Science.gov

Sample records for dynamic species exchange

  1. Exchange frequency in replica exchange molecular dynamics

    NASA Astrophysics Data System (ADS)

    Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.

    2008-01-01

    The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.

  2. Contrasting nuclear and cytoplasmic exchanges between phylogenetically distant oak species (Quercus suber L. and Q. ilex L.) in Southern France: inferring crosses and dynamics.

    PubMed

    Mir, C; Jarne, P; Sarda, V; Bonin, A; Lumaret, R

    2009-03-01

    Gene flow is particularly frequent in the genus Quercus (oaks), especially between closely related species. We focus here on Quercus ilex and the cork-producing Quercus suber, which occasionally hybridize although they are phylogenetically markedly separated. Morphological observations were combined with both allozymic and chloroplastic diagnostic markers to characterize hybridization and introgression and to infer their dynamics in two French regions (French Catalonia and Provence), which are separated by several hundred kilometres. Some hybrids were found in both regions, indicating recent hybridization events. As expected from previous studies, most hybrids resulted from female symbol Q. ilex x male symbol Q. suber crosses, but our data showed that the reciprocal cross is also possible. Partial independence between nuclear and chloroplastic introgression was observed in the two species. Nuclear introgression was limited in both species and both regions, with no preferred direction. In Provence, chloroplastic introgression was very rare in both species. Conversely, all Q. suber individuals from French Catalonia were introgressed by Q. ilex chlorotypes. This might be explained by introgression in the Iberian Peninsula antedating the first occurrence of the two species in French Catalonia. We also observed a new chlorotype that was created locally, and was exchanged between the two species. However, the two species still remain genetically differentiated. The dynamics and complexity of exchanges and the factors determining them (including human management of Q. suber) are discussed.

  3. 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.

  4. Nonadiabatic exchange dynamics during adiabatic frequency sweeps.

    PubMed

    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.

  5. Intracellular guest exchange between dynamic supramolecular hosts.

    PubMed

    Swaminathan, Subramani; Fowley, Colin; McCaughan, Bridgeen; Cusido, Janet; Callan, John F; Raymo, Françisco M

    2014-06-04

    Decyl and oligo(ethylene glycol) chains were appended to the same poly(methacrylate) backbone to generate an amphiphilic polymer with a ratio between hydrophobic and hydrophilic segments of 2.5. At concentrations greater than 10 μg mL(-1) in neutral buffer, multiple copies of this particular macromolecule assemble into nanoparticles with a hydrodynamic diameter of 15 nm. In the process of assembling, these nanoparticles can capture anthracene donors and borondipyrromethene acceptors within their hydrophobic interior and permit the transfer of excitation energy with an efficiency of 95%. Energy transfer is observed also if nanocarriers containing exclusively the donors are mixed with nanoparticles preloaded separately with the acceptors in aqueous media. The two sets of supramolecular assemblies exchange their guests with fast kinetics upon mixing to co-localize complementary chromophores within the same nanostructured container and enable energy transfer. After guest exchange, the nanoparticles can cross the membrane of cervical cancer cells and bring the co-entrapped donors and acceptors within the intracellular environment. Alternatively, intracellular energy transfer is also established after sequential cell incubation with nanoparticles containing the donors first and then with nanocarriers preloaded with the acceptors or vice versa. Under these conditions, the nanoparticles exchange their cargo only after internalization and allow energy transfer exclusively within the cell interior. Thus, the dynamic character of such supramolecular containers offers the opportunity to transport independently complementary species inside cells and permit their interaction only within the intracellular space.

  6. 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

  7. 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.

  8. 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.

  9. Spread dynamics of invasive species.

    PubMed

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

    2006-01-10

    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.

  10. 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

  11. Do Heliconius butterfly species exchange mimicry alleles?

    PubMed Central

    Smith, Joel; Kronforst, Marcus R.

    2013-01-01

    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. PMID:23864282

  12. 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.

  13. Dynamic conservation for migratory species

    PubMed Central

    Reynolds, Mark D.; Sullivan, Brian L.; Hallstein, Eric; Matsumoto, Sandra; Kelling, Steve; Merrifield, Matthew; Fink, Daniel; Johnston, Alison; Hochachka, Wesley M.; Bruns, Nicholas E.; Reiter, Matthew E.; Veloz, Sam; Hickey, Catherine; Elliott, Nathan; Martin, Leslie; Fitzpatrick, John W.; Spraycar, Paul; Golet, Gregory H.; McColl, Christopher; Morrison, Scott A.

    2017-01-01

    In an era of unprecedented and rapid global change, dynamic conservation strategies that tailor the delivery of habitat to when and where it is most needed can be critical for the persistence of species, especially those with diverse and dispersed habitat requirements. We demonstrate the effectiveness of such a strategy for migratory waterbirds. We analyzed citizen science and satellite data to develop predictive models of bird populations and the availability of wetlands, which we used to determine temporal and spatial gaps in habitat during a vital stage of the annual migration. We then filled those gaps using a reverse auction marketplace to incent qualifying landowners to create temporary wetlands on their properties. This approach is a cost-effective way of adaptively meeting habitat needs for migratory species, optimizes conservation outcomes relative to investment, and can be applied broadly to other conservation challenges. PMID:28845449

  14. Longitudinal exchange: an alternative strategy towards quantification of dynamics parameters in ZZ exchange spectroscopy.

    PubMed

    Kloiber, Karin; Spitzer, Romana; Grutsch, Sarina; Kreutz, Christoph; Tollinger, Martin

    2011-09-01

    Longitudinal exchange experiments facilitate the quantification of the rates of interconversion between the exchanging species, along with their longitudinal relaxation rates, by analyzing the time-dependence of direct correlation and exchange cross peaks. Here we present a simple and robust alternative to this strategy, which is based on the combination of two complementary experiments, one with and one without resolving exchange cross peaks. We show that by combining the two data sets systematic errors that are caused by differential line-broadening of the exchanging species are avoided and reliable quantification of kinetic and relaxation parameters in the presence of additional conformational exchange on the ms-μs time scale is possible. The strategy is applied to a bistable DNA oligomer that displays different line-broadening in the two exchanging species.

  15. 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.

  16. A Unified Approach to Dynamic Matching and Barter Exchange

    DTIC Science & Technology

    2016-09-01

    barter exchange, market design, dynamic matching markets , kidney exchange, combinatorial optimization To my parents, for their unwavering support in...addresses the design, analysis, and real-world fielding of dynamic matching markets and barter exchanges. We present new mathematical models for static... markets , and develop provably optimal market clearing algo- rithms for models of these markets that can be deployed in practice. We show that taking a

  17. Species radiation by DNA replication that systematically exchanges nucleotides?

    PubMed

    Seligmann, Hervé

    2014-12-21

    RNA and DNA syntheses share many properties. Therefore, the existence of 'swinger' RNAs, presumed 'orphan' transcripts matching genomic sequences only if transcription systematically exchanged nucleotides, suggests replication producing swinger DNA. Transcripts occur in many short-lived copies, the few cellular DNA molecules are long-lived. Hence pressures for functional swinger DNAs are greater than for swinger RNAs. Protein coding properties of swinger sequences differ from original sequences, suggesting rarity of corresponding swinger DNA. For genes producing structural RNAs, such as tRNAs and rRNAs, three exchanges (A<->T, C<->G and A<->T+C<->G) conserve self-hybridization properties. All nuclear eukaryote swinger DNA sequences detected in GenBank are for rRNA genes assuming A<->T+C<->G exchanges. In brachyuran crabs, 25 species had A<->T+C<->G swinger 18S rDNA, all matching the reverse-exchanged version of regular 18S rDNA of a related species. In this taxon, swinger replication of 18S rDNA apparently associated with, or even resulted in species radiation. A<->T+C<->G transformation doesn't invert sequence direction, differing from inverted repeats. Swinger repeats (detectable only assuming swinger transformations, A<->T+C<->G swinger repeats most frequent) within regular human rRNAs, independently confirm swinger polymerizations for most swinger types. Swinger replication might be an unsuspected molecular mechanism for ultrafast speciation.

