Populus angustifolia James (narrowleaf cottonwood), in a long-term, common garden experiment using a bipartite "genotype-species" network perspective. We combine this empirical work with a simulation experiment designed to further investigate how variation among individual tree genotypes can impact network structure. Three findings emerged: (1) the empirical "genotype-species network" exhibited significant network structure with modularity being greater than the highly conservative null model; (2) as would be expected given a modular network structure, the empirical network displayed significant positive arthropod co-occurrence patterns; and (3) furthermore, the simulations of "genotype-species" networks displayed variation in network structure, with modularity in particular clearly increasing, as genotypic variation increased. These results support the conclusion that genetic variation in a single species contributes to the structure of ecological interaction networks, which could influence eco-ogical dynamics (e.g., assembly and stability) and evolution in a community context. PMID:27197399

  16. Temperature tolerance and energetics: a dynamic energy budget-based comparison of North Atlantic marine species

    PubMed Central

    Freitas, Vânia; Cardoso, Joana F. M. F.; Lika, Konstadia; Peck, Myron A.; Campos, Joana; Kooijman, Sebastiaan A. L. M.; van der Veer, Henk W.

    2010-01-01

    Temperature tolerance and sensitivity were examined for some North Atlantic marine species and linked to their energetics in terms of species-specific parameters described by dynamic energy budget (DEB) theory. There was a general lack of basic information on temperature tolerance and sensitivity for many species. Available data indicated that the ranges in tolerable temperatures were positively related to optimal growth temperatures. However, no clear relationships with temperature sensitivity were established and no clear differences between pelagic and demersal species were observed. The analysis was complicated by the fact that for pelagic species, experimental data were completely absent and even for well-studied species, information was incomplete and sometimes contradictory. Nevertheless, differences in life-history strategies were clearly reflected in parameter differences between related species. Two approaches were used in the estimation of DEB parameters: one based on the assumption that reserve hardly contributes to physical volume; the other does not make this assumption, but relies on body-size scaling relationships, using parameter values of a generalized animal as pseudo-data. Temperature tolerance and sensitivity seemed to be linked with the energetics of a species. In terms of growth, relatively high temperature optima, sensitivity and/or tolerance were related to lower relative assimilation rates as well as lower maintenance costs. Making the step from limited observations to underlying mechanisms is complicated and extrapolations should be carefully interpreted. Special attention should be devoted to the estimation of parameters using body-size scaling relationships predicted by the DEB theory. PMID:20921053

  17. Genotypic variation in foundation species generates network structure that may drive community dynamics and evolution.

    PubMed

    Lau, Matthew K; Keith, Arthur R; Borrett, Stuart R; Shuster, Stephen M; Whitham, Thomas G

    2016-03-01

    Although genetics in a single species is known to impact whole communities, little is known about how genetic variation influences species interaction networks in complex ecosystems. Here, we examine the interactions in a community of arthropod species on replicated genotypes (clones) of a foundation tree species, Populus angustifolia James (narrowleaf cottonwood), in a long-term, common garden experiment using a bipartite "genotype-species" network perspective. We combine this empirical work with a simulation experiment designed to further investigate how variation among individual tree genotypes can impact network structure. Three findings emerged: (1) the empirical "genotype-species network" exhibited significant network structure with modularity being greater than the highly conservative null model; (2) as would be expected given a modular network structure, the empirical network displayed significant positive arthropod co-occurrence patterns; and (3) furthermore, the simulations of "genotype-species" networks displayed variation in network structure, with modularity in particular clearly increasing, as genotypic variation increased. These results support the conclusion that genetic variation in a single species contributes to the structure of ecological interaction networks, which could influence eco-ogical dynamics (e.g., assembly and stability) and evolution in a community context.

  18. The effects of tropospheric ozone on the species dynamics of calcareous grassland.

    PubMed

    Thwaites, R H; Ashmore, M R; Morton, A J; Pakeman, R J

    2006-11-01

    Although ozone has been shown to reduce the growth of individual species and to alter the composition of simple species mixtures, there is little understanding of its long-term effects on species dynamics and composition in real communities. Intact turfs of calcareous grassland were exposed to four different ozone regimes in open-top chambers over three consecutive summers. Treatments provided a mean seasonal AOT40 ranging from approximately zero to 15 ppm h. Cumulative ozone exposure was a significant factor in compositional change, but only explained 4.6% of the variation. The dominant grass species (Festuca rubra) showed a consistent decline in cover in the high ozone treatment over time and the forb Campanula rotundifolia was lost from all three ozone treatments. The frequency of some species (Galium verum and Plantago lanceolata) increased with ozone exposure. Long-term effects of ozone on species composition in chalk grassland may be a function of both the sensitivity of individual species and the response of the dominant species. PMID:16533548

  19. Placing the Dynamics of Syringe Exchange Programs in the United States

    PubMed Central

    2007-01-01

    Drawing upon the broader health, social, and political geography literature this paper outlines a framework for considering place-based processes through which syringe exchange availability may be understood. It is argued that the geographic distribution of syringe exchange programs (SEPs) in the United States is linked to the social and political conditions of particular localities through three place characteristics: (1) structural constraints; (2) social and spatial distancing of injection drug users; and (3) localized action. Although SEPs remain a controversial issue and face ongoing obstacles from the government, law enforcement and local communities, they continue to operate through the efforts of grassroots organizations and local activists. Action on this issue occurs locally, and the characteristics of place-based factors will affect whether particular areas adopt SEPs. PMID:16797217

  20. Screened exchange dynamical mean-field theory and its relation to density functional theory: SrVO3 and SrTiO3

    NASA Astrophysics Data System (ADS)

    van Roekeghem, Ambroise; Biermann, Silke

    2014-12-01

    We present the first application of a recently proposed electronic-structure scheme to transition metal oxides: screened exchange dynamical mean-field theory includes non-local exchange beyond the local density approximation and dynamical correlations beyond standard dynamical mean-field theory. Our results for the spectral function of SrVO3 are in agreement with the available experimental data, including photoemission spectroscopy and thermodynamics. Finally, the 3d0 compound SrTiO3 serves as a test case to illustrate how the theory reduces to the band structure of standard electronic-structure techniques for weakly correlated compounds.

  1. Dynamic C and N stocks - key factors controlling the C gas exchange of maize in heterogenous peatland

    NASA Astrophysics Data System (ADS)

    Pohl, M.; Hoffmann, M.; Hagemann, U.; Giebels, M.; Albiac Borraz, E.; Sommer, M.; Augustin, J.

    2015-05-01

    The drainage and cultivation of fen peatlands create complex small-scale mosaics of soils with extremely variable soil organic carbon (SOC) stocks and groundwater levels (GWLs). To date, the significance of such sites as sources or sinks for greenhouse gases such as CO2 and CH4 is still unclear, especially if the sites are used for cropland. As individual control factors such as GWL fail to account for this complexity, holistic approaches combining gas fluxes with the underlying processes are required to understand the carbon (C) gas exchange of drained fens. It can be assumed that the stocks of SOC and N located above the variable GWL - defined as dynamic C and N stocks - play a key role in the regulation of the plant- and microbially mediated CO2 fluxes in these soils and, inversely, for CH4. To test this assumption, the present study analysed the C gas exchange (gross primary production - GPP; ecosystem respiration - Reco; net ecosystem exchange - NEE; CH4) of maize using manual chambers for 4 years. The study sites were located near Paulinenaue, Germany, where we selected three soil types representing the full gradient of GWL and SOC stocks (0-1 m) of the landscape: (a) Haplic Arenosol (AR; 8 kg C m-2); (b) Mollic Gleysol (GL; 38 kg C m-2); and (c) Hemic Histosol (HS; 87 kg C m-2). Daily GWL data were used to calculate dynamic SOC (SOCdyn) and N (Ndyn) stocks. Average annual NEE differed considerably among sites, ranging from 47 ± 30 g C m-2 yr-1 in AR to -305 ± 123 g C m-2 yr-1 in GL and -127 ± 212 g C m-2 yr-1 in HS. While static SOC and N stocks showed no significant effect on C fluxes, SOCdyn and Ndyn and their interaction with GWL strongly influenced the C gas exchange, particularly NEE and the GPP : Reco ratio. Moreover, based on nonlinear regression analysis, 86% of NEE variability was explained by GWL and SOCdyn. The observed high relevance of dynamic SOC and N stocks in the aerobic zone for plant and soil gas exchange likely originates from the

  2. Dynamic C and N stocks - key factors controlling the C gas exchange of maize in a heterogenous peatland

    NASA Astrophysics Data System (ADS)

    Pohl, M.; Hoffmann, M.; Hagemann, U.; Giebels, M.; Albiac Borraz, E.; Sommer, M.; Augustin, J.

    2014-11-01

    Drainage and cultivation of fen peatlands creates complex small-scale mosaics of soils with extremely variable soil organic carbon (SOC) stocks and groundwater-level (GWL). To date, it remains unclear if such sites are sources or sinks for greenhouse gases like CO2 and CH4, especially if used for cropland. As individual control factors like GWL fail to account for this complexity, holistic approaches combining gas fluxes with the underlying processes are required to understand the carbon (C) gas exchange of drained fens. It can be assumed that the stocks of SOC and N located above the variable GWL - defined as dynamic C and N stocks - play a key role in the regulation of plant- and microbially mediated C gas fluxes of these soils. To test this assumption, the present study analysed the C gas exchange (gross primary production - GPP, ecosystem respiration - Reco, net ecosystem exchange - NEE, CH4) of maize using manual chambers for four years. The study sites were located near Paulinenaue, Germany. Here we selected three soils, which represent the full gradient in pedogenesis, GWL and SOC stocks (0-1 m) of the fen peatland: (a) Haplic Arenosol (AR; 8 kg C m-2); (b) Mollic Gleysol (GL; 38 kg C m-2); and (c) Hemic Histosol (HS; 87 kg C m-2). Daily GWL data was used to calculate dynamic SOC (SOCdyn) and N (Ndyn) stocks. Average annual NEE differed considerably among sites, ranging from 47 ± 30 g C m-2 a-1 at AR to -305 ± 123 g C m-2 a-1 at GL and -127 ± 212 g C m-2 a-1 at HS. While static SOC and N stocks showed no significant effect on C fluxes, SOCdyn and Ndyn and their interaction with GWL strongly influenced the C gas exchange, particularly NEE and the GPP:Reco ratio. Moreover, based on nonlinear regression analysis, 86% of NEE variability was explained by GWL and SOCdyn. The observed high relevance of dynamic SOC and N stocks in the aerobic zone for plant and soil gas exchange likely originates from the effects of GWL-dependent N availability on C formation and

  3. Interactions among K+-Ca2+ exchange, sorption of m-dinitrobenzene, and smectite quasicrystal dynamics.

    PubMed

    Chatterjee, Ritushree; Laird, David A; Thompson, Michael L

    2008-12-15

    The fate of organic contaminants in soils and sediments is influenced by sorption of the compounds to surfaces of soil materials. We investigated the interaction among sorption of an organic compound, cation exchange reactions, and both the size and swelling of smectite quasicrystals. Two reference smectites that vary in location and amount of layer charge, SPV (a Wyoming bentonite) and SAz-1 were initially Ca- and K-saturated and then equilibrated with mixed 0.01 M KCl and 0.005 M CaCl2 salt solutions both with and without the presence of 200 mg L(-1) m-dinitrobenzene (m-DNB). In general, sorption of m-DNB increased with the amount of K+ in the system for both clays, and the SPV sorbed more m-DNB than the SAz-1. Sorption of m-DNB increased the preference of Ca-SPV for K+ relative to Ca2+ but had little effect on K+-Ca2+ selectivity for K-SPV. Selectivity for K+ relative to Ca2+ was slightly higher for both K-SAz-1 and Ca-SAz-1 in the presence of m-DNB than in its absence. Distinct hysteresis loops were observed for the K+-Ca2+ cation exchange reactions for both clays, and the legacy of having been initially Ca- or K-saturated influenced sorption of m-DNB by SPV but had little effect for SAz-1. Suspension X-ray diffraction was used to measure changes in d-spacing and the relative thickness of smectite quasicrystals during the cation exchange and m-DNB sorption reactions. The results suggest that interactions among cation exchange and organic sorption reactions are controlled byan inherently hysteretic complex feedback process that is regulated by changes in the size and extent of swelling of smectite quasicrystals. PMID:19174877

  4. The roles of competition and habitat in the dynamics of populations and species distributions.

    PubMed

    Yackulic, Charles B; Reid, Janice; Nichols, James D; Hines, James E; Davis, Raymond; Forsman, Eric

    2014-02-01

    The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition's importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading species (Barred Owl, Strix varia) and a resident species (Northern Spotted Owl, Strix occidentalis caurina) in a 1000-km study area over a 22-year period. Past studies of these competitors have focused on the dynamics of one species at a time, hindering efforts to parse out the roles of habitat and competition and to forecast the future of the resident species. In addition, while these studies accounted for the imperfect detection of the focal species, no multi-season analysis of these species has accounted for the imperfect detection of the secondary species, potentially biasing inference. We analyzed survey data using models that combine the general multistate-multi-season occupancy modeling framework with autologistic modeling, allowing us to account for important aspects of our study system. We found that local extinction probability increases for each species when the other is present; however, the effect of the invader on the resident is greater. Although the species prefer different habitats, these habitats are highly correlated at the patch scale, and the impacts of invader on the resident are greatest in patches that would otherwise be optimal. As a consequence, competition leads to a weaker relationship between habitat and Northern Spotted Owl occupancy. Colonization and extinction rates of the invader are closely related to neighborhood occupancy, and over the first half of the study the availability of colonists limited the rate of population growth. Competition is likely to exclude the resident species, both through its immediate effects on local extinction and by indirectly lowering colonization rates as

  5. Vaults are dynamically unconstrained cytoplasmic nanoparticles capable of half vault exchange.

    PubMed

    Yang, Jian; Kickhoefer, Valerie A; Ng, Benny C; Gopal, Ajaykumar; Bentolila, Laurent A; John, Scott; Tolbert, Sarah H; Rome, Leonard H

    2010-12-28

    Vaults are naturally occurring ribonucleoprotein particles with an enormous interior volume, large enough to encapsulate hundreds of proteins. They are highly conserved and are present in nearly all eukaryotic cells ranging from 10(4) to 10(7) particles per cell. Recombinant vaults can be produced in vitro and engineered to allow cell targeting and protein packaging. These nanometer-sized particles have many desirable characteristics that may give them advantages for use as drug delivery vehicles. Using photoactivatable green fluorescent protein (PAGFP) labeled vaults, we demonstrate that the particles rapidly diffuse throughout the cytoplasm following single pixel photoactivation in live cells. Their in vivo movement remained relatively unchanged despite exposure to a variety of cellular stresses, suggesting that vaults are largely unconstrained in the cytoplasm. Fluorescence resonance energy transfer (FRET) was observed from polyethylene glycol (PEG) fused hybrid cells that expressed either CFP or YFP labeled vaults, indicating that vaults can exchange major vault protein (MVP) subunits in vivo. Investigation into the mechanism of this exchange in vitro using recombinant vaults demonstrated that they were capable of rapidly separating at the particle waist and reassembling back into whole vaults, supporting a half vault exchange mechanism. This data suggests a means whereby vaults can functionally interact with their cellular environment and deliver materials packaged within their interior.

  6. Cation Exchange in Dynamic 3D Porous Magnets: Improvement of the Physical Properties.

    PubMed

    Grancha, Thais; Acosta, Alvaro; Cano, Joan; Ferrando-Soria, Jesús; Seoane, Beatriz; Gascon, Jorge; Pasán, Jorge; Armentano, Donatella; Pardo, Emilio

    2015-11-16

    We report two novel three-dimensional porous coordination polymers (PCPs) of formulas Li4{Mn4[Cu2(Me3mpba)2]3}·68H2O (2) and K4{Mn4[Cu2(Me3mpba)2]3}·69H2O (3) obtained-via alkali cation exchange in a single-crystal to single-crystal process-from the earlier reported anionic manganese(II)-copper(II) PCP of formula Na4{Mn4[Cu2(Me3mpba)2]3}·60H2O (1) [Me3mpba(4-) = N,N'-2,4,6-trimethyl-1,3-phenylenebis(oxamate)]. This postsynthetic process succeeds where the direct synthesis in solution from the corresponding building blocks fails and affords significantly more robust PCPs with enhanced magnetic properties [long-range 3D magnetic ordering temperatures for the dehydrated phases (1'-3') of 2.0 (1'), 12.0 (2'), and 20.0 K (3')]. Changes in the adsorptive properties upon postsynthetic exchange suggest that the nature, electrostatic properties, mobility, and location of the cations within the framework are crucial for the enhanced structural stability. Overall, these results further confirm the potential of postsynthetic methods (including cation exchange) to obtain PCPs with novel or enhanced physical properties while maintaining unaltered their open-framework structures. PMID:26492551

  7. Cation Exchange in Dynamic 3D Porous Magnets: Improvement of the Physical Properties.

    PubMed

    Grancha, Thais; Acosta, Alvaro; Cano, Joan; Ferrando-Soria, Jesús; Seoane, Beatriz; Gascon, Jorge; Pasán, Jorge; Armentano, Donatella; Pardo, Emilio

    2015-11-16

    We report two novel three-dimensional porous coordination polymers (PCPs) of formulas Li4{Mn4[Cu2(Me3mpba)2]3}·68H2O (2) and K4{Mn4[Cu2(Me3mpba)2]3}·69H2O (3) obtained-via alkali cation exchange in a single-crystal to single-crystal process-from the earlier reported anionic manganese(II)-copper(II) PCP of formula Na4{Mn4[Cu2(Me3mpba)2]3}·60H2O (1) [Me3mpba(4-) = N,N'-2,4,6-trimethyl-1,3-phenylenebis(oxamate)]. This postsynthetic process succeeds where the direct synthesis in solution from the corresponding building blocks fails and affords significantly more robust PCPs with enhanced magnetic properties [long-range 3D magnetic ordering temperatures for the dehydrated phases (1'-3') of 2.0 (1'), 12.0 (2'), and 20.0 K (3')]. Changes in the adsorptive properties upon postsynthetic exchange suggest that the nature, electrostatic properties, mobility, and location of the cations within the framework are crucial for the enhanced structural stability. Overall, these results further confirm the potential of postsynthetic methods (including cation exchange) to obtain PCPs with novel or enhanced physical properties while maintaining unaltered their open-framework structures.

  8. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall, G.E.

    2011-05-31

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  9. Gas-Phase Molecular Dynamics: High Resolution Spectroscopy and Collision Dynamics of Transient Species

    SciTech Connect

    Hall G. E.; Goncharov, V.

    2012-05-29

    This research is carried out as part of the Gas-Phase Molecular Dynamics program in the Chemistry Department at Brookhaven National Laboratory. Chemical intermediates in the elementary gas-phase reactions involved in combustion chemistry are investigated by high resolution spectroscopic tools. Production, reaction, and energy transfer processes are investigated by transient, double resonance, polarization and saturation spectroscopies, with an emphasis on technique development and connection with theory, as well as specific molecular properties.

  10. 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.

  11. Spatio-temporal dynamics of a three interacting species mathematical model inspired in physics

    NASA Astrophysics Data System (ADS)

    Sánchez-Garduño, Faustino; Breña-Medina, Víctor F.

    2008-02-01

    In this paper we study both, analytically and numerically, the spatio-temporal dynamics of a three interacting species mathematical model. The populations take the form of pollinators, a plant and herbivores; the model consists of three nonlinear reaction-diffusion-advection equations. In view of considering the full model, as a previous step we firstly analyze a mutualistic interaction (pollinator-plant), later on a predator-prey (plant-herbivore) interaction model is studied and finally, we consider the full model. In all cases, the purely temporal dynamics is given; meanwhile for the spatio-temporal dynamics, we use numerical simulations, corresponding to those parameter values for which we obtain interesting temporal dynamics.

  12. Impacts of land cover data selection and trait parameterisation on dynamic modelling of species' range expansion.

    PubMed

    Heikkinen, Risto K; Bocedi, Greta; Kuussaari, Mikko; Heliölä, Janne; Leikola, Niko; Pöyry, Juha; Travis, Justin M J

    2014-01-01

    Dynamic models for range expansion provide a promising tool for assessing species' capacity to respond to climate change by shifting their ranges to new areas. However, these models include a number of uncertainties which may affect how successfully they can be applied to climate change oriented conservation planning. We used RangeShifter, a novel dynamic and individual-based modelling platform, to study two potential sources of such uncertainties: the selection of land cover data and the parameterization of key life-history traits. As an example, we modelled the range expansion dynamics of two butterfly species, one habitat specialist (Maniola jurtina) and one generalist (Issoria lathonia). Our results show that projections of total population size, number of occupied grid cells and the mean maximal latitudinal range shift were all clearly dependent on the choice made between using CORINE land cover data vs. using more detailed grassland data from three alternative national databases. Range expansion was also sensitive to the parameterization of the four considered life-history traits (magnitude and probability of long-distance dispersal events, population growth rate and carrying capacity), with carrying capacity and magnitude of long-distance dispersal showing the strongest effect. Our results highlight the sensitivity of dynamic species population models to the selection of existing land cover data and to uncertainty in the model parameters and indicate that these need to be carefully evaluated before the models are applied to conservation planning. PMID:25265281

  13. Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation.

    PubMed

    Swails, Jason M; York, Darrin M; Roitberg, Adrian E

    2014-03-11

    By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simulations (CpHMD) run in Generalized Born (GB) implicit solvent for long time scales can yield poor pKa predictions as a result of sampling unrealistic conformations. To address this shortcoming, we present a method for performing constant pH molecular dynamics simulations (CpHMD) in explicit solvent using a discrete protonation state model. The method involves standard molecular dynamics (MD) being propagated in explicit solvent followed by protonation state changes being attempted in GB implicit solvent at fixed intervals. Replica exchange along the pH-dimension (pH-REMD) helps to obtain acceptable titration behavior with the proposed method. We analyzed the effects of various parameters and settings on the titration behavior of CpHMD and pH-REMD in explicit solvent, including the size of the simulation unit cell and the length of the relaxation dynamics following protonation state changes. We tested the method with the amino acid model compounds, a small pentapeptide with two titratable sites, and hen egg white lysozyme (HEWL). The proposed method yields superior predicted pKa values for HEWL over hundreds of nanoseconds of simulation relative to corresponding predicted values from simulations run in implicit solvent.

  14. The roles of competition and habitat in the dynamics of populations and species distributions

    USGS Publications Warehouse

    Yackulic, Charles Brandon; Reid, Janice; Nichols, James D.; Hines, James E.; Davis, Raymond; Forsman, Eric

    2014-01-01

    The role of competition in structuring biotic communities at fine spatial scales is well known from detailed process-based studies. Our understanding of competition's importance at broader scales is less resolved and mainly based on static species distribution maps. Here, we bridge this gap by examining the joint occupancy dynamics of an invading (barred owl: Strix varia) and a resident species (Northern spotted owl: Strix occidentalis caurina) in a 1000 km2 study area over a 22 - year period. Past studies of these competitors have focused on the dynamics of one species at a time, hindering efforts to parse out the roles of habitat and competition and to forecast the future of the resident species. In addition, while these studies accounted for the imperfect detection of the focal species, no multiseason analysis of these species has accounted for the imperfect detection of the secondary species, potentially biasing inference. We analyze survey data using models that combine the general multistate-multiseason occupancy modeling framework with autologistic modeling - allowing us to account for important aspects of our study system. We find that local extinction probability increases for each species when the other is present; however, the effect of the invader on the resident is greater. Although the species prefer different habitats, these habitats are highly correlated at the patch scale and the impacts of invader on the resident are greatest in patches that would otherwise be optimal. As a consequence, competition leads to a weaker relationship between habitat and Northern spotted owl occupancy. Colonization and extinction rates of the invader are closely related to neighborhood occupancy, and over the first half of the study the availability of colonists limited the rate of population growth. Competition is likely to exclude the resident species both through its immediate effects on local extinction, and by indirectly lowering colonization rates as Northern

  15. Io's Atmospheric Freeze-out Dynamics in the Presence of a Non-condensable Species

    SciTech Connect

    Moore, Chris H.; Goldstein, David B.; Varghese, Philip L.; Trafton, Laurence M.; Stewart, Benedicte D.; Walker, Andrew C.

    2008-12-31

    One dimensional direct simulation Monte Carlo (DSMC) simulations are used to examine the effect of a trace non-condensable species on the freeze-out dynamics of Io's sulfur dioxide sublimation atmosphere during eclipse and egress. Due to finite ballistic times, essentially no collapse occurs during the first 10 minutes of eclipse at altitudes above {approx}100 km, and hence immediately after ingress auroral emission morphology above 100 km should resemble that of the immediate pre-eclipse state. In the absence of a non-condensable species the sublimation SO2 atmosphere will freeze-out (collapse) during eclipse as the surface temperature drops. However, rapid collapse is prevented by the presence of even a small amount of a perfect non-condensable species due to the formation of a static diffusion layer several mean free paths thick near the surface. The higher the non-condensable mole fraction, the longer the collapse time. The effect of a weakly condensable gas species (non-zero sticking/reaction coefficient) was examined since real gas species may not be perfectly non-condensable at realistic surface temperatures. It is found that even a small sticking coefficient dramatically reduces the effect of the diffusion layer on the dynamics. If the sticking coefficient of the non-condensable exceeds {approx}0.25 the collapse dynamics are effectively the same as if there was no non-condensable present. This sensitivity results because the loss of non-condensable to the surface reduces the effective diffusion layer size and the formation of an effective diffusion layer requires that the layer be stationary which does not occur if the surface is a sink. As the surface temperature increases during egress from eclipse the sublimating SO2 gas pushes the non-condensable diffusion layer up to higher altitudes once it becomes dense enough to be collisional. This vertical species stratification should alter the auroral emissions after egress.

  16. Species Traits Predict Assemblage Dynamics at Ephemeral Resource Patches Created by Carrion

    PubMed Central

    Barton, Philip S.; Cunningham, Saul A.; Macdonald, Ben C. T.; McIntyre, Sue; Lindenmayer, David B.; Manning, Adrian D.

    2013-01-01

    Carrion is an ephemeral and spatially patchy resource that supports a diverse subset of species linked to nutrient cycling and the decomposition process. A number of studies have separately documented changes in the diversity of plants, arthropods and vertebrates at individual carcasses, but there are few studies that have examined how functional traits of different groups of organisms underpin their responses to carrion patches. We used a carrion addition experiment to compare changes in composition and functional traits of insect and plant assemblages at carcasses compared with control sites. We found that significant changes in insect assemblage evenness and heterogeneity was associated with species’ dispersal traits, and that plant assemblage responses to subsequent soil nitrogen changes was most apparent among graminoids and exotic species. Beetles at carcasses were twice as large as their counterparts at control sites during the first week of carrion decomposition, and also had higher wing loadings. Plants with high specific leaf area responded faster to the carcass addition, and twice as many species recolonised the centre of carcasses in exotic-dominated grassland compared with carcasses in native-dominated grassland. These results provide an example of how traits of opportunist species enable them to exploit patchy and dynamic resources. This increases our understanding of how carcasses can drive biodiversity dynamics, and has implications for the way carrion might be managed in ecosystems, such as appropriate consideration of spatial and temporal continuity in carrion resources to promote heterogeneity in nutrient cycling and species diversity within landscapes. PMID:23326549

  17. Spatio-temporal dynamics of species richness in coastal fish communities.

    PubMed Central

    Lekve, Kyrre; Boulinier, Thierry; Stenseth, Nils Chr; Gjøsaeter, Jakob; Fromentin, Jean-Marc; Hines, James E; Nichols, James D

    2002-01-01

    Determining patterns of change in species richness and the processes underlying the dynamics of biodiversity are of key interest within the field of ecology, but few studies have investigated the dynamics of vertebrate communities at a decadal temporal scale. Here, we report findings on the spatio-temporal variability in the richness and composition of fish communities along the Norwegian Skagerrak coast having been surveyed for more than half a century. Using statistical models incorporating non-detection and associated sampling variance, we estimate local species richness and changes in species composition allowing us to compute temporal variability in species richness. We tested whether temporal variation could be related to distance to the open sea and to local levels of pollution. Clear differences in mean species richness and temporal variability are observed between fjords that were and were not exposed to the effects of pollution. Altogether this indicates that the fjord is an appropriate scale for studying changes in coastal fish communities in space and time. The year-to-year rates of local extinction and turnover were found to be smaller than spatial differences in community composition. At the regional level, exposure to the open sea plays a homogenizing role, possibly due to coastal currents and advection. PMID:12350265

  18. Nectar production dynamics and sugar composition in two Mucuna species (Leguminosae, Faboideae) with different specialized pollinators.

    PubMed

    Agostini, Kayna; Sazima, Marlies; Galetto, Leonardo

    2011-11-01

    Nectar is secreted in particular rhythms throughout the lifespan of a flower, which allows determining the nectar production dynamics. This paper compares nectar features in Mucuna japira and Mucuna urens describing: dynamics of nectar production, floral response to nectar removal, resorption, nectar sugar composition, and variation in nectar sugar composition. M. japira inflorescence bears 12-21 yellow flowers, which are in anthesis for 7 days, whereas M. urens inflorescence bears 36-54 greenish flowers, but only 1-3 flowers are in anthesis simultaneously that last one night. Nectar volume and sugar concentration were measured, and the amount of sugar was estimated. Qualitative and quantitative nectar sugar composition was determined. Both species had a constant nectar sugar concentration (ca. 10% for M. japira and ca. 16% for M. urens) and secreted high volumes of nectar (ca. 340 μl per flower for M. japira and 310 μl per flower for M. urens), during 5 days for M. japira and 6 h for M. urens, but after the first removal, i.e., when flower opening mechanism is triggered, nectar production stops immediately. Nectar resorption occurred in both species. Nectar sugar composition showed some similarities between the species. Variation in nectar sugar composition occurred in both species. The Mucuna species are dependent on their pollinators to produce fruits and seeds, and they have different strategies to promote the necessary interaction with birds or bats, especially related to nectar and flower characteristics.

  19. Dynamics of mtDNA introgression during species range expansion: insights from an experimental longitudinal study.

    PubMed

    Mastrantonio, V; Porretta, D; Urbanelli, S; Crasta, G; Nascetti, G

    2016-01-01

    Introgressive hybridization represents one of the long-lasting debated genetic consequences of species range expansion. Mitochondrial DNA has been shown to heavily introgress between interbreeding animal species that meet in new sympatric areas and, often, asymmetric introgression from local to the colonizing populations has been observed. Disentangling among the evolutionary and ecological processes that might shape this pattern remains difficult, because they continuously act across time and space. In this context, long-term studies can be of paramount importance. Here, we investigated the dynamics of mitochondrial introgression between two mosquito species (Aedes mariae and Ae. zammitii ) during a colonization event that started in 1986 after a translocation experiment. By analyzing 1,659 individuals across 25 years, we showed that introgression occurred earlier and at a higher frequency in the introduced than in the local species, showing a pattern of asymmetric introgression. Throughout time, introgression increased slowly in the local species, becoming reciprocal at most sites. The rare opportunity to investigate the pattern of introgression across time during a range expansion along with the characteristics of our study-system allowed us to support a role of demographic dynamics in determining the observed introgression pattern.

  20. Dynamics of mtDNA introgression during species range expansion: insights from an experimental longitudinal study.

    PubMed

    Mastrantonio, V; Porretta, D; Urbanelli, S; Crasta, G; Nascetti, G

    2016-01-01

    Introgressive hybridization represents one of the long-lasting debated genetic consequences of species range expansion. Mitochondrial DNA has been shown to heavily introgress between interbreeding animal species that meet in new sympatric areas and, often, asymmetric introgression from local to the colonizing populations has been observed. Disentangling among the evolutionary and ecological processes that might shape this pattern remains difficult, because they continuously act across time and space. In this context, long-term studies can be of paramount importance. Here, we investigated the dynamics of mitochondrial introgression between two mosquito species (Aedes mariae and Ae. zammitii ) during a colonization event that started in 1986 after a translocation experiment. By analyzing 1,659 individuals across 25 years, we showed that introgression occurred earlier and at a higher frequency in the introduced than in the local species, showing a pattern of asymmetric introgression. Throughout time, introgression increased slowly in the local species, becoming reciprocal at most sites. The rare opportunity to investigate the pattern of introgression across time during a range expansion along with the characteristics of our study-system allowed us to support a role of demographic dynamics in determining the observed introgression pattern. PMID:27460445

  1. Dynamics of mtDNA introgression during species range expansion: insights from an experimental longitudinal study

    PubMed Central

    Mastrantonio, V.; Porretta, D.; Urbanelli, S.; Crasta, G.; Nascetti, G.

    2016-01-01

    Introgressive hybridization represents one of the long-lasting debated genetic consequences of species range expansion. Mitochondrial DNA has been shown to heavily introgress between interbreeding animal species that meet in new sympatric areas and, often, asymmetric introgression from local to the colonizing populations has been observed. Disentangling among the evolutionary and ecological processes that might shape this pattern remains difficult, because they continuously act across time and space. In this context, long-term studies can be of paramount importance. Here, we investigated the dynamics of mitochondrial introgression between two mosquito species (Aedes mariae and Ae. zammitii ) during a colonization event that started in 1986 after a translocation experiment. By analyzing 1,659 individuals across 25 years, we showed that introgression occurred earlier and at a higher frequency in the introduced than in the local species, showing a pattern of asymmetric introgression. Throughout time, introgression increased slowly in the local species, becoming reciprocal at most sites. The rare opportunity to investigate the pattern of introgression across time during a range expansion along with the characteristics of our study-system allowed us to support a role of demographic dynamics in determining the observed introgression pattern. PMID:27460445

  2. Nectar production dynamics and sugar composition in two Mucuna species (Leguminosae, Faboideae) with different specialized pollinators

    NASA Astrophysics Data System (ADS)

    Agostini, Kayna; Sazima, Marlies; Galetto, Leonardo

    2011-11-01

    Nectar is secreted in particular rhythms throughout the lifespan of a flower, which allows determining the nectar production dynamics. This paper compares nectar features in Mucuna japira and Mucuna urens describing: dynamics of nectar production, floral response to nectar removal, resorption, nectar sugar composition, and variation in nectar sugar composition. M. japira inflorescence bears 12-21 yellow flowers, which are in anthesis for 7 days, whereas M. urens inflorescence bears 36-54 greenish flowers, but only 1-3 flowers are in anthesis simultaneously that last one night. Nectar volume and sugar concentration were measured, and the amount of sugar was estimated. Qualitative and quantitative nectar sugar composition was determined. Both species had a constant nectar sugar concentration (ca. 10% for M. japira and ca. 16% for M. urens) and secreted high volumes of nectar (ca. 340 μl per flower for M. japira and 310 μl per flower for M. urens), during 5 days for M. japira and 6 h for M. urens, but after the first removal, i.e., when flower opening mechanism is triggered, nectar production stops immediately. Nectar resorption occurred in both species. Nectar sugar composition showed some similarities between the species. Variation in nectar sugar composition occurred in both species. The Mucuna species are dependent on their pollinators to produce fruits and seeds, and they have different strategies to promote the necessary interaction with birds or bats, especially related to nectar and flower characteristics.

  3. Seasonal dynamics of tick species in an urban park of Rome.

    PubMed

    Di Luca, Marco; Toma, Luciano; Bianchi, Riccardo; Quarchioni, Elisa; Marini, Luca; Mancini, Fabiola; Ciervo, Alessandra; Khoury, Cristina

    2013-12-01

    Regular collections were obtained in the Natural Reserve of the Insugherata of Rome during 2011 in order to obtain the tick species composition and the respective seasonal dynamics of the area. A total of 325 ticks was collected in selected sites by means of drag sampling. Among the identified species, Rhipicephalus turanicus was the most abundant (72.3%), followed by Ixodes ricinus (19.7%), Dermacentor marginatus (6.5%), Haemaphysalis punctata (1.2%), and Rhipicephalus bursa (0.3%). R. turanicus occurred mainly in pastures, showing a mono-modal seasonal activity pattern from spring to early summer. Questing I. ricinus were prevalent in woodland from October to May, and the seasonal trend of specimens showed a weak peak in winter. Although adult D. marginatus exhibited seasonal dynamics similar to I. ricinus, with an activity period from October to April, this species occurred in a different environment (pasture) and with considerably lower densities. Haemaphysalis punctata and R. bursa were rare, with an apparent autumn and autumn-winter seasonal activity, respectively. While the species diversity recorded appears as an unequivocal consequence of the natural state of the park, the remarkable R. turanicus density could be a direct effect of the recent introduction of wild boar, as carriers, from the close Veio Park. The presence of the species, a proven vector of various diseases in humans and domestic animals, is discussed in the light of the possible risk of tick-bite exposure of park workers and visitors.

  4. Spatio-temporal dynamics of species richness in coastal fish communities

    USGS Publications Warehouse

    Lekve, K.; Boulinier, T.; Stenseth, N.C.; Gjøsaeter, J.; Fromentin, J-M.; Hines, J.E.; Nichols, J.D.

    2002-01-01

    Determining patterns of change in species richness and the processes underlying the dynamics of biodiversity are of key interest within the field of ecology, but few studies have investigated the dynamics of vertebrate communities at a decadal temporal scale. Here, we report findings on the spado-temporal variability in the richness and composition of fish communities along the Norwegian Skagerrak coast having been surveyed for more than half a century. Using statistical models incorporating non-detection and associated sampling variance, we estimate local species richness and changes in species composition allowing us to compute temporal variability in species richness. We tested whether temporal variation could be related to distance to the open sea and to local levels of pollution. Clear differences in mean species richness and temporal variability are observed between fjords that were and were not exposed to the effects of pollution. Altogether this indicates that the fjord is an appropriate scale for studying changes in coastal fish communities in space and time. The year-to-year rates of local extinction and turnover were found to be smaller than spatial differences in community composition. At the regional level, exposure to the open sea plays a homogenizing role, possibly due to coastal currents and advection.

  5. Nectar production dynamics and sugar composition in two Mucuna species (Leguminosae, Faboideae) with different specialized pollinators.

    PubMed

    Agostini, Kayna; Sazima, Marlies; Galetto, Leonardo

    2011-11-01

    Nectar is secreted in particular rhythms throughout the lifespan of a flower, which allows determining the nectar production dynamics. This paper compares nectar features in Mucuna japira and Mucuna urens describing: dynamics of nectar production, floral response to nectar removal, resorption, nectar sugar composition, and variation in nectar sugar composition. M. japira inflorescence bears 12-21 yellow flowers, which are in anthesis for 7 days, whereas M. urens inflorescence bears 36-54 greenish flowers, but only 1-3 flowers are in anthesis simultaneously that last one night. Nectar volume and sugar concentration were measured, and the amount of sugar was estimated. Qualitative and quantitative nectar sugar composition was determined. Both species had a constant nectar sugar concentration (ca. 10% for M. japira and ca. 16% for M. urens) and secreted high volumes of nectar (ca. 340 μl per flower for M. japira and 310 μl per flower for M. urens), during 5 days for M. japira and 6 h for M. urens, but after the first removal, i.e., when flower opening mechanism is triggered, nectar production stops immediately. Nectar resorption occurred in both species. Nectar sugar composition showed some similarities between the species. Variation in nectar sugar composition occurred in both species. The Mucuna species are dependent on their pollinators to produce fruits and seeds, and they have different strategies to promote the necessary interaction with birds or bats, especially related to nectar and flower characteristics. PMID:21928066

  6. Dynamics of leaf gas exchange, chlorophyll fluorescence and stem diameter changes during freezing and thawing of Scots pine seedlings.

    PubMed

    Lindfors, Lauri; Hölttä, Teemu; Lintunen, Anna; Porcar-Castell, Albert; Nikinmaa, Eero; Juurola, Eija

    2015-12-01

    Boreal trees experience repeated freeze-thaw cycles annually. While freezing has been extensively studied in trees, the dynamic responses occurring during the freezing and thawing remain poorly understood. At freezing and thawing, rapid changes take place in the water relations of living cells in needles and in stem. While freezing is mostly limited to extracellular spaces, living cells dehydrate, shrink and their osmotic concentration increases. We studied how the freezing-thawing dynamics reflected on leaf gas exchange, chlorophyll fluorescence and xylem and living bark diameter changes of Scots pine (Pinus sylvestris L.) saplings in controlled experiments. Photosynthetic rate quickly declined following ice nucleation and extracellular freezing in xylem and needles, almost parallel to a rapid shrinking of xylem diameter, while that of living bark followed with a slightly longer delay. While xylem and living bark diameters responded well to decreasing temperature and water potential of ice, the relationship was less consistent in the case of increasing temperature. Xylem showed strong temporal swelling at thawing suggesting water movement from bark. After thawing xylem diameter recovered to a pre-freezing level but living bark remained shrunk. We found that freezing affected photosynthesis at multiple levels. The distinct dynamics of photosynthetic rate and stomatal conductance reveals that the decreased photosynthetic rate reflects impaired dark reactions rather than stomatal closure. Freezing also inhibited the capacity of the light reactions to dissipate excess energy as heat, via non-photochemical quenching, whereas photochemical quenching of excitation energy decreased gradually with temperature in agreement with the gas exchange data. PMID:26423334

  7. Magnetization dynamics and damping due to electron-phonon scattering in a ferrimagnetic exchange model

    NASA Astrophysics Data System (ADS)

    Baral, Alexander; Vollmar, Svenja; Schneider, Hans Christian

    2014-07-01

    We present a microscopic calculation of magnetization damping for a magnetic "toy model." The magnetic system consists of itinerant carriers coupled antiferromagnetically to a dispersionless band of localized spins, and the magnetization damping is due to coupling of the itinerant carriers to a phonon bath in the presence of spin-orbit coupling. Using a mean-field approximation for the kinetic exchange model and assuming the spin-orbit coupling to be of the Rashba form, we derive Boltzmann scattering integrals for the distributions and spin conherences in the case of an antiferromagnetic exchange splitting, including a careful analysis of the connection between lifetime broadening and the magnetic gap. For incoherent scattering of itinerant carriers with the phonon bath, i.e., the Elliott-Yafet mechanism, we extract dephasing and magnetization times T1 and T2 from initial conditions corresponding to a tilt of the magnetization vector and draw a comparison to phenomenological equations such as the Landau-Lifshitz (LL) or the Gilbert damping. We also analyze magnetization precession and damping for this system including an anisotropy field and find a carrier mediated dephasing of the localized spin via the mean-field coupling.

  8. Free energies and mechanisms of water exchange around Uranyl from first principles molecular dynamics

    SciTech Connect

    Atta-Fynn, Raymond; Bylaska, Eric J.; De Jong, Wibe A.

    2012-02-01

    From density functional theory (DFT) based ab initio (Car-Parrinello) metadynamics, we compute the activation energies and mechanisms of water exchange between the first and second hydration shells of aqueous Uranyl (UO{sub 2}{sup 2+}) using the primary hydration number of U as the reaction coordinate. The free energy and activation barrier of the water dissociation reaction [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) {yields} [UO{sub 2}(OH{sub 2})4]{sup 2+}(aq) + H{sub 2}O are 0.7 kcal and 4.7 kcal/mol respectively. The free energy is in good agreement with previous theoretical (-2.7 to +1.2 kcal/mol) and experimental (0.5 to 2.2 kcal/mol) data. The associative reaction [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) + H{sub 2}O {yields} [UO{sub 2}(OH{sub 2})6]{sup 2+}(aq) is short-lived with a free energy and activation barrier of +7.9 kcal/mol and +8.9 kca/mol respectively; it is therefore classified as associative-interchange. On the basis of the free energy differences and activation barriers, we predict that the dominant exchange mechanism between [UO{sub 2}(OH{sub 2}){sub 5}]{sup 2+}(aq) and bulk water is dissociative.

  9. Dynamics of the fully stripped ion-hydrogen atom charge exchange process in dense quantum plasmas

    SciTech Connect

    Zhang, Ling-yu; Wan, Jiang-feng; Zhao, Xiao-ying; Xiao, Guo-qing; Duan, Wen-shan; Qi, Xin; Yang, Lei

    2014-09-15

    The plasma screening effects of dense quantum plasmas on charge exchange processes of a fully stripped ion colliding with a hydrogen atom are studied by the classical trajectory Monte Carlo method. The inter-particle interactions are described by the exponential cosine-screened Coulomb potentials. It is found that in weak screening conditions, cross sections increase with the increase of the ionic charge Z. However, in strong screening conditions, the dependence of cross sections on the ionic charge is related to the incident particle energy. At high energies, cross sections show a linear increase with the increase of Z, whereas at low energies, cross sections for Z≥4 become approximately the same. The He{sup 2+} and C{sup 6+} impacting charge exchange cross sections in dense quantum plasmas are also compared with those in weakly coupled plasmas. The interactions are described by the static screened Coulomb potential. It is found that for both He{sup 2+} and C{sup 6+}, the oscillatory screening effects of dense quantum plasmas are almost negligible in weak screening conditions. However, in strong screening conditions, the oscillatory screening effects enhance the screening effects of dense quantum plasmas, and the enhancement becomes more and more significant with the increase of the screening parameter and the ionic charge.

  10. Gas-dynamics characteristics of wave energy exchanger as high-temperature preheater-compressor

    SciTech Connect

    Zubatov, N.

    1983-12-01

    In the magnetohydrodynamic (MHD) energy conversion and high-temperature steel production technological processes the air preheater is an essential component. It preheats the air used in fuel combustion, so that the flame temperature can reach the high levels required by the process. Many studies have indicated that air preheat temperature significantly affects MHD plant efficiency and blast-furnace performance. Combustion air preheating can be accomplished by either of two methods. One method (MHD power plant) utilizes the heat energy of the MHD generator exhaust gas directly. In this case, the preheater, classified as directly-fired, is located in the MHD generator exhaust gas stream as part of the bottoming plant. The alternate method of preheating the combustion air (blast-furnace systems) utilizes a separate heat source and fires the preheater with a clean fuel. This type of preheater is classified as indirectly-fired. The regenerative heat exchangers are used for both methods to achieve the high air preheat temperature required for combustion. Such heat exchangers operate on the principle of transferring heat through a separating medium that is heated for a time by a hot fluid, then cooled by a fluid of lower temperature. The preheater system requires several regenerators, arranged in parallel and with switchover valves, in order to deliver a continuous flow of preheated air.

  11. Price dynamics and market power in an agent-based power exchange

    NASA Astrophysics Data System (ADS)

    Cincotti, Silvano; Guerci, Eric; Raberto, Marco

    2005-05-01

    This paper presents an agent-based model of a power exchange. Supply of electric power is provided by competing generating companies, whereas demand is assumed to be inelastic with respect to price and is constant over time. The transmission network topology is assumed to be a fully connected graph and no transmission constraints are taken into account. The price formation process follows a common scheme for real power exchanges: a clearing house mechanism with uniform price, i.e., with price set equal across all matched buyer-seller pairs. A single class of generating companies is considered, characterized by linear cost function for each technology. Generating companies compete for the sale of electricity through repeated rounds of the uniform auction and determine their supply functions according to production costs. However, an individual reinforcement learning algorithm characterizes generating companies behaviors in order to attain the expected maximum possible profit in each auction round. The paper investigates how the market competitive equilibrium is affected by market microstructure and production costs.

  12. Spatial, temporal, and environmental dynamics of a multi-species epinephelid spawning aggregation in Pohnpei, Micronesia

    NASA Astrophysics Data System (ADS)

    Rhodes, K. L.; Nemeth, R. S.; Kadison, E.; Joseph, E.

    2014-09-01

    Long-term and short-term underwater visual censuses using SCUBA, technical Nitrox, and closed circuit rebreathers (CCR) were carried out in Pohnpei, Micronesia, to define spatial and temporal dynamics within a semi-protected multi-species epinephelid (fish) spawning aggregation (FSA) of brown-marbled grouper, Epinephelus fuscoguttatus, camouflage grouper, Epinephelus polyphekadion, and squaretail coralgrouper, Plectropomus areolatus. Results identified species-specific patterns of habitat use, abundance, residency, and dispersal of FSAs. Fish spawning aggregations formed and dispersed monthly within a 21-160-d period after winter solstice within adjacent yet distinct outer reef habitats. The reproductive season coincided with periods of seasonally low sub-surface seawater temperature. Peaks in density varied among species both within the calendar year and relative to the winter solstice. Significant long-term declines in FSA density were observed for all three species, suggesting population-level fishery-induced impacts, similar to those previously reported for E. polyphekadion. Differences in density estimates were also observed between dive gear, with a threefold difference in densities measured by CCR for E. polyphekadion versus SCUBA that suggest a disturbance effect from exhaled SCUBA bubbles for this species. CCR also allowed surveys to be conducted over a larger area in a single dive, thereby improving the potential to gauge actual abundance and density within FSAs. Based on these findings, a combination of long-term and intensive short-term monitoring strategies is recommended to fully characterize trends in seasonal abundance and habitat use for aggregating species at single or multi-species FSA sites. Inherent variations in the timing and distribution of species within FSA make fine-scale temporal management protocols less effective than blanket protective coverage of these species at (e.g., marine protected areas covering FSAs and adjacent migratory

  13. Population dynamics of Scirtothrips dorsalis (Thysanoptera: Thripidae) and other thrips species on two ornamental host plant species in Southern Florida.

    PubMed

    Mannion, Catharine M; Derksen, Andrew I; Seal, Dakshina R; Osborne, Lance S; Martin, Cliff G

    2014-08-01

    Since its 2005 introduction into the United States, chilli thrips, Scirtothrips dorsalis Hood (Thysanoptera: Thripidae), has become a problematic pest of agronomic, vegetable, fruit, and ornamental plants. Knowledge of its population dynamics may help managers better monitor and control S. dorsalis. Population estimates were recorded for S. dorsalis and other thrips species on Knock-Out rose (Rosa 'Radrazz') and green buttonwood (Conocarpus erectus L.) from July 2007 to September 2008 in two field plots (one per plant species) in Homestead, FL. Yellow sticky card traps and samples of terminals, flowers, buds, and leaves were collected. S. dorsalis accounted for 95% of all thrips individuals collected from plants and 84% from traps with the remainder including at least 18 other thrips species. More thrips were caught on or flying near rose plants (47,438) than on or near buttonwoods (5,898), and on-plant densities of S. dorsalis appeared higher for rose than for buttonwood. Compared with rose leaves, rose buds, terminals, and flowers each had higher numbers of S. dorsalis, and buds and terminals had higher densities. On each host plant species, S. dorsalis density fluctuated over time with peaks in the late spring, summer, and fall, but populations were consistently low in the late winter and early spring. On roses, increased plant damage ratings correlated with reduced numbers of flowers and buds, reduced mean flower areas, and increased on-plant number and density of S. dorsalis. There were positive correlations over time between S. dorsalis density and plant damage rating for rose flowers (R = 0.78; P = 0.0003) and for buttonwood terminals (R = 0.90; P = 0.0001). Yellow sticky card traps were effective for monitoring S. dorsalis and may be especially useful and economically justified for the most susceptible hosts, but they also work well for less susceptible hosts. A good S. dorsalis scouting program should hence consider trap catches and symptoms such as leaf

  14. Beam dynamics simulations of the transverse-to-longitudinal emittance exchange proof-of-principle experiment at the Argonne Wakefield Accelerator

    SciTech Connect

    Rihaoui, M.; Gai, W.; Kim, K.-J.; Power, J. G.; Piot, P.; Sun, Y.-E.

    2009-01-22

    Transverse-to-longitudinal emittance exchange has promising applications in various advanced acceleration and light source concepts. A proof-of-principle experiment to demonstrate this phase space manipulation method is currently being planned at the Argonne Wakefield Accelerator. The experiment focuses on exchanging a low longitudinal emittance with a high transverse horizontal emittance and also incorporates room for possible parametric studies e.g. using an incoming flat beam with tunable horizontal emittance. In this paper, we present realistic start-to-end beam dynamics simulation of the scheme, explore the limitations of this phase space exchange.

  15. Beam dynamics simulations of the transverse-to-longitudinal emittance exchange proof-of-principle experiment at the Argonne Wakefield Accelerator.

    SciTech Connect

    Gao, F.; Gai, W.; Power, J. G.; Kim, K. J.; Sun, Y. E.; Piot, P.; Rihaoui, M.; High Energy Physics; Northern Illinois Univ.; FNAL

    2009-01-01

    Transverse-to-longitudinal emittance exchange has promising applications in various advanced acceleration and light source concepts. A proof-of-principle experiment to demonstrate this phase space manipulation method is currently being planned at the Argonne Wakefield Accelerator. The experiment focuses on exchanging a low longitudinal emittance with a high transverse horizontal emittance and also incorporates room for possible parametric studies e.g. using an incoming flat beam with tunable horizontal emittance. In this paper, we present realistic start-to-end beam dynamics simulation of the scheme, explore the limitations of this phase space exchange.

  16. Beam dynamics simulations of the transverse-to-longitudinal emittance exchange proof-of-principle experiment at the Argonne Wakefield Accelerator

    SciTech Connect

    Rihaoui, M.; Gai, W.; Kim, K.J.; Piot, Philippe; Power, John Gorham; Sun, Y.E.; /Fermilab

    2009-01-01

    Transverse-to-longitudinal emittance exchange has promising applications in various advanced acceleration and light source concepts. A proof-of-principle experiment to demonstrate this phase space manipulation method is currently being planned at the Argonne Wakefield Accelerator. The experiment focuses on exchanging a low longitudinal emittance with a high transverse horizontal emittance and also incorporates room for possible parametric studies e.g. using an incoming flat beam with tunable horizontal emittance. In this paper, we present realistic start-to-end beam dynamics simulation of the scheme, explore the limitations of this phase space exchange.

  17. Application of the electron nuclear dynamics method to hydrogen abstraction and exchange reactions of hydrogen + HOD and deuterium + ammonium ion

    NASA Astrophysics Data System (ADS)

    Coutinho Neto, Mauricio Domingues

    2001-07-01

    The field of quantum molecular dynamics have flourished in the last 20 years. Methods that propose the solution of the time dependent Schrodinger equation for a molecular reactive process abound in the literature. However the majority of these methods focus on solving the nuclear Schrodinger equation subject to a known electronic potential. The electron nuclear dynamics (END) method proposes a framework of a hierarchy of approximations to the Schrodinger equation based on the time dependent variational Principle (TDVP). A general approach is sought to solve the electronic and nuclear problem simultaneously without making use of the Born-Oppenheimer approximation. The purpose of this work is to apply the minimal END to areas where its unique qualities can give new insight into the relevant dynamics of a chemical or physical process. Minimal END is a method for direct non-adiabatic dynamics. It describes the electrons with a family of complex determinantal wave-functions in terms of non-orthogonal spin orbitals and treats the nuclei as classical particles. In the first two studies, we apply the END method to hydrogen abstraction and exchange reactions at hyper-thermal collision energies. We investigate the D2+ NH+3 reaction at collision energies ranging from 6 to 16 eV and the H + HOD reaction at a collision energy of 1.575 eV. Collision energies refer to center of mass energies. Emphasis is put on the details of the abstraction and exchange reaction mechanisms for ground state reactants. In a final application we use minimal END to study the interaction of a strong laser field with the diatomic molecules HF and LiH. Effects of the polarization of the electronic potential on the dynamics are investigated. Emphasis is also placed on the development of a general method for interpreting the final time dependent wave-function of the product fragments. The purpose is to analyze the final state wave-function in terms of charge transfer channels as well as individual

  18. 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.

  19. Dynamics of host plant use and species diversity in Polygonia butterflies (Nymphalidae).

    PubMed

    Weingartner, E; Wahlberg, N; Nylin, S

    2006-03-01

    The ability of insects to utilize different host plants has been suggested to be a dynamic and transient phase. During or after this phase, species can shift to novel host plants or respecialize on ancestral ones. Expanding the range of host plants might also be a factor leading to higher levels of net speciation rates. In this paper, we have studied the possible importance of host plant range for diversification in the genus Polygonia (Nymphalidae, Nymphalini). We have compared species richness between sistergroups in order to find out if there are any differences in number of species between clades including species that utilize only the ancestral host plants ('urticalean rosids') and their sisterclades with a broader (or in some cases potentially broader) host plant repertoire. Four comparisons could be made, and although these are not all phylogenetically or statistically independent, all showed clades including butterfly species using other or additional host plants than the urticalean rosids to be more species-rich than their sisterclade restricted to the ancestral host plants. These results are consistent with the theory that expansions in host plant range are involved in the process of diversification in butterflies and other phytophagous insects, in line with the general theory that plasticity may drive speciation.

  20. Density dynamics of diverse Spiroplasma strains naturally infecting different species of Drosophila

    PubMed Central

    Haselkorn, Tamara S; Watts, Thomas D; Markow, Therese A

    2013-01-01

    Facultative heritable bacterial endosymbionts can have dramatic effects on their hosts, ranging from mutualistic to parasitic. Within-host bacterial endosymbiont density plays a critical role in maintenance of a symbiotic relationship, as it can affect levels of vertical transmission and expression of phenotypic effects, both of which influence the infection prevalence in host populations. Species of genus Drosophila are infected with Spiroplasma, whose characterized phenotypic effects range from that of a male-killing reproductive parasite to beneficial defensive endosymbiont. For many strains of Spiroplasma infecting at least 17 species of Drosophila, however, the phenotypic effects are obscure. The infection prevalence of these Spiroplasma vary within and among Drosophila species, and little is known about the within-host density dynamics of these diverse strains. To characterize the patterns of Spiroplasma density variation among Drosophila we used quantitative PCR to assess bacterial titer at various life stages of three species of Drosophila naturally-infected with two different types of Spiroplasma. For naturally infected Drosophila species we found that non-male-killing infections had consistently lower densities than the male-killing infection. The patterns of Spiroplasma titer change during aging varied among Drosophila species infected with different Spiroplasma strains. Bacterial density varied within and among populations of Drosophila, with individuals from the population with the highest prevalence of infection having the highest density. This density variation underscores the complex interaction of Spiroplasma strain and host genetic background in determining endosymbiont density. PMID:23846301

  1. Weak coordination among petiole, leaf, vein, and gas-exchange traits across 41 Australian angiosperm species and its possible implications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background and Aims Close coordination between leaf gas exchange and maximal hydraulic supply has been reported across diverse plant life-forms. However, recent reports suggest that this relationship may become weak or break down completely within the angiosperms. Methods To examine this possi...

  2. Floral scent of brazilian Passiflora: five species analised by dynamic headspace.

    PubMed

    Montero, Daniel A V; Marques, Marcia Ortiz M; Meletti, Laura M M; Kampen, Maria H VAN; Polozzi, Sandra C

    2016-09-01

    This study describes for the first time the chemical composition and olfactive description of floral scent from Brazilian Passiflora (Passiflora edulis Sim, Passiflora alata Curtis, Passiflora cincinnata Mast., Passiflora coccinea Aubl. and Passiflora quadrangularis L.). Five species were grown in greenhouse at the Agronomic Institute (IAC), São Paulo, Brazil. Volatile compounds were collected using dynamic headspace. Analyses of scent composition were performed by gas chromatograph coupled to mass spectrometer. Identification of chemical constituents was conducted through of retention index followed by comparative analysis of mass spectra with specialized databases. The olfactive descriptions of floral scent from each species was evaluated for a professional perfumer. High interspecific diversity was found between chemical compositions of floral scent within Passiflora and different bouquets were observed amount the studied species. Mayor constituents were linalool (P. alata), geraniol (P. quadrangularis), 1,4-dimethoxybenzene (P. edulis), benzaldehyde (P. cincinnata) and 2-methyl-3-pentanone (P. coccinea). PMID:27598839

  3. The tropics: cradle, museum or casino? A dynamic null model for latitudinal gradients of species diversity.

    PubMed

    Arita, Héctor T; Vázquez-Domínguez, Ella

    2008-07-01

    Several ecological and evolutionary hypotheses have been proposed to explain the latitudinal diversity gradient (LDG), but a general model for this conspicuous pattern remains elusive. Mid-domain effect (MDE) models generate gradients of species diversity by randomly placing the geographic ranges of species in one- or two-dimensional spaces, thus excluding both evolutionary processes and the effect of contemporary climate. Traditional MDE models are statistical and static because they determine the size of ranges either randomly or based on empirical frequency distributions. Here we present a simple dynamic null model for the LDG that simulates stochastic processes of range shifts, extinction and speciation. The model predicts higher species diversity and higher extinction and speciation rates in the tropics, and a strong influence of range movements in shaping the LDG. These null expectations should be taken into consideration in studies aimed at understanding the many factors that generate latitudinal diversity gradients.

  4. Species richness patterns and water-energy dynamics in the drylands of Northwest China.

    PubMed

    Li, Liping; Wang, Zhiheng; Zerbe, Stefan; Abdusalih, Nurbay; Tang, Zhiyao; Ma, Ming; Yin, Linke; Mohammat, Anwar; Han, Wenxuan; Fang, Jingyun

    2013-01-01

    Dryland ecosystems are highly vulnerable to climatic and land-use changes, while the mechanisms underlying patterns of dryland species richness are still elusive. With distributions of 3637 native vascular plants, 154 mammals, and 425 birds in Xinjiang, China, we tested the water-energy dynamics hypothesis for species richness patterns in Central Asian drylands. Our results supported the water-energy dynamics hypothesis. We found that species richness of all three groups was a hump-shaped function of energy availability, but a linear function of water availability. We further found that water availability had stronger effects on plant richness, but weaker effects on vertebrate richness than energy availability. We conducted piecewise linear regressions to detect the breakpoints in the relationship between species richness and potential evapotranspiration which divided Xinjiang into low and high energy regions. The concordance between mammal and plant richness was stronger in high than in low energy regions, which was opposite to that between birds and plants. Plant richness had stronger effects than climate on mammal richness regardless of energy levels, but on bird richness only in high energy regions. The changes in the concordance between vertebrate and plant richness along the climatic gradient suggest that cautions are needed when using concordance between taxa in conservation planning.

  5. Species Richness Patterns and Water-Energy Dynamics in the Drylands of Northwest China

    PubMed Central

    Zerbe, Stefan; Abdusalih, Nurbay; Tang, Zhiyao; Ma, Ming; Yin, Linke; Mohammat, Anwar; Han, Wenxuan; Fang, Jingyun

    2013-01-01

    Dryland ecosystems are highly vulnerable to climatic and land-use changes, while the mechanisms underlying patterns of dryland species richness are still elusive. With distributions of 3637 native vascular plants, 154 mammals, and 425 birds in Xinjiang, China, we tested the water-energy dynamics hypothesis for species richness patterns in Central Asian drylands. Our results supported the water-energy dynamics hypothesis. We found that species richness of all three groups was a hump-shaped function of energy availability, but a linear function of water availability. We further found that water availability had stronger effects on plant richness, but weaker effects on vertebrate richness than energy availability. We conducted piecewise linear regressions to detect the breakpoints in the relationship between species richness and potential evapotranspiration which divided Xinjiang into low and high energy regions. The concordance between mammal and plant richness was stronger in high than in low energy regions, which was opposite to that between birds and plants. Plant richness had stronger effects than climate on mammal richness regardless of energy levels, but on bird richness only in high energy regions. The changes in the concordance between vertebrate and plant richness along the climatic gradient suggest that cautions are needed when using concordance between taxa in conservation planning. PMID:23840472

  6. Structural dynamics of soluble chloride intracellular channel protein CLIC1 examined by amide hydrogen-deuterium exchange mass spectrometry.