  18. Crossing species' range borders: interspecies gene exchange mediated by hybridogenesis

    PubMed Central

    Schmeller, Dirk S; Seitz, Alfred; Crivelli, Alain; Veith, Michael

    2005-01-01

    The distribution of species is limited by their ability to adapt to local environments. For adaptation by selection, genetic variability is crucial. As founder effects reduce genetic variability, extension of species' range borders is usually slow due to the reduced probability of successful colonization. However, the range limit might be extended by incorporating locally adapted genes. In western Palaearctic waterfrogs, interspecies hybrids show hemiclonal gametogenesis, are fertile and reproductively mimic one parental species. Genetic analysis, using allozyme loci, shows that they mediate gene exchange between the two parental species. Selection analysis provides evidence for local adaptation of single locus genotypes. This suggests that hybridogenesis presents a process which increases the number of neoform parental genotypes, exposing these to selection, and thereby revealing locally adapted genotypes which are essential for species range expansion. PMID:16048778

  19. Dynamics and topology of species networks

    NASA Astrophysics Data System (ADS)

    Bastolla, Ugo; Laessig, Michael; Manrubia, Susanna C.; Valleriani, Angelo

    We study communities formed by a large number of species, which are an example of dynamical networks in biology. Interactions between species, such as prey-predator relationships and mutual competition, define the links of these networks. They also govern the dynamics of their population sizes. This dynamics acts as a selection mechanism, which can lead to the extinction of species. Adaptive changes of the interactions or the generation of new species involve random mutations as well as selection. We show how this dynamics determines key topological characteristics of species networks. The results are in agreement with observations.

  20. 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

  1. 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.

  2. 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.

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

    PubMed

    2012-07-05

    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.

  4. Dynamic enhancement of the exchange bias training effect

    NASA Astrophysics Data System (ADS)

    Sahoo, S.; Polisetty, S.; Binek, Ch.; Berger, A.

    2007-03-01

    Exchange bias in coupled magnetic thin films and its accompanying training effect are fundamental interface phenomena with significant impact in spintronic applications. Both effects are well known in heterosystems of ferro- and antiferromagnetic thin films. Here, we report on the dynamic enhancement of the training effect in an exchange coupled bilayer of soft and hard ferromagnetic materials. Training is referred to as a gradual change of the bias field, which evolves upon cycling the soft layer through consecutive hysteresis loops. Its dynamic enhancement is observed with increasing sweep rate of the applied magnetic field from quasistatic to the fully dynamic range. A dynamically generalized theory based on triggered relaxation is in excellent agreement with the training data. Additionally, we evidence the remarkable universality of our theoretical approach when applying it to the dynamically altered training effect of a conventional exchange bias system involving an antiferromagnetic pinning layer.

  5. 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.

  6. 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.

  7. Dynamic tube/support interaction in heat exchanger tubes

    SciTech Connect

    Chen, S.S.

    1991-01-01

    The supports for heat exchanger tubes are usually plates with drilled holes; other types of supports also have been used. To facilitate manufacture and to allow for thermal expansion of the tubes, small clearances are used between tubes and tube supports. The dynamics of tube/support interaction in heat exchangers is fairly complicated. Understanding tube dynamics and its effects is important for heat exchangers. This paper summarizes the current state of the art on this subject and to identify future research needs. Specifically, the following topics are discussed: dynamics of loosely supported tubes, tube/support gap dynamics, tube response in flow, tube damage and wear, design considerations, and future research needs. 55 refs., 1 fig.

  8. Dynamics of water and salt exchange at Maryland Coastal Bays

    NASA Astrophysics Data System (ADS)

    Kang, Xinyi; Xia, Meng; Pitula, Joseph S.; Chigbu, Paulinus

    2017-04-01

    The exchange processes between the Maryland Coastal Bays system (MCBs) and their adjacent coastal ocean were simulated using a three-dimensional unstructured-grid based hydrodynamic model, which was validated by observed data including water level, current velocity and salinity. Idealized experiments were then carried out to investigate the impact of wind forcing on water exchange and salt flux. Through these experiments, the exchanges between the MCBs and coastal ocean were investigated at two inlets (Ocean City Inlet and Chincoteague Inlet). Given that winds and tides are two key external forces known to impact estuarine dynamics, the effect of each individual force on the exchange processes was studied to evaluate the corresponding influence on the inlet dynamics. It was found that wind forcing significantly impacts the inlet dynamics: the effect of wind directions on exchange processes under strong wind speeds is substantial; for example, northwesterly winds push flux to the southern part of the bays, while southwesterly winds pile up flux towards northern Chincoteague Bay. The effect of wind forcing on the exchange dynamics becomes stronger with the augmentation of its speed. Meanwhile, tidal forcing is the major driver of exchange dynamics at weak wind speeds (e.g., 3 m/s), and its effect on exchange process gradually weakens with stronger wind speeds (e.g., 7 m/s, 15 m/s). In addition, sensitivity tests elucidated that closing either inlet results in a significant impact on the water elevation, current velocity and salinity nearby the relevant cut-off inlet areas.

  9. Modeling of the Bosphorus exchange flow dynamics

    NASA Astrophysics Data System (ADS)

    Sözer, Adil; Özsoy, Emin

    2017-04-01

    The fundamental hydrodynamic behavior of the Bosphorus Strait is investigated through a numerical modeling study using alternative configurations of idealized or realistic geometry. Strait geometry and basin stratification conditions allow for hydraulic controls and are ideally suited to support the maximal-exchange regime, which determines the rate of exchange of waters originating from the adjacent Black and Mediterranean Seas for a given net transport. Steady-state hydraulic controls are demonstrated by densimetric Froude number calculations under layered flow approximations when corrections are applied to account for high velocity shears typically observed in the Bosphorus. Analyses of the model results reveal many observed features of the strait, including critical transitions at hydraulic controls and dissipation by turbulence and hydraulic jumps. It is found that the solution depends on initialization, especially with respect to the basin initial conditions. Significant differences between the controlled maximal-exchange and drowned solutions suggest that a detailed modeling implementation involving coupling with adjacent basins needs to take full account of the Bosphorus Strait in terms of the physical processes to be resolved.

  10. Modeling of the Bosphorus exchange flow dynamics

    NASA Astrophysics Data System (ADS)

    Sözer, Adil; Özsoy, Emin

    2017-01-01

    The fundamental hydrodynamic behavior of the Bosphorus Strait is investigated through a numerical modeling study using alternative configurations of idealized or realistic geometry. Strait geometry and basin stratification conditions allow for hydraulic controls and are ideally suited to support the maximal-exchange regime, which determines the rate of exchange of waters originating from the adjacent Black and Mediterranean Seas for a given net transport. Steady-state hydraulic controls are demonstrated by densimetric Froude number calculations under layered flow approximations when corrections are applied to account for high velocity shears typically observed in the Bosphorus. Analyses of the model results reveal many observed features of the strait, including critical transitions at hydraulic controls and dissipation by turbulence and hydraulic jumps. It is found that the solution depends on initialization, especially with respect to the basin initial conditions. Significant differences between the controlled maximal-exchange and drowned solutions suggest that a detailed modeling implementation involving coupling with adjacent basins needs to take full account of the Bosphorus Strait in terms of the physical processes to be resolved.

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

    PubMed

    Della Sala, Flavio; Kay, Euan R

    2015-03-27

    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.