    PubMed

    Stoychev, Stoyan H; Nathaniel, Christos; Fanucchi, Sylvia; Brock, Melissa; Li, Sheng; Asmus, Kyle; Woods, Virgil L; Dirr, Heini W

    2009-09-01

    Chloride intracellular channel protein 1 (CLIC1) functions as an anion channel in plasma and nuclear membranes when its soluble monomeric form converts to an integral-membrane form. The transmembrane region of CLIC1 is located in its thioredoxin-like domain 1, but the mechanism whereby the protein converts to its membrane conformation has yet to be determined. Since channel formation in membranes is enhanced at low pH (5 to 5.5), a condition that is found at the surface of membranes, the structural dynamics of soluble CLIC1 was studied at pH 7 and at pH 5.5 in the absence of membranes by amide hydrogen-deuterium exchange mass spectrometry (DXMS). Rapid hydrogen exchange data indicate that CLIC1 displays a similar core structure at these pH values. Domain 1 is less stable than the all-helical domain 2, and, while the structure of domain 1 remains intact, its conformational flexibility is further increased in an acidic environment (pH 5.5). In the absence of membrane, an acidic environment appears to prime the solution structure of CLIC1 by destabilizing domain 1 in order to lower the activation energy barrier for its conversion to the membrane-insertion conformation. The significantly enhanced H/D-exchange rates at pH 5.5 displayed by two segments (peptides 11-31 and 68-82) could be due to the protonation of acidic residues in salt bridges. One of these segments (peptide 11-31) includes part of the transmembrane region which, in the solution structure, consists of helix alpha1. This helix is intrinsically stable and is most likely retained in the membrane conformation. Strand beta2, another element of the transmembrane region, displays a propensity to form a helical structure and has putative N- and C-capping motifs, suggesting that it too most likely forms a helix in a lipid bilayer.

  7. Long-term dynamics of production, respiration, and net CO2 exchange in two sagebrush-steppe ecosystems

    USGS Publications Warehouse

    Gilmanov, T.G.; Svejcar, T.J.; Johnson, D.A.; Angell, R.F.; Saliendra, Nicanor Z.; Wylie, B.K.

    2006-01-01

    We present a synthesis of long-term measurements of CO2 exchange in 2 US Intermountain West sagebrush-steppe ecosystems. The locations near Burns, Oregon (1995-2001), and Dubois, Idaho (1996-2001), are part of the AgriFlux Network of the Agricultural Research Service, United States Department of Agriculture. Measurements of net ecosystem CO2 exchange (F c) during the growing season were continuously recorded at flux towers using the Bowen ratio-energy balance technique. Data were partitioned into gross primary productivity (Pg) and ecosystem respiration (Re) using the light-response function method. Wintertime fluxes were measured during 1999/2000 and 2000/2001 and used to model fluxes in other winters. Comparison of daytime respiration derived from light-response analysis with nighttime tower measurements showed close correlation, with daytime respiration being on the average higher than nighttime respiration. Maxima of Pg and Re at Burns were both 20 g CO2?? m-2??d-1 in 1998. Maxima of Pg and R e at Dubois were 37 and 35 g CO2??m -2??d-1, respectively, in 1997. Mean annual gross primary production at Burns was 1 111 (range 475-1 715) g CO2?? m-2??y-1 about 30% lower than that at Dubois (1 602, range 963-2 162 g CO2??m-2??y-1). Across the years, both ecosystems were net sinks for atmospheric CO2 with a mean net ecosystem CO2 exchange of 82 g CO2?? m-2??y-1 at Burns and 253 g CO2?? m-2??y-1 at Dubois, but on a yearly basis either site could be a C sink or source, mostly depending on precipitation timing and amount. Total annual precipitation is not a good predictor of carbon sequestration across sites. Our results suggest that Fc should be partitioned into Pg and Re components to allow prediction of seasonal and yearly dynamics of CO2 fluxes.

  8. Neutral dynamics with environmental noise: Age-size statistics and species lifetimes

    NASA Astrophysics Data System (ADS)

    Kessler, David; Suweis, Samir; Formentin, Marco; Shnerb, Nadav M.

    2015-08-01

    Neutral dynamics, where taxa are assumed to be demographically equivalent and their abundance is governed solely by the stochasticity of the underlying birth-death process, has proved itself as an important minimal model that accounts for many empirical datasets in genetics and ecology. However, the restriction of the model to demographic [O (√{N }) ] noise yields relatively slow dynamics that appears to be in conflict with both short-term and long-term characteristics of the observed systems. Here we analyze two of these problems—age-size relationships and species extinction time—in the framework of a neutral theory with both demographic and environmental stochasticity. It turns out that environmentally induced variations of the demographic rates control the long-term dynamics and modify dramatically the predictions of the neutral theory with demographic noise only, yielding much better agreement with empirical data. We consider two prototypes of "zero mean" environmental noise, one which is balanced with regard to the arithmetic abundance, another balanced in the logarithmic (fitness) space, study their species lifetime statistics, and discuss their relevance to realistic models of community dynamics.

  9. Mathematical Models of Quasi-Species Theory and Exact Results for the Dynamics.

    PubMed

    Saakian, David B; Hu, Chin-Kun

    2016-01-01

    We formulate the Crow-Kimura, discrete-time Eigen model, and continuous-time Eigen model. These models are interrelated and we established an exact mapping between them. We consider the evolutionary dynamics for the single-peak fitness and symmetric smooth fitness. We applied the quantum mechanical methods to find the exact dynamics of the evolution model with a single-peak fitness. For the smooth symmetric fitness landscape, we map exactly the evolution equations into Hamilton-Jacobi equation (HJE). We apply the method to the Crow-Kimura (parallel) and Eigen models. We get simple formulas to calculate the dynamics of the maximum of distribution and the variance. We review the existing mathematical tools of quasi-species theory.

  10. Mathematical Models of Quasi-Species Theory and Exact Results for the Dynamics.

    PubMed

    Saakian, David B; Hu, Chin-Kun

    2016-01-01

    We formulate the Crow-Kimura, discrete-time Eigen model, and continuous-time Eigen model. These models are interrelated and we established an exact mapping between them. We consider the evolutionary dynamics for the single-peak fitness and symmetric smooth fitness. We applied the quantum mechanical methods to find the exact dynamics of the evolution model with a single-peak fitness. For the smooth symmetric fitness landscape, we map exactly the evolution equations into Hamilton-Jacobi equation (HJE). We apply the method to the Crow-Kimura (parallel) and Eigen models. We get simple formulas to calculate the dynamics of the maximum of distribution and the variance. We review the existing mathematical tools of quasi-species theory. PMID:26342705

  11. Phase transition of dynamical herd behaviors for Yen Dollar exchange rates

    NASA Astrophysics Data System (ADS)

    Yoon, Seong-Min; Choi, J. S.; Kim, Y.; Kim, Kyungsik

    2006-01-01

    We study the herd behavior and the phase transition for the yen-dollar exchange rate in the Japanese financial market. It is obtained that the probability distribution of returns satisfies the power-law behavior P(R)≃R with scaling exponents β=3.11, 2.81, and 2.29 at time intervals τ=1min, 30min, and 1 h. The crash region in which the probability density increases with the increasing return appears, when the herding parameter h satisfies h⩾2.33 for the case of τ<30min. We especially obtain that no crash occurs τ>30min and that the probability distribution of price returns occurs in the phase transition at τ=30min.

  12. An Autoethnographic Exchange: Exploring the Dynamics of Selves as Adult Learners and Adult Educators

    ERIC Educational Resources Information Center

    Plakhotnik, Maria S.; Delgado, Antonio; Seepersad, Rehana

    2015-01-01

    This article explores four former doctoral students' perceptions about their selves as adult learners and adult educators through the use of autoethnography and reflective dialogue. The dynamics between the two selves were explored to identify emerging themes and implications for practice in adult education. The duality of their roles as learners…

  13. Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

    PubMed Central

    2015-01-01

    We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values. PMID:25061443

  14. Species composition, abundance, and seasonal dynamics of stink bugs (Hemiptera: Pentatomidae) in Minnesota soybean fields.

    PubMed

    Koch, Robert L; Pahs, Tiffany

    2014-08-01

    Stink bugs (Hemiptera: Pentatomidae) have historically not been pests of soybean in Minnesota. In response to the invasion of Halyomorpha halys (Stål) and reports of increasing abundance of species native to North America, a state-wide survey of soybean was conducted over 3 yr in Minnesota to determine species composition, abundance, and seasonal dynamics of Pentatomidae associated with soybean. Fourteen species of Pentatomidae (12 herbivorous and two predatory) were collected from soybean. H. halys was not detected in this survey. Among the herbivorous species found, adults of Euschistus variolarius (Palisot de Beauvois) had the greatest relative abundance (60.51%) and frequency of detection (18.44%), followed by Euschistus servus euschistoides (Say) (19.37 and 3.04%, respectively) and Chinavia hilaris (Say) (5.50 and 1.69%, respectively). Abundance of herbivorous nymphs and adults exceeded an economic threshold (20 nymphs and adults per 100 sweeps) in 0.82% of fields in 2012 but not in 2011 or 2013. The frequency of detection of herbivorous species and ratio of nymphs to adults increased with increasing reproductive growth stage of soybean. In two of three years, herbivorous adults were more abundant in the edge compared with interior of fields. Two predatory Pentatomidae, Podisus maculiventris (Say) and Podisus placidus Uhler, comprised 5.95 and 1.62% of the pentatomid adults. Though the species composition of Pentatomidae in Minnesota soybean differs from that in eastern and southern states, the spatial (i.e., greater abundance near field edge) and seasonal dynamics (i.e., increasing abundance and reproduction with increasing reproductive maturity of soybean) in soybean appear similar.

  15. Dynamics and energy exchanges between a linear oscillator and a nonlinear absorber with local and global potentials

    NASA Astrophysics Data System (ADS)

    Charlemagne, S.; Lamarque, C.-H.; Ture Savadkoohi, A.

    2016-08-01

    The dynamical behavior of a two degree-of-freedom system made up of a linear oscillator and a coupled nonlinear energy sink with nonlinear global and local potentials is studied. The nonlinear global potential of the energy sink performs direct interactions with the linear oscillator, while its local potential depends only on its own behavior during vibratory energy exchanges between two oscillators. A time multiple scale method around 1:1:1 resonance is used to detect slow invariant manifold of the system, its equilibrium and singular points. Detected equilibrium points permit us to predict periodic regime(s) while singular points can lead the system to strongly modulated responses characterized by persistent bifurcations. Several possible scenarios occurring during these strongly modulated regimes are highlighted. All analytical predictions are compared with those which are obtained by direct numerical integration of system equations.

  16. Structure, dynamics, and function of the hammerhead ribozyme in bulk water and at a clay mineral surface from replica exchange molecular dynamics.

    PubMed

    Swadling, Jacob B; Wright, David W; Suter, James L; Coveney, Peter V

    2015-03-01

    Compared with proteins, the relationship between structure, dynamics, and function of RNA enzymes (known as ribozymes) is far less well understood, despite the fact that ribozymes are found in many organisms and are often conceived as "molecular fossils" of the first self-replicating molecules to have arisen on Earth. To investigate how ribozymal function is governed by structure and dynamics, we study the full hammerhead ribozyme in bulk water and in an aqueous clay mineral environment by computer simulation using replica-exchange molecular dynamics. Through extensive sampling of the major conformational states of the hammerhead ribozyme, we are able to show that the hammerhead manifests a free-energy landscape reminiscent of that which is well known in proteins, exhibiting a "funnel" topology that guides the ribozyme into its globally most stable conformation. The active-site geometry is found to be closely correlated to the tertiary structure of the ribozyme, thereby reconciling conflicts between previously proposed mechanisms for the self-scission of the hammerhead. The conformational analysis also accounts for the differences reported experimentally in the catalytic activity of the hammerhead ribozyme, which is reduced when interacting with clay minerals as compared with bulk water.

  17. Climate, invasive species and land use drive population dynamics of a cold-water specialist

    USGS Publications Warehouse

    Kovach, Ryan P.; Al-Chokhachy, Robert K.; Whited, Diane C.; Schmetterling, David A.; Dux, Andrew M; Muhlfeld, Clint C.

    2016-01-01

    Climate change is an additional stressor in a complex suite of threats facing freshwater biodiversity, particularly for cold-water fishes. Research addressing the consequences of climate change on cold-water fish has generally focused on temperature limits defining spatial distributions, largely ignoring how climatic variation influences population dynamics in the context of other existing stressors.We used long-term data from 92 populations of bull trout Salvelinus confluentus – one of North America's most cold-adapted fishes – to quantify additive and interactive effects of climate, invasive species and land use on population dynamics (abundance, variability and growth rate).Populations were generally depressed, more variable and declining where spawning and rearing stream habitat was limited, invasive species and land use were prevalent and stream temperatures were highest. Increasing stream temperature acted additively and independently, whereas land use and invasive species had additive and interactive effects (i.e. the impact of one stressor depended on exposure to the other stressor).Most (58%–78%) of the explained variation in population dynamics was attributed to the presence of invasive species, differences in life history and management actions in foraging habitats in rivers, lakes and reservoirs. Although invasive fishes had strong negative effects on populations in foraging habitats, proactive control programmes appeared to effectively temper their negative impact.Synthesis and applications. Long-term demographic data emphasize that climate warming will exacerbate imperilment of cold-water specialists like bull trout, yet other stressors – especially invasive fishes – are immediate threats that can be addressed by proactive management actions. Therefore, climate-adaptation strategies for freshwater biodiversity should consider existing abiotic and biotic stressors, some of which provide potential and realized opportunity for conservation

  18. Optimal variable flip angle schemes for dynamic acquisition of exchanging hyperpolarized substrates

    NASA Astrophysics Data System (ADS)

    Xing, Yan; Reed, Galen D.; Pauly, John M.; Kerr, Adam B.; Larson, Peder E. Z.

    2013-09-01

    In metabolic MRI with hyperpolarized contrast agents, the signal levels vary over time due to T1 decay, T2 decay following RF excitations, and metabolic conversion. Efficient usage of the nonrenewable hyperpolarized magnetization requires specialized RF pulse schemes. In this work, we introduce two novel variable flip angle schemes for dynamic hyperpolarized MRI in which the flip angle is varied between excitations and between metabolites. These were optimized to distribute the magnetization relatively evenly throughout the acquisition by accounting for T1 decay, prior RF excitations, and metabolic conversion. Simulation results are presented to confirm the flip angle designs and evaluate the variability of signal dynamics across typical ranges of T1 and metabolic conversion. They were implemented using multiband spectral-spatial RF pulses to independently modulate the flip angle at various chemical shift frequencies. With these schemes we observed increased SNR of [1-13C]lactate generated from [1-13C]pyruvate, particularly at later time points. This will allow for improved characterization of tissue perfusion and metabolic profiles in dynamic hyperpolarized MRI.

  19. Analyzing slowly exchanging protein conformations by ion mobility mass spectrometry: study of the dynamic equilibrium of prolyl oligopeptidase.

    PubMed

    López, Abraham; Vilaseca, Marta; Madurga, Sergio; Varese, Monica; Tarragó, Teresa; Giralt, Ernest

    2016-07-01

    Ion mobility mass spectrometry (IMMS) is a biophysical technique that allows the separation of isobaric species on the basis of their size and shape. The high separation capacity, sensitivity and relatively fast time scale measurements confer IMMS great potential for the study of proteins in slow (µs-ms) conformational equilibrium in solution. However, the use of this technique for examining dynamic proteins is still not generalized. One of the major limitations is the instability of protein ions in the gas phase, which raises the question as to what extent the structures detected reflect those in solution. Here, we addressed this issue by analyzing the conformational landscape of prolyl oligopeptidase (POP) - a model of a large dynamic enzyme in the µs-ms range - by native IMMS and compared the results obtained in the gas phase with those obtained in solution. In order to interpret the experimental results, we used theoretical simulations. In addition, the stability of POP gaseous ions was explored by charge reduction and collision-induced unfolding experiments. Our experiments disclosed two species of POP in the gas phase, which correlated well with the open and closed conformations in equilibrium in solution; moreover, a gas-phase collapsed form of POP was also detected. Therefore, our findings not only support the potential of IMMS for the study of multiple co-existing conformations of large proteins in slow dynamic equilibrium in solution but also stress the need for careful data analysis to avoid artifacts. Copyright © 2016 John Wiley & Sons, Ltd.

  20. Photosynthesis in Grass Species Differing in Carbon Dioxide Fixation Pathways: II. A Search for Species with Intermediate Gas Exchange and Anatomical Characteristics.

    PubMed

    Morgan, J A; Brown, R H

    1979-08-01

    Thirty-three grass species were examined in two experiments in an attempt to locate plants with photosynthetic responses to O(2), CO(2) compensation concentrations, and leaf anatomy intermediate to those of C(3) and C(4) species. Species examined included seven from the Laxa group in the Panicum genus, one of which, P. milioides Nees ex Trin., has been reported earlier to have intermediate characteristics. The species with O(2)-sensitive photosynthesis typical of C(3) plants showed more than 37% increase in apparent photosynthesis at 2% O(2) compared to 21% O(2) at 25 C and 335 microliters per liter CO(2), whereas in Panicum milioides, P. schenckii Hack., and P. decipiens Nees ex Trin., members of the Laxa group of Panicum, increases ranged from 25 to 30%. The remainder of the species did not respond to O(2). Species with O(2) responses characteristic of C(3) plants exhibited CO(2) compensation concentrations of 44 microliters per liter or higher at 21% O(2) and 25 to 27.5 C and species characterized as O(2)-insensitive had values of microliters per liter or less. The CO(2) compensation concentration (capital GHE, Cyrillic) values of P. milioides, P. schenckii, and P. decipiens ranged from 10.3 to 23.3 microliters per liter. Other species of the Laxa group of Panicum exhibited O(2) response and capital GHE, Cyrillic values of either C(3) (P. laxum Sw., P. hylaeicum Mez., and P. rivulare Trin.) or C(4) (P. prionitis Griseb.) plants. Leaves of species with O(2) response and CO(2) compensation values typical of C(3) plants had poorly developed or nearly empty bundle sheath cells, and much larger distances and mesophyll cell numbers between veins than did the O(2)-insensitive ones. Vein spacings in P. milioides, P. schenckii, and P. decipiens ranged from 0.18 to 0.28 millimeter and mesophyll cell number between veins from 5.2 to 7.8. While these vein spacings are closer than those of most C(3) grasses, two O(2)-sensitive species of Dactylis had vein spacings similar to

  1. Dextran-grafted cation exchanger based on superporous agarose gel: adsorption isotherms, uptake kinetics and dynamic protein adsorption performance.

    PubMed

    Shi, Qing-Hong; Jia, Guo-Dong; Sun, Yan

    2010-07-30

    A novel chromatographic medium for high-capacity protein adsorption was fabricated by grafting dextran (40kDa) onto the pore surfaces of superporous agarose (SA) beads. The bead was denoted as D-SA. D-SA, SA and homogeneous agarose (HA) beads were modified with sulfopropyl (SP) group to prepare cation exchangers, and the adsorption and uptake of lysozyme on all three cation-exchange chromatographic beads (SP-HA, SP-SA and SP-D-SA) were investigated at salt concentrations of 6-50mmol/L. Static adsorption experiments showed that the adsorption capacity of SP-D-SA (2.24mmol/g) was 78% higher than that of SP-SA (1.26mmol/g) and 54% higher than that of SP-HA (1.45mmol/g) at a salt concentration of 6mmol/L. Moreover, salt concentration had less influence on the adsorption capacity and dissociation constant of SP-D-SA than it did on SP-HA, suggesting that dextran-grafted superporous bead is a more potent architecture for chromatographic beads. In the dynamic uptake of lysozyme to the three cation-exchange beads, the D(e)/D(0) (the ratio of effective pore diffusivity to free solution diffusivity) values of 1.6-2.0 were obtained in SA-D-SA, indicating that effective pore diffusivities of SP-D-SA were about two times higher than free solution diffusivity for lysozyme. At 6mmol/L NaCl, the D(e) value in SA-D-SA (22.0x10(-11)m(2)/s) was 14.4-fold greater than that in SP-HA. Due to the superior uptake kinetics in SA-D-SA, the highest dynamic binding capacity (DBC) and adsorption efficiency (the ratio of DBC to static adsorption capacity) was likewise found in SP-D-SA. It is thus confirmed that SP-D-SA has combined the advantages of superporous matrix structure and drafted ligand chemistry in mass transport and offers a new opportunity for the development of high-performance protein chromatography.

  2. Ozone dynamics and snow-atmosphere exchanges during ozone depletion events at Barrow, Alaska

    NASA Astrophysics Data System (ADS)

    Helmig, Detlev; Boylan, Patrick; Johnson, Bryan; Oltmans, Sam; Fairall, Chris; Staebler, Ralf; Weinheimer, Andrew; Orlando, John; Knapp, David J.; Montzka, Denise D.; Flocke, Frank; Frieß, Udo; Sihler, Holger; Shepson, Paul B.

    2012-10-01

    The behavior of lower atmospheric ozone and ozone exchanges at the snow surface were studied using a suite of platforms during the Ocean-Atmosphere-Sea Ice-Snow (OASIS) Spring 2009 experiment at an inland, coastal site east of Barrow, Alaska. A major objective was to investigate if and how much chemistry at the snow surface at the site contributes to springtime ozone depletion events (ODEs). Between March 8 and April 16, seven ODEs, with atmospheric ozone dropping below 1.0 ppbv, were observed. The depth of the ozone-depleted layer was variable, extending from the surface to ˜200-800 m. ODEs most commonly occurred during low wind speed conditions with flow coming from the Arctic Ocean. Two high-sensitivity ozone chemiluminescence instruments were used to accurately define the remaining sub-ppbv ozone levels during ODEs. These measurements showed variable residual ODE ozone levels ranging between 0.010 and 0.100 ppbv. During the most extended ODE, when ozone remained below 1.0 ppbv for over 78 h, these measurements showed a modest ozone recovery or production in the early afternoon hours, resulting in increases in the ozone mixing ratio of 0.100 to 0.800 ppbv. The comparison between high-sensitivity ozone measurements and BrO measured by longpath differential absorption spectroscopy (DOAS) during ODEs indicated that at low ozone levels formation of BrO is controlled by the amount of available ozone. Measurements of ozone in air drawn from below the snow surface showed depleted ozone in the snowpack, with levels consistently remaining <6 ppbv independent of above-surface ambient air concentrations. The snowpack was always a sink of ozone. Ozone deposition velocities determined from ozone surface flux measurements by eddy covariance were on the order of 0.01 cm s-1, which is of similar magnitude as ozone uptake rates found over snow at other polar sites that are not subjected to ODEs. The results from these multiple platform measurements unequivocally show that snow

  3. Comparison of CO2 Dynamics and Air-Sea Exchange in Contrasting Tropical Reef Environments

    NASA Astrophysics Data System (ADS)

    Drupp, P. S.; De Carlo, E. H.; Mackenzie, F. T.; Shamberger, K. E.; Musielewicz, S. B.; Maenner-Jones, S.; Sabine, C. L.; Feely, R. A.

    2011-12-01

    Multiyear high temporal resolution CO2 records in three differing coral reef settings were obtained using buoys deployed in coastal waters of Oahu since June 2008. The buoys are located on the barrier reef of Kaneohe Bay and offshore of Honolulu, on the south shore of Oahu. Annualized CO2 air-sea fluxes at the three buoys ranged from +0.05 mol C/m2/yr offshore Honolulu on a fringing reef well mixed with the open ocean to -1.12 mol C/m2/yr on a barrier reef flat in Kaneohe Bay (positive values represent CO2 sinks from the atmosphere and negative values represent sources). These fluxes compare well to those estimated from previous studies in Kaneohe Bay as well as in other tropical reef environments. pCO2 measurements, made every 3 hours, at each location show strong temporal cycles on multiple time scales ranging from diel to seasonal at each buoy and an anticorrelation with pO2. These records, when combined with those of a prior buoy deployment in southern Kaneohe Bay and several synoptic studies, allow us to examine how the principal biological cycles of productivity/respiration and calcification/carbonate dissolution are influenced by changing water column properties, physical processes (e.g. residence time) and atmospheric conditions and how these processes ultimately impact the exchange of CO2 between the ocean and atmosphere on hourly to interannual cycles. The data clearly demonstrate the need for high frequency pCO2 data to characterize completely and accurately short-term local changes in the CO2-carbonic acid system parameters and how these changes overprint the longer scale process of ocean acidification as a result of invasion of CO2 into the ocean due to emissions of anthropogenic CO2 to the atmosphere. Since many coral reef ecosystems are still sources of CO2 to the atmosphere because of positive net ecosystem calcification, and in some instances net heterotrophy, such data are even more critical in terms of assessing future changes in the direction

  4. Frequent cytoplasmic exchanges between oak species that are not closely related: Quercus suber and Q. ilex in Morocco.

    PubMed

    Belahbib, N; Pemonge, M H; Ouassou, A; Sbay, H; Kremer, A; Petit, R J

    2001-08-01

    Chloroplast (cp) and mitochondrial (mt) DNA variation were studied in 97 populations of cork oak (Quercus suber) in Morocco; in 31 of these populations, holm oak (Quercus ilex), a clearly distinct species, also occurred and was compared with Q. suber. Three cpDNA and one mtDNA primer pairs were used in the survey, each in combination with one restriction enzyme. Six haplotypes belonging to two very divergent lineages were detected; one lineage predominates in each species, and is probably ancestral, as inferred from comparisons with other oak species. In the mixed-species populations, cytoplasmic genomes were frequently shared across species, as indicated by an introgression ratio of 0.63. This index is a new measure of the propensity of species to share locally genetic markers, varying from zero (complete differentiation) to one (no differentiation). By contrast, more closely related deciduous oak species (Q. robur, Q. petraea and Q. pubescens) have introgression ratios varying from 0.82 to 0.97. The introgression events appear to have been more frequent in the direction Q. ilex (female) x Q. suber (male), a finding which seems attributable to the flowering phenology of these two species. This asymmetry may have favoured immigration of Q. suber beyond its main range, in regions already colonized by Q. ilex. There, rare hybridization and further introgression through long distance pollen flow have established populations that are morphologically indistinguishable from Q. suber but that have cytoplasmic genomes originating from the local Q. ilex populations.

  5. Cross-Cordillera exchange mediated by the Panama Canal increased the species richness of local freshwater fish assemblages.

    PubMed Central

    Smith, Scott A.; Bell, Graham; Bermingham, Eldredge

    2004-01-01

    Completion of the Panama Canal in 1914 breached the continental divide and set into motion a natural experiment of unprecedented magnitude by bringing previously isolated freshwater fish communities into contact. The construction of a freshwater corridor connecting evolutionarily isolated communities in Pacific and Caribbean watersheds dramatically increased the rate of dispersal, without directly affecting species interactions. Here, we report that a large fraction of species have been able to establish themselves on the other side of the continental divide, whereas no species have become extinct, leading to a local increase in species richness. Our results suggest that communities are not saturated and that competitive exclusion does not occur over the time-scale previously envisioned. Moreover, the results of this unintentional experiment demonstrate that community composition and species richness were regulated by the regional process of dispersal, rather than by local processes such as competition and predation. PMID:15347510

  6. Cross-Cordillera exchange mediated by the Panama Canal increased the species richness of local freshwater fish assemblages.

    PubMed

    Smith, Scott A; Bell, Graham; Bermingham, Eldredge

    2004-09-22

    Completion of the Panama Canal in 1914 breached the continental divide and set into motion a natural experiment of unprecedented magnitude by bringing previously isolated freshwater fish communities into contact. The construction of a freshwater corridor connecting evolutionarily isolated communities in Pacific and Caribbean watersheds dramatically increased the rate of dispersal, without directly affecting species interactions. Here, we report that a large fraction of species have been able to establish themselves on the other side of the continental divide, whereas no species have become extinct, leading to a local increase in species richness. Our results suggest that communities are not saturated and that competitive exclusion does not occur over the time-scale previously envisioned. Moreover, the results of this unintentional experiment demonstrate that community composition and species richness were regulated by the regional process of dispersal, rather than by local processes such as competition and predation. PMID:15347510

  7. Novel wireless sensor system for dynamic characterization of borehole heat exchangers.

    PubMed

    Martos, Julio; Montero, Álvaro; Torres, José; Soret, Jesús; Martínez, Guillermo; García-Olcina, Raimundo

    2011-01-01

    The design and field test of a novel sensor system based in autonomous wireless sensors to measure the temperature of the heat transfer fluid along a borehole heat exchanger (BHE) is presented. The system, by means of two special valves, inserts and extracts miniaturized wireless sensors inside the pipes of the borehole, which are carried by the thermal fluid. Each sensor is embedded in a small sphere of just 25 mm diameter and 8 gr weight, containing a transceiver, a microcontroller, a temperature sensor and a power supply. A wireless data processing unit transmits to the sensors the acquisition configuration before the measurements, and also downloads the temperature data measured by the sensor along its way through the BHE U-tube. This sensor system is intended to improve the conventional thermal response test (TRT) and it allows the collection of information about the thermal characteristics of the geological structure of subsurface and its influence in borehole thermal behaviour, which in turn, facilitates the implementation of TRTs in a more cost-effective and reliable way.

  8. Novel Wireless Sensor System for Dynamic Characterization of Borehole Heat Exchangers

    PubMed Central

    Martos, Julio; Montero, Álvaro; Torres, José; Soret, Jesús; Martínez, Guillermo; García-Olcina, Raimundo

    2011-01-01

    The design and field test of a novel sensor system based in autonomous wireless sensors to measure the temperature of the heat transfer fluid along a borehole heat exchanger (BHE) is presented. The system, by means of two specials valves, inserts and extracts miniaturized wireless sensors inside the pipes of the borehole, which are carried by the thermal fluid. Each sensor is embedded in a small sphere of just 25 mm diameter and 8 gr weight, containing a transceiver, a microcontroller, a temperature sensor and a power supply. A wireless data processing unit transmits to the sensors the acquisition configuration before the measurements, and also downloads the temperature data measured by the sensor along its way through the BHE U-tube. This sensor system is intended to improve the conventional thermal response test (TRT) and it allows the collection of information about the thermal characteristics of the geological structure of subsurface and its influence in borehole thermal behaviour, which in turn, facilitates the implementation of TRTs in a more cost-effective and reliable way. PMID:22164005

  9. Dynamics of carbon dioxide exchange of a wheat community grown in a semi-closed environment

    NASA Technical Reports Server (NTRS)

    Corey, Kenneth A.

    1989-01-01

    A wheat (Triticum aestivum Yecora Rojo) community was grown in the semi-closed conditions of the NASA/KSC Biomass Production Chamber (BPC). Experiments were conducted to determine whole community carbon dioxide exchange rates as influenced by growth and development, carbon dioxide concentration, time within the photoperiod, irradiance, and temperature. Plants were grown at a population of about 1500 per sq meter using a 20 hour light/4 hour dark daily regime. Light was supplied by HPS vapor lamps and irradiance was maintained in the range of 590 to 675 mu mol per sq meter. The temperature regime was 20 C light/16 C dark and nutrients were supplied hydroponically as a thin film. Fractional interception of PPF by the community increased rapidly during growth reaching a maximum of 0.96, 24 days after planting. This time corresponded to canopy closure and maximum rates of net photosynthesis (NP). Net daily CO2 utilization rates were calculated to day 48 and a 4th order regression equation integrated to obtain total moles of CO2 fixed by the community. This procedure may be useful for monitoring and prediction of biomass yields in a closed ecology life support system (CELSS).

  10. Novel wireless sensor system for dynamic characterization of borehole heat exchangers.

    PubMed

    Martos, Julio; Montero, Álvaro; Torres, José; Soret, Jesús; Martínez, Guillermo; García-Olcina, Raimundo

    2011-01-01

    The design and field test of a novel sensor system based in autonomous wireless sensors to measure the temperature of the heat transfer fluid along a borehole heat exchanger (BHE) is presented. The system, by means of two special valves, inserts and extracts miniaturized wireless sensors inside the pipes of the borehole, which are carried by the thermal fluid. Each sensor is embedded in a small sphere of just 25 mm diameter and 8 gr weight, containing a transceiver, a microcontroller, a temperature sensor and a power supply. A wireless data processing unit transmits to the sensors the acquisition configuration before the measurements, and also downloads the temperature data measured by the sensor along its way through the BHE U-tube. This sensor system is intended to improve the conventional thermal response test (TRT) and it allows the collection of information about the thermal characteristics of the geological structure of subsurface and its influence in borehole thermal behaviour, which in turn, facilitates the implementation of TRTs in a more cost-effective and reliable way. PMID:22164005

  11. Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species.

    PubMed

    Klie, Sebastian; Osorio, Sonia; Tohge, Takayuki; Drincovich, María F; Fait, Aaron; Giovannoni, James J; Fernie, Alisdair R; Nikoloski, Zoran

    2014-01-01

    Computational analyses of molecular phenotypes traditionally aim at identifying biochemical components that exhibit differential expression under various scenarios (e.g. environmental and internal perturbations) in a single species. High-throughput metabolomics technologies allow the quantification of (relative) metabolite levels across developmental stages in different tissues, organs, and species. Novel methods for analyzing the resulting multiple data tables could reveal preserved dynamics of metabolic processes across species. The problem we address in this study is 2-fold. (1) We derive a single data table, referred to as a compromise, which captures information common to the investigated set of multiple tables containing data on different fruit development and ripening stages in three climacteric (i.e. peach [Prunus persica] and two tomato [Solanum lycopersicum] cultivars, Ailsa Craig and M82) and two nonclimacteric (i.e. strawberry [Fragaria × ananassa] and pepper [Capsicum chilense]) fruits; in addition, we demonstrate the power of the method to discern similarities and differences between multiple tables by analyzing publicly available metabolomics data from three tomato ripening mutants together with two tomato cultivars. (2) We identify the conserved dynamics of metabolic processes, reflected in the data profiles of the corresponding metabolites that contribute most to the determined compromise. Our analysis is based on an extension to principal component analysis, called STATIS, in combination with pathway overenrichment analysis. Based on publicly available metabolic profiles for the investigated species, we demonstrate that STATIS can be used to identify the metabolic processes whose behavior is similarly affected during fruit development and ripening. These findings ultimately provide insights into the pathways that are essential during fruit development and ripening across species. PMID:24243932

  12. Conservation of species in dynamic landscapes: divergent fates of Silene tatarica populations in riparian habitats.

    PubMed

    Jäkäläniemi, Anne; Tuomi, Juha; Siikamäki, Pirkko

    2006-06-01

    In transient environments, where local extinctions occur as a result of destruction or deterioration of the local habitat, the long-term persistence of a species requires successful colonizations at new, suitable sites. This kind of habitat tracking should be associated with the asynchronous dynamics of local populations, and it can be especially important for the conservation of rare plant species in riparian habitats. We determined spatiotemporal variation in the demography of the perennial Silene tatarica (L.) Pers. in 15 populations (1998-2003) located in periodically disturbed riparian habitats. The habitats differed according to their morphology (flat shores, slopes) and the amount of bare ground (open, intermediate, closed) along a successional gradient. We used elasticity and life-table response analyses and stochastic simulations to study the variation in population demography. Finite population growth rate was higher in intermediate habitats than in open and closed habitats. In stochastic simulations population size increased in most cases, but four populations were projected to become extinct within 12-70 years. The viability of local populations depended most on the survival and growth of juvenile individuals and on the fecundity of large fertile individuals. On a regional scale, the persistence of this species will require a viable network of local populations as protection against local extinctions caused by natural disturbances and succession. Accordingly, the long-term persistence of riparian species may depend on habitat changes; thus, their conservation requires maintenance of natural disturbance dynamics. Along regulated rivers, management activities such as the creation of open habitats for new colonization should be implemented. Similarly, these activities can be rather general requirements for the conservation of endangered species dependent on transient habitats along successional gradients.

  13. Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species.

    PubMed

    Klie, Sebastian; Osorio, Sonia; Tohge, Takayuki; Drincovich, María F; Fait, Aaron; Giovannoni, James J; Fernie, Alisdair R; Nikoloski, Zoran

    2014-01-01

    Computational analyses of molecular phenotypes traditionally aim at identifying biochemical components that exhibit differential expression under various scenarios (e.g. environmental and internal perturbations) in a single species. High-throughput metabolomics technologies allow the quantification of (relative) metabolite levels across developmental stages in different tissues, organs, and species. Novel methods for analyzing the resulting multiple data tables could reveal preserved dynamics of metabolic processes across species. The problem we address in this study is 2-fold. (1) We derive a single data table, referred to as a compromise, which captures information common to the investigated set of multiple tables containing data on different fruit development and ripening stages in three climacteric (i.e. peach [Prunus persica] and two tomato [Solanum lycopersicum] cultivars, Ailsa Craig and M82) and two nonclimacteric (i.e. strawberry [Fragaria × ananassa] and pepper [Capsicum chilense]) fruits; in addition, we demonstrate the power of the method to discern similarities and differences between multiple tables by analyzing publicly available metabolomics data from three tomato ripening mutants together with two tomato cultivars. (2) We identify the conserved dynamics of metabolic processes, reflected in the data profiles of the corresponding metabolites that contribute most to the determined compromise. Our analysis is based on an extension to principal component analysis, called STATIS, in combination with pathway overenrichment analysis. Based on publicly available metabolic profiles for the investigated species, we demonstrate that STATIS can be used to identify the metabolic processes whose behavior is similarly affected during fruit development and ripening. These findings ultimately provide insights into the pathways that are essential during fruit development and ripening across species.

  14. Riparian plant species loss alters trophic dynamics in detritus-based stream ecosystems.

    PubMed

    Lecerf, Antoine; Dobson, Michael; Dang, Christian K; Chauvet, Eric

    2005-12-01

    Riparian vegetation is closely connected to stream food webs through input of leaf detritus as a primary energy supply, and therefore, any alteration of plant diversity may influence aquatic ecosystem functioning. We measured leaf litter breakdown rate and associated biological parameters in mesh bags in eight headwater streams bordered either with mixed deciduous forest or with beech forest. The variety of leaf litter types in mixed forest results in higher food quality for large-particle invertebrate detritivores ('shredders') than in beech forest, which is dominated by a single leaf species of low quality. Breakdown rate of low quality (oak) leaf litter in coarse mesh bags was lower in beech forest streams than in mixed forest streams, a consequence of lower shredder biomass. In contrast, high quality (alder) leaf litter broke down at similar rates in both stream categories as a result of similar shredder biomass in coarse mesh bags. Microbial breakdown rate of oak and alder leaves, determined in fine mesh bags, did not differ between the stream categories. We found however aquatic hyphomycete species richness on leaf litter to positively co-vary with riparian plant species richness. Fungal species richness may enhance leaf litter breakdown rate through positive effects on resource quality for shredders. A feeding experiment established a positive relationship between fungal species richness per se and leaf litter consumption rate by an amphipod shredder (Gammarus fossarum). Our results show therefore that plant species richness may indirectly govern ecosystem functioning through complex trophic interactions. Integrating microbial diversity and trophic dynamics would considerably improve the prediction of the consequences of species loss.

  15. Ligand binding and proton exchange dynamics in site-specific mutants of human myoglobin

    SciTech Connect

    Lambright, D.G.

    1992-01-01

    Site specific mutagenesis was used to make substitutions of four residues in the distal heme pocket of human myoglobin: Val68, His64, Lys45, and Asp60. Strongly diffracting crystals of the conservative mutation K45R in the met aquo form were grown in the trigonal space group P3[sub 2]21 and the X-ray crystal structure determined at 1.6 [angstrom] resolution. The overall structure is similar to that of sperm whale met aquo myoglobin. Several of the mutant proteins were characterized by 2-D NMR spectroscopy. The NMR data suggest the structural changes are localized to the region of the mutation. The dynamics of ligand binding to myoglobin mutants were studied by transient absorption spectroscopy following photolysis of the CO complexes. Transient absorption kinetics and spectra on the ns to ms timescale were measured in aqueous solution from 280 K to 310 K and in 75% glycerol: water from 250 K to 310 K. Two significant basis spectra were obtained from singular value decomposition of the matrix of time dependent spectra. The information was used to obtain approximations for the extent of ligand rebinding and the kinetics of conformational relaxation. Except for K45R, substitutions at Lys45 or Asp60 produce changes in the kinetics for ligand rebinding. Replacement of Lys45 with Arg increases the rate of ligand rebinding from the protein matrix by a factor of 2, but does not alter the rates for ligand escape or entry into the protein or the dynamics of the conformational relaxation. Substitutions at His64 and Val68 influence the kinetics of ligand rebinding and the dynamics of conformational relaxation. The results do not support the hypothesis that ligand migration between the heme pocket and solvent is determined solely by fluctuations of Arg45 and His64 between open and closed conformations of the heme pocket but can be rationalized if ligand diffusion through the protein matrix involves multiple competing pathways.

  16. Seasonal source-sink dynamics at the edge of a species' range

    USGS Publications Warehouse

    Kanda, L.L.; Fuller, T.K.; Sievert, P.R.; Kellogg, R.L.

    2009-01-01

    The roles of dispersal and population dynamics in determining species' range boundaries recently have received theoretical attention but little empirical work. Here we provide data on survival, reproduction, and movement for a Virginia opossum (Didelphis virginiana) population at a local distributional edge in central Massachusetts (USA). Most juvenile females that apparently exploited anthropogenic resources survived their first winter, whereas those using adjacent natural resources died of starvation. In spring, adult females recolonized natural areas. A life-table model suggests that a population exploiting anthropogenic resources may grow, acting as source to a geographically interlaced sink of opossums using only natural resources, and also providing emigrants for further range expansion to new human-dominated landscapes. In a geographical model, this source-sink dynamic is consistent with the local distribution identified through road-kill surveys. The Virginia opossum's exploitation of human resources likely ameliorates energetically restrictive winters and may explain both their local distribution and their northward expansion in unsuitable natural climatic regimes. Landscape heterogeneity, such as created by urbanization, may result in source-sink dynamics at highly localized scales. Differential fitness and individual dispersal movements within local populations are key to generating regional distributions, and thus species ranges, that exceed expectations. ?? 2009 by the Ecological Society of America.

  17. Seasonal source-sink dynamics at the edge of a species' range.

    PubMed

    Kanda, L Leann; Fuller, Todd K; Sievert, Paul R; Kellogg, Robert L

    2009-06-01

    The roles of dispersal and population dynamics in determining species' range boundaries recently have received theoretical attention but little empirical work. Here we provide data on survival, reproduction, and movement for a Virginia opossum (Didelphis virginiana) population at a local distributional edge in central Massachusetts (USA). Most juvenile females that apparently exploited anthropogenic resources survived their first winter, whereas those using adjacent natural resources died of starvation. In spring, adult females recolonized natural areas. A life-table model suggests that a population exploiting anthropogenic resources may grow, acting as source to a geographically interlaced sink of opossums using only natural resources, and also providing emigrants for further range expansion to new human-dominated landscapes. In a geographical model, this source-sink dynamic is consistent with the local distribution identified through road-kill surveys. The Virginia opossum's exploitation of human resources likely ameliorates energetically restrictive winters and may explain both their local distribution and their northward expansion in unsuitable natural climatic regimes. Landscape heterogeneity, such as created by urbanization, may result in source-sink dynamics at highly localized scales. Differential fitness and individual dispersal movements within local populations are key to generating regional distributions, and thus species ranges, that exceed expectations.

  18. Could beaked whales get the bends? Effect of diving behaviour and physiology on modelled gas exchange for three species: Ziphius cavirostris, Mesoplodon densirostris and Hyperoodon ampullatus.

    PubMed

    Hooker, Sascha K; Baird, Robin W; Fahlman, Andreas

    2009-07-31

    A mathematical model, based on current knowledge of gas exchange and physiology of marine mammals, was used to predict blood and tissue tension N2 (P(N2)) using field data from three beaked whale species: northern bottlenose whales, Cuvier's beaked whales, and Blainville's beaked whales. The objective was to determine if physiology (body mass, diving lung volume, dive response) or dive behaviour (dive depth and duration, changes in ascent rate, diel behaviour) would lead to differences in P(N2) levels and thereby decompression sickness (DCS) risk between species. Diving lung volume and extent of the dive response had a large effect on end-dive P(N2). The dive profile had a larger influence on end-dive P(N2) than body mass differences between species. Despite diel changes in dive behaviour, P(N2) levels showed no consistent trend. Model output suggested that all three species live with tissue P(N2) levels that would cause a significant proportion of DCS cases in terrestrial mammals. Cuvier's beaked whale diving behaviour appears to put them at higher risk than the other species, which may explain their prevalence in strandings after the use of mid-frequency sonar.

  19. Population dynamics in changing environments: the case of an eruptive forest pest species.

    PubMed

    Kausrud, Kyrre; Okland, Bjørn; Skarpaas, Olav; Grégoire, Jean-Claude; Erbilgin, Nadir; Stenseth, Nils Chr

    2012-02-01

    In recent decades we have seen rapid and co-occurring changes in landscape structure, species distributions and even climate as consequences of human activity. Such changes affect the dynamics of the interaction between major forest pest species, such as bark beetles (Coleoptera: Curculionidae, Scolytinae), and their host trees. Normally breeding mostly in broken or severely stressed spruce; at high population densities some bark beetle species can colonise and kill healthy trees on scales ranging from single trees in a stand to multi-annual landscape-wide outbreaks. In Eurasia, the largest outbreaks are caused by the spruce bark beetle, Ips typographus (Linnaeus), which is common and shares a wide distribution with its main host, Norway spruce (Picea abies Karst.). A large literature is now available, from which this review aims to synthesize research relevant for the population dynamics of I. typographus and co-occurring species under changing conditions. We find that spruce bark beetle population dynamics tend to be metastable, but that mixed-species and age-heterogeneous forests with good site-matching tend to be less susceptible to large-scale outbreaks. While large accumulations of logs should be removed and/or debarked before the next swarming period, intensive removal of all coarse dead wood may be counterproductive, as it reduces the diversity of predators that in some areas may play a role in keeping I. typographus populations below the outbreak threshold, and sanitary logging frequently causes edge effects and root damage, reducing the resistance of remaining trees. It is very hard to predict the outcome of interspecific interactions due to invading beetle species or I. typographus establishing outside its current range, as they can be of varying sign and strength and may fluctuate depending on environmental factors and population phase. Most research indicates that beetle outbreaks will increase in frequency and magnitude as temperature, wind speed and

  20. The orbital-based view on reaction dynamics: ligand exchange of Fe(CO)5 in solution

    NASA Astrophysics Data System (ADS)

    Föhlisch, Alexander

    2015-03-01

    Time resolved soft X-ray spectroscopy has proven recently, that it can beat the complexity of dynamics in materials and chemical processes by its high selectivity towards elemental, chemical, and magnetic properties. Changes in chemical bonding, in particular bond breaking and bond creation seem conceptually simple, but as a result of coherent wave packet motion it is difficult to catch the dynamic pathways in a multidimensional potential energy landscape. In this contribution we exploit the unique approach of femtosecond time resolved resonant inelastic X-ray scattering at LCLS to derive how ultrafast spin-crossover and ligation determines the pathways of ligand exchange of Ironpentacarbonyl (Fe(CO)5) in solution. As an outlook, it will be discussed, how non-linear X-ray processes can push time resolved soft X-ray spectroscopy in a new phase. In particular, stimulated Raman scattering and amplified spontaneous emission can overcome the weak scattering cross-sections of spontaneous processes, help to suppress sample damage and increase spectral resolution and excited state selectivity through the exploitation of Anti-Stokes Raman Scattering.

  1. Applications of hydrogen deuterium exchange (HDX) for the characterization of conformational dynamics in light-activated photoreceptors

    PubMed Central

    Lindner, Robert; Heintz, Udo; Winkler, Andreas

    2015-01-01

    Rational design of optogenetic tools is inherently linked to the understanding of photoreceptor function. Structural analysis of elements involved in signal integration in individual sensor domains provides an initial idea of their mode of operation, but understanding how local structural rearrangements eventually affect signal transmission to output domains requires inclusion of the effector regions in the characterization. However, the dynamic nature of these assemblies renders their structural analysis challenging and therefore a combination of high- and low-resolution techniques is required to appreciate functional aspects of photoreceptors. This review focuses on the potential of hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) for complementing the structural characterization of photoreceptors. In this respect, the ability of HDX-MS to provide information on conformational dynamics and the possibility to address multiple functionally relevant states in solution render this methodology ideally suitable. We highlight recent examples demonstrating the potential of HDX-MS and discuss how these results can help to improve existing optogenetic systems or guide the design of novel optogenetic tools. PMID:26157802

  2. Molecular dynamics simulation of energy exchanges during hydrogen collision with graphite sheets

    NASA Astrophysics Data System (ADS)

    Sun, Jizhong; Li, Shouyang; Stirner, Thomas; Chen, Junlin; Wang, Dezhen

    2010-06-01

    Experiments show that the energy of particles incident on divertor plates in fusion devices seldom exceeds 100 eV. Trim code and its variants are not suitable to predict the sputtering yield of carbon-based divertor plates for this energy range and, therefore, a dynamic model, taking into account the C-H bond formation and breaking, and the structure of carbon, is needed. In this paper, the molecular dynamics method is employed to investigate collision processes between incident hydrogen atoms and a graphene sheet. The simulation results demonstrate that the collision processes cannot be adequately described by a simple binary approximation. The energy transfer from the projectile to the graphite sheet exhibits a very complicated behavior when the kinetic energy of the incident hydrogen atom is below 30 eV, strongly depending on the impact position. When its kinetic energy is lower than 0.35 eV, the incident hydrogen is always reflected back from the single, perfect graphite sheet; when its kinetic energy is higher than 0.35 eV, then whether the incident particle penetrates the graphite sheet, is reflected back or is adsorbed depends on the impact position. In certain areas of the graphite sheet, either adsorption or reflection of an incident hydrogen atom can occur in two different energy ranges.

  3. The Dynamics of Lateral Gene Transfer in Genus Leishmania - A Route for Adaptation and Species Diversification

    PubMed Central

    Vikeved, Elisabet; Backlund, Anders; Alsmark, Cecilia

    2016-01-01

    Background The genome of Leishmania major harbours a comparably high proportion of genes of prokaryote origin, acquired by lateral gene transfer (LGT). Some of these are present in closely related trypanosomatids, while some are detected in Leishmania only. We have evaluated the impact and destiny of LGT in genus Leishmania. Methodology/Principal Findings To study the dynamics and fate of LGTs we have performed phylogenetic, as well as nucleotide and amino acid composition analyses within orthologous groups of LGTs detected in Leishmania. A set of universal trypanosomatid LGTs was added as a reference group. Both groups of LGTs have, to some extent, ameliorated to resemble the recipient genomes. However, while virtually all of the universal trypanosomatid LGTs are distributed and conserved in the entire genus Leishmania, the LGTs uniquely present in genus Leishmania are more prone to gene loss and display faster rates of evolution. Furthermore, a PCR based approach has been employed to ascertain the presence of a set of twenty LGTs uniquely present in genus Leishmania, and three universal trypanosomatid LGTs, in ten additional strains of Leishmania. Evolutionary rates and predicted expression levels of these LGTs have also been estimated. Ten of the twenty LGTs are distributed and conserved in all species investigated, while the remainder have been subjected to modifications, or undergone pseudogenization, degradation or loss in one or more species. Conclusions/Significance LGTs unique to the genus Leishmania have been acquired after the divergence of Leishmania from the other trypanosomatids, and are evolving faster than their recipient genomes. This implies that LGT in genus Leishmania is a continuous and dynamic process contributing to species differentiation and speciation. This study also highlights the importance of carefully evaluating these dynamic genes, e.g. as LGTs have been suggested as potential drug targets. PMID:26730948

  4. Influence of the exchange-correlation functional on the quasi-harmonic lattice dynamics of II-VI semiconductors.

    PubMed

    Skelton, Jonathan M; Tiana, Davide; Parker, Stephen C; Togo, Atsushi; Tanaka, Isao; Walsh, Aron

    2015-08-14

    We perform a systematic comparison of the finite-temperature structure and properties of four bulk semiconductors (PbS, PbTe, ZnS, and ZnTe) predicted by eight popular exchange-correlation functionals from quasi-harmonic lattice-dynamics calculations. The performance of the functionals in reproducing the temperature dependence of a number of material properties, including lattice parameters, thermal-expansion coefficients, bulk moduli, heat capacities, and phonon frequencies, is evaluated quantitatively against available experimental data. We find that the phenomenological over- and under-binding characteristics of the local-density approximation and the PW91 and Perdew-Burke-Enzerhof (PBE) generalised-gradient approximation (GGA) functionals, respectively, are exaggerated at finite temperature, whereas the PBEsol GGA shows good general performance across all four systems. The Tao-Perdew-Staroverov-Scuseria (TPSS) and revTPSS meta-GGAs provide relatively small improvements over PBE, with the latter being better suited to calculating structural and dynamical properties, but both are considerably more computationally demanding than the simpler GGAs. The dispersion-corrected PBE-D2 and PBE-D3 functionals perform well in describing the lattice dynamics of the zinc chalcogenides, whereas the lead chalcogenides appear to be challenging for these functionals. These findings show that quasi-harmonic calculations with a suitable functional can predict finite-temperature structure and properties with useful accuracy, and that this technique can serve as a means of evaluating the performance of new functionals in the future. PMID:26277159

  5. Unmodeled observation error induces bias when inferring patterns and dynamics of species occurrence via aural detections

    USGS Publications Warehouse

    McClintock, Brett T.; Bailey, Larissa L.; Pollock, Kenneth H.; Simons, Theodore R.

    2010-01-01

    The recent surge in the development and application of species occurrence models has been associated with an acknowledgment among ecologists that species are detected imperfectly due to observation error. Standard models now allow unbiased estimation of occupancy probability when false negative detections occur, but this is conditional on no false positive detections and sufficient incorporation of explanatory variables for the false negative detection process. These assumptions are likely reasonable in many circumstances, but there is mounting evidence that false positive errors and detection probability heterogeneity may be much more prevalent in studies relying on auditory cues for species detection (e.g., songbird or calling amphibian surveys). We used field survey data from a simulated calling anuran system of known occupancy state to investigate the biases induced by these errors in dynamic models of species occurrence. Despite the participation of expert observers in simplified field conditions, both false positive errors and site detection probability heterogeneity were extensive for most species in the survey. We found that even low levels of false positive errors, constituting as little as 1% of all detections, can cause severe overestimation of site occupancy, colonization, and local extinction probabilities. Further, unmodeled detection probability heterogeneity induced substantial underestimation of occupancy and overestimation of colonization and local extinction probabilities. Completely spurious relationships between species occurrence and explanatory variables were also found. Such misleading inferences would likely have deleterious implications for conservation and management programs. We contend that all forms of observation error, including false positive errors and heterogeneous detection probabilities, must be incorporated into the estimation framework to facilitate reliable inferences about occupancy and its associated vital rate parameters.

  6. Complex Dynamics of an Impulsive Control System in which Predator Species Share a Common Prey

    NASA Astrophysics Data System (ADS)

    Pei, Yongzhen; Liu, Shaoying; Li, Changguo

    2009-06-01

    In an ecosystem, multiple predator species often share a common prey and the interactions between the predators are neutral. In view of this fact, we propose a three-species prey-predator system with the functional responses and impulsive controls to model the process of pest management. It is proved that the system has a locally stable pest-eradication periodic solution under the assumption that the impulsive period is less than some critical value. In particular, two single control strategies (biological control alone or chemical control alone) are proposed. Finally, we compare three pest control strategies and find that if we choose narrow-spectrum pesticides that are targeted to a specific pest’s life cycle to kill the pest, then the combined strategy is preferable. Numerical results show that our system has complex dynamics including period-doubling bifurcation, quasi-periodic oscillation, chaos, intermittency and crises.

  7. Dynamics of species interaction strength in space, time and with developmental stage.

    PubMed

    Kordas, Rebecca L; Dudgeon, Steve

    2011-06-22

    Quantifying species interaction strengths enhances prediction of community dynamics, but variability in the strength of species interactions in space and time complicates accurate prediction. Interaction strengths can vary in response to density, indirect effects, priority effects or a changing environment, but the mechanism(s) causing direction and magnitudes of change are often unclear. We designed an experiment to characterize how environmental factors influence the direction and the strength of priority effects between sessile species. We estimated per capita non-trophic effects of barnacles (Semibalanus balanoides) on newly settled germlings of the fucoid, Ascophyllum nodosum, in the presence and absence of consumers in experiments on rocky shores throughout the Gulf of Maine, USA. Per capita effects on germlings varied among environments and barnacle life stages, and these interaction strengths were largely unaltered by changing consumer abundance. Whereas previous evidence shows adult barnacles facilitate fucoids, here, we show that recent settlers and established juveniles initially compete with germlings. As barnacles mature, they switch to become facilitators of fucoids. Consumers caused variable mortality of germlings through time comparable to that from competition. Temporally variable effects of interactors (e.g. S. balanoides), or spatial variation in their population structure, in different regions differentially affect target populations (e.g. A. nodosum). This may affect abundance of critical stages and the resilience of target species to environmental change in different geographical regions.

  8. Dynamics of species interaction strength in space, time and with developmental stage.

    PubMed

    Kordas, Rebecca L; Dudgeon, Steve

    2011-06-22

    Quantifying species interaction strengths enhances prediction of community dynamics, but variability in the strength of species interactions in space and time complicates accurate prediction. Interaction strengths can vary in response to density, indirect effects, priority effects or a changing environment, but the mechanism(s) causing direction and magnitudes of change are often unclear. We designed an experiment to characterize how environmental factors influence the direction and the strength of priority effects between sessile species. We estimated per capita non-trophic effects of barnacles (Semibalanus balanoides) on newly settled germlings of the fucoid, Ascophyllum nodosum, in the presence and absence of consumers in experiments on rocky shores throughout the Gulf of Maine, USA. Per capita effects on germlings varied among environments and barnacle life stages, and these interaction strengths were largely unaltered by changing consumer abundance. Whereas previous evidence shows adult barnacles facilitate fucoids, here, we show that recent settlers and established juveniles initially compete with germlings. As barnacles mature, they switch to become facilitators of fucoids. Consumers caused variable mortality of germlings through time comparable to that from competition. Temporally variable effects of interactors (e.g. S. balanoides), or spatial variation in their population structure, in different regions differentially affect target populations (e.g. A. nodosum). This may affect abundance of critical stages and the resilience of target species to environmental change in different geographical regions. PMID:21106597

  9. Plant Species Anaerobiosis and DOC Dynamics in a Peat-Forming Wetland, New York State

    NASA Astrophysics Data System (ADS)

    Yavitt, J. B.; Williams, C. J.

    2004-05-01

    We quantified spatial and temporal patterns of dissolved organic carbon (DOC) concentrations in the shallow peat soil of a freshwater wetland (located in central New York State) and correlated the patterns with anaerobiosis in roots of the dominant plant species. Sampling was stratified in zones dominated by: lakebank sedge (Carex lacustris), common cattail (Typha latifolia), purple loosestrife (Lythrum salicaria) or soft rush (Juncus effusus). Concentrations of DOC peaked in late summer and were much greater in wet years (14.3 mg C/L) than during summer drought (5.3 mg C/L). DOC concentrations did not vary significantly as a function of plant species and were greater in subsurface peat (13.3 mg C/L at 20 cm depth) than in surface peat (8.6 mg C/L at 5 cm depth). Anaerobiosis was pronounced in cattail in the spring and autumn, in purple loosestrife in mid summer, but showed little seasonal pattern in rush and in sedge. Although recent ecological research has shown that plant species can control belowground processes, we found little evidence for plant species control of DOC dynamics in this wetland.

  10. Modeling spatiotemporal dynamics of outbreaking species: influence of environment and migration in a locust.

    PubMed

    Veran, Sophie; Simpson, Stephen J; Sword, Gregory A; Deveson, Edward; Piry, Sylvain; Hines, James E; Berthier, Karine

    2015-03-01

    Many pest species exhibit huge fluctuations in population abundance. Understanding their large-scale and long-term dynamics is necessary to develop effective control and management strategies. Occupancy models represent a promising approach to unravel interactions between environmental factors and spatiotemporal dynamics of outbreaking populations. Here, we investigated population dynamics of the Australian plague locust, Chortoicetes terminifera, using density data collected between 1988 and 2010 by the Australian Plague Locust Commission over more than 3 million km2 in eastern Australia. We applied multistate and autologistic multi-season occupancy models to test competing hypotheses about environmental and demographic processes affecting the large-scale dynamics of the Australian plague locust. We found that rainfall and land cover predictors best explained the spatial variability in outbreak probability across eastern Australia. Outbreaks are more likely to occur in temperate than tropical regions, with a faster and more continuous response to rainfall in desert than in agricultural areas. Our results also support the hypothesis that migration tends to propagate outbreaks only locally (over distances lower than 400 km) rather than across climatic regions. Our study suggests that locust outbreak forecasting and management systems could be improved by implementing key environmental factors and migration in hierarchical spatial models. Finally, our modeling framework can be seen as a step towards bridging the gap between mechanistic and more phenomenological models in the spatial analysis of fluctuating populations. PMID:26236870

  11. High population variability and source-sink dynamics in a solitary bee species.

    PubMed

    Franzén, Markus; Nilsson, Sven G

    2013-06-01

    Although solitary bees are considered to play key roles in ecosystem functions, surprisingly few studies have explored their population dynamics. We investigated the population dynamics of a rare, declining, solitary bee (Andrena humilis) in a landscape of 80 km2 in southern Sweden from 2003 to 2011. Only one population was persistent throughout all years studied; most likely this population supplied the surrounding landscape with 11 smaller, temporary local populations. Despite stable pollen availability, the size of the persistent population fluctuated dramatically in a two-year cycle over the nine years, with 490-1230 nests in odd-numbered years and 21-48 nests in even-numbered years. These fluctuations were not significantly related to climatic variables or pollen availability. Nineteen colonization and 14 extinction events were recorded. Occupancy decreased with distance from the persistent population and increased with increasing resource (pollen) availability. There were significant positive correlations between the size of the persistent population and patch occupancy and colonization. Colonizations were generally more common in patches closer to the persistent population, whereas extinctions were independent of distance from the persistent population. Our results highlight the complex population dynamics that exist for this solitary bee species, which could be due to source-sink dynamics, a prolonged diapause, or can represent a bet-hedging strategy to avoid natural enemies and survive in small habitat patches. If large fluctuations in solitary bee populations prove to be widespread, it will have important implications for interpreting ecological relationships, bee conservation, and pollination.