  12. Dynamic Response of Exchange Bias in Graphene Nanoribbons

    DTIC Science & Technology

    2012-01-01

    1 Dynamic response of exchange bias in graphene nanoribbons S. Narayana Jammalamadaka a, b* , S. S. Rao c, d, e* , J. Vanacken a , V. V...investigated in exchange-coupled potassium split graphene nanoribbons (GNRs). We find that, at low field sweep rate, the pronounced absolute training... graphene nanoribbons 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT

  13. Solvent Exchange Leading to Nanobubble Nucleation: A Molecular Dynamics Study

    PubMed Central

    2017-01-01

    The solvent exchange procedure has become the most-used protocol to produce surface nanobubbles, while the molecular mechanisms behind the solvent exchange are far from being fully understood. In this paper, we build a simple model and use molecular dynamics simulations to investigate the dynamic characteristics of solvent exchange for producing nanobubbles. We find that at the first stage of solvent exchange, there exists an interface between interchanging solvents of different gas solubility. This interface moves toward the substrate gradually as the exchange process proceeds. Our simulations reveal directed diffusion of gas molecules against the gas concentration gradient, driven by the solubility gradient of the liquid composition across the moving solvent–solvent interface. It is this directed diffusion that causes gas retention and produces a local gas oversaturation much higher near the substrate than far from it. At the second stage of solvent exchange, the high local gas oversaturation leads to bubble nucleation either on the solid surface or in the bulk solution, which is found to depend on the substrate hydrophobicity and the degree of local gas oversaturation. Our findings suggest that solvent exchange could be developed into a standard procedure to produce oversaturation and used to a variety of nucleation applications other than generating nanobubbles. PMID:28742364

  14. Solvent Exchange Leading to Nanobubble Nucleation: A Molecular Dynamics Study.

    PubMed

    Xiao, Qianxiang; Liu, Yawei; Guo, Zhenjiang; Liu, Zhiping; Lohse, Detlef; Zhang, Xianren

    2017-08-15

    The solvent exchange procedure has become the most-used protocol to produce surface nanobubbles, while the molecular mechanisms behind the solvent exchange are far from being fully understood. In this paper, we build a simple model and use molecular dynamics simulations to investigate the dynamic characteristics of solvent exchange for producing nanobubbles. We find that at the first stage of solvent exchange, there exists an interface between interchanging solvents of different gas solubility. This interface moves toward the substrate gradually as the exchange process proceeds. Our simulations reveal directed diffusion of gas molecules against the gas concentration gradient, driven by the solubility gradient of the liquid composition across the moving solvent-solvent interface. It is this directed diffusion that causes gas retention and produces a local gas oversaturation much higher near the substrate than far from it. At the second stage of solvent exchange, the high local gas oversaturation leads to bubble nucleation either on the solid surface or in the bulk solution, which is found to depend on the substrate hydrophobicity and the degree of local gas oversaturation. Our findings suggest that solvent exchange could be developed into a standard procedure to produce oversaturation and used to a variety of nucleation applications other than generating nanobubbles.

  15. Phase transitions and relaxation dynamics of Ising models exchanging particles

    NASA Astrophysics Data System (ADS)

    Goh, Segun; Fortin, Jean-Yves; Choi, M. Y.

    2017-01-01

    A variety of systems in nature and in society are open and subject to exchanging their constituents with other systems (e.g., environments). For instance, in biological systems, cells collect necessary energy and material by exchange of molecules or ions. Similarly, countries, cities or research institutes evolve as their constituents move in or out. To probe the corresponding particle exchange dynamics in such systems, we consider two Ising models exchanging particles and establish a master equation describing the equilibrium phases as well as the non-equilibrium dynamics of the system. It is found that an additional stable phase emerges as a consequence of the particle exchange process. Furthermore, we formulate the Ginzburg-Landau theory which allows to probe correlation effects. Accordingly, critical slowing down is manifested and the associated dynamic exponent is computed in the linear relaxation regime. In particular, this approach is relevant for investigating the grand canonical description of the system plus environment, with particle exchange and state transitions taken into account explicitly.

  16. Species pool and dynamics of marine paleocommunities.

    PubMed

    Buzas, M A; Culver, S J

    1994-06-03

    Foraminiferal communities in the Cenozoic shelf deposits of the North American Atlantic Coastal Plain exhibit little unity during almost 55 million years of successive transgressions and regressions. Transgression communities are composed of a dynamic mixture of immigrants and newly evolved species. During regressions, species within these communities either became extinct or emigrated. Some emigrants returned during subsequent transgressions, but many did not. The neritic species of the Atlantic and Gulf continental margins constitute a species pool. Immigrants and emigrants transferred into and out of the species pool, while extinctions and originations repeatedly altered its species composition. While the results indicate a lack of local community unity, at the same time they demonstrate the necessity of a species pool to sustain species diversity.

  17. Modeling hyporheic exchange with unsteady stream discharge and bedform dynamics

    NASA Astrophysics Data System (ADS)

    Boano, Fulvio; Revelli, Roberto; Ridolfi, Luca

    2013-07-01

    Water exchange between streams and hyporheic zones is highly dynamic, and its temporal variation is related to the hydrologic fluctuations of stream discharge and groundwater levels. Unfortunately, predictions of temporal patterns of exchange are difficult due to the many hydrodynamic and morphodynamic processes that are involved and also to their complex nonlinear interactions. Examples of these processes include the evolution of streambed morphology in response to changing streamflow as well as the feedback on surface flow induced by drag resistance due to evolving bed forms. In this work, we have employed a stochastic method to analyze the temporal dynamics of bed form-driven hyporheic exchange in a stream characterized by subcritical flow and daily discharge variations. The method is an extension of previous studies that includes current-induced alterations of bedform size and celerity and their effect on water exchange. The modeling results show that during high flows, stream water penetrates deeper and for longer times in the sediments. At the same time, the predicted rate of water exchange per unit streambed area decreases because the streambed area occupied by each bed form increases faster than the volumetric rate of stream water exchange induced by the same bed form. This reduction can be compensated by the increase in wetted area with discharge, which may provide additional streambed area for water exchange. One the main finding of the study is that the time-averaged values of exchange flux and depths are quite similar to those modeled for a steady mean discharge, while residence times are somewhat lower. Predicted temporal variations of exchange depths and times around their time-averaged values are moderate compared to steady state values.

  18. Ultrafast 2D-IR and simulation investigations of preferential solvation and cosolvent exchange dynamics.

    PubMed

    Dunbar, Josef A; Arthur, Evan J; White, Aaron M; Kubarych, Kevin J

    2015-05-21

    Using a derivative of the vitamin biotin labeled with a transition-metal carbonyl vibrational probe in a series of aqueous N,N-dimethylformamide (DMF) solutions, we observe a striking slowdown in spectral diffusion dynamics with decreased DMF concentration. Equilibrium solvation dynamics, measured with the rapidly acquired spectral diffusion (RASD) technique, a variant of heterodyne-detected photon-echo peak shift experiments, range from 1 ps in neat DMF to ∼3 ps in 0.07 mole fraction DMF/water solution. Molecular dynamics simulations of the biotin-metal carbonyl solute in explicit aqueous DMF solutions show marked preferential solvation by DMF, which becomes more pronounced at lower DMF concentrations. The simulations and the experimental data are consistent with an interpretation where the slowdown in spectral diffusion is due to solvent exchange involving distinct cosolvent species. A simple two-component model reproduces the observed spectral dynamics as well as the DMF concentration dependence, enabling the extraction of the solvent exchange time scale of 8 ps. This time scale corresponds to the diffusive motion of a few Å, consistent with a solvent-exchange mechanism. Unlike most previous studies of solvation dynamics in binary mixtures of polar solvents, our work highlights the ability of vibrational probes to sense solvent exchange as a new, slow component in the spectral diffusion dynamics.

  19. 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).

  20. 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.

  1. Ab initio dynamical exchange interactions in frustrated antiferromagnets

    NASA Astrophysics Data System (ADS)

    Simoni, Jacopo; Stamenova, Maria; Sanvito, Stefano

    2017-08-01

    The ultrafast response to an optical pulse excitation of the spin-spin exchange interaction in transition metal antiferromagnets is studied within the framework of the time-dependent spin-density functional theory. We propose a formulation for the full dynamical exchange interaction, which is nonlocal in space, and it is derived starting from ab initio arguments. Then, we investigate the effect of the laser pulse on the onset of the dynamical process. It is found that we can distinguish two types of excitations, both activated immediately after the action of the laser pulse. While the first one can be associated to a Stoner-like excitation and involves the transfer of spin from one site to another, the second one is related to the ultrafast modification of a Heisenberg-like exchange interaction and can trigger the formation of spin waves in the first few hundred femtoseconds of the time evolution.

  2. 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…

  3. 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…

  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. 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.

  6. 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…

  7. Diffusive and Arrestedlike Dynamics in Currency Exchange Markets

    NASA Astrophysics Data System (ADS)

    Clara-Rahola, J.; Puertas, A. M.; Sánchez-Granero, M. A.; Trinidad-Segovia, J. E.; de las Nieves, F. J.