  12. Roche-lobe overflow systems powered by black holes in young star clusters: the importance of dynamical exchanges

    SciTech Connect

    Mapelli, Michela; Zampieri, Luca

    2014-10-10

    We have run 600 N-body simulations of intermediate-mass (∼3500 M {sub ☉}) young star clusters (SCs; with three different metallicities (Z = 0.01, 0.1, and 1 Z {sub ☉}). The simulations include the dependence of stellar properties and stellar winds on metallicity. Massive stellar black holes (MSBHs) with mass >25 M {sub ☉} are allowed to form through direct collapse of very massive metal-poor stars (Z < 0.3 Z {sub ☉}). We focus on the demographics of black hole (BH) binaries that undergo mass transfer via Roche lobe overflow (RLO). We find that 44% of all binaries that undergo an RLO phase (RLO binaries) formed through dynamical exchange. RLO binaries that formed via exchange (RLO-EBs) are powered by more massive BHs than RLO primordial binaries (RLO-PBs). Furthermore, the RLO-EBs tend to start the RLO phase later than the RLO-PBs. In metal-poor SCs (0.01-0.1 Z {sub ☉}), >20% of all RLO binaries are powered by MSBHs. The vast majority of RLO binaries powered by MSBHs are RLO-EBs. We have produced optical color-magnitude diagrams of the simulated RLO binaries, accounting for the emission of both the donor star and the irradiated accretion disk. We find that RLO-PBs are generally associated with bluer counterparts than RLO-EBs. We compare the simulated counterparts with the observed counterparts of nine ultraluminous X-ray sources. We discuss the possibility that IC 342 X-1, Ho IX X-1, NGC 1313 X-2, and NGC 5204 X-1 are powered by an MSBH.

  13. Post-clearcut dynamics of carbon, water and energy exchanges in a midlatitude temperate, deciduous broadleaf forest environment.

    PubMed

    Williams, Christopher A; Vanderhoof, Melanie K; Khomik, Myroslava; Ghimire, Bardan

    2014-03-01

    Clearcutting and other forest disturbances perturb carbon, water, and energy balances in significant ways, with corresponding influences on Earth's climate system through biogeochemical and biogeophysical effects. Observations are needed to quantify the precise changes in these balances as they vary across diverse disturbances of different types, severities, and in various climate and ecosystem type settings. This study combines eddy covariance and micrometeorological measurements of surface-atmosphere exchanges with vegetation inventories and chamber-based estimates of soil respiration to quantify how carbon, water, and energy fluxes changed during the first 3 years following forest clearing in a temperate forest environment of the northeastern US. We observed rapid recovery with sustained increases in gross ecosystem productivity (GEP) over the first three growing seasons post-clearing, coincident with large and relatively stable net emission of CO2 because of overwhelmingly large ecosystem respiration. The rise in GEP was attributed to vegetation changes not environmental conditions (e.g., weather), but attribution to the expansion of leaf area vs. changes in vegetation composition remains unclear. Soil respiration was estimated to contribute 44% of total ecosystem respiration during summer months and coarse woody debris accounted for another 18%. Evapotranspiration also recovered rapidly and continued to rise across years with a corresponding decrease in sensible heat flux. Gross short-wave and long-wave radiative fluxes were stable across years except for strong wintertime dependence on snow covered conditions and corresponding variation in albedo. Overall, these findings underscore the highly dynamic nature of carbon and water exchanges and vegetation composition during the regrowth following a severe forest disturbance, and sheds light on both the magnitude of such changes and the underlying mechanisms with a unique example from a temperate, deciduous

  14. Confirmatory analysis of the AP1000 passive residual heat removal heat exchanger with 3-D computational fluid dynamic analysis

    SciTech Connect

    Schwall, James R.; Karim, Naeem U.; Thakkar, Jivan G.; Taylor, Creed; Schulz, Terry; Wright, Richard F.

    2006-07-01

    The AP1000 is an 1100 MWe advanced nuclear power plant that uses passive safety features to enhance plant safety and to provide significant and measurable improvements in plant simplification, reliability, investment protection and plant costs. The AP1000 received final design approval from the US-NRC in 2004. The AP1000 design is based on the AP600 design that received final design approval in 1999. Wherever possible, the AP1000 plant configuration and layout was kept the same as AP600 to take advantage of the maturity of the design and to minimize new design efforts. As a result, the two-loop configuration was maintained for AP1000, and the containment vessel diameter was kept the same. It was determined that this significant power up-rate was well within the capability of the passive safety features, and that the safety margins for AP1000 were greater than those of operating PWRs. A key feature of the passive core cooling system is the passive residual heat removal heat exchanger (PRHR HX) that provides decay heat removal for postulated LOCA and non-LOCA events. The PRHR HX is a C-tube heat exchanger located in the in-containment refueling water storage tank (IRWST) above the core promoting natural circulation heat removal between the reactor cooling system and the tank. Component testing was performed for the AP600 PRHR HX to determine the heat transfer characteristics and to develop correlations to be used for the AP1000 safety analysis codes. The data from these tests were confirmed by subsequent integral tests at three separate facilities including the ROSA facility in Japan. Owing to the importance of this component, an independent analysis has been performed using the ATHOS-based computational fluid dynamics computer code PRHRCFD. Two separate models of the PRHR HX and IRWST have been developed representing the ROSA test geometry and the AP1000 plant geometry. Confirmation of the ROSA test results were used to validate PRHRCFD, and the AP1000 plant model

  15. {sup 1}H and {sup 23}Na MAS NMR spectroscopy of cationic species in CO{sub 2} selective alkaline earth metal porous silicoaluminophosphates prepared via liquid and solid state ion exchange

    SciTech Connect

    Arevalo-Hidalgo, Ana G.; Dugar, Sneha; Fu, Riqiang; Hernandez-Maldonado, Arturo J.

    2012-07-15

    The location of extraframework cations in Sr{sup 2+} and Ba{sup 2+} ion-exchanged SAPO-34 was estimated by means of {sup 1}H and {sup 23}Na MAS NMR spectroscopy and spectral deconvolution. Incorporation of the alkaline earth metal cations onto the SAPO framework was achieved via liquid state ion exchange, coupled partial detemplation/solid-state ion exchange, and combination of both techniques. MAS NMR revealed that the level of ion exchange was limited by the presence of protons and sodium cations near hexagonal prisms (site SI), which are relatively difficult to exchange with the alkaline earth metal due to steric and charge repulsion criteria. In addition, the presence of ammonium cations in the supercages facilitated the exchange of otherwise tenacious hydrogen as corroborated by unit cell compositional data as well as enhanced CO{sub 2} adsorption at low partial pressures. The extraframework ammonium species were produced from partial detemplation of the structure-directing agent employed for the SAPO-34 synthesis, tetraethylammonium. - Graphical abstract: MAS NMR was used to elucidate the position the cationic species in alkaline earth metal exchanged silicoaluminophosphates. These species played a significant role during the ion exchange process and, therefore, the materials ultimate CO{sub 2} adsorption performance. Highlights: Black-Right-Pointing-Pointer Location of extraframework Sr{sup 2+} or Ba{sup 2+} cations was estimated by means of {sup 1}H and {sup 23}Na MAS NMR. Black-Right-Pointing-Pointer Level of Sr{sup 2+} or Ba{sup 2+} ion exchange was limited by the presence of protons and sodium cations. Black-Right-Pointing-Pointer Presence of ammonium cations in the supercages facilitated the exchange. Black-Right-Pointing-Pointer Sr{sup 2+} and Ba{sup 2+} ion exchanged SAPOs are outstanding CO{sub 2} adsorbents.

  16. Injectable and Self-Healing Dynamic Hydrogels Based on Metal(I)-Thiolate/Disulfide Exchange as Biomaterials with Tunable Mechanical Properties.

    PubMed

    Casuso, Pablo; Odriozola, Ibon; Pérez-San Vicente, Adrián; Loinaz, Iraida; Cabañero, Germán; Grande, Hans-Jürgen; Dupin, Damien

    2015-11-01

    Despite numerous strategies involving dynamic covalent bonds to produce self-healing hydrogels with similar frequency-dependent stiffness to native tissues, it remains challenging to use biologically relevant thiol/disulfide exchange to confer such properties to polymeric networks. Herein, we report a new method based on Metal(I) [Au(I) or Ag(I)] capping to protect thiolates from aerial oxidation without preventing thiolate/disulfide exchange. Dynamic hydrogels were readily prepared by injecting simultaneously aqueous solutions of commercially available HAuCl4 and 4-arm thiol-terminated polyethylene glycol [(PEGSH)4], resulting in a network containing a mixture of Au(I)-thiolate (Au-S) and disulfide bonds (SS). While the dynamic properties of the hydrogel were closely dependent on the pH, the mechanical properties could be easily tuned by adjusting (PEGSH)4 concentration and amount of Au-S, as judged by dynamic rheology studies. Permanent Au-S/SS exchange at physiological pH conferred self-healing behavior and frequency-dependent stiffness to the hydrogel. In addition, in vitro studies confirmed that Au-based dynamic material was not cytotoxic to human dermal fibroblasts, demonstrating its potential use as a medical device. Dynamic hydrogels obtained using Ag(I) ions demonstrated that the exchange reaction was not affected by the nature of the Metal(I) capping. Finally, this efficient thiolate capping strategy offers a simple way to produce injectable and self-healing dynamic hydrogels from virtually any thiol-containing polymers. PMID:26418440

  17. Characterization of the internal dynamics and conformational space of zinc-bound amyloid β peptides by replica-exchange molecular dynamics simulations.

    PubMed

    Xu, Liang; Wang, Xiaojuan; Wang, Xicheng

    2013-07-01

    Amyloid β (Aβ) peptides and metal ions have been associated with the pathogenesis of Alzheimer's disease. The conformational space of Aβ fragments of different length with and without binding of metal ions has been extensively investigated by replica-exchange molecular dynamics (REMD) simulation. However, only trajectories extracted at relatively low temperatures have been used for this analysis. The capability of REMD simulations to characterize the internal dynamics of such intrinsically disordered proteins (IDPs) as Aβ has been overlooked. In this work, we use an approach recently developed by Xue and Skrynnikov (J Am Chem Soc 133:14614-14628, 2011) to calculate NMR observables, including (15)N relaxation rates and (15)N-(1)H nuclear Overhauser enhancement (NOE), from the high-temperature trajectory of REMD simulations for zinc-bound Aβ peptides. The time axis of the trajectory was rescaled to correct for the effect of the high temperature (408 K) compared with the experimental temperature (278 K). Near-quantitative agreement between simulated values and experimental results was obtained. When the structural properties and free-energy surfaces of zinc-bound Aβ(1-40) and Aβ(1-42) were compared at the physiological temperature 310 K it was found that zinc-bound Aβ(1-42) was more rigid than Aβ(1-40) at the C terminus, and its conformational transitions were also more preferred. The self-consistent results derived from trajectories at high and low temperatures demonstrate the capability of REMD simulations to capture the internal dynamics of IDPs.

  18. Proton exchange membrane fuel cell degradation: A parametric analysis using Computational Fluid Dynamics

    NASA Astrophysics Data System (ADS)

    Ozden, Ender; Tari, Ilker

    2016-02-01

    A Polymer Electrolyte Membrane (PEM) fuel cell is numerically investigated both as fresh and as degraded with the help of observed degradation patterns reported in the literature. The fresh fuel cell model is validated and verified with the data from the literature. Modifying the model by varying the parameters affected by degradation, a degraded PEM fuel cell model is created. The degraded fuel cell is parametrically analyzed by using a commercial Computational Fluid Dynamics (CFD) software. The investigated parameters are the membrane equivalent weight, the Catalyst Layer (CL) porosity and viscous resistance, the Gas Diffusion Layer (GDL) porosity and viscous resistance, and the bipolar plate contact resistance. It is shown for the first time that PEM fuel cell overall degradation can be numerically estimated by combining experimental data from degraded individual components. By comparing the simulation results for the fresh and the degraded PEM fuel cells for two years of operation, it is concluded that the effects of overall degradation on cell potential is significant - estimated to be 17% around the operating point of the fuel cell at 0.95 V open circuit voltage and 70 °C operating temperature.

  19. Investigation of mercury exchange between forest canopy vegetation and the atmosphere using a new dynamic chamber

    USGS Publications Warehouse

    Graydon, J.A.; St. Louis, V.L.; Lindberg, S.E.; Hintelmann, H.; Krabbenhoft, D.P.

    2006-01-01

    This paper presents the design of a dynamic chamber system that allows full transmission of PAR and UV radiation and permits enclosed intact foliage to maintain normal physiological function while Hg(0) flux rates are quantified in the field. Black spruce and jack pine foliage both emitted and absorbed Hg(0), exhibiting compensation points near atmospheric Hg(0) concentrations of ???2-3 ng m-3. Using enriched stable Hg isotope spikes, patterns of spike Hg(II) retention on foliage were investigated. Hg(0) evasion rates from foliage were simultaneously measured using the chamber to determine if the decline of foliar spike Hg(II) concentrations overtime could be explained by the photoreduction and re-emission of spike Hg to the atmosphere. This mass balance approach suggested that spike Hg(0) fluxes alone could not account for the measured decrease in spike Hg(II) on foliage following application, implying that either the chamber underestimates the true photoreduction of Hg(II) to Hg(0) on foliage, or other mechanisms of Hg(II) loss from foliage, such as cuticle weathering, are in effect. The radiation spectrum responsible for the photoreduction of newly deposited Hg(II) on foliage was also investigated. Our spike experiments suggest that some of the Hg(II) in wet deposition retained by the forest canopy may be rapidly photoreduced to Hg(0) and re-emitted back to the atmosphere, while another portion may be retained by foliage at the end of the growing season, with some being deposited in litterfall. This finding has implications for the estimation of Hg dry deposition based on throughfall and litterfall fluxes. ?? 2006 American Chemical Society.

  20. Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution

    PubMed Central

    Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J.; Golovanov, Alexander P.

    2016-01-01

    The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (SosCat) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of SosCat, while SosCat also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos. PMID:27412770

  1. Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution.

    PubMed

    Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J; Golovanov, Alexander P

    2016-01-01

    The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (Sos(Cat)) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of Sos(Cat), while Sos(Cat) also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos. PMID:27412770

  2. Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution.

    PubMed

    Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J; Golovanov, Alexander P

    2016-07-14

    The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (Sos(Cat)) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of Sos(Cat), while Sos(Cat) also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos.

  3. Constraints on Genome Dynamics Revealed from Gene Distribution among the Ralstonia solanacearum Species

    PubMed Central

    Lefeuvre, Pierre; Cellier, Gilles; Remenant, Benoît; Chiroleu, Frédéric; Prior, Philippe

    2013-01-01

    Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens. PMID:23723974

  4. Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix

    PubMed Central

    Springer, Mark S.; Meredith, Robert W.; Gatesy, John; Emerling, Christopher A.; Park, Jong; Rabosky, Daniel L.; Stadler, Tanja; Steiner, Cynthia; Ryder, Oliver A.; Janečka, Jan E.; Fisher, Colleen A.; Murphy, William J.

    2012-01-01

    Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (“Grande Coupure”) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts. PMID:23166696

  5. Dynamics of novel forests of Castilla elastica in Puerto Rico: from species to ecosystems.

    PubMed

    Fonseca da Silva, Jéssica

    2015-08-01

    Novel forests (NFs)-forests that contain a combination of introduced and native species-are a consequence of intense anthropogenic disturbances and the natural resilience of disturbed ecosystems. The extent to which NFs have similar forest function as comparable native secondary forests is a matter of debate in the scientific community. Little is known about the performance of individual species in those forests. This study focuses on the functional attributes of Castilla elastica NFs in Puerto Rico and on the differences between introduced and native species growing side by side in these forests. Rates of processes measured here were later compared with data from literature about NSFs. I hypothesize that juvenile plants of C. elastica in NFs have higher survival rate than those of native species and that C. elastica trees have faster biomass fluxes than native trees. To test the hypotheses, I measured survival rates of juvenile plants and tree growth and characterized the aboveground litter fluxes and storage. Although juvenile plants of native species displayed higher survival rates than those of C. elastica (53% vs. 28%), the latter was dominant in the understory (96%). Stand biomass growth rate was 2.0 ± 0.4 (average ± one standard deviation) Mg·ha(-1)·year(-1) for the whole forest, and Guarea guidonia, a native species, exhibited the highest tree growth. Total litter fall was 9.6 ± 0.5 Mg·ha(-1)·year(-1), and mean litter standing stock was 4.4 ± 0.1 Mg·ha(-1). Castilla elastica litter fall decomposed twice as fast as that of native species (5.8 ± 1.1 vs. 3.03 ± 1 k·year(-1)). Literature comparisons show that the present NFs differ in some rates of processes from NSFs. This study brings unique and detailed supporting data about the ecological dynamics under mature novel forest stands. Further comprehensive studies about NFs are important to strengthen the body of knowledge about the wide range of variation of emerging tropical ecosystems. Due to the

  6. Dynamics of novel forests of Castilla elastica in Puerto Rico: from species to ecosystems.

    PubMed

    Fonseca da Silva, Jéssica

    2015-08-01

    Novel forests (NFs)-forests that contain a combination of introduced and native species-are a consequence of intense anthropogenic disturbances and the natural resilience of disturbed ecosystems. The extent to which NFs have similar forest function as comparable native secondary forests is a matter of debate in the scientific community. Little is known about the performance of individual species in those forests. This study focuses on the functional attributes of Castilla elastica NFs in Puerto Rico and on the differences between introduced and native species growing side by side in these forests. Rates of processes measured here were later compared with data from literature about NSFs. I hypothesize that juvenile plants of C. elastica in NFs have higher survival rate than those of native species and that C. elastica trees have faster biomass fluxes than native trees. To test the hypotheses, I measured survival rates of juvenile plants and tree growth and characterized the aboveground litter fluxes and storage. Although juvenile plants of native species displayed higher survival rates than those of C. elastica (53% vs. 28%), the latter was dominant in the understory (96%). Stand biomass growth rate was 2.0 ± 0.4 (average ± one standard deviation) Mg·ha(-1)·year(-1) for the whole forest, and Guarea guidonia, a native species, exhibited the highest tree growth. Total litter fall was 9.6 ± 0.5 Mg·ha(-1)·year(-1), and mean litter standing stock was 4.4 ± 0.1 Mg·ha(-1). Castilla elastica litter fall decomposed twice as fast as that of native species (5.8 ± 1.1 vs. 3.03 ± 1 k·year(-1)). Literature comparisons show that the present NFs differ in some rates of processes from NSFs. This study brings unique and detailed supporting data about the ecological dynamics under mature novel forest stands. Further comprehensive studies about NFs are important to strengthen the body of knowledge about the wide range of variation of emerging tropical ecosystems. Due to the

  7. Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation.

    PubMed

    Laureys, David; De Vuyst, Luc

    2014-04-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product. PMID:24532061

  8. Population dynamics of two diplectanid species (Monogenea) parasitising sparid hosts (Sparidae).

    PubMed

    Emre, Yilmaz; Emre, Nesrin; Aydogdu, Ali; Bušelić, Ivana; Smales, Lesley R; Mladineo, Ivona

    2015-03-01

    Economically important sparid fish species, gilthead (Sparus aurata) and white seabream (Diplodus sargus) (Sparidae) are frequently parasitised by diplectanid monogeneans, known to induce severe losses in farming conditions. We have analysed population dynamic of two diplectanid species, Lamellodiscus echeneis and Lamellodiscus ignoratus (Monogenea: Diplectanidae) collected from two bream species in the Beymelek Lagoon (southwest coast of Turkey), comparing it between different host variables (fish size, age and sex) in order to have insight in parasites' ecology, important for managing parasitosis in the intensive aquaculture system. In seabream (N = 127), L. echeneis prevalence was 46.5 % (exact 95 % confidence limits 38.90-54.14), mean abundance 5.64 (bootstrap 95 % confidence limits 4.20-7.65) and mean intensity 12.14 (bootstrap 95 % confidence limits 9.49-15.59). In white seabream (N = 102), L. ignoratus prevalence was 24.5 % (exact 95 % confidence limits 16.53-34.03), mean abundance 1.73 (bootstrap 95 % confidence limits 0.98-3.21) and mean intensity 7.04 (bootstrap 95 % confidence limits 4.60-11.40). Parasites' parameters differed only between seasons in both hosts and between age categories in gilthead, but not in white seabream.

  9. Microbial Species Diversity, Community Dynamics, and Metabolite Kinetics of Water Kefir Fermentation

    PubMed Central

    Laureys, David

    2014-01-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product. PMID:24532061

  10. Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation.

    PubMed

    Laureys, David; De Vuyst, Luc

    2014-04-01

    Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product.

  11. Delineation of the dynamic properties of individual lipid species in native and synthetic pulmonary surfactants.

    PubMed

    Farver, Suzanne; Smith, Adam N; Mills, Frank D; Egri, Adam G; Long, Joanna R

    2015-01-01

    Pulmonary surfactant (PS) is characterized by a highly conserved lipid composition and the formation of unique multilamellar structures within the lung. An unusually high concentration of DPPC is a hallmark of PS and is critical to the formation of a high surface area, stable air/water interface; the unusual lipid polymorphisms observed in PS are dependent on surfactant proteins, particularly lung surfactant protein B (SP-B). The molecular mechanisms of lipid trafficking and assembly in PS remain largely uncharacterized. Using (2)H and (31)P NMR, we characterize the dynamics and polymorphisms of the major lipid species in native PS and synthetic lipid mixtures as a function of SP-B1-25 addition. Our findings point to increased dynamics and a departure from a lamellar behavior for DPPC on addition of the peptide, consistent with our observations of DPPC phase separation in native surfactant. The monounsaturated lipids POPC, POPG and POPE remain in a lamellar phase and are less affected than DPPC by surfactant peptide addition. Additionally, we demonstrate that the properties of a native PS can be successfully mimicked by using a fully synthetic lipid mixture allowing the efficient evaluation of peptidomimetics under development for PS replacement therapies via NMR spectroscopy. The specificity of the dynamic changes in DPPC relative to POPC suggests the importance of tuning partitioning properties in successful peptidomimetic design.

  12. Quantum dynamics of {sup 16}O + {sup 36}O{sub 2} and {sup 18}O + {sup 32}O{sub 2} exchange reactions

    SciTech Connect

    Rajagopala Rao, T.; Mahapatra, S.; Guillon, G.; Honvault, P.

    2015-05-07

    We present quantum dynamical investigations of {sup 16}O + {sup 36}O{sub 2} and {sup 18}O + {sup 32}O{sub 2} exchange reactions using a time-independent quantum mechanical method and an accurate global potential energy surface of ozone [Dawes et al., J. Chem. Phys. 135, 081102 (2011)]. Initial state-selected integral cross sections, rate constants, and Boltzmann averaged thermal rate constants are obtained and compared with earlier experimental and theoretical results. The computed thermal rate constants for the oxygen exchange reactions exhibit a negative temperature dependence, as found experimentally. They are in better agreement with the experiments than the previous studies on the same reactions.

  13. Similarity measure and topology evolution of foreign exchange markets using dynamic time warping method: Evidence from minimal spanning tree

    NASA Astrophysics Data System (ADS)

    Wang, Gang-Jin; Xie, Chi; Han, Feng; Sun, Bo

    2012-08-01

    In this study, we employ a dynamic time warping method to study the topology of similarity networks among 35 major currencies in international foreign exchange (FX) markets, measured by the minimal spanning tree (MST) approach, which is expected to overcome the synchronous restriction of the Pearson correlation coefficient. In the empirical process, firstly, we subdivide the analysis period from June 2005 to May 2011 into three sub-periods: before, during, and after the US sub-prime crisis. Secondly, we choose NZD (New Zealand dollar) as the numeraire and then, analyze the topology evolution of FX markets in terms of the structure changes of MSTs during the above periods. We also present the hierarchical tree associated with the MST to study the currency clusters in each sub-period. Our results confirm that USD and EUR are the predominant world currencies. But USD gradually loses the most central position while EUR acts as a stable center in the MST passing through the crisis. Furthermore, an interesting finding is that, after the crisis, SGD (Singapore dollar) becomes a new center currency for the network.

  14. Miniature sodium-selective ion-exchange optode with fluorescent pH chromoionophores and tunable dynamic range.

    PubMed

    Shortreed, M; Bakker, E; Kopelman, R

    1996-08-01

    An extension into the fluorescence mode of ion-exchange optodes is described, allowing miniaturization and its concomitant benefits. A micrometer-size, fluorescent fiber-optic sodium sensor is described, based on a highly sodium-selective, crown ether-capped calix[4]arene ionophore, capable of ratiometric operation. Three sensor configurations are given, employing different lipophilic, fluorescent pH chromoionophores (Nile Blue derivatives), demonstrating the ability to improve the detection limit and tune the dynamic range to the desired region of interest. Two of the sensors are of special interest in that their working ranges lie within those desired for measuring intracellular cytosolic or blood levels of sodium at the respective physiological pH. These optodes have excellent sodium selectivity, with other physiologically relevant cations (e.g., potassium, calcium, and magnesium) being highly discriminated. Three simple mathematical relationships are given for the three experimentally used fluorescent signal mechanisms (intensity, intensity ratios, and inner-filter or energy transfer effects), permitting visualization on a single graph and enabling direct comparison of the different sensors' optical responses on a common platform. Finally, these optodes measure the sample's sodium activity, rather than the concentration, provided that the sample's pH is measured simultaneously by another sensor, such as a glass electrode. PMID:8694263

  15. Quantifying humpback whale song sequences to understand the dynamics of song exchange at the ocean basin scale.

    PubMed

    Garland, Ellen C; Noad, Michael J; Goldizen, Anne W; Lilley, Matthew S; Rekdahl, Melinda L; Garrigue, Claire; Constantine, Rochelle; Daeschler Hauser, Nan; Poole, M Michael; Robbins, Jooke

    2013-01-01

    Humpback whales have a continually evolving vocal sexual display, or "song," that appears to undergo both evolutionary and "revolutionary" change. All males within a population adhere to the current content and arrangement of the song. Populations within an ocean basin share similarities in their songs; this sharing is complex as multiple variations of the song (song types) may be present within a region at any one time. To quantitatively investigate the similarity of song types, songs were compared at both the individual singer and population level using the Levenshtein distance technique and cluster analysis. The highly stereotyped sequences of themes from the songs of 211 individuals from populations within the western and central South Pacific region from 1998 through 2008 were grouped together based on the percentage of song similarity, and compared to qualitatively assigned song types. The analysis produced clusters of highly similar songs that agreed with previous qualitative assignments. Each cluster contained songs from multiple populations and years, confirming the eastward spread of song types and their progressive evolution through the study region. Quantifying song similarity and exchange will assist in understanding broader song dynamics and contribute to the use of vocal displays as population identifiers.

  16. Effect of gas composition and gas utilisation on the dynamic response of a proton exchange membrane fuel cell

    NASA Astrophysics Data System (ADS)

    Weydahl, Helge; Møller-Holst, Steffen; Børresen, Børre

    The transient response of a proton exchange membrane fuel cell (PEMFC) was measured for various cathode gas compositions and gas utilisations (fraction of supplied reactant gas which is consumed in the fuel cell reaction). For a PEMFC operated on pure hydrogen and oxygen, the cell voltage response to current steps was fast, with response times in the range 0.01-1 s, depending on the applied current. For a PEMFC supplied with air as cathode gas, an additional relaxation process related to oxygen transport caused a slower response (approximately 0.1-2 s depending on the applied current). Response curves up to approximately 0.01 s were apparently unaffected by gas composition and utilisation and were most likely dominated by capacitive discharge of the double layer and reaction with surplus oxygen residing in the cathode. The utilisation of hydrogen had only a minor effect on the response curves, while the utilisation of air severely influenced the PEMFC dynamics. Results suggested that air flow rates should be high to obtain rapid PEMFC response.

  17. Investigation of dynamic driving cycle effect on the degradation of proton exchange membrane fuel cell by segmented cell technology

    NASA Astrophysics Data System (ADS)

    Lin, R.; Xiong, F.; Tang, W. C.; Técher, L.; Zhang, J. M.; Ma, J. X.

    2014-08-01

    Durability is one of the most important limiting factors for the commercialization of proton exchange membrane fuel cell (PEMFC). Fuel cells are more vulnerable to degradation under operating conditions as dynamic load cycle or start up/shut down. The purpose of this study is to evaluate influences of driving cycles on the durability of fuel cells through analyzing the degradation mechanism of a segmented cell in real time. This study demonstrates that the performance of the fuel cell significantly decreases after 200 cycles. The segmented cell technology is used to measure the local current density distribution, which shows that the current density at the exit region and the inlet region declines much faster than the other parts. Meanwhile, electro-chemical impedance spectroscopy (EIS) reveals that after 200 cycles the ohmic resistance of fuel cell increases, especially at the cathode, and electro-chemical surface area (ESA) decreases from 392 to 307 cm2 mg-1. Furthermore, scanning electron microscopy (SEM) images of the membrane-electrode assembly (MEA) in cross-section demonstrate crackle flaw on the surface of the catalyst layer and the delamination of the electrodes from the membrane. Transmission electron microscope (TEM) results also show that the Pt particle size increases distinctly after driving cycles.

  18. New Insights into Active Site Conformation Dynamics of E. coli PNP Revealed by Combined H/D Exchange Approach and Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Kazazić, Saša; Bertoša, Branimir; Luić, Marija; Mikleušević, Goran; Tarnowski, Krzysztof; Dadlez, Michal; Narczyk, Marta; Bzowska, Agnieszka

    2016-01-01

    The biologically active form of purine nucleoside phosphorylase (PNP) from Escherichia coli (EC 2.4.2.1) is a homohexamer unit, assembled as a trimer of dimers. Upon binding of phosphate, neighboring monomers adopt different active site conformations, described as open and closed. To get insight into the functions of the two distinctive active site conformations, virtually inactive Arg24Ala mutant is complexed with phosphate; all active sites are found to be in the open conformation. To understand how the sites of neighboring monomers communicate with each other, we have combined H/D exchange (H/DX) experiments with molecular dynamics (MD) simulations. Both methods point to the mobility of the enzyme, associated with a few flexible regions situated at the surface and within the dimer interface. Although H/DX provides an average extent of deuterium uptake for all six hexamer active sites, it was able to indicate the dynamic mechanism of cross-talk between monomers, allostery. Using this technique, it was found that phosphate binding to the wild type (WT) causes arrest of the molecular motion in backbone fragments that are flexible in a ligand-free state. This was not the case for the Arg24Ala mutant. Upon nucleoside substrate/inhibitor binding, some release of the phosphate-induced arrest is observed for the WT, whereas the opposite effects occur for the Arg24Ala mutant. MD simulations confirmed that phosphate is bound tightly in the closed active sites of the WT; conversely, in the open conformation of the active site of the WT phosphate is bound loosely moving towards the exit of the active site. In Arg24Ala mutant binary complex Pi is bound loosely, too.

  19. Evidence of Allosteric Enzyme Regulation via Changes in Conformational Dynamics: A Hydrogen/Deuterium Exchange Investigation of Dihydrodipicolinate Synthase.