    2017-02-01

    This work studies the symmetry between colloidal dynamics and the dynamics of the Euro-U.S. dollar currency exchange market (EURUSD). We consider the EURUSD price in the time range between 2001 and 2015, where we find significant qualitative symmetry between fluctuation distributions from this market and the ones belonging to colloidal particles in supercooled or arrested states. In particular, we find that models used for arrested physical systems are suitable for describing the EURUSD fluctuation distributions. Whereas the corresponding mean-squared price displacement (MSPD) to the EURUSD is diffusive for all years, when focusing in selected time frames within a day, we find a two-step MSPD when the New York Stock Exchange market closes, comparable to the dynamics in supercooled systems. This is corroborated by looking at the price correlation functions and non-Gaussian parameters and can be described by the theoretical model. We discuss the origin and implications of this analogy.

  8. Diffusive and Arrestedlike Dynamics in Currency Exchange Markets.

    PubMed

    Clara-Rahola, J; Puertas, A M; Sánchez-Granero, M A; Trinidad-Segovia, J E; de Las Nieves, F J

    2017-02-10

    This work studies the symmetry between colloidal dynamics and the dynamics of the Euro-U.S. dollar currency exchange market (EURUSD). We consider the EURUSD price in the time range between 2001 and 2015, where we find significant qualitative symmetry between fluctuation distributions from this market and the ones belonging to colloidal particles in supercooled or arrested states. In particular, we find that models used for arrested physical systems are suitable for describing the EURUSD fluctuation distributions. Whereas the corresponding mean-squared price displacement (MSPD) to the EURUSD is diffusive for all years, when focusing in selected time frames within a day, we find a two-step MSPD when the New York Stock Exchange market closes, comparable to the dynamics in supercooled systems. This is corroborated by looking at the price correlation functions and non-Gaussian parameters and can be described by the theoretical model. We discuss the origin and implications of this analogy.

  9. 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.

  10. Computer simulation of methanol exchange dynamics around cations and anions

    SciTech Connect

    Roy, Santanu; Dang, Liem X.

    2016-03-03

    In this paper, we present the first computer simulation of methanol exchange dynamics between the first and second solvation shells around different cations and anions. After water, methanol is the most frequently used solvent for ions. Methanol has different structural and dynamical properties than water, so its ion solvation process is different. To this end, we performed molecular dynamics simulations using polarizable potential models to describe methanol-methanol and ion-methanol interactions. In particular, we computed methanol exchange rates by employing the transition state theory, the Impey-Madden-McDonald method, the reactive flux approach, and the Grote-Hynes theory. We observed that methanol exchange occurs at a nanosecond time scale for Na+ and at a picosecond time scale for other ions. We also observed a trend in which, for like charges, the exchange rate is slower for smaller ions because they are more strongly bound to methanol. 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.

  11. Ligand and proton exchange dynamics in recombinant human myoglobin mutants.

    PubMed

    Lambright, D G; Balasubramanian, S; Boxer, S G

    1989-05-05

    Site-specific mutants of human myoglobin have been prepared in which lysine 45 is replaced by arginine (K45R) and aspartate 60 by glutamate (D60E), in order to examine the influence of these residues and their interaction on the dynamics of the protein. These proteins were studied by a variety of methods, including one and two-dimensional proton nuclear magnetic resonance spectroscopy, exchange kinetics for the distal and proximal histidine NH protons as a function of pH in the met cyano forms, flash photolysis of the CO forms, and ligand replacement kinetics. The electronic absorption and proton nuclear magnetic resonance spectra of the CO forms of these proteins are virtually identical, indicating that the structure of the heme pocket is unaltered by these mutations. There are, however, substantial changes in the dynamics of both CO binding and proton exchange for the mutant K45R, whereas the mutant D60E exhibits behavior indistinguishable from the reference human myoglobin. K45R has a faster CO bimolecular recombination rate and slower CO off-rate relative to the reference. The kinetics for CO binding are independent of pH (6.5 to 10) as well as ionic strength (0 to 1 M-NaCl). The exchange rate for the distal histidine NH is substantially lower for K45R than the reference, whereas the proximal histidine NH exchange rate is unaltered. The exchange behavior of the human proteins is similar to that reported for a comparison of the exchange rates for myoglobins having lysine at position 45 with sperm whale myoglobin, which has arginine at this position. This indicates that the differences in exchange rates reflects largely the Lys----Arg substitution. The lack of a simple correlation for the CO kinetics with this substitution means that these are sensitive to other factors as well. Specific kinetic models, whereby substitution of arginine for lysine at position 45 can affect ligand binding dynamics, are outlined. These experiments demonstrate that a relatively

  12. 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.

  13. Why the long hours? Job demands and social exchange dynamics.

    PubMed

    Genin, Emilie; Haines, Victor Y; Pelletier, David; Rousseau, Vincent; Marchand, Alain

    2016-11-22

    This study investigates the determinants of long working hours from the perspectives of the demand-control model [Karasek, 1979] and social exchange theory [Blau, 1964; Goulder, 1960]. These two theoretical perspectives are tested to understand why individuals work longer (or shorter) hours. The hypotheses are tested with a representative sample of 1,604 employed Canadians. In line with Karasek's model, the results support that high job demands are positively associated with longer work hours. The social exchange perspective would predict a positive association between skill discretion and work hours. This hypothesis was supported for individuals with a higher education degree. Finally, the results support a positive association between active jobs and longer work hours. Our research suggests that job demands and social exchange dynamics need to be considered together in the explanation of longer (or shorter) work hours.

  14. 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.

  15. 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

  16. NASA data exchange standards for computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Blake, Matthew

    1993-01-01

    This paper covers the following topics in viewgraph format: purpose of data exchange standards; data exchange in engineering analysis/CFD; geometry data exchange through existing product data exchange standards, NASA Data Exchange Committee, and NASA-IGES (Initial Graphics Exchange Specification); CFD grid and solution data exchange; and data exchange for multi-disciplinary engineering.

  17. 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

  18. Kinetic model of mass exchange with dynamic Arrhenius transition rates

    NASA Astrophysics Data System (ADS)

    Hristopulos, Dionissios T.; Muradova, Aliki

    2016-02-01

    We study a nonlinear kinetic model of mass exchange between interacting grains. The transition rates follow the Arrhenius equation with an activation energy that depends dynamically on the grain mass. We show that the activation parameter can be absorbed in the initial conditions for the grain masses, and that the total mass is conserved. We obtain numerical solutions of the coupled, nonlinear, ordinary differential equations of mass exchange for the two-grain system, and we compare them with approximate theoretical solutions in specific neighborhoods of the phase space. Using phase plane methods, we determine that the system exhibits regimes of diffusive and growth-decay (reverse diffusion) kinetics. The equilibrium states are determined by the mass equipartition and separation nullcline curves. If the transfer rates are perturbed by white noise, numerical simulations show that the system maintains the diffusive and growth-decay regimes; however, the noise can reverse the sign of equilibrium mass difference. Finally, we present theoretical analysis and numerical simulations of a system with many interacting grains. Diffusive and growth-decay regimes are established as well, but the approach to equilibrium is considerably slower. Potential applications of the mass exchange model involve coarse-graining during sintering and wealth exchange in econophysics.

  19. 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.

  20. Predicting Carbonate Species Ionic Conductivity in Alkaline Anion Exchange Membranes

    DTIC Science & Technology

    2012-06-01

    anion exchange membranes. Andrew M. Kiss, Timothy D . Myles, Kyle N. Grew, Aldo A. Peracchio, George J. Nelson, and Wilson K. S. Chiu University of...Alkaline Anion Exchange Membranes Andrew M. Kiss1, Timothy D . Myles1, Kyle N. Grew2, Aldo A. Peracchio1, George J. Nelson1, and Wilson K. S. Chiu1* 1...Vol. 301, 93-106, 2007. 16. Satterfleld,M.B., Benziger,J.B., J. Phys. Chem. B, Vol. 112,12, 3693 -3704, 2008. 17. Motupally,S., Becker,A.J

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

    Treesearch

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

    2014-01-01

    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,...

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

    Treesearch

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

    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...