    PubMed

    Sowole, Modupeola A; Simpson, Sarah; Skovpen, Yulia V; Palmer, David R J; Konermann, Lars

    2016-09-27

    Dihydrodipicolinate synthase is a tetrameric enzyme of the diaminopimelate pathway in bacteria and plants. The protein catalyzes the condensation of pyruvate (Pyr) and aspartate semialdehyde en route to the end product lysine (Lys). Dihydrodipicolinate synthase from Campylobacter jejuni (CjDHDPS) is allosterically inhibited by Lys. CjDHDPS is a promising antibiotic target, as highlighted by the recent development of a potent bis-lysine (bisLys) inhibitor. The mechanism whereby Lys and bisLys allosterically inhibit CjDHDPS remains poorly understood. In contrast to the case for other allosteric enzymes, crystallographically detectable conformational changes in CjDHDPS upon inhibitor binding are very minor. Also, it is difficult to envision how Pyr can access the active site; the available X-ray data seemingly imply that each turnover step requires diffusion-based mass transfer through a narrow access channel. This study employs hydrogen/deuterium exchange mass spectrometry for probing the structure and dynamics of CjDHDPS in a native solution environment. The deuteration kinetics reveal that the most dynamic protein regions are in the direct vicinity of the substrate access channel. This finding is consistent with the view that transient opening/closing fluctuations facilitate access of the substrate to the active site. Under saturating conditions, both Lys and bisLys cause dramatically reduced dynamics in the inhibitor binding region. In addition, rigidification extends to regions close to the substrate access channel. This finding strongly suggests that allosteric inhibitors interfere with conformational fluctuations that are required for CjDHDPS substrate turnover. In particular, our data imply that Lys and bisLys suppress opening/closing events of the access channel, thereby impeding diffusion of the substrate into the active site. Overall, this work illustrates why allosteric control does not have to be associated with crystallographically detectable large

  20. The non-statistical dynamics of the 18O + 32O2 isotope exchange reaction at two energies

    NASA Astrophysics Data System (ADS)

    Van Wyngarden, Annalise L.; Mar, Kathleen A.; Quach, Jim; Nguyen, Anh P. Q.; Wiegel, Aaron A.; Lin, Shi-Ying; Lendvay, Gyorgy; Guo, Hua; Lin, Jim J.; Lee, Yuan T.; Boering, Kristie A.

    2014-08-01

    The dynamics of the 18O(3P) + 32O2 isotope exchange reaction were studied using crossed atomic and molecular beams at collision energies (Ecoll) of 5.7 and 7.3 kcal/mol, and experimental results were compared with quantum statistical (QS) and quasi-classical trajectory (QCT) calculations on the O3(X1A') potential energy surface (PES) of Babikov et al. [D. Babikov, B. K. Kendrick, R. B. Walker, R. T. Pack, P. Fleurat-Lesard, and R. Schinke, J. Chem. Phys. 118, 6298 (2003)]. In both QS and QCT calculations, agreement with experiment was markedly improved by performing calculations with the experimental distribution of collision energies instead of fixed at the average collision energy. At both collision energies, the scattering displayed a forward bias, with a smaller bias at the lower Ecoll. Comparisons with the QS calculations suggest that 34O2 is produced with a non-statistical rovibrational distribution that is hotter than predicted, and the discrepancy is larger at the lower Ecoll. If this underprediction of rovibrational excitation by the QS method is not due to PES errors and/or to non-adiabatic effects not included in the calculations, then this collision energy dependence is opposite to what might be expected based on collision complex lifetime arguments and opposite to that measured for the forward bias. While the QCT calculations captured the experimental product vibrational energy distribution better than the QS method, the QCT results underpredicted rotationally excited products, overpredicted forward-bias and predicted a trend in the strength of forward-bias with collision energy opposite to that measured, indicating that it does not completely capture the dynamic behavior measured in the experiment. Thus, these results further underscore the need for improvement in theoretical treatments of dynamics on the O3(X1A') PES and perhaps of the PES itself in order to better understand and predict non-statistical effects in this reaction and in the formation

  1. Trophic-dynamic considerations in relating species diversity to ecosystem resilience.

    PubMed

    Johnson, K H

    2000-08-01

    Complexity in the networks of interactions among and between the living and abiotic components forming ecosystems confounds the ability of ecologists to predict the economic consequences of perturbations such as species deletions in nature. Such uncertainty hampers prudent decision making about where and when to invest most intensively in species conservation programmes. Demystifying ecosystem responses to biodiversity alterations may be best achieved through the study of the interactions allowing biotic communities to compensate internally for population changes in terms of contributing to ecosystem function, or their intrinsic functional redundancy. Because individual organisms are the biologically discrete working components of ecosystems and because environmental changes are perceived at the scale of the individual, a mechanistic understanding of functional redundancy will hinge upon understanding how individuals' behaviours influence population dynamics in the complex community setting. Here, I use analytical and graphical modelling to construct a conceptual framework for predicting the conditions under which varying degrees of interspecific functional redundancy can be found in dynamic ecosystems. The framework is founded on principles related to food web successional theory, which provides some evolutionary insights for mechanistically linking functional roles of discrete, interacting organisms with the dynamics of ecosystems because energy is the currency both for ecological fitness and for food web commerce. Net productivity is considered the most contextually relevant ecosystem process variable because of its socioeconomic significance and because it ultimately subsumes all biological processes and interactions. Redundancy relative to productivity is suggested to manifest most directly as compensatory niche shifts among adaptive foragers in exploitation ecosystems, facilitating coexistence and enhancing ecosystem recovery after disturbances which alter

  2. Dynamics of novel forests of Castilla elastica in Puerto Rico: from species to ecosystems

    PubMed Central

    Fonseca da Silva, Jéssica

    2015-01-01

    Novel forests (NFs)—forests that contain a combination of introduced and native species—are a consequence of intense anthropogenic disturbances and the natural resilience of disturbed ecosystems. The extent to which NFs have similar forest function as comparable native secondary forests is a matter of debate in the scientific community. Little is known about the performance of individual species in those forests. This study focuses on the functional attributes of Castilla elastica NFs in Puerto Rico and on the differences between introduced and native species growing side by side in these forests. Rates of processes measured here were later compared with data from literature about NSFs. I hypothesize that juvenile plants of C. elastica in NFs have higher survival rate than those of native species and that C. elastica trees have faster biomass fluxes than native trees. To test the hypotheses, I measured survival rates of juvenile plants and tree growth and characterized the aboveground litter fluxes and storage. Although juvenile plants of native species displayed higher survival rates than those of C. elastica (53% vs. 28%), the latter was dominant in the understory (96%). Stand biomass growth rate was 2.0 ± 0.4 (average ± one standard deviation) Mg·ha−1·year−1 for the whole forest, and Guarea guidonia, a native species, exhibited the highest tree growth. Total litter fall was 9.6 ± 0.5 Mg·ha−1·year−1, and mean litter standing stock was 4.4 ± 0.1 Mg·ha−1. Castilla elastica litter fall decomposed twice as fast as that of native species (5.8 ± 1.1 vs. 3.03 ± 1 k·year−1). Literature comparisons show that the present NFs differ in some rates of processes from NSFs. This study brings unique and detailed supporting data about the ecological dynamics under mature novel forest stands. Further comprehensive studies about NFs are important to strengthen the body of knowledge about the wide range of variation of emerging tropical ecosystems. Due to

  3. Dynamics of CO2-exchange and C-budgets due to soil erosion: Insights from a 4 years observation period

    NASA Astrophysics Data System (ADS)

    Hoffmann, Mathias; Albiac Borraz, Elisa; Garcia Alba, Juana; Augustin, Jürgen; Sommer, Michael

    2015-04-01

    Agriculture in the hummocky ground moraine landscape of NE-Germany is characterized by an increase in energy crop cultivation, like maize or sorghum. Both enhance lateral C fluxes by erosion and induce feedbacks on C dynamics of agroecosystems as a result of reduced wintertime plant cover and vigorous crop growth during summer. However, the actual impact of these phenomena on the CO2-sink/-source function of agricultural landscapes, is still not clear. Therefore, the interdisciplinary project "CarboZALF" was established in Dedelow/Prenzlau (NE-Germany) in 2009. Within the field experiment CarboZALF-D, CO2 fluxes for the soil-plant systems were monitored, covering typical landscape relevant soil states in respect to erosion and deposition, like Calcic Cutanic Luvisol and Endogleyic Colluvic Regosol. Automated chamber systems, each consisting of four transparent chambers (2.5 m height, basal area 2.25 m2), were placed along gradients at both measurement sites. Monitored CO2 fluxes were gap-filled on a high-temporal resolution by modelling ecosystem respiration (Reco), gross primary productivity (GPP) and net ecosystem exchange (NEE) based on parallel and continuous measurements of the CO2 exchange, soil and air temperatures as well as photosynthetic active radiation (PAR). Gap-filling was e.g. needed in case of chamber malfunctions and abrupt disturbances by farming practice. The monitored crop rotation was corn-winter wheat (2 a), sorghum-winter triticale and alfalfa (1.5 a). In our presentation we would like to show insights from a 4 years observation period, with prounounced differences between the eroded and the colluvial soil: The Endogleyic Colluvic Regosol showed higher flux rates for Reco, GPP and NEE compared to the Calcic Cutanic Luvisol. Site-specific NEE and C-balances were positively related to soil C-stocks as well as biomass production, and generated a minor C-sink in case of the Calcic Cutanic Luvisol and a highly variable C-source in case of the

  4. Studies of ground-state dynamics in isolated species by ionization-detected stimulated Raman techniques

    SciTech Connect

    Felker, P.M.

    1993-12-01

    First, the author aims to develop methods of nonlinear Raman spectroscopy for application in studies of sparse samples. Second, the author wishes to apply such methods to structural and dynamical studies of species (molecules, complexes, and clusters) in supersonic molecular beams. In the past year, the author has made progress in several areas. The first pertains to the application of mass-selective ionization-detected stimulated Raman spectroscopies (IDSRS) to the size-specific vibrational spectroscopy of solute-solvent{sub n} clusters. The second involves the application of IDSRS methods to studies of jet-cooled benzene clusters. The third pertains to the use of IDSRS methods in the study of intermolecular vibrational transitions in van der Waals complexes.

  5. The Role of Explicitly Modeling Bryophytes in Simulating Carbon Exchange and Permafrost Dynamics of an Arctic Coastal Tundra at Barrow, Alaska

    NASA Astrophysics Data System (ADS)

    Yuan, F.; Thornton, P. E.; McGuire, A. D.; Oechel, W. C.; Yang, B.; Tweedie, C. E.; Rogers, A.; Norby, R. J.

    2013-12-01

    Bryophyte cover is greater than 50% in many Arctic tundra ecosystems. In regions of the Arctic where shrubs are expanding it is expected that bryophyte cover will be substantially reduced. Such a loss in cover could influence the hydrological, biogeochemical, and permafrost dynamics of Arctic tundra ecosystems. The explicit representation of bryophyte physiological and biophysical processes in large-scale ecological and land surface models is rare, and we hypothesize that the representation of bryophytes has consequences for estimates of the exchange of water, energy, and carbon by these models. This study explicitly represents the effects of bryophyte function and structure on the exchange of carbon (e.g., summer photosynthesis effects) and energy (e.g., summer insulation effects) with the atmosphere in the Community Land Model (CLM-CN). The modified model was evaluated for its ability to simulate C exchange, soil temperature, and soil moisture since the 1970s at Barrow, Alaska through comparison with data from AmeriFlux sites, USDA Soil Climate Networks observation sites at Barrow, and other sources. We also compare the outputs of the CLM-CN simulations with those of the recently developed Dynamical Organic Soil coupled Terrestrial Ecosystem Model (DOS-TEM). Overall, our evaluation indicates that bryophytes are important contributors to land-atmospheric C exchanges in Arctic tundra and that they play an important role to permafrost thermal and hydrological processes which are critical to permafrost stability. Our next step in this study is to examine the climate system effects of explicitly representing bryophyte dynamics in the land surface model. Key Words: Bryophytes, Arctic coastal tundra, Vegetation composition, Net Ecosystem Exchange, Permafrost, Land Surface Model, Terrestrial Ecosystem Model

  6. Evolution and Emergence of Enteroviruses through Intra- and Inter-species Recombination: Plasticity and Phenotypic Impact of Modular Genetic Exchanges in the 5' Untranslated Region.

    PubMed

    Muslin, Claire; Joffret, Marie-Line; Pelletier, Isabelle; Blondel, Bruno; Delpeyroux, Francis

    2015-01-01

    Genetic recombination shapes the diversity of RNA viruses, including enteroviruses (EVs), which frequently have mosaic genomes. Pathogenic circulating vaccine-derived poliovirus (cVDPV) genomes consist of mutated vaccine poliovirus (PV) sequences encoding capsid proteins, and sequences encoding nonstructural proteins derived from other species' C EVs, including certain coxsackieviruses A (CV-A) in particular. Many cVDPV genomes also have an exogenous 5' untranslated region (5' UTR). This region is involved in virulence and includes the cloverleaf (CL) and the internal ribosomal entry site, which play major roles in replication and the initiation of translation, respectively. We investigated the plasticity of the PV genome in terms of recombination in the 5' UTR, by developing an experimental model involving the rescue of a bipartite PV/CV-A cVDPV genome rendered defective by mutations in the CL, following the co-transfection of cells with 5' UTR RNAs from each of the four human EV species (EV-A to -D). The defective cVDPV was rescued by recombination with 5' UTR sequences from the four EV species. Homologous and nonhomologous recombinants with large deletions or insertions in three hotspots were isolated, revealing a striking plasticity of the 5' UTR. By contrast to the recombination of the cVDPV with the 5' UTR of group II (EV-A and -B), which can decrease viral replication and virulence, recombination with the 5' UTRs of group I (EV-C and -D) appeared to be evolutionarily neutral or associated with a gain in fitness. This study illustrates how the genomes of positive-strand RNA viruses can evolve into mosaic recombinant genomes through intra- or inter-species modular genetic exchanges, favoring the emergence of new recombinant lineages.

  7. Soil-related variations in the population dynamics of six dipterocarp tree species with strong habitat preferences.

    PubMed

    Yamada, Toshihiro; Yamada, Yuko; Okuda, Toshinori; Fletcher, Christine

    2013-07-01

    Differences in the density of conspecific tree individuals in response to environmental gradients are well documented for many tree species, but how such density differences are generated and maintained is poorly understood. We examined the segregation of six dipterocarp species among three soil types in the Pasoh tropical forest, Malaysia. We examined how individual performance and population dynamics changed across the soil types using 10-year demographic data to compare tree performance across soil types, and constructed population matrix models to analyze the population dynamics. Species showed only minor changes in mortality and juvenile growth across soil types, although recruitment differed greatly. Clear, interspecific demographic trade-offs between growth and mortality were found in all soil types. The relative trade-offs by a species did not differ substantially among the soil types. Population sizes were projected to remain stable in all soil types for all species with one exception. Our life-table response experiment demonstrated that the population dynamics of a species differed only subtly among soil types. Therefore, species with strong density differences across soil types do not necessarily differ greatly in their population dynamics across the soil types. In contrast, interspecific differences in population dynamics were large. The trade-off between mortality and growth led to a negative correlation between the contributions of mortality and growth to variations in the population growth rate (λ) and thus reduced their net contributions. Recruitment had little impact on the variation in λ. The combination of these factors resulted in little variation in λ among species.

  8. The effect of flooding on the exchange of the volatile C2-compounds ethanol, acetaldehyde and acetic acid between leaves of Amazonian floodplain tree species and the atmosphere

    NASA Astrophysics Data System (ADS)

    Rottenberger, S.; Kleiss, B.; Kuhn, U.; Wolf, A.; Piedade, M. T. F.; Junk, W.; Kesselmeier, J.

    2008-08-01

    The effect of root inundation on the leaf emissions of ethanol, acetaldehyde and acetic acid in relation to assimilation and transpiration was investigated with 2 3 years old tree seedlings of four Amazonian floodplain species by applying dynamic cuvette systems under greenhouse conditions. Emissions were monitored over a period of several days of inundation using a combination of Proton Transfer Reaction Mass Spectrometry (PTR-MS) and conventional techniques (HPLC, ion chromatography). Under non-flooded conditions, none of the species exhibited measurable emissions of any of the compounds, but rather low deposition of acetaldehyde and acetic acid was observed instead. Tree species specific variations in deposition velocities were largely due to variations in stomatal conductance. Flooding of the roots resulted in leaf emissions of ethanol and acetaldehyde by all species, while emissions of acetic acid were only observed from the species exhibiting the highest ethanol and acetaldehyde emission rates. All three compounds showed a similar diurnal emission profile, each displaying an emission burst in the morning, followed by a decline in the evening. This concurrent behavior supports the conclusion, that all three compounds emitted by the leaves are derived from ethanol produced in the roots by alcoholic fermentation, transported to the leaves with the transpiration stream and finally partly converted to acetaldehyde and acetic acid by enzymatic processes. Co-emissions and peaking in the early morning suggest that root ethanol, after transportation with the transpiration stream to the leaves and enzymatic oxidation to acetaldehyde and acetate, is the metabolic precursor for all compounds emitted, though we can not totally exclude other production pathways. Emission rates substantially varied among tree species, with maxima differing by up to two orders of magnitude (25 1700 nmol m-2 min-1 for ethanol and 5 500 nmol m-2 min-1 for acetaldehyde). Acetic acid emissions

  9. The effect of flooding on the exchange of the volatile C2-compounds ethanol, acetaldehyde and acetic acid between leaves of Amazonian floodplain tree species and the atmosphere

    NASA Astrophysics Data System (ADS)

    Rottenberger, S.; Kleiss, B.; Kuhn, U.; Wolf, A.; Piedade, M. T. F.; Junk, W.; Kesselmeier, J.

    2008-02-01

    The effect of root inundation on the leaf emissions of ethanol, acetaldehyde and acetic acid was investigated with 2-3 years old tree seedlings of four Amazonian floodplain species by applying dynamic cuvette systems under greenhouse conditions. Emissions were monitored over a period of several days of inundation using a combination of Proton Transfer Reaction Mass Spectrometry (PTR-MS) and conventional techniques (HPLC, ion chromatography). Under non-flooded conditions, none of the species exhibited significant emissions of any of the compounds. A slight deposition of acetaldehyde and acetic acid was mainly observed, instead. Tree species specific variations in deposition velocities were largely due to variations in stomatal conductance. Flooding of the roots resulted in leaf emissions of ethanol and acetaldehyde by all species, while emissions of acetic acid occurred only by the species exhibiting the highest ethanol and acetaldehyde emission rates. All three compounds showed a similar diurnal emission profile, each displaying an emission burst in the morning, followed by a decline in the evening. This concurrent behavior supports the conclusion, that all three compounds emitted by the leaves are derived from ethanol produced in the roots by alcoholic fermentation, transported to the leaves with the transpiration stream and finally partly converted to acetaldehyde and acetic acid by enzymatic processes. Co-emissions and peaking in the early morning confirmed that root ethanol, after transportation with the transpiration stream to the leaves and enzymatic oxidation to acetaldehyde and acetate, is the metabolic precursor for all compounds emitted. Emission rates substantially varied among tree species, with maxima differing by up to two orders of magnitude (3-200 nmol m-2 min-1 for ethanol and 5-500 nmol m-2 min-1 for acetaldehyde). Acetic acid emissions reached 12 nmol m-2 min-1. The observed differences in emission rates between the tree species are discussed

  10. Flow-Induced New Channels of Energy Exchange in Multi-Scale Plasma Dynamics - Revisiting Perturbative Hybrid Kinetic-MHD Theory.

    PubMed

    Shiraishi, Junya; Miyato, Naoaki; Matsunaga, Go

    2016-05-10

    It is found that new channels of energy exchange between macro- and microscopic dynamics exist in plasmas. They are induced by macroscopic plasma flow. This finding is based on the kinetic-magnetohydrodynamic (MHD) theory, which analyses interaction between macroscopic (MHD-scale) motion and microscopic (particle-scale) dynamics. The kinetic-MHD theory is extended to include effects of macroscopic plasma flow self-consistently. The extension is realised by generalising an energy exchange term due to wave-particle resonance, denoted by δ WK. The first extension is generalisation of the particle's Lagrangian, and the second one stems from modification to the particle distribution function due to flow. These extensions lead to a generalised expression of δ WK, which affects the MHD stability of plasmas.

  11. Flow-Induced New Channels of Energy Exchange in Multi-Scale Plasma Dynamics – Revisiting Perturbative Hybrid Kinetic-MHD Theory

    PubMed Central

    Shiraishi, Junya; Miyato, Naoaki; Matsunaga, Go

    2016-01-01

    It is found that new channels of energy exchange between macro- and microscopic dynamics exist in plasmas. They are induced by macroscopic plasma flow. This finding is based on the kinetic-magnetohydrodynamic (MHD) theory, which analyses interaction between macroscopic (MHD-scale) motion and microscopic (particle-scale) dynamics. The kinetic-MHD theory is extended to include effects of macroscopic plasma flow self-consistently. The extension is realised by generalising an energy exchange term due to wave-particle resonance, denoted by δ WK. The first extension is generalisation of the particle’s Lagrangian, and the second one stems from modification to the particle distribution function due to flow. These extensions lead to a generalised expression of δ WK, which affects the MHD stability of plasmas. PMID:27160346

  12. Population dynamics, distribution, and species diversity of fruit flies on cucurbits in Kashmir Valley, India.

    PubMed

    Ganie, S A; Khan, Z H; Ahangar, R A; Bhat, H A; Hussain, Barkat

    2013-01-01

    Given the economic importance of cucurbits and the losses incurred by fruit fly infestation, the population dynamics of fruit flies in cucurbit crops and the influence of abiotic parameters, such as temperature, relative humidity, rainfall, and total sunshine hours per day on the fruit fly population were studied. The study was carried out at six locations; in district Srinagar the locations were Batmaloo, Shalimar, and Dal, while in district Budgam the locations were Chadoora, Narkara, and Bugam (Jammu and Kashmir, India). Various cucurbit crops, such as cucumber, bottle gourd, ridge gourd and bitter gourd, were selected for the study. With regard to locations, mean fruit fly population was highest (6.09, 4.55, 3.87, and 3.60 flies/trap/week) at Batamaloo and Chadoora (4.73, 3.93, 2.73, and 2.73 flies/trap/week) on cucumber, bottle gourd, ridge gourd, and bitter gourd, respectively. The population of fruit flies was significantly correlated with the minimum and maximum temperature. The maximum species diversity of fruit flies was 0.511, recorded in Chadoora. Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae) was the most predominant species in both Srinagar and Budgam, followed by B. dorsalis (Hendel) and B. tau (Walker), while B. scutellaris (Bezzi) was found only in Chadoora. Results of the present investigation may be utilized in developing a sustainable pest management strategy in the agroecological system.

  13. Species diversity, community dynamics, and metabolite kinetics of spontaneous leek fermentations.

    PubMed

    Wouters, D; Bernaert, N; Conjaerts, W; Van Droogenbroeck, B; De Loose, M; De Vuyst, L

    2013-04-01

    Leek (Allium ampeloprasum var. porrum) is one of Belgium's most important vegetables. All or part of the green leek parts are often left on the fields because of their limited cooking applications compared to the white leek parts. Therefore, the possibility to perform leek fermentations in view of product valorization and diversification was investigated. This study deals with the community dynamics, species diversity, and metabolite kinetics of spontaneous leek fermentations, thereby studying the influence of added NaCl concentration, harvesting season, and duration of the fermentation. The combination of a culture-dependent and culture-independent approach revealed the prevalence of lactic acid bacteria (LAB) from the third day of fermentation onwards, which was not influenced by the fermentation conditions applied. Enterobacteriaceae, Pseudomonadaceae, and yeasts disappeared after one week of fermentation. Leuconostoc mesenteroides, Lactobacillus sakei, and Lactobacillus plantarum, Lactobacillus brevis, and Lactobacillus parabrevis were the most frequently isolated LAB species. Both added NaCl concentrations were suitable to perform successful fermentations within three weeks. By that time, glucose and fructose, the main leek carbohydrates, were metabolized into mainly lactic acid, acetic acid, ethanol, and mannitol. A sensory analysis revealed that the fermented white leek parts were generally more appreciated than the fermented green leek parts. PMID:23200651

  14. Constructing Time-Resolved Species Sensitivity Distributions Using a Hierarchical Toxico-Dynamic Model.

    PubMed

    Kon Kam King, Guillaume; Delignette-Muller, Marie Laure; Kefford, Ben J; Piscart, Christophe; Charles, Sandrine

    2015-10-20

    Classical species sensitivity distribution (SSD) is used to assess the threat to ecological communities posed by a contaminant and derive a safe concentration. It suffers from several well-documented weaknesses regarding its ecological realism and statistical soundness. Criticism includes that SSD does not take time-dependence of the data into account, that safe concentrations obtained from SSD might not be entirely protective of the target communities, and that there are issues of statistical representativity and of uncertainty propagation from the experimental data. We present a hierarchical toxico-dynamic (TD) model to simultaneously address these weaknesses: TD models incorporate time-dependence and allow improvement of the ecological relevance of safe concentrations, while the hierarchical approach affords appropriate propagation of uncertainty from the original data. We develop this model on a published data set containing the salinity tolerance over 72 h of 217 macroinvertebrate taxa, obtained through rapid toxicity testing (RTT). The shrinkage properties of the hierarchical model prove particularly adequate for modeling inhomogeneous RTT data. Taking into account the large variability in the species response, the model fits the whole data set well. Moreover, the model predicts a time-independent safe concentration below that obtained with classical SSD at 72 h, demonstrating under-protectiveness of the classical approach. PMID:26406398

  15. Bacterial-biota dynamics of eight bryophyte species from different ecosystems.

    PubMed

    Koua, Faisal Hammad Mekky; Kimbara, Kazuhide; Tani, Akio

    2015-03-01

    Despite the importance of bryophyte-associated microorganisms in various ecological aspects including their crucial roles in the soil-enrichment of organic mass and N2 fixation, nonetheless, little is known about the microbial diversity of the bryophyte phyllospheres (epi-/endophytes). To get insights into bacterial community structures and their dynamics on the bryophyte habitats in different ecosystems and their potential biological roles, we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan. Forty-two bacterial species belonging to γ-proteobacteria and Firmicutes with 71.4% and 28.6%, respectively, were identified among 90 DGGE gel band population. These DGGE-bands were assigned to 13 different genera with obvious predomination the genus Clostridium with 21.4% from the total bacterial community. These analyses provide new insights into bryophyte-associated bacteria and their relations to the ecosystems. PMID:25737654

  16. Population dynamics, distribution, and species diversity of fruit flies on cucurbits in Kashmir Valley, India.

    PubMed

    Ganie, S A; Khan, Z H; Ahangar, R A; Bhat, H A; Hussain, Barkat

    2013-01-01

    Given the economic importance of cucurbits and the losses incurred by fruit fly infestation, the population dynamics of fruit flies in cucurbit crops and the influence of abiotic parameters, such as temperature, relative humidity, rainfall, and total sunshine hours per day on the fruit fly population were studied. The study was carried out at six locations; in district Srinagar the locations were Batmaloo, Shalimar, and Dal, while in district Budgam the locations were Chadoora, Narkara, and Bugam (Jammu and Kashmir, India). Various cucurbit crops, such as cucumber, bottle gourd, ridge gourd and bitter gourd, were selected for the study. With regard to locations, mean fruit fly population was highest (6.09, 4.55, 3.87, and 3.60 flies/trap/week) at Batamaloo and Chadoora (4.73, 3.93, 2.73, and 2.73 flies/trap/week) on cucumber, bottle gourd, ridge gourd, and bitter gourd, respectively. The population of fruit flies was significantly correlated with the minimum and maximum temperature. The maximum species diversity of fruit flies was 0.511, recorded in Chadoora. Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae) was the most predominant species in both Srinagar and Budgam, followed by B. dorsalis (Hendel) and B. tau (Walker), while B. scutellaris (Bezzi) was found only in Chadoora. Results of the present investigation may be utilized in developing a sustainable pest management strategy in the agroecological system. PMID:23906383

  17. Time-variant species pools shape competitive dynamics and biodiversity-ecosystem function relationships.

    PubMed

    Armitage, David W

    2016-09-14

    Biodiversity-ecosystem function (BEF) experiments routinely employ common garden designs, drawing samples from a local biota. The communities from which taxa are sampled may not, however, be at equilibrium. To test for temporal changes in BEF relationships, I assembled the pools of aquatic bacterial strains isolated at different time points from leaves on the pitcher plant Darlingtonia californica in order to evaluate the strength, direction and drivers of the BEF relationship across a natural host-associated successional gradient. I constructed experimental communities using bacterial isolates from each time point and measured their respiration rates and competitive interactions. Communities assembled from mid-successional species pools showed the strongest positive relationships between community richness and respiration rates, driven primarily by linear additivity among isolates. Diffuse competition was common among all communities but greatest within mid-successional isolates. These results demonstrate the dependence of the BEF relationship on the temporal dynamics of the local species pool, implying that ecosystems may respond differently to the addition or removal of taxa at different points in time during succession. PMID:27629035

  18. Species diversity, community dynamics, and metabolite kinetics of spontaneous leek fermentations.

    PubMed

    Wouters, D; Bernaert, N; Conjaerts, W; Van Droogenbroeck, B; De Loose, M; De Vuyst, L

    2013-04-01

    Leek (Allium ampeloprasum var. porrum) is one of Belgium's most important vegetables. All or part of the green leek parts are often left on the fields because of their limited cooking applications compared to the white leek parts. Therefore, the possibility to perform leek fermentations in view of product valorization and diversification was investigated. This study deals with the community dynamics, species diversity, and metabolite kinetics of spontaneous leek fermentations, thereby studying the influence of added NaCl concentration, harvesting season, and duration of the fermentation. The combination of a culture-dependent and culture-independent approach revealed the prevalence of lactic acid bacteria (LAB) from the third day of fermentation onwards, which was not influenced by the fermentation conditions applied. Enterobacteriaceae, Pseudomonadaceae, and yeasts disappeared after one week of fermentation. Leuconostoc mesenteroides, Lactobacillus sakei, and Lactobacillus plantarum, Lactobacillus brevis, and Lactobacillus parabrevis were the most frequently isolated LAB species. Both added NaCl concentrations were suitable to perform successful fermentations within three weeks. By that time, glucose and fructose, the main leek carbohydrates, were metabolized into mainly lactic acid, acetic acid, ethanol, and mannitol. A sensory analysis revealed that the fermented white leek parts were generally more appreciated than the fermented green leek parts.

  19. Synthesis of Formamide and Related Organic Species in the Interstellar Medium via Chemical Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Spezia, Riccardo; Jeanvoine, Yannick; Hase, William L.; Song, Kihyung; Largo, Antonio

    2016-08-01

    We show, by means of direct dynamics simulations, how it is possible to define possible reactants and mechanisms leading to the formation of formamide in the interstellar medium. In particular, different ion-molecule reactions in the gas phase were considered: NH3OH+, NH2OH{}2+, H2COH+, and NH4 + for the ions and NH2OH, H2CO, and NH3 for the partner neutrals. These calculations were combined with high level ab initio calculations to investigate possible further evolution of the products observed. In particular, for formamide, we propose that the NH2OH{}2+ + H2CO reaction can produce an isomer, NH2OCH{}2+, that, after dissociative recombination, can produce neutral formamide, which was observed in space. The direct dynamics do not pre-impose any reaction pathways and in other reactions, we did not observe the formation of formamide or any possible precursor. On the other hand, we obtained other interesting reactions, like the formation of NH2CH{}2+. Finally, some radiative association processes are proposed. All of the results obtained are discussed in light of the species observed in radioastronomy.

  20. Synthesis of Formamide and Related Organic Species in the Interstellar Medium via Chemical Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Spezia, Riccardo; Jeanvoine, Yannick; Hase, William L.; Song, Kihyung; Largo, Antonio

    2016-08-01

    We show, by means of direct dynamics simulations, how it is possible to define possible reactants and mechanisms leading to the formation of formamide in the interstellar medium. In particular, different ion–molecule reactions in the gas phase were considered: NH3OH+, NH2OH{}2+, H2COH+, and NH4 + for the ions and NH2OH, H2CO, and NH3 for the partner neutrals. These calculations were combined with high level ab initio calculations to investigate possible further evolution of the products observed. In particular, for formamide, we propose that the NH2OH{}2+ + H2CO reaction can produce an isomer, NH2OCH{}2+, that, after dissociative recombination, can produce neutral formamide, which was observed in space. The direct dynamics do not pre-impose any reaction pathways and in other reactions, we did not observe the formation of formamide or any possible precursor. On the other hand, we obtained other interesting reactions, like the formation of NH2CH{}2+. Finally, some radiative association processes are proposed. All of the results obtained are discussed in light of the species observed in radioastronomy.