  3. Dynamic pupillary exchange engages brain regions encoding social salience.

    PubMed

    Harrison, Neil A; Gray, Marcus A; Critchley, Hugo D

    2009-01-01

    Covert exchange of autonomic responses may shape social affective behavior, as observed in mirroring of pupillary responses during sadness processing. We examined how, independent of facial emotional expression, dynamic coherence between one's own and another's pupil size modulates regional brain activity. Fourteen subjects viewed pairs of eye stimuli while undergoing fMRI. Using continuous pupillometry biofeedback, the size of the observed pupils was varied, correlating positively or negatively with changes in participants' own pupils. Viewing both static and dynamic stimuli activated right fusiform gyrus. Observing dynamically changing pupils activated STS and amygdala, regions engaged by non-static and salient facial features. Discordance between observed and observer's pupillary changes enhanced activity within bilateral anterior insula, left amygdala and anterior cingulate. In contrast, processing positively correlated pupils enhanced activity within left frontal operculum. Our findings suggest pupillary signals are monitored continuously during social interactions and that incongruent changes activate brain regions involved in tracking motivational salience and attentionally meaningful information. Naturalistically, dynamic coherence in pupillary change follows fluctuations in ambient light. Correspondingly, in social contexts discordant pupil response is likely to reflect divergence of dispositional state. Our data provide empirical evidence for an autonomically mediated extension of forward models of motor control into social interaction.

  4. Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

    PubMed

    Cooke, Ben; Schmidler, Scott C

    2008-10-28

    We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

  5. Driven Nonlinear Dynamics of Two Coupled Exchange-Only Qubits

    NASA Astrophysics Data System (ADS)

    Pal, Arijeet; Rashba, Emmanuel I.; Halperin, Bertrand I.

    2014-01-01

    Inspired by the creation of a fast exchange-only qubit [Medford et al., Phys. Rev. Lett. 111, 050501 (2013)], we develop a theory describing the nonlinear dynamics of two such qubits that are capacitively coupled, when one of them is driven resonantly at a frequency equal to its level splitting. We include conditions of strong driving, where the Rabi frequency is a significant fraction of the level splitting, and we consider situations where the splitting for the second qubit may be the same as or different than the first. We demonstrate that coupling between qubits can be detected by reading the response of the second qubit, even when the coupling between them is only of about 1% of their level splittings, and we calculate entanglement between qubits. Patterns of nonlinear dynamics of coupled qubits and their entanglement are strongly dependent on the geometry of the system, and the specific mechanism of interqubit coupling deeply influences dynamics of both qubits. In particular, we describe the development of irregular dynamics in a two-qubit system, explore approaches for inhibiting it, and demonstrate the existence of an optimal range of coupling strength maintaining stability during the operational time.

  6. Challenges in quantifying biosphere-atmosphere exchange of nitrogen species.

    PubMed

    Sutton, M A; Nemitz, E; Erisman, J W; Beier, C; Bahl, K Butterbach; Cellier, P; de Vries, W; Cotrufo, F; Skiba, U; Di Marco, C; Jones, S; Laville, P; Soussana, J F; Loubet, B; Twigg, M; Famulari, D; Whitehead, J; Gallagher, M W; Neftel, A; Flechard, C R; Herrmann, B; Calanca, P L; Schjoerring, J K; Daemmgen, U; Horvath, L; Tang, Y S; Emmett, B A; Tietema, A; Peñuelas, J; Kesik, M; Brueggemann, N; Pilegaard, K; Vesala, T; Campbell, C L; Olesen, J E; Dragosits, U; Theobald, M R; Levy, P; Mobbs, D C; Milne, R; Viovy, N; Vuichard, N; Smith, J U; Smith, P; Bergamaschi, P; Fowler, D; Reis, S

    2007-11-01

    Recent research in nitrogen exchange with the atmosphere has separated research communities according to N form. The integrated perspective needed to quantify the net effect of N on greenhouse-gas balance is being addressed by the NitroEurope Integrated Project (NEU). Recent advances have depended on improved methodologies, while ongoing challenges include gas-aerosol interactions, organic nitrogen and N(2) fluxes. The NEU strategy applies a 3-tier Flux Network together with a Manipulation Network of global-change experiments, linked by common protocols to facilitate model application. Substantial progress has been made in modelling N fluxes, especially for N(2)O, NO and bi-directional NH(3) exchange. Landscape analysis represents an emerging challenge to address the spatial interactions between farms, fields, ecosystems, catchments and air dispersion/deposition. European up-scaling of N fluxes is highly uncertain and a key priority is for better data on agricultural practices. Finally, attention is needed to develop N flux verification procedures to assess compliance with international protocols.

  7. Correlation between CAM-Cycling and Photosynthetic Gas Exchange in Five Species of Talinum (Portulacaceae) 1

    PubMed Central

    Harris, Fred S.; Martin, Craig E.

    1991-01-01

    Photosynthetic gas exchange and malic acid fluctuations were monitored in 69 well-watered plants from five morphologically similar species of Talinum in an investigation of the ecophysiological significance of the Crassulacean acid metabolism (CAM)-cycling mode of photosynthesis. Unlike CAM, atmospheric CO2 uptake in CAM-cycling occurs exclusively during the day; at night, the stomata are closed and respiratory CO2 is recaptured to form malic acid. All species showed similar patterns of day-night gas exchange and overnight malic acid accumulation, confirming the presence of CAM-cycling. Species averages for gas exchange parameters and malic acid fluctuation were significantly different such that the species with the highest daytime gas exchange had the lowest malic acid accumulation and vice versa. Also, daytime CO2 exchange and transpiration were negatively correlated with overnight malic acid fluctuation for all individuals examined together, as well as within one species. This suggests that malic acid may effect reductions in both atmospheric CO2 uptake and transpiration during the day. No significant correlation between malic acid fluctuation and water-use efficiency was found, although a nonsignificant trend of increasing water-use efficiency with increasing malic acid fluctuation was observed among species averages. This study provides evidence that CO2 recycling via malic acid is negatively correlated with daytime transpirational water losses in well-watered plants. Thus, CAM-cycling could be important for survival in the thin, frequently desiccated soils of rock outcrops on which these plants occur. PMID:16668307

  8. Contrasting dynamics of leaf potential and gas exchange during progressive drought cycles and recovery in Amorpha fruticosa and Robinia pseudoacacia.

    PubMed

    Yan, Weiming; Zheng, Shuxia; Zhong, Yangquanwei; Shangguan, Zhouping

    2017-06-30

    Leaf gas exchange is closely associated with water relations; however, less attention has been given to this relationship over successive drought events. Dynamic changes in gas exchange and water potential in the seedlings of two woody species, Amorpha fruticosa and Robinia pseudoacacia, were monitored during recurrent drought. The pre-dawn leaf water potential declined in parallel with gas exchange in both species, and sharp declines in gas exchange occurred with decreasing water potential. A significant correlation between pre-dawn water potential and gas exchange was observed in both species and showed a right shift in R. pseudoacacia in the second drought. The results suggested that stomatal closure in early drought was mediated mainly by elevated foliar abscisic acid (ABA) in R. pseudoacacia, while a shift from ABA-regulated to leaf-water-potential-driven stomatal closure was observed in A. fruticosa. After re-watering, the pre-dawn water potential recovered quickly, whereas stomatal conductance did not fully recover from drought in R. pseudoacacia, which affected the ability to tightly control transpiration post-drought. The dynamics of recovery from drought suggest that stomatal behavior post-drought may be restricted mainly by hydraulic factors, but non-hydraulic factors may also be involved in R. pseudoacacia.

  9. 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.

  10. Energy exchange dynamics across L-H transitions in NSTX

    NASA Astrophysics Data System (ADS)

    Diallo, A.; Banerjee, S.; Zweben, S. J.; Stoltzfus-Dueck, T.