  1. Incongruent range dynamics between co-occurring Asian temperate tree species facilitated by life history traits.

    PubMed

    Zhao, Yun-Peng; Yan, Xiao-Ling; Muir, Graham; Dai, Qiong-Yan; Koch, Marcus A; Fu, Cheng-Xin

    2016-04-01

    Postglacial expansion to former range limits varies substantially among species of temperate deciduous forests in eastern Asia. Isolation hypotheses (with or without gene flow) have been proposed to explain this variance, but they ignore detailed population dynamics spanning geological time and neglect the role of life history traits. Using population genetics to uncover these dynamics across their Asian range, we infer processes that formed the disjunct distributions of Ginkgo biloba and the co-occurring Cercidiphyllum japonicum (published data). Phylogenetic, coalescent, and comparative data suggest that Ginkgo population structure is regional, dichotomous (to west-east refugia), and formed ˜51 kya, resulting from random genetic drift during the last glaciation. This split is far younger than the north-south population structure of Cercidiphyllum (~1.89 Mya). Significant (recent) unidirectional gene flow has not homogenized the two Ginkgo refugia, despite 2Nm > 1. Prior to this split, gene flow was potentially higher, resulting in conflicting support for a priori hypotheses that view isolation as an explanation for the variation in postglacial range limits. Isolation hypotheses (with or without gene flow) are thus not necessarily mutually exclusive due to temporal variation of gene flow and genetic drift. In comparison with Cercidiphyllum, the restricted range of Ginkgo has been facilitated by uncompetitive life history traits associated with seed ecology, highlighting the importance of both demography and lifetime reproductive success when interpreting range shifts.

  2. Incongruent range dynamics between co-occurring Asian temperate tree species facilitated by life history traits.

    PubMed

    Zhao, Yun-Peng; Yan, Xiao-Ling; Muir, Graham; Dai, Qiong-Yan; Koch, Marcus A; Fu, Cheng-Xin

    2016-04-01

    Postglacial expansion to former range limits varies substantially among species of temperate deciduous forests in eastern Asia. Isolation hypotheses (with or without gene flow) have been proposed to explain this variance, but they ignore detailed population dynamics spanning geological time and neglect the role of life history traits. Using population genetics to uncover these dynamics across their Asian range, we infer processes that formed the disjunct distributions of Ginkgo biloba and the co-occurring Cercidiphyllum japonicum (published data). Phylogenetic, coalescent, and comparative data suggest that Ginkgo population structure is regional, dichotomous (to west-east refugia), and formed ˜51 kya, resulting from random genetic drift during the last glaciation. This split is far younger than the north-south population structure of Cercidiphyllum (~1.89 Mya). Significant (recent) unidirectional gene flow has not homogenized the two Ginkgo refugia, despite 2Nm > 1. Prior to this split, gene flow was potentially higher, resulting in conflicting support for a priori hypotheses that view isolation as an explanation for the variation in postglacial range limits. Isolation hypotheses (with or without gene flow) are thus not necessarily mutually exclusive due to temporal variation of gene flow and genetic drift. In comparison with Cercidiphyllum, the restricted range of Ginkgo has been facilitated by uncompetitive life history traits associated with seed ecology, highlighting the importance of both demography and lifetime reproductive success when interpreting range shifts. PMID:27069572

  3. Effects of invasive species on ecosystem carbon dynamics in a restored tallgrass prairie

    NASA Astrophysics Data System (ADS)

    Matamala, R.; Graham, S. L.; Cook, D. R.; Gonzalez-Meler, M. A.

    2007-12-01

    Land cover is an important determinant of soil C storage and dynamics. Restoration of degraded ecosystems and soils represents a target sink for offsetting rising atmospheric CO2 levels by increasing carbon sequestration in soils. The Conservation Reserve Program (CRP) and other initiatives to halt land degradation after cessation of cultivation present opportunities to assess the C sequestration potential of restoration practices. Our aim is to study what key ecosystem and climatic components exert the largest leverage for these lands to be sustainable C sinks. When considering controls on ecosystem C cycling, biodiversity has the potential to be a strong biotic influence. Invasive species can disrupt ecosystem processes by exhibiting functional characteristics which are distinct from their native counterparts. Invasive species, while affecting nearly all ecosystems, may pose a particular threat to restorations and impact rates of C accrual. We measured net ecosystem production (NEP) at a 18 years-old restored tallgrass prairie using the eddy covariance technique coupled to biometric estimates of biomass and soil C in a two year study where climatic conditions and plant species dominance varied. In 2005, the prairie restoration was a strong C sink with a NEP 438 gCm-2, despite a pronounced spring drought. In 2006, with above normal precipitation, a Melilotus alba dominance dramatically reduced NEP when compared to 2005. The loss of ecosystem functional diversity that resulted from the dominance of the invasive M. alba led to a 42% reduction in the length of the photosynthetically active season, as compared to the previous year. These results suggest that understudied biotic limitations to NEP may outweigh the effects of more commonly studied abiotic limitations. Ecosystem models and management strategies should consider biotic limitations to NEP in grasslands in order to maximize long term C sequestration of restorations and CRP management practices.

  4. Species assembly in model ecosystems, I: Analysis of the population model and the invasion dynamics.

    PubMed

    Capitán, José A; Cuesta, José A

    2011-01-21

    Recently we have introduced a simplified model of ecosystem assembly (Capitán et al., 2009) for which we are able to map out all assembly pathways generated by external invasions in an exact manner. In this paper we provide a deeper analysis of the model, obtaining analytical results and introducing some approximations which allow us to reconstruct the results of our previous work. In particular, we show that the population dynamics equations of a very general class of trophic-level structured food-web have an unique interior equilibrium point which is globally stable. We show analytically that communities found as end states of the assembly process are pyramidal and we find that the equilibrium abundance of any species at any trophic level is approximately inversely proportional to the number of species in that level. We also find that the per capita growth rate of a top predator invading a resident community is key to understand the appearance of complex end states reported in our previous work. The sign of these rates allows us to separate regions in the space of parameters where the end state is either a single community or a complex set containing more than one community. We have also built up analytical approximations to the time evolution of species abundances that allow us to determine, with high accuracy, the sequence of extinctions that an invasion may cause. Finally we apply this analysis to obtain the communities in the end states. To test the accuracy of the transition probability matrix generated by this analytical procedure for the end states, we have compared averages over those sets with those obtained from the graph derived by numerical integration of the Lotka-Volterra equations. The agreement is excellent.

  5. Human-facilitated metapopulation dynamics in an emerging pest species, Cimex lectularius

    PubMed Central

    FOUNTAIN, TOBY; DUVAUX, LUDOVIC; HORSBURGH, GAVIN; REINHARDT, KLAUS; BUTLIN, ROGER K

    2014-01-01

    The number and demographic history of colonists can have dramatic consequences for the way in which genetic diversity is distributed and maintained in a metapopulation. The bed bug (Cimex lectularius) is a re-emerging pest species whose close association with humans has led to frequent local extinction and colonization, that is, to metapopulation dynamics. Pest control limits the lifespan of subpopulations, causing frequent local extinctions, and human-facilitated dispersal allows the colonization of empty patches. Founder events often result in drastic reductions in diversity and an increased influence of genetic drift. Coupled with restricted migration, this can lead to rapid population differentiation. We therefore predicted strong population structuring. Here, using 21 newly characterized microsatellite markers and approximate Bayesian computation (ABC), we investigate simplified versions of two classical models of metapopulation dynamics, in a coalescent framework, to estimate the number and genetic composition of founders in the common bed bug. We found very limited diversity within infestations but high degrees of structuring across the city of London, with extreme levels of genetic differentiation between infestations (FST = 0.59). ABC results suggest a common origin of all founders of a given subpopulation and that the numbers of colonists were low, implying that even a single mated female is enough to found a new infestation successfully. These patterns of colonization are close to the predictions of the propagule pool model, where all founders originate from the same parental infestation. These results show that aspects of metapopulation dynamics can be captured in simple models and provide insights that are valuable for the future targeted control of bed bug infestations. PMID:24446663

  6. Highly dynamic metal exchange in anthrax lethal factor involves the occupation of an inhibitory metal binding site.

    PubMed

    Young, Calvin J; Siemann, Stefan

    2016-10-11

    Metal exchange is a common strategy to replace the zinc ion of many zinc proteins with other transition metals amenable to spectroscopic investigations. We here demonstrate that in anthrax lethal factor (and likely other zinc proteases), metal exchange is a fast process, and involves the occupation of an inhibitory metal site by the incoming ion prior to the release of zinc. PMID:27517100

  7. Structure and Dynamics of NBD1 from CFTR Characterized Using Crystallography and Hydrogen/Deuterium Exchange Mass Spectrometry

    SciTech Connect

    Lewis, H.A.; Wang, C.; Zhao, X.; Hamuro, Y.; Conners, K.; Kearins, M.C.; Lu, F.; Sauder, J.M.; Molnar, K.S.; Coales, S.J.; Maloney, P.C.; Guggino, W.B.; Wetmore, D.R.; Weber, P.C.; Hunt, J.F.

    2012-04-30

    The {Delta}F508 mutation in nucleotide-binding domain 1 (NBD1) of the cystic fibrosis transmembrane conductance regulator (CFTR) is the predominant cause of cystic fibrosis. Previous biophysical studies on human F508 and {Delta}F508 domains showed only local structural changes restricted to residues 509-511 and only minor differences in folding rate and stability. These results were remarkable because {Delta}F508 was widely assumed to perturb domain folding based on the fact that it prevents trafficking of CFTR out of the endoplasmic reticulum. However, the previously reported crystal structures did not come from matched F508 and {Delta}F508 constructs, and the {Delta}F508 structure contained additional mutations that were required to obtain sufficient protein solubility. In this article, we present additional biophysical studies of NBD1 designed to address these ambiguities. Mass spectral measurements of backbone amide {sup 1}H/{sup 2}H exchange rates in matched F508 and {Delta}F508 constructs reveal that {Delta}F508 increases backbone dynamics at residues 509-511 and the adjacent protein segments but not elsewhere in NBD1. These measurements also confirm a high level of flexibility in the protein segments exhibiting variable conformations in the crystal structures. We additionally present crystal structures of a broader set of human NBD1 constructs, including one harboring the native F508 residue and others harboring the {Delta}F508 mutation in the presence of fewer and different solubilizing mutations. The only consistent conformational difference is observed at residues 509-511. The side chain of residue V510 in this loop is mostly buried in all non-{Delta}F508 structures but completely solvent exposed in all {Delta}F508 structures. These results reinforce the importance of the perturbation {Delta}F508 causes in the surface topography of NBD1 in a region likely to mediate contact with the transmembrane domains of CFTR. However, they also suggest that increased

  8. A Coupled Formulation for Vadose Zone Transport of Multiple Gas Species With Plant Exchange Under Variable Gravity

    NASA Astrophysics Data System (ADS)

    Stothoff, S. A.

    2008-12-01

    Most plants require a balance between water availability and oxygen availability in the rooting zone. Procedures for raising plants under microgravity conditions, such as might be encountered in long-term space missions, face a special challenge: water redistribution is not affected by gravity, leading to difficulty in maintaining both water and oxygen levels in the rooting zone because flow is dominated by capillary properties. The plant substrate used for microgravity conditions is typically a coarse material that drains extremely rapidly under the fluctuating gravity conditions (0 to 1.8 G) experienced on KC-135 aircraft during flight parabolas. To evaluate control strategies for meeting plant water uptake and respiration needs under microgravity and to characterize flow redistribution under fluctuating gravity, a single formulation considering partial to full saturation was developed to cover this range of conditions. The fully coupled system of equations considers N>1 gaseous species, including water, that are all constituents in the liquid phase and in equilibrium between the gas and liquid phases where both phases are present. Plants are considered as separate quasi steady continua. Plant uptake and respiration, when considered, are defined using (possibly age dependent) transfer functions characterized by root length density. The formulation avoids complexities arising from switching variables when going from very dry to saturated conditions by using variables that are continuous throughout the domain: liquid pressure and N-1 mass fraction variables, expressed as partial capillary pressure. The mass fractions of all species in both phases are recovered from the standard equilibrium conditions used to define the partial capillary pressures. The use of partial capillary pressure state variables is inspired by mass balance considerations near saturation (where capillary pressure is almost zero), because mass balance convergence rates are dominated by the phase

  9. Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges.

    PubMed

    Villalobos, Fabricio; Carotenuto, Francesco; Raia, Pasquale; Diniz-Filho, José Alexandre F

    2016-04-01

    Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes--speciation, extinction and dispersal--in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity.

  10. Phylogenetic fields through time: temporal dynamics of geographical co-occurrence and phylogenetic structure within species ranges.

    PubMed

    Villalobos, Fabricio; Carotenuto, Francesco; Raia, Pasquale; Diniz-Filho, José Alexandre F

    2016-04-01

    Species co-occur with different sets of other species across their geographical distribution, which can be either closely or distantly related. Such co-occurrence patterns and their phylogenetic structure within individual species ranges represent what we call the species phylogenetic fields (PFs). These PFs allow investigation of the role of historical processes--speciation, extinction and dispersal--in shaping species co-occurrence patterns, in both extinct and extant species. Here, we investigate PFs of large mammalian species during the last 3 Myr, and how these correlate with trends in diversification rates. Using the fossil record, we evaluate species' distributional and co-occurrence patterns along with their phylogenetic structure. We apply a novel Bayesian framework on fossil occurrences to estimate diversification rates through time. Our findings highlight the effect of evolutionary processes and past climatic changes on species' distributions and co-occurrences. From the Late Pliocene to the Recent, mammal species seem to have responded in an individualistic manner to climate changes and diversification dynamics, co-occurring with different sets of species from different lineages across their geographical ranges. These findings stress the difficulty of forecasting potential effects of future climate changes on biodiversity. PMID:26977061

  11. Inclusion of Additional Plant Species and Trait Information in Dynamic Vegetation Modeling of Arctic Tundra and Boreal Forest Ecosystem

    NASA Astrophysics Data System (ADS)

    Euskirchen, E. S.; Patil, V.; Roach, J.; Griffith, B.; McGuire, A. D.

    2015-12-01

    Dynamic vegetation models (DVMs) have been developed to model the ecophysiological characteristics of plant functional types in terrestrial ecosystems. They have frequently been used to answer questions pertaining to processes such as disturbance, plant succession, and community composition under historical and future climate scenarios. While DVMs have proved useful in these types of applications, it has often been questioned if additional detail, such as including plant dynamics at the species-level and/or including species-specific traits would make these models more accurate and/or broadly applicable. A sub-question associated with this issue is, 'How many species, or what degree of functional diversity, should we incorporate to sustain ecosystem function in modeled ecosystems?' Here, we focus on how the inclusion of additional plant species and trait information may strengthen dynamic vegetation modeling in applications pertaining to: (1) forage for caribou in northern Alaska, (2) above- and belowground carbon storage in the boreal forest and lake margin wetlands of interior Alaska, and (3) arctic tundra and boreal forest leaf phenology. While the inclusion of additional information generally proved valuable in these three applications, this additional detail depends on field data that may not always be available and may also result in increased computational complexity. Therefore, it is important to assess these possible limitations against the perceived need for additional plant species and trait information in the development and application of dynamic vegetation models.

  12. Differences in plant cover and species composition of semiarid grassland communities of Central Mexico and its effects on net ecosystem exchange

    NASA Astrophysics Data System (ADS)

    Delgado-Balbuena, J.; Arredondo, J. T.; Loescher, H. W.; Huber-Sannwald, E.; Chavez-Aguilar, G.; Luna-Luna, M.; Barretero-Hernandez, R.

    2012-12-01

    Changes in land use across the semiarid grasslands of Northern Mexico have driven a decline of plant cover and alteration of plant species composition. A number of different plant communities have resulted from these changes, however, their implications on the carbon cycle and regional carbon balance are still poorly understood. Here, we examined the effects of plant cover loss and changes in species composition on net ecosystem CO2 exchange (NEE) and their biotic and abiotic controls. Five typical plant community types were examined in the semiarid grassland by encasing the entire above-ground ecosystem using the geodesic dome method. Sites included an oat crop (crop), a moderately grazed grassland (moderate grazing), a 28 yr-old grazing exclosure (exclosure), an overgrazed site with low perennial grass cover (overgrazed), and an overgrazed site presenting shrub encroachment (shrub encroachment). For natural vegetation, rates of daytime NEE for sites with a high plant cover (exclosure and moderate grazing) were similar (P>0.05) as compared to sites with low plant cover (overgrazed and shrub encroachment). However, night time NEE (carbon loss) was more than double (P<0.05) for sites with high plant cover compared to sites with low cover, resulting into slight C sinks for the low plant cover sites and neutral or sources for the high plant cover sites on an annual basis. Differences in plant cover and its associated biomass defined the sensitivity to environmental controls. Thus, daytime NEE in low plant cover sites reached light compensation points at lower PPFD values than those from high plant cover sites. Differences in species composition did not influence NEE rates even though there were transient or permanent changes in C3 vs. C4 functional groups.

  13. Evolution and Emergence of Enteroviruses through Intra- and Inter-species Recombination: Plasticity and Phenotypic Impact of Modular Genetic Exchanges in the 5’ Untranslated Region

    PubMed Central

    Muslin, Claire; Joffret, Marie-Line; Pelletier, Isabelle; Blondel, Bruno; Delpeyroux, Francis

    2015-01-01

    Genetic recombination shapes the diversity of RNA viruses, including enteroviruses (EVs), which frequently have mosaic genomes. Pathogenic circulating vaccine-derived poliovirus (cVDPV) genomes consist of mutated vaccine poliovirus (PV) sequences encoding capsid proteins, and sequences encoding nonstructural proteins derived from other species’ C EVs, including certain coxsackieviruses A (CV-A) in particular. Many cVDPV genomes also have an exogenous 5’ untranslated region (5’ UTR). This region is involved in virulence and includes the cloverleaf (CL) and the internal ribosomal entry site, which play major roles in replication and the initiation of translation, respectively. We investigated the plasticity of the PV genome in terms of recombination in the 5’ UTR, by developing an experimental model involving the rescue of a bipartite PV/CV-A cVDPV genome rendered defective by mutations in the CL, following the co-transfection of cells with 5’ UTR RNAs from each of the four human EV species (EV-A to -D). The defective cVDPV was rescued by recombination with 5’ UTR sequences from the four EV species. Homologous and nonhomologous recombinants with large deletions or insertions in three hotspots were isolated, revealing a striking plasticity of the 5’ UTR. By contrast to the recombination of the cVDPV with the 5’ UTR of group II (EV-A and -B), which can decrease viral replication and virulence, recombination with the 5’ UTRs of group I (EV-C and -D) appeared to be evolutionarily neutral or associated with a gain in fitness. This study illustrates how the genomes of positive-strand RNA viruses can evolve into mosaic recombinant genomes through intra- or inter-species modular genetic exchanges, favoring the emergence of new recombinant lineages. PMID:26562151

  14. Contrasting submergence tolerance in two species of stem-succulent halophytes is not determined by differences in stem internal oxygen dynamics

    PubMed Central

    Konnerup, Dennis; Moir-Barnetson, Louis; Pedersen, Ole; Veneklaas, Erik J.; Colmer, Timothy D.

    2015-01-01

    Background and Aims Many stem-succulent halophytes experience regular or episodic flooding events, which may compromise gas exchange and reduce survival rates. This study assesses submergence tolerance, gas exchange and tissue oxygen (O2) status of two stem-succulent halophytes with different stem diameters and from different elevations of an inland marsh. Methods Responses to complete submergence in terms of stem internal O2 dynamics, photosynthesis and respiration were studied for the two halophytic stem-succulents Tecticornia auriculata and T. medusa. Plants were submerged in a glasshouse experiment for 3, 6 and 12 d and O2 levels within stems were measured with microelectrodes. Photosynthesis by stems in air after de-submergence was also measured. Key Results Tecticornia medusa showed 100 % survival in all submergence durations whereas T. auriculata did not survive longer than 6 d of submergence. O2 profiles and time traces showed that when submerged in water at air-equilibrium, the thicker stems of T. medusa were severely hypoxic (close to anoxic) when in darkness, whereas the smaller diameter stems of T. auriculata were moderately hypoxic. During light periods, underwater photosynthesis increased the internal O2 concentrations in the succulent stems of both species. Stems of T. auriculata temporally retained a gas film when first submerged, whereas T. medusa did not. The lower O2 in T. medusa than in T. auriculata when submerged in darkness was largely attributed to a less permeable epidermis. The submergence sensitivity of T. auriculata was associated with swelling and rupturing of the succulent stem tissues, which did not occur in T. medusa. Conclusions The higher submergence tolerance of T. medusa was not associated with better internal aeration of stems. Rather, this species has poor internal aeration of the succulent stems due to its less permeable epidermis; the low epidermal permeability might be related to resistance to swelling of succulent stem

  15. Carbon dynamics in aboveground biomass of co-dominant plant species: related rather to leaf life span than to species

    NASA Astrophysics Data System (ADS)

    Ostler, Ulrike; Schleip, Inga; Lattanzi, Fernando A.; Schnyder, Hans

    2016-04-01

    This study investigates the role of individual organisms in whole ecosystem carbon (C) fluxes. It is currently unknown if different plant community members share the same or different kinetics of C pools in aboveground biomass, thereby adding (or not) variability to the first steps in ecosystem C cycling. We assessed the residence times in metabolic and non-metabolic (or structural) C pools and the allocation pattern of assimilated C in aboveground plant parts of four co-existing, co-dominant species from different functional groups in a temperate grassland community. For this purpose continuous, 14-16 day long 13CO2/12CO2-labeling experiments were performed in Sept. 2006, May 2007 and Sept. 2007, and the tracer kinetics were analysed with compartmental modeling. In all experimental periods, the species shared vastly similar residence times in metabolic C (5-8 d). In contrast, the residence times in non-metabolic C ranged from 20 to 58 d (except one outlier) and the fraction of fixed C allocated to the non-metabolic pool from 7 to 45%. These variations in non-metabolic C kinetics were not systematically associated with species or experimental periods, but exhibited close relationships with (independent estimates of) leaf life span, particularly in the grasses. This adds new meaning to leaf life span as a functional trait in the leaf and plant economics spectrum and its implication for C cycle studies in grassland and also forest systems. As the four co-dominant species accounted for ~80% of total community shoot biomass, we should also expect that the observed similarities in pool kinetics and allocation will scale up to similar relationships at the community level.

  16. The Ecuadorian Artisanal Fishery for Large Pelagics: Species Composition and Spatio-Temporal Dynamics.

    PubMed

    Martínez-Ortiz, Jimmy; Aires-da-Silva, Alexandre M; Lennert-Cody, Cleridy E; Maunder, Mark N

    2015-01-01

    The artisanal fisheries of Ecuador operate within one of the most dynamic and productive marine ecosystems of the world. This study investigates the catch composition of the Ecuadorian artisanal fishery for large pelagic fishes, including aspects of its spatio-temporal dynamics. The analyses of this study are based on the most extensive dataset available to date for this fishery: a total of 106,963 trip-landing inspection records collected at its five principal ports during 2008 ‒ 2012. Ecuadorian artisanal fisheries remove a substantial amount of biomass from the upper trophic-level predatory fish community of the eastern tropical Pacific Ocean. It is estimated that at least 135 thousand metric tons (mt) (about 15.5 million fish) were landed in the five principal ports during the study period. The great novelty of Ecuadorian artisanal fisheries is the "oceanic-artisanal" fleet component, which consists of mother-ship (nodriza) boats with their towed fiber-glass skiffs (fibras) operating with pelagic longlines. This fleet has fully expanded into oceanic waters as far offshore as 100°W, west of the Galapagos Archipelago. It is estimated that nodriza operations produce as much as 80% of the total catches of the artisanal fishery. The remainder is produced by independent fibras operating in inshore waters with pelagic longlines and/or surface gillnets. A multivariate regression tree analysis was used to investigate spatio-environmental effects on the nodriza fleet (n = 6,821 trips). The catch species composition of the nodriza fleet is strongly influenced by the northwesterly circulation of the Humboldt Current along the coast of Peru and its associated cold waters masses. The target species and longline gear-type used by nodrizas change seasonally with the incursion of cool waters (< 25°C) from the south and offshore. During this season, dolphinfish (Coryphaena hippurus) dominates the catches. However, in warmer waters, the fishery changes to tuna

  17. The Ecuadorian Artisanal Fishery for Large Pelagics: Species Composition and Spatio-Temporal Dynamics

    PubMed Central

    Martínez-Ortiz, Jimmy; Aires-da-Silva, Alexandre M.; Lennert-Cody, Cleridy E.; Maunder, Mark N.

    2015-01-01

    The artisanal fisheries of Ecuador operate within one of the most dynamic and productive marine ecosystems of the world. This study investigates the catch composition of the Ecuadorian artisanal fishery for large pelagic fishes, including aspects of its spatio-temporal dynamics. The analyses of this study are based on the most extensive dataset available to date for this fishery: a total of 106,963 trip-landing inspection records collected at its five principal ports during 2008 ‒ 2012. Ecuadorian artisanal fisheries remove a substantial amount of biomass from the upper trophic-level predatory fish community of the eastern tropical Pacific Ocean. It is estimated that at least 135 thousand metric tons (mt) (about 15.5 million fish) were landed in the five principal ports during the study period. The great novelty of Ecuadorian artisanal fisheries is the “oceanic-artisanal” fleet component, which consists of mother-ship (nodriza) boats with their towed fiber-glass skiffs (fibras) operating with pelagic longlines. This fleet has fully expanded into oceanic waters as far offshore as 100°W, west of the Galapagos Archipelago. It is estimated that nodriza operations produce as much as 80% of the total catches of the artisanal fishery. The remainder is produced by independent fibras operating in inshore waters with pelagic longlines and/or surface gillnets. A multivariate regression tree analysis was used to investigate spatio-environmental effects on the nodriza fleet (n = 6,821 trips). The catch species composition of the nodriza fleet is strongly influenced by the northwesterly circulation of the Humboldt Current along the coast of Peru and its associated cold waters masses. The target species and longline gear-type used by nodrizas change seasonally with the incursion of cool waters (< 25°C) from the south and offshore. During this season, dolphinfish (Coryphaena hippurus) dominates the catches. However, in warmer waters, the fishery changes to tuna

  18. The Ecuadorian Artisanal Fishery for Large Pelagics: Species Composition and Spatio-Temporal Dynamics.

    PubMed

    Martínez-Ortiz, Jimmy; Aires-da-Silva, Alexandre M; Lennert-Cody, Cleridy E; Maunder, Mark N

    2015-01-01

    The artisanal fisheries of Ecuador operate within one of the most dynamic and productive marine ecosystems of the world. This study investigates the catch composition of the Ecuadorian artisanal fishery for large pelagic fishes, including aspects of its spatio-temporal dynamics. The analyses of this study are based on the most extensive dataset available to date for this fishery: a total of 106,963 trip-landing inspection records collected at its five principal ports during 2008 ‒ 2012. Ecuadorian artisanal fisheries remove a substantial amount of biomass from the upper trophic-level predatory fish community of the eastern tropical Pacific Ocean. It is estimated that at least 135 thousand metric tons (mt) (about 15.5 million fish) were landed in the five principal ports during the study period. The great novelty of Ecuadorian artisanal fisheries is the "oceanic-artisanal" fleet component, which consists of mother-ship (nodriza) boats with their towed fiber-glass skiffs (fibras) operating with pelagic longlines. This fleet has fully expanded into oceanic waters as far offshore as 100°W, west of the Galapagos Archipelago. It is estimated that nodriza operations produce as much as 80% of the total catches of the artisanal fishery. The remainder is produced by independent fibras operating in inshore waters with pelagic longlines and/or surface gillnets. A multivariate regression tree analysis was used to investigate spatio-environmental effects on the nodriza fleet (n = 6,821 trips). The catch species composition of the nodriza fleet is strongly influenced by the northwesterly circulation of the Humboldt Current along the coast of Peru and its associated cold waters masses. The target species and longline gear-type used by nodrizas change seasonally with the incursion of cool waters (< 25°C) from the south and offshore. During this season, dolphinfish (Coryphaena hippurus) dominates the catches. However, in warmer waters, the fishery changes to tuna

  19. Dynamic control of osmolality and ionic composition of the xylem sap in two mangrove species.

    PubMed

    López-Portillo, Jorge; Ewers, Frank W; Méndez-Alonzo, Rodrigo; Paredes López, Claudia L; Angeles, Guillermo; Alarcón Jiménez, Ana Luisa; Lara-Domínguez, Ana Laura; Torres Barrera, María Del Carmen

    2014-06-01

    • Premise of the study: Xylem sap osmolality and salinity is a critical unresolved issue in plant function with impacts on transport efficiency, pressure gradients, and living cell turgor pressure, especially for halophytes such as mangrove trees.• Methods: We collected successive xylem vessel sap samples from stems and shoots of Avicennia germinans and Laguncularia racemosa using vacuum and pressure extraction and measured their osmolality. Following a series of extractions with the pressure chamber, we depressurized the shoot and pressurized again after various equilibration periods (minutes to hours) to test for dynamic control of osmolality. Transpiration and final sap osmolality were measured in shoots perfused with deionized water or different seawater dilutions.• Key results: For both species, the sap osmolality values of consecutive samples collected by vacuum extraction were stable and matched those of the initial samples extracted with the pressure chamber. Further extraction of samples with the pressure chamber decreased sap osmolality, suggesting reverse osmosis occurred. However, sap osmolalities increased when longer equilibration periods after sap extraction were allowed. Analysis of expressed sap with HPLC indicated a 1:1 relation between measured osmolality and the osmolality of the inorganic ions in the sap (mainly Na(+), K(+), and Cl(-)), suggesting no contamination by organic compounds. In stems perfused with deionized water, the sap osmolality increased to mimic the native sap osmolality.• Conclusions: Xylem sap osmolality and ionic contents are dynamically adjusted by mangroves and may help modulate turgor pressure, hydraulic conductivity, and water potential, thus being important for mangrove physiology, survival, and distribution.

  20. Statistical analysis of polychaete population density: dynamics of dominant species and scaling properties in relative abundance fluctuations

    NASA Astrophysics Data System (ADS)

    Quiroz-Martinez, B.; Schmitt, F. G.; Dauvin, J.-C.

    2012-01-01

    We consider here the dynamics of two polychaete populations based on a 20 yr temporal benthic survey of two muddy fine sand communities in the Bay of Morlaix, Western English Channel. These populations display high temporal variability, which is analyzed here using scaling approaches. We find that population densities have heavy tailed probability density functions. We analyze the dynamics of relative species abundance in two different communities of polychaetes by estimating in a novel way a "mean square drift" coefficient which characterizes their fluctuations in relative abundance over time. We show the usefulness of using new tools to approach and model such highly variable population dynamics in marine ecosystems.

  1. [Effects of dynamic aerodynamic parameters on simulating the land-atmosphere flux exchange in maize field: a case study of BATS1e model].

    PubMed

    Cai, Fu; Ming, Hui-qing; Li, Rong-ping; Zhou, Guang-sheng

    2013-08-01

    Based on the continuous observations on the land-atmosphere flux exchange and the meteorological and biological elements in a maize field at the Jinzhou Agricultural Ecosystem Research Station in Liaoning Province of Northeast China from 2006 to 2008, and by using the dynamic roughness (z0) and zero-displacement (d) parameterization scheme considering the effects of leaf area index, canopy height and wind speed at different developmental stages of maize, the BATS1e model was modified, and applied to investigate the effects of dynamic aerodynamic parameters on the flux exchange between maize agroecosystem and atmosphere. Compared with the original model, the drag coefficient (C(D)) simulated by the modified model increased, and its diurnal variation was more obvious with increasing vegetation coverage, which was more accordant with practical circumstances. The simulation accuracies of sensible heat (H), latent heat (lambdaE) and soil heat flux were improved in varying degree, and the Nash-Sutcliffes (NSs) were increased by 0.0569, 0.0194 and 0. 0384, with the improvement quantities in the growth season being 0.9%, 1.1% and 1.2% of global radiation, respectively. The dynamic parameterizations of z0 and d played a more remarkable role to increase the simulation accuracies of H and lambdaE with the actual observation of soil water content introduced into the improved model. This research proved that more reasonable dynamic aerodynamic parameterizations could fulfill an obvious function to improve the land surface processes simulation.