    2017-06-01

    We studied the energy exchange dynamics across the low-to-high-confinement (L-H) transition in NSTX discharges using the gas-puff imaging (GPI) diagnostic. The investigation focused on the energy exchange between flows and turbulence to help clarify the mechanism of the L-H transition. We applied this study to three types of heating schemes, including a total of 17 shots from the NSTX 2010 campaign run. Results show that the edge fluctuation characteristics (fluctuation levels, radial and poloidal correlation lengths) measured using GPI do not vary just prior to the H-mode transition, but change after the transition. Using a velocimetry approach (orthogonal-dynamics programming), velocity fields of a 24× 30 cm GPI view during the L-H transition were obtained with good spatial (˜1 cm) and temporal (˜2.5 μs) resolutions. Analysis using these velocity fields shows that the production term is systematically negative just prior to the L-H transition, indicating a transfer from mean flows to turbulence, which is inconsistent with the predator-prey paradigm. Moreover, the inferred absolute value of the production term is two orders of magnitude too small to explain the observed rapid L-H transition. These discrepancies are further reinforced by consideration of the ratio between the kinetic energy in the mean flow to the thermal free energy, which is estimated to be much less than 1, suggesting again that the turbulence depletion mechanism may not play an important role in the transition to the H-mode. Although the Reynolds work therefore appears to be too small to directly deplete the turbulent free energy reservoir, order-of-magnitude analysis shows that the Reynolds stress may still make a non-negligible contribution to the observed poloidal flows.

  11. Energy exchange dynamics across L–H transitions in NSTX

    DOE PAGES

    Diallo, A.; Banerjee, S.; Zweben, S. J.; ...

    2017-05-10

    Here, we studied the energy exchange dynamics across the low-to-high-confinement (L–H) transition in NSTX discharges using the gas-puff imaging (GPI) diagnostic. The investigation focused on the energy exchange between flows and turbulence to help clarify the mechanism of the L–H transition. We applied this study to three types of heating schemes, including a total of 17 shots from the NSTX 2010 campaign run. Results show that the edge fluctuation characteristics (fluctuation levels, radial and poloidal correlation lengths) measured using GPI do not vary just prior to the H-mode transition, but change after the transition. Using a velocimetry approach (orthogonal-dynamics programming), velocity fields of amore » $$24\\times 30$$ cm GPI view during the L–H transition were obtained with good spatial (~1 cm) and temporal (~2.5 μs) resolutions. Analysis using these velocity fields shows that the production term is systematically negative just prior to the L–H transition, indicating a transfer from mean flows to turbulence, which is inconsistent with the predator–prey paradigm. Moreover, the inferred absolute value of the production term is two orders of magnitude too small to explain the observed rapid L–H transition. These discrepancies are further reinforced by consideration of the ratio between the kinetic energy in the mean flow to the thermal free energy, which is estimated to be much less than 1, suggesting again that the turbulence depletion mechanism may not play an important role in the transition to the H-mode. Although the Reynolds work therefore appears to be too small to directly deplete the turbulent free energy reservoir, order-of-magnitude analysis shows that the Reynolds stress may still make a non-negligible contribution to the observed poloidal flows.« less

  12. Evaluating an invasive species policy: ballast water exchange in the Great Lakes.

    PubMed

    Costello, Christopher; Drake, John M; Lodge, David M

    2007-04-01

    Improvements in environmental policy require an accurate diagnosis of the shortcomings of existing policy. We develop a model for assessing the efficacy of policy instruments aimed at reducing the introduction of nonindigenous species. The model identifies and accounts for several features of the nonindigenous species introduction-detection process that complicate interpretations of monitoring data. Specifically, the model includes explicit attention to the pathway of introduction, a probabilistic description of species detection, and the possibility of attenuation of species introductions over time. We apply this theoretical model to the case of mid-ocean ballast water exchange, which was implemented by the United States in 1990 for the North American Great Lakes. Contrary to other authors who take the recent increase in discoveries of nonindigeneous species (NIS) in the Great Lakes as evidence that ballast water exchange is ineffective, we find that the observed detection record could just as plausibly be explained by a lag of a few years between introduction and detection, even if ballast water exchange was 100% effective. Model results suggest that, under current monitoring regimes, several more years of data would be required to make a conclusive evaluation of ballast water exchange. Better estimation of the lag time between introduction and detection, and a shortening of that lag time with better monitoring, would allow more precise and timely evaluation of the efficacy of ballast water exchange and other policy instruments.

  13. 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.

  14. 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.

  15. 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.

  16. Investigating existence of chaos in short and long term dynamics of Moroccan exchange rates

    NASA Astrophysics Data System (ADS)

    Lahmiri, Salim

    2017-01-01

    This paper proposes a new methodology to investigate presence of chaos in exchange rate time series by combining wavelet transform and Lyapunov exponent estimation. In particular, stationary wavelet transform (SWT) is applied to exchange rate original time series for decomposition purpose. As a result, approximation and details coefficients are extracted. They are used to represent long and short term dynamics of the original exchange rate time series. Then, largest Lyapunov exponent is estimated for each type of dynamics to check for presence of chaos. Our methodology is applied to several Moroccan exchange rate time series. The empirical results show that, in general, the hypothesis of chaotic structure is accepted for currency levels but it is rejected for currency returns on both long and short dynamics. In addition, long and short dynamics exhibit different chaotic patterns in some exchange rate time series. Our approach may be useful to understand chaotic behaviour in original exchange rate time series.

  17. Tailoring of ion species composition in complex plasmas with charge exchange collisions

    NASA Astrophysics Data System (ADS)

    Ostrikov, K.

    2005-06-01

    A generic approach towards tailoring of ion species composition in reactive plasmas used for nanofabrication of various functional nanofilms and nanoassemblies, based on a simplified model of a parallel-plate rf discharge, is proposed. The model includes an idealized reactive plasma containing two neutral and two ionic species interacting via charge exchange collisions in the presence of a microdispersed solid component. It is shown that the number densities of the desired ionic species can be efficiently managed by adjusting the dilution of the working gas in a buffer gas, rates of electron impact ionization, losses of plasma species on the discharge walls, and surfaces of fine particles, charge exchange rates, and efficiency of three-body recombination processes in the plasma bulk. The results are relevant to the plasma-aided nanomanufacturing of ordered patterns of carbon nanotip and nanopyramid microemitters.

  18. 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

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

    PubMed

    2016-03-01

    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.

  20. Exchange dynamics of nitric oxide in the human nose.

    PubMed

    Chambers, D C; Carpenter, D A; Ayres, J G

    2001-11-01

    Nasal nitric oxide (NO) exchange dynamics are poorly understood but potentially are of importance, inasmuch as they may provide insight into the NO-related physiology of the bronchial tree. In healthy human volunteers, NO output was assessed by isolating the nasal cavity through elevation of the soft palate and application of tight-fitting nasal olives. Mean NO output was 334 nl/min and was a positive function of gas flow. With the use of a mathematical model and the introduction of nonzero concentrations of NO, the diffusing capacity for NO in the nose (DNO) and the mucosal NO concentration (Cw) were determined. DNO ranged from 0.52 to 2.98 x 10(-3) nl x s(-1) x ppb(-1) and Cw from 1,236 to 8,947 ppb. Cw declined with increasing gas flow, while DNO was constant. NO output declined with luminal hypoxia, particularly at oxygen tensions <10%. Measurement of nasal DNO and Cw is easy using this method, and the range of intersubject values of Cw raises the possibility of interindividual differences in NO-dependent nasal physiology.

  1. Dynamical exchange-correlation potentials beyond the local density approximation

    NASA Astrophysics Data System (ADS)

    Tao, Jianmin; Vignale, Giovanni

    2006-03-01

    Approximations for the static exchange-correlation (xc) potential of density functional theory (DFT) have reached a high level of sophistication. By contrast, time-dependent xc potentials are still being treated in a local (although velocity-dependent) approximation [G. Vignale, C. A. Ullrich and S. Conti, PRL 79, 4879 (1997)]. Unfortunately, one of the assumptions upon which the dynamical local approximation is based appears to break down in the important case of d.c. transport. Here we propose a new approximation scheme, which should allow a more accurate treatment of molecular transport problems. As a first step, we separate the exact adiabatic xc potential, which has the same form as in the static theory and can be treated by a generalized gradient approximation (GGA) or a meta-GGA. In the second step, we express the high-frequency limit of the xc stress tensor (whose divergence gives the xc force density) in terms of the exact static xc energy functional. Finally, we develop a perturbative scheme for the calculation of the frequency dependence of the xc stress tensor in terms of the ground-state Kohn-Sham orbitals and eigenvalues.

  2. 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.