  2. Magnetization dynamics in an exchange-coupled NiFe/CoFe bilayer studied by x-ray detected ferromagnetic resonance

    NASA Astrophysics Data System (ADS)

    Stenning, G. B. G.; Shelford, L. R.; Cavill, S. A.; Hoffmann, F.; Haertinger, M.; Hesjedal, T.; Woltersdorf, G.; Bowden, G. J.; Gregory, S. A.; Back, C. H.; de Groot, P. A. J.; van der Laan, G.

    2015-01-01

    Exchange-coupled hard and soft magnetic layers find extensive use in data storage applications, for which their dynamical response has great importance. With bulk techniques, such as ferromagnetic resonance (FMR), it is difficult to access the behaviour and precise influence of each individual layer. By contrast, the synchrotron radiation-based technique of x-ray detected ferromagnetic resonance (XFMR) allows element-specific and phase-resolved FMR measurements in the frequency range 0.5-11 GHz. Here, we report the study of the magnetization dynamics of an exchange-coupled Ni0.81Fe0.19 (43.5 nm)/Co0.5Fe0.5 (30 nm) bilayer system using magnetometry and vector network analyser FMR, combined with XFMR at the Ni and Co L2 x-ray absorption edges. The epitaxially grown bilayer exhibits two principal resonances denoted as the acoustic and optical modes. FMR experiments show that the Kittel curves of the two layers cannot be taken in isolation, but that their modelling needs to account for an interlayer exchange coupling. The angular dependence of FMR indicates a collective effect for the modes of the magnetically hard CoFe and soft NiFe layer. The XFMR precessional scans show that the acoustic mode is dominated by the Ni signal with the Co and Ni magnetization precessing in phase, whereas the optical mode is dominated by the Co signal with the Co and Ni magnetization precessing in anti-phase. The response of the Co signal at the Ni resonance, and vice versa, show induced changes in both amplitude and phase, which can be ascribed to the interface exchange coupling. An interesting aspect of phase-resolved XFMR is the ability to distinguish between static and dynamic exchange coupling. The element-specific precessional scans of the NiFe/CoFe bilayer clearly have the signature of static exchange coupling, in which the effective field in one layer is aligned along the magnetization direction of the other layer.

  3. Genomes of Ellobius species provide insight into the evolutionary dynamics of mammalian sex chromosomes.

    PubMed

    Mulugeta, Eskeatnaf; Wassenaar, Evelyne; Sleddens-Linkels, Esther; van IJcken, Wilfred F J; Heard, Edith; Grootegoed, J Anton; Just, Walter; Gribnau, Joost; Baarends, Willy M

    2016-09-01

    The X and Y sex chromosomes of placental mammals show hallmarks of a tumultuous evolutionary past. The X Chromosome has a rich and conserved gene content, while the Y Chromosome has lost most of its genes. In the Transcaucasian mole vole Ellobius lutescens, the Y Chromosome including Sry has been lost, and both females and males have a 17,X diploid karyotype. Similarly, the closely related Ellobius talpinus, has a 54,XX karyotype in both females and males. Here, we report the sequencing and assembly of the E. lutescens and E. talpinus genomes. The results indicate that the loss of the Y Chromosome in E. lutescens and E. talpinus occurred in two independent events. Four functional homologs of mouse Y-Chromosomal genes were detected in both female and male E. lutescens, of which three were also detected in the E. talpinus genome. One of these is Eif2s3y, known as the only Y-derived gene that is crucial for successful male meiosis. Female and male E. lutescens can carry one and the same X Chromosome with a largely conserved gene content, including all genes known to function in X Chromosome inactivation. The availability of the genomes of these mole vole species provides unique models to study the dynamics of sex chromosome evolution. PMID:27510564

  4. Species sorting and patch dynamics in harlequin metacommunities affect the relative importance of environment and space.

    PubMed

    Leibold, Mathew A; Loeuille, Nicolas

    2015-12-01

    Metacommunity theory indicates that variation in local community structure can be partitioned into components including those related to local environmental conditions vs. spatial effects and that these can be quantified using statistical methods based on variation partitioning. It has been hypothesized that joint associations of community composition with environment and space could be due to patch dynamics involving colonization-extinction processes in environmentally heterogeneous landscapes but this has yet to be theoretically shown. We develop a two-patch, type-two, species competition model in such a "harlequin" landscape (where different patches have different environments) to evaluate how composition is related to environmental and spatial effects as a function of background extinction rate. Using spatially implicit analytical models, we find that the environmental association of community composition declines with extinction rate as expected. Using spatially explicit simulation models, we further find that there is an increase in the spatial structure with extinction due to spatial patterning into clusters that are not related to environmental conditions but that this increase is limited. Natural metacommunities often show both environment and spatial determination even under conditions of relatively high isolation and these could be more easily explained by our model than alternative metacommunity models. PMID:26909428

  5. Strategy Dependent Swimming Dynamics Change among a Predatory Algae Species with Different Strains

    NASA Astrophysics Data System (ADS)

    Katz, Joseph; Sheng, Jian; Malkiel, Edwin; Adolf, Jason; Place, Allen

    2008-11-01

    Digital holographic microscopic cinematography is used for measuring the 3D, time resolved, swimming behavior of toxic and non-toxic strains the marine dinoflagellate Karlodinium veneficum. We focus on the response of predators of the same species, but with different predation strategy, to the presence of prey, Storeatula major. Experiments are performed in a 3x3 mm cuvette, at densities extending to 100,000 cells/ml. Holograms are recorded at 60fps and at 20X magnification. In each case, we simultaneously track 200-500 cells in the 3mm deep sample, at a spatial resolution of 0.4x0.4x2 μm. We show that responses are largely dependent on the predation strategy. K. veneficum 2064, a toxic mixotroph, slows down and decreases the helix radius and clusters around the prey. Conversely, MD5, a non-toxic, autotrophic-like strain is completely oblivious to prey. Strain 1974, which is toxic and twice as motile, shows heterotrophic-like responses with characteristics of an active hunter. Also, on going spectral analysis of the 3-D motion provides quantitative insight on the swimming dynamics of microorganisms.

  6. Species sorting and patch dynamics in harlequin metacommunities affect the relative importance of environment and space.

    PubMed

    Leibold, Mathew A; Loeuille, Nicolas

    2015-12-01

    Metacommunity theory indicates that variation in local community structure can be partitioned into components including those related to local environmental conditions vs. spatial effects and that these can be quantified using statistical methods based on variation partitioning. It has been hypothesized that joint associations of community composition with environment and space could be due to patch dynamics involving colonization-extinction processes in environmentally heterogeneous landscapes but this has yet to be theoretically shown. We develop a two-patch, type-two, species competition model in such a "harlequin" landscape (where different patches have different environments) to evaluate how composition is related to environmental and spatial effects as a function of background extinction rate. Using spatially implicit analytical models, we find that the environmental association of community composition declines with extinction rate as expected. Using spatially explicit simulation models, we further find that there is an increase in the spatial structure with extinction due to spatial patterning into clusters that are not related to environmental conditions but that this increase is limited. Natural metacommunities often show both environment and spatial determination even under conditions of relatively high isolation and these could be more easily explained by our model than alternative metacommunity models.

  7. Carbon and Nitrogen dynamics in forest soils depending on light conditions and tree species

    NASA Astrophysics Data System (ADS)

    Veselinovic, Bojana; Hager, Herbert

    2013-04-01

    Climate change mitigation actions under the Kyoto Protocol apply among other decreases of CO2-emissions and/or increases of carbon (C) stocks. As soils represent the second biggest C-reservoir on Earth, an exact estimation of the stocks and reliable knowledge on C-dynamics in forest soils is of high importance. Anyhow, here, the accurate GHG-accounting, emission reductions and increase in C stocks is hampered due to lack of reliable data and solid statistical methods for the factors which influence C-sequestration in and its release from these systems. In spite of good progress in the scientific research, these factors are numerous and diverse in their interactions. This work focuses on influence of the economically relevant tree species - Picea abies, Fagus sylvatica and Quercus spp. - and light conditions on forest floor and mineral soil C and N dynamics in forest soils. Spruce monocultures have been widely used management practices in central European forests during the past century. Such stands are in lower altitudes and on heavy and water logged soils unstable and prone to disturbances, especially to windthrows. We hypothesize that windthrow areas loose C & N and that the establishment of the previous nutrient stocks is, if at all, only possible to be reached over the longer periods of time. We research also how the increased OM depletion affects the change of C & N stocks in forest floor vs. mineral soil. Conversion of such secondary spruce monocultures to site adequate beech and oak forests may enable higher stocks allocated predominantly as stable organic carbon and as plant available nitrogen. For this purpose sites at 300-700 m altitude with planosols were chosen in the region of the Northern Alpine Foothills. A false chronosequence approach was used in order to evaluate the impacts of the tree species and change in light conditions on dynamic of C & N in the forest floor and mineral soil, over the period 0-100 (for oak 120 y.) years. The C- and N

  8. Occupancy dynamics in a tropical bird community: unexpectedly high forest use by birds classified as non-forest species

    USGS Publications Warehouse

    Ruiz-Gutierrez, Viviana; Zipkin, Elise F.; Dhondt, Andre A.

    2010-01-01

    1. Worldwide loss of biodiversity necessitates a clear understanding of the factors driving population declines as well as informed predictions about which species and populations are at greatest risk. The biggest threat to the long-term persistence of populations is the reduction and changes in configuration of their natural habitat. 2. Inconsistencies have been noted in the responses of populations to the combined effects of habitat loss and fragmentation. These have been widely attributed to the effects of the matrix habitats in which remnant focal habitats are typically embedded. 3. We quantified the potential effects of the inter-patch matrix by estimating occupancy and colonization of forest and surrounding non-forest matrix (NF). We estimated species-specific parameters using a dynamic, multi-species hierarchical model on a bird community in southwestern Costa Rica. 4. Overall, we found higher probabilities of occupancy and colonization of forest relative to the NF across bird species, including those previously categorized as open habitat generalists not needing forest to persist. Forest dependency was a poor predictor of occupancy dynamics in our study region, largely predicting occupancy and colonization of only non-forest habitats. 5. Our results indicate that the protection of remnant forest habitats is key for the long-term persistence of all members of the bird community in this fragmented landscape, including species typically associated with open, non-forest habitats. 6.Synthesis and applications. We identified 39 bird species of conservation concern defined by having high estimates of forest occupancy, and low estimates of occupancy and colonization of non-forest. These species survive in forest but are unlikely to venture out into open, non-forested habitats, therefore, they are vulnerable to the effects of habitat loss and fragmentation. Our hierarchical community-level model can be used to estimate species-specific occupancy dynamics for focal

  9. Joint effects of habitat heterogeneity and species' life-history traits on population dynamics in spatially structured landscapes.

    PubMed

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

    2014-01-01

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

  10. The role of dynamic surface water-groundwater exchange on streambed denitrification in a first-order, low-relief agricultural watershed

    USGS Publications Warehouse

    Rahimi Kazerooni, Mina N.; Essaid, Hedeff I.; Wilson, John T.

    2015-01-01

    The role of temporally varying surface water-groundwater (SW-GW) exchange on nitrate removal by streambed denitrification was examined along a reach of Leary Weber Ditch (LWD), Indiana, a small, first-order, low-relief agricultural watershed within the Upper Mississippi River basin, using data collected in 2004 and 2005. Stream stage, GW heads (H), and temperatures (T) were continuously monitored in streambed piezometers and stream bank wells for two transects across LWD accompanied by synoptic measurements of stream stage, H, T, and nitrate (NO3) concentrations along the reach. The H and T data were used to develop and calibrate vertical two-dimensional, models of streambed water flow and heat transport across and along the axis of the stream. Model-estimated SW-GW exchange varied seasonally and in response to high-streamflow events due to dynamic interactions between SW stage and GW H. Comparison of 2004 and 2005 conditions showed that small changes in precipitation amount and intensity, evapotranspiration, and/or nearby GW levels within a low-relief watershed can readily impact SW-GW interactions. The calibrated LWD flow models and observed stream and streambed NO3 concentrations were used to predict temporal variations in streambed NO3 removal in response to dynamic SW-GW exchange. NO3 removal rates underwent slow seasonal changes, but also underwent rapid changes in response to high-flow events. These findings suggest that increased temporal variability of SW-GW exchange in low-order, low-relief watersheds may be a factor contributing their more efficient removal of NO3.

  11. The role of dynamic surface water-groundwater exchange on streambed denitrification in a first-order, low-relief agricultural watershed

    NASA Astrophysics Data System (ADS)

    Rahimi, Mina; Essaid, Hedeff I.; Wilson, John T.

    2015-12-01

    The role of temporally varying surface water-groundwater (SW-GW) exchange on nitrate removal by streambed denitrification was examined along a reach of Leary Weber Ditch (LWD), Indiana, a small, first-order, low-relief agricultural watershed within the Upper Mississippi River basin, using data collected in 2004 and 2005. Stream stage, GW heads (H), and temperatures (T) were continuously monitored in streambed piezometers and stream bank wells for two transects across LWD accompanied by synoptic measurements of stream stage, H, T, and nitrate (NO3) concentrations along the reach. The H and T data were used to develop and calibrate vertical two-dimensional, models of streambed water flow and heat transport across and along the axis of the stream. Model-estimated SW-GW exchange varied seasonally and in response to high-streamflow events due to dynamic interactions between SW stage and GW H. Comparison of 2004 and 2005 conditions showed that small changes in precipitation amount and intensity, evapotranspiration, and/or nearby GW levels within a low-relief watershed can readily impact SW-GW interactions. The calibrated LWD flow models and observed stream and streambed NO3 concentrations were used to predict temporal variations in streambed NO3 removal in response to dynamic SW-GW exchange. NO3 removal rates underwent slow seasonal changes, but also underwent rapid changes in response to high-flow events. These findings suggest that increased temporal variability of SW-GW exchange in low-order, low-relief watersheds may be a factor contributing their more efficient removal of NO3.

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

    USGS Publications Warehouse

    Beerens, J.M.; Gawlik, D.E.; Herring, G.; 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. ?? The American Ornithologists' Union, 2011.

  13. The dynamics of reductive sorption of oxygen by a granular bed of electron-ion exchangers with different copper dispersities

    NASA Astrophysics Data System (ADS)

    Konev, D. V.; Kravchenko, T. A.; Kalinichev, A. I.; Kipriyanova, E. S.

    2009-05-01

    The behavior of an immobile granular sorbent bed in one-component sorption in a column reactor is described in terms of the kinetic model of redox sorption taking into consideration the dispersity of metal particles, their radial distribution, peculiarities of chemical oxidation, and the relation of the overall rate of the process to the properties of the ion exchange matrix. The mathematical problem is formulated and solved numerically; the solution is analyzed theoretically in relation to the basic parameters of the sorption system. A satisfactory agreement is obtained between the experimental and calculated data on the reductive sorption of molecular oxygen from water on a copper-containing electron-ion exchanger.

  14. Differences in plant cover and species composition of semiarid grassland communities of central Mexico and its effects on net ecosystem exchange

    NASA Astrophysics Data System (ADS)

    Delgado-Balbuena, J.; Arredondo, J. T.; Loescher, H. W.; Huber-Sannwald, E.; Chavez-Aguilar, G.; Luna-Luna, M.; Barretero-Hernandez, R.

    2013-07-01

    Changes in land use across the semiarid grasslands of northern Mexico have driven a decline of plant cover and alteration of plant species composition. A number of different plant communities have resulted from these changes. Their implications, however, on the carbon (C) cycle and regional carbon balance are still poorly understood. Here, we examined the effects of plant cover loss and changes in species composition on net ecosystem CO2 exchange (NEE) and their biotic and abiotic controls. NEE was measured in five representative plant community types within a semiarid grassland by temporarily enclosing the entire aboveground ecosystem using a chamber method (i.e., geodesic dome). Sites included an oat crop (crop), a moderately grazed grassland (moderate grazing), a 28 yr-old grazing exclosure (exclosure), an overgrazed site with low perennial grass cover (overgrazed), and an overgrazed site presenting shrub encroachment (shrub encroachment). For natural vegetation, rates of standardized daytime NEE for sites with a high plant cover (exclosure and moderate grazing) were similar (P > 0.05) as compared to sites with low plant cover (overgrazed and shrub encroachment). However, yearly total nighttime NEE (carbon loss) was more than double (P < 0.05) for sites with high plant cover compared to sites with low cover, resulting to slight C sinks for the low plant cover sites, and neutral or sources for the high plant cover sites as accounted by daytime and nighttime NEE annual balance. Differences in plant cover and its associated biomass defined the sensitivity to environmental controls. Thus, daytime NEE in low plant cover sites reached light compensation points at lower photosynthetic photon flux density than those from high plant cover sites. Differences in species composition did not influence NEE rates even though there were transient or permanent changes in C3 vs. C4 functional groups. Our results allowed the detection of the large variability and contribution of

  15. Population dynamics of Aspergillus section Nigri species on vineyard samples of grapes and raisins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several species of Aspergillus section Nigri, including potential mycotoxin producers, are common residents of grape vineyards, but the relative population size of individual species throughout the growing season is difficult to determine using traditional isolation and identification methods. Using...

  16. Seasonal Dynamics of Phlebotomine Sand Fly Species Proven Vectors of Mediterranean Leishmaniasis Caused by Leishmania infantum

    PubMed Central

    Alten, Bulent; Maia, Carla; Afonso, Maria Odete; Campino, Lenea; Jiménez, Maribel; González, Estela; Molina, Ricardo; Bañuls, Anne Laure; Prudhomme, Jorian; Vergnes, Baptiste; Toty, Celine; Cassan, Cécile; Rahola, Nil; Thierry, Magali; Sereno, Denis; Bongiorno, Gioia; Bianchi, Riccardo; Khoury, Cristina; Tsirigotakis, Nikolaos; Dokianakis, Emmanouil; Antoniou, Maria; Christodoulou, Vasiliki; Mazeris, Apostolos; Karakus, Mehmet; Ozbel, Yusuf; Arserim, Suha K.; Erisoz Kasap, Ozge; Gunay, Filiz; Oguz, Gizem; Kaynas, Sinan; Tsertsvadze, Nikoloz; Tskhvaradze, Lamzira; Gramiccia, Marina; Volf, Petr; Gradoni, Luigi

    2016-01-01

    Background The recent geographical expansion of phlebotomine vectors of Leishmania infantum in the Mediterranean subregion has been attributed to ongoing climate changes. At these latitudes, the activity of sand flies is typically seasonal; because seasonal phenomena are also sensitive to general variations in climate, current phenological data sets can provide a baseline for continuing investigations on sand fly population dynamics that may impact on future scenarios of leishmaniasis transmission. With this aim, in 2011–2013 a consortium of partners from eight Mediterranean countries carried out entomological investigations in sites where L. infantum transmission was recently reported. Methods/Principal Findings A common protocol for sand fly collection included monthly captures by CDC light traps, complemented by sticky traps in most of the sites. Collections were replicated for more than one season in order to reduce the effects of local weather events. In each site, the trapping effort was left unchanged throughout the survey to legitimate inter-seasonal comparisons. Data from 99,000 collected specimens were analyzed, resulting in the description of seasonal dynamics of 56,000 sand flies belonging to L. infantum vector species throughout a wide geographical area, namely P. perniciosus (Portugal, Spain and Italy), P. ariasi (France), P. neglectus (Greece), P. tobbi (Cyprus and Turkey), P. balcanicus and P. kandelakii (Georgia). Time of sand fly appearance/disappearance in collections differed between sites, and seasonal densities showed variations in each site. Significant correlations were found between latitude/mean annual temperature of sites and i) the first month of sand fly appearance, that ranged from early April to the first half of June; ii) the type of density trend, varying from a single peak in July/August to multiple peaks increasing in magnitude from May through September. A 3-modal trend, recorded for P. tobbi in Cyprus, represents a novel

  17. Stable conformation of full-length amyloid-β (1-42) monomer in water: Replica exchange molecular dynamics and ab initio molecular orbital simulations

    NASA Astrophysics Data System (ADS)

    Okamoto, Akisumi; Yano, Atsushi; Nomura, Kazuya; Higai, Shin'ichi; Kurita, Noriyuki

    2013-07-01

    Aggregation of amyloid β-proteins (Aβ) plays a key role in the mechanism of molecular pathogenesis of Alzheimer’s disease (AD). It is known that full-length Aβ(1-42) is more prone to aggregation than Aβ(1-40). We here search stable conformations of solvated Aβ(1-42) monomer by replica exchange molecular dynamics simulations based on classical force fields, and the most stable conformation is determined from the total energies evaluated by the ab initio fragment molecular orbital (FMO) calculations. In addition, based on the FMO results, the amino acid residues of Aβ(1-42) contributing to the stabilization of the monomer are highlighted.

  18. Magnetic friction of a nanometer-sized tip scanning a magnetic surface: Dynamics of a classical spin system with direct exchange and dipolar interactions between the spins

    NASA Astrophysics Data System (ADS)

    Fusco, C.; Wolf, D. E.; Nowak, U.

    2008-05-01

    We theoretically study the occurrence of magnetic friction of a nanometer-sized tip scanning a magnetic surface by studying the dynamics of a model of classical spins interacting through dipolar and exchange interactions, neglecting thermal effects. We find that for small scanning velocities, the friction force linearly scales with the velocity, with a slope proportional to the phenomenological damping parameter of the Landau-Lifshitz-Gilbert equation. At higher velocities, the friction vs velocity relationship becomes rather complex with the presence of a maximum that is explained by the excitations of spin-wave resonances in the sample.

  19. Species frequency dynamics in an old-field succession: Effects of disturbance, fertilization and scale

    USGS Publications Warehouse

    Gibson, D.J.; Middleton, B.A.; Foster, K.; Honu, Y.A.K.; Hoyer, E.W.; Mathis, M.

    2005-01-01

    Question: Can patterns of species frequency in an old-field be explained within the context of a metapopulation model? Are the patterns observed related to time, spatial scale, disturbance, and nutrient availability? Location: Upland and lowland old-fields in Illinois, USA. Method: Species richness was recorded annually for seven years following plowing of an upland and lowland old-field subject to crossed fertilizer and disturbance treatments (mowing and rototilling). Species occupancy distributions were assessed with respect to the numbers of core and satellite species. Results: In both fields, species richness became higher in disturbed plots than in undisturbed plots over time, and decreased in fertilized plots irrespective of time. A bimodal pattern of species richness consistent with the Core-satellite species (CSS) hypothesis occurred in the initial seed bank and through the course of early succession. The identity of native and exotic core species (those present in > 90% of blocks) changed with time. Some core species from the seed bank became core species in the vegetation, albeit after several years. At the scale of individual plots, a bimodal fit consistent with the CSS hypothesis applied only in year 1 and rarely thereafter. Conclusions: The CSS hypothesis provides a metapopulation perspective for understanding patterns of species richness but requires the assessment of spatial and temporal scaling effects. Regional processes (e.g. propagule availability) at the largest scale have the greatest impact influencing community structure during early secondary succession. Local processes (e.g., disturbance and soil nutrients) are more important at smaller scales and place constraints on species establishment and community structure of both native and exotic species. Under the highest intensity of disturbance, exotic species may be able to use resources unavailable to, or unused by, native species. ?? IAVS; Opulus Press.

  20. Characterization of IgG1 Conformation and Conformational Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry

    SciTech Connect

    Houde, Damian; Arndt, Joseph; Domeier, Wayne; Berkowitz, Steven; Engen, John R.

    2009-04-22

    Protein function is dictated by protein conformation. For the protein biopharmaceutical industry, therefore, it is important to have analytical tools that can detect changes in protein conformation rapidly, accurately, and with high sensitivity. In this paper we show that hydrogen/deuterium exchange mass spectrometry (H/DX-MS) can play an important role in fulfilling this need within the industry. H/DX-MS was used to assess both global and local conformational behavior of a recombinant monoclonal IgG1 antibody, a major class of biopharmaceuticals. Analysis of exchange into the intact, glycosylated IgG1 (and the Fab and Fc regions thereof) showed that the molecule was folded, highly stable, and highly amenable to analysis by this method using less than a nanomole of material. With improved chromatographic methods, peptide identification algorithms and data-processing steps, the analysis of deuterium levels in peptic peptides produced after labeling was accomplished in 1--2 days. On the basis of peptic peptide data, exchange was localized to specific regions of the antibody. Changes to IgG1 conformation as a result of deglycosylation were determined by comparing exchange into the glycosylated and deglycosylated forms of the antibody. Two regions of the IgG1 (residues 236-253 and 292-308) were found to have altered exchange properties upon deglycosylation. These results are consistent with previous findings concerning the role of glycosylation in the interaction of IgG1 with Fc receptors. Moreover, the data clearly illustrate how H/DX-MS can provide important characterization information on the higher order structure of antibodies and conformational changes that these molecules may experience upon modification.

  1. Dynamics of the abundance of some bivalve species in Russian waters of the Sea of Japan and its prognosis

    NASA Astrophysics Data System (ADS)

    Gabaev, D. D.

    2009-04-01

    The abundance dynamics of several species of bivalve mollusks spats were studied on scallop collectors situated in Minonosok bay of Pos’eta Gulf for 27 years and for 4 years in Kit bay of the Sea of Japan (Russia). A significant positive relation was found between the species having similar thermopathy: the Japanese scallop Mizuhopecten yessoensis and Swift’s scallop Swiftopecten swifti, as well as between the wrinkled rock borer Hiatella arctica and Swift’s scallop Swiftopecten swifti. A significant reverse relation was found between the bay mussel Mytilus trossulus and the Northern Pacific seastar Asterias amurensis. Some of the studied mollusks of Minonosok bay and the remote Kit bay display a significant reversed interrelation in their abundance dynamics caused by the precipitation regime. The one-way dispersion analysis a revealed significant influence of the water temperature in June and the precipitation abundance in the summer on Swift’s scallop’s dynamic abundance. The two-way dispersion analysis showed a significant influence of the ice period duration and the solar activity expressed in Wolf’s numbers on the Japanese scallop abundance dynamics. The uneven years in the period from 1977 to 1984 were usually productive for M. yessoensis and S. swifti spat. After 1985, the even years became more productive (there was asynchronicity in the abundance dynamics compared with 1977-1984). Such asynchronicity appeared with the advent of the new 22-year solar cycle, which caused a change in the magnet polarity in 1986.

  2. [Dynamics of species diversity in artificial restoration process of subalpine coniferous forest].

    PubMed

    Wu, Yan; Liu, Qing; He, Hai; Lin, Bo

    2004-08-01

    Through plot investigation and by adopting the concept of space as a substitute for time, the developments of species diversity of trees, shrubs and herbaceous plants in subalpine coniferous plantations at different restoration stages were studied, and the correlation coefficients of species in each layer were discussed. The results indicated that in the restoration process, the species richness, diversity and evenness in subalpine coniferous plantations were gradually increased in a fluctuating way. The restoration process of Picea asperata plantations showed a tendency of development that in favor of resuming species diversity. The indices of species richness (species number and Margalef index) and species diversity (Shannon-Wiener index and Simpson index) of trees increased rapidly from the early stages of plantation establishment to the stage of canopy closing (about 30 yr of stand age) and then presented a tendency of decrease with some slight fluctuations, while the index of species evenness showed a periodical rising trend. For the shrub layer, the indices of species richness (Simpson index and Macintosh index) gradually increased with increasing restoration years, whereas the indices of species diversity (Shannon-Wiener index) decreased in the early stages, sharply increased during the stages of canopy closing, and then slowly decreased, which exhibited a tendency of high-->low-->high. In the layer of herbaceous plants, the indices of species richness (Margalef index and number of species) and species diversity (Simpson index, Macintosh index and Shannon-Wiener index) presented a trend of decrease in the early stages of plantations establishment to canopy closing and increased later on. During this process, herbaceous species and their life forms changed greatly, with shade tolerant species gradually substituting the intolerant species. Among the plantations of different stand ages, the average correlation coefficients of trees, shrubs and herbaceous

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

    PubMed

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

    2016-08-01

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

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

    PubMed

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

    2016-08-01

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

  5. Limited Population Structure, Genetic Drift and Bottlenecks Characterise an Endangered Bird Species in a Dynamic, Fire-Prone Ecosystem

    PubMed Central

    Brown, Sarah M.; Harrisson, Katherine A.; Clarke, Rohan H.; Bennett, Andrew F.; Sunnucks, Paul

    2013-01-01

    Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems. PMID:23626668

  6. Limited population structure, genetic drift and bottlenecks characterise an endangered bird species in a dynamic, fire-prone ecosystem.

    PubMed

    Brown, Sarah M; Harrisson, Katherine A; Clarke, Rohan H; Bennett, Andrew F; Sunnucks, Paul

    2013-01-01

    Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems.

  7. Population dynamics and the economics of invasive species management: the greenhouse whitefly in California-grown strawberries.

    PubMed

    McKee, Gregory J; Goodhue, Rachael E; Zalom, Frank G; Carter, Colin A; Chalfant, James A

    2009-01-01

    In agriculture, relatively few efficacious control measures may be available for an invasive pest. In the case of a new insect pest, insecticide use decisions are affected by regulations associated with its registration, insect population dynamics, and seasonal market price cycles. We assess the costs and benefits of environmental regulations designed to regulate insecticide applications on an invasive species. We construct a bioeconomic model, based on detailed scientific data, of management decisions for a specific invasion: greenhouse whiteflies in California-grown strawberries. The empirical model integrates whitefly population dynamics, the effect of whitefly feeding on strawberry yields, and weekly strawberry price. We use the model to assess the optimality of alternative treatment programs on a simulated greenhouse whitefly population. Our results show that regulations may lead growers to "under-spray" when placed in an economic context, and provide some general lessons about the design of optimal invasive species control policies.

  8. [The conformational dynamic of the tetramer hemoglobin molecule as revealed by hydrogen exchange. II. Influence of the intersubunit contact splitting].

    PubMed

    Abaturov, L V; Molchanova, T P; Nosova, N G; Shliapnikov, S V; Faĭzulin, D A

    2006-01-01

    The rate of the H-D exchange of the peptide NH atoms of the isolated alpha and beta subunits of human Hb were studied at the pH range 5.5-9.0 and 20 degrees C by the IR spectroscopy. The factor retardation of the exchange rate of subunits -P in the range -10(2)-10(7). In comparison with tetramer Hb the probability of local fluctuations (1/P) is increased to a slightly greater extent for the monomeric alpha subunits then for the tetramer beta subunits. Unlike Hb oxygenation of subunits does not influence on the probability of the local fluctuations and subunits have no the pH-dependent change of the value 1/P observable for the ligand Hb. The possible mechanisms of the overall intensification of the local fluctuations upon the splitting of the Hb tetrameric contacts between subunits are discussed with the inviting of the structural crystallographic data.

  9. Dynamics of competing species in a model of adaptive radiation and macroevolution

    NASA Astrophysics Data System (ADS)

    de Blasio, Birgitte Freiesleben; de Blasio, Fabio Vittorio

    2005-09-01

    We present a simple model of adaptive radiation in evolution based on species competition. Competition is found to promote species divergence and branching, and to dampen the net species production. In the model simulations, hi