  3. Dynamics of inorganic nutrient species in the Bohai seawaters

    NASA Astrophysics Data System (ADS)

    Zhang, J.; Yu, Z. G.; Raabe, T.; Liu, S. M.; Starke, A.; Zou, L.; Gao, H. W.; Brockmann, U.

    2004-02-01

    Within the frame of a Sino-German Joint Research Program, two cruises of "R/V Dong Fang Hong 2" were carried out in September-October 1998 and April-May 1999, respectively, to understand the dynamics of nutrients in the Bohai. Nutrient species (NO 3-, NO 2-, NH 4+, PO 43- and SiO 32-) are determined colorimetrically on board for five anchor and 30 grid stations. In situ incubation experiments are performed to determine planktonic nutrient uptake and benthic exchange flux. Nutrient concentrations display short-term variability and seasonal change in the Bohai, with higher levels in shallow coastal waters than in the Central Bohai. The influence of riverine discharge on nutrient levels can be seen from salinity isopleths, nutrient distribution and species ratios. Near-bottom (nb) waters have similar nutrient concentrations as to the surface waters in the Central Bohai, whereas stratification takes place in the Bohai Strait and North Yellow Sea. In situ incubation experiments provide evidence that the uptake ratio (i.e. N, P) by phytoplankton is proportional to the ratios among nutrient species in ambient waters. Based on the data of this study and previously publications, a preliminary estimate of nutrient budgets via riverine input and atmospheric deposition is established. The results indicate that atmospheric deposition gains importance over rivers in delivering nutrients into the Bohai and sustain the new production, following recent decrease in riverine inflow caused by drought periods in North China and damming practices. A historical review of nutrient data indicates that concentrations of nitrogen increase and phosphorus and silica decrease in the Central Bohai over last 40 years. This potentially has an important influence on the health of ecosystem in Bohai (e.g. food web and community structure), though further study is needed to examine the scenario in more detail.

  4. 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…

  5. 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…

  6. 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.

  7. Dynamics of the hydrogen exchange reaction using the photoloc technique

    NASA Astrophysics Data System (ADS)

    Fernandez-Alonso, Felix

    2000-08-01

    The dynamics of the H + D2 exchange reaction has been studied experimentally using laser, velocity- sensitive time-of-flight (TOF) methods. Chemical reaction is initiated by laser photolysis of a suitable HX precursor resulting in a collision energy spread of 50 MeV. HD(v ', J') products are detected via (2+1) resonance-enhanced multiphoton ionization (REMPI) inside a Wiley-McLaren time-of-flight spectrometer. Integral cross section measurements are performed by measuring the total ion yield into different product rovibrational states. In addition, core extraction of the ion packet prior to detection allows an unambiguous inversion of the laboratory product velocity distribution into a corresponding center-of-mass differential cross section with an angular resolution ranging from 3° for backward to 15° for forward scattering. The measured rotational distributions for the HD(v' = 1, 2, J) vibrational manifolds at collision energies ca. 1.6 eV agree closely with quasiclassical trajectory calculations. These distributions are colder than the ``prior'' limit indicating that other constraints besides energy conservation are dictating energy disposal into the rotational degree of Freedom of the diatomic product. Further insight into the dynamics of this reaction is given by the differential cross section measurements into particular HD(v' = 1, J') and HD(v' = 2, J') quantum states. In each vibrational manifold, the product angular distributions are completely back ward scattered for low- J' states, and they shift toward side scattering as the rotational excitation of the product increases. Experimental data at a lower angular resolution for HD(v' = 3, J' ) also show a similar trend in the angular distributions. The differential cross section data can be qualitatively explained by invoking a line- of-centers with nearly elastic specular scattering model which links the most probable scattering angle for a given HD(v', J') product state with initial impact parameter

  8. 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.

  9. Contribution of different grass species to plant-atmosphere ammonia exchange in intensively managed grassland

    NASA Astrophysics Data System (ADS)

    Mattsson, M.; Herrmann, B.; Jones, S.; Neftel, A.; Sutton, M. A.; Schjoerring, J. K.

    2008-06-01

    Species diversity in grasslands usually declines with increasing input of nitrogen from fertilizers or atmospheric nitrogen deposition. Conversely, species diversity may also impact the build-up of soil nitrogen pools. Limited information is available on how plant-atmosphere ammonia exchange is related to species diversity in grasslands. We have here investigated grass species abundance and different foliar nitrogen pools in 4-year-old intensively managed grassland. Apoplastic pH and NH4+ concentrations of the 8 most abundant species were used to calculate stomatal NH3 compensation points. Apoplastic NH4+ concentrations differed considerably among the species, ranging from 13 to 117 μM, with highest values in Festuca pratensis. Also apoplastic pH values varied, from pH 6.0 in Phleum pratense to 6.9 in Dactylis glomerata. The observed differences in apoplastic NH4+ and pH resulted in a large span of predicted values for the stomatal NH3 compensation point which ranged from 0.20 to 6.57 nmol mol-1. Three species (Lolium perenne, Festuca pratensis and Dactylis glomerata) had sufficiently high NH3 compensation points and abundance to contribute to the NH3 emission of the whole field. At the same time, other grass species such as Phleum pratense and Lolium multiflorum had NH3 compensation points below the atmospheric NH3 concentration and could thus contribute to NH3 uptake from the atmosphere. Evaluated across species, leaf bulk-tissue NH4+ concentrations correlated well (r2=0.902) with stomatal NH3 compensation points calculated on the basis of the apoplastic bioassay. This suggests that leaf tissue NH4+ concentrations combined with data for the frequency distribution of the corresponding species can be used for predicting the NH3 exchange potential of a mixed grass sward.

  10. Imaging Local Diffusive Dynamics Using Diffusion Exchange Spectroscopy MRI

    NASA Astrophysics Data System (ADS)

    Benjamini, Dan; Komlosh, Michal E.; Basser, Peter J.

    2017-04-01

    The movement of water between microenvironments presents a central challenge in the physics of soft matter and porous media. Diffusion exchange spectroscopy (DEXSY) is a powerful 2D nuclear magnetic resonance method for measuring such exchange, yet it is rarely used because of its long scan time requirements. Moreover, it has never been combined with magnetic resonance imaging (MRI). Using probability theory, we vastly reduce the required data, making DEXSY MRI feasible for the first time. Experiments are performed on a composite nerve tissue phantom with restricted and free water-exchanging compartments.

  11. 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

  12. Transformations of metal species in ageing humic hydrocolloids studied by competitive ligand and metal exchange.

    PubMed

    Burba, Peter; Van den Bergh, Johan

    2004-03-01

    Transformations of metal species (particularly Al, Ca, Fe, Mg, Mn, Zn) in ageing humic hydrocolloids were studied, applying a competitive ligand and metal exchange approach. For this purpose, metal-containing hydrocolloids, freshly collected from humic-rich German bog lake waters (Hohlohsee (HO), Black Forest; Venner Moor (VM), Muensterland; Arnsberger Wald (AW), Northrhine-Westfalia) and conventionally pre-filtered through 0.45 microm membranes, were subjected on-site to an exchange with EDTA and Cu(II) ions, respectively, as a function of time. EDTA complexes gradually formed, metal fractions exchanged by Cu(II) (as well as free Cu(II) concentrations) were operationally discriminated by means of a small time-controlled tangential-flow ultrafiltration unit (nominal cutoff: 1 kDa). Metal and DOM (dissolved organic matter) fractions obtained this way were determined off-site using instrumental methods (AAS, ICP-OES, carbon analyzer). After weeks of storage, the collected hydrocolloids were studied again by this approach. The EDTA availability of colloid-bound metals (particularly Al and Fe) exhibited different ageing trends, dependent on the sample (VM: decrease of Fe availability (98-76%), HO: increase of Fe availability (76-82%)). In contrast, the Cu(II) exchange equilibria of colloid-bound metals revealed merely low availability of Al (16-38%) and Fe (5-11%) towards Cu(II) ions, also dependent on ageing effects. In particular, the conditional copper exchange constants Kex obtained from the exchange between Cu(II) ions and available metal species (such as Ca, Mg, Mn, Zn) exhibited a strong decrease (by a factor of 2-100) during sample storage, indicating considerable non-equilibria complexation of these metal ions in the original bogwaters studied on-site.

  13. 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.

  14. Genome Sequencing Reveals Widespread Virulence Gene Exchange among Human Neisseria Species

    PubMed Central

    Marri, Pradeep Reddy; Paniscus, Mary; Hernández, Diana R.; Higashi, Dustin L.; Sodergren, Erica; Weinstock, George M.; Rounsley, Steven D.; So, Magdalene

    2010-01-01

    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. PMID:20676376

  15. Foliar trichomes, boundary layers, and gas exchange in 12 species of epiphytic Tillandsia (Bromeliaceae).

    PubMed

    Benz, Brett W; Martin, Craig E

    2006-04-01

    We examined the relationships between H2O and CO2 gas exchange parameters and leaf trichome cover in 12 species of Tillandsia that exhibit a wide range in trichome size and trichome cover. Previous investigations have hypothesized that trichomes function to enhance boundary layers around Tillandsioid leaves thereby buffering the evaporative demand of the atmosphere and retarding transpirational water loss. Data presented herein suggest that trichome-enhanced boundary layers have negligible effects on Tillandsia gas exchange, as indicated by the lack of statistically significant relationships in regression analyses of gas exchange parameters and trichome cover. We calculated trichome and leaf boundary layer components, and their associated effects on H2O and CO2 gas exchange. The results further indicate trichome-enhanced boundary layers do not significantly reduce transpirational water loss. We conclude that although the trichomes undoubtedly increase the thickness of the boundary layer, the increase due to Tillandsioid trichomes is inconsequential in terms of whole leaf boundary layers, and any associated reduction in transpirational water loss is also negligible within the whole plant gas exchange pathway.

  16. Dynamics of Charged Species in Ionic-Neutral Block Copolymer and Surfactant Complexes

    DOE PAGES

    Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.; ...

    2017-06-21

    Structure–property relationships of ionic block copolymer (BCP) surfactant complexes are critical toward the progress of favorable engineering design of efficient charge-transport materials. In this paper, molecular dynamics simulations are used to understand the dynamics of charged-neutral BCP and surfactant complexes. The dynamics are examined for two different systems: charged-neutral double-hydrophilic and hydrophobic–hydrophilic block copolymers with oppositely charged surfactant moieties. The dynamics of the surfactant head, tails, and charges are studied for five different BCP volume fractions. We observe that the dynamics of the different species solely depend on the balance between electrostatic and entropic interactions between the charged species andmore » the neutral monomers. The favorable hydrophobic–hydrophobic interactions and the unfavorable hydrophobic–hydrophilic interactions determine the mobilities of the monomers. The dynamical properties of the charge species influence complex formation. Structural relaxations exhibit length-scale dependent behavior, with slower relaxation at the radius of gyration length-scale and faster relaxation at the segmental length-scale, consistent with previous results. The dynamical analysis correlates ion-exchange kinetics to the self-assembly behavior of the complexes.« less

  17. 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

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

    PubMed

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

    2014-09-15

    Carefully controlled gas exchange across the eggshell is essential for the development of the avian embryo. Water vapour conductance (G(H2O)) 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 G(H2O) and putative life-history correlates of adult birds, ecological nest parameters and physical characteristics of the egg itself to investigate how variation in G(H2O) 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 G(H2O) 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 G(H2O) 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 G(H2O) 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 G(H2O) 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 G(H2O) to overcome this constraint and still

  19. Respiratory and cuticular water loss in insects with continuous gas exchange: comparison across five ant species.

    PubMed

    Schilman, Pablo E; Lighton, John R B; Holway, David A

    2005-12-01

    Respiratory water loss (RWL) in insects showing continuous emission of CO(2) is poorly studied because few methodologies can measure it. Comparisons of RWL between insects showing continuous and discontinuous gas exchange cycles (DGC) are therefore difficult. We used two recently developed methodologies (the hyperoxic switch and correlation between water-loss and CO(2) emission rates) to compare cuticular permeabilities and rates of RWL in five species of ants, the Argentine ant (Linepithema humile) and four common native ant competitors. Our results showed that RWL in groups of ants with moderate levels of activity and continuous gas exchange were similar across the two measurement methods, and were similar to published values on insects showing the DGC. Furthermore, ants exposed to anoxia increased their total water loss rates by 50-150%. These results suggest that spiracular control under continuous gas exchange can be as effective as the DGC in reducing RWL. Finally, the mesic-adapted Argentine ant showed significantly higher rates of water loss and cuticular permeability compared to four ant species native to dry environments. Physiological limitations may therefore be responsible for restricting the distribution of this invasive species in seasonally dry environments.

  20. Pairing dynamics and the origin of species.

    PubMed

    Puebla, Oscar; Bermingham, Eldredge; Guichard, Frédéric

    2012-03-22

    Whether sexual selection alone can drive the evolution of assortative mating in the presence of gene flow is a long-standing question in evolutionary biology. Here, we report a role for pairing dynamics of individuals when mate choice is mutual, which is sufficient for the evolution of assortative mating by sexual selection alone in the presence of gene flow. Through behavioural observation, individual-based simulation and population genetic analysis, we evaluate the pairing dynamics of coral reef fish in the genus Hypoplectrus (Serranidae), and the role these dynamics can play for the evolution of assortative mating. When mate choice is mutual and the stability of mating pairs is critical for reproductive success, the evolution of assortative mating in the presence of gene flow is not only possible, but is also a robust evolutionary outcome.

  1. Pairing dynamics and the origin of species

    PubMed Central

    Puebla, Oscar; Bermingham, Eldredge; Guichard, Frédéric

    2012-01-01

    Whether sexual selection alone can drive the evolution of assortative mating in the presence of gene flow is a long-standing question in evolutionary biology. Here, we report a role for pairing dynamics of individuals when mate choice is mutual, which is sufficient for the evolution of assortative mating by sexual selection alone in the presence of gene flow. Through behavioural observation, individual-based simulation and population genetic analysis, we evaluate the pairing dynamics of coral reef fish in the genus Hypoplectrus (Serranidae), and the role these dynamics can play for the evolution of assortative mating. When mate choice is mutual and the stability of mating pairs is critical for reproductive success, the evolution of assortative mating in the presence of gene flow is not only possible, but is also a robust evolutionary outcome. PMID:21937496

  2. Contribution of different grass species to plant-atmosphere ammonia exchange in intensively managed grassland

    NASA Astrophysics Data System (ADS)

    Mattsson, M.; Herrmann, B.; Jones, S.; Neftel, A.; Sutton, M. A.; Schjoerring, J. K.

    2009-01-01

    Species diversity in grasslands usually declines with increasing input of nitrogen from fertilizers or atmospheric deposition. Conversely, species diversity may also impact the build-up of soil and plant nitrogen pools. One important pool is NH3/NH4+ which also can be exchanged between plant leaves and the atmosphere. Limited information is available on how plant-atmosphere ammonia exchange is related to species diversity in grasslands. We have here investigated grass species abundance and different foliar nitrogen pools in 4-year-old intensively managed grassland. Apoplastic pH and NH4+ concentrations of the 8 most abundant species (Lolium perenne, Phleum pratense, Festuca pratensis, Lolium multiflorum, Poa pratensis, Dactylis glomerata, Holcus lanatus, Bromus mollis) were used to calculate stomatal NH3 compensation points. Apoplastic NH4+ concentrations differed considerably among the species, ranging from 13 to 117 μM, with highest values in Festuca pratensis. Also apoplastic pH values varied, from pH 6.0 in Phleum pratense to 6.9 in Dactylis glomerata. The observed differences in apoplastic NH4+ and pH resulted in a large span of predicted values for the stomatal NH3 compensation point which ranged between 0.20 and 6.57 nmol mol-1. Three species (Lolium perenne, Festuca pratensis and Dactylis glomerata) had sufficiently high NH3 compensation point and abundance to contribute to the bi-directional NH3 fluxes recorded over the whole field. The other 5 grass species had NH3 compensation points considerably below the atmospheric NH3 concentration and were thus not likely to contribute to NH3 emission but only to NH3 uptake from the atmosphere. Evaluated across species, leaf bulk-tissue NH4+ concentrations correlated well (r2=0.902) with stomatal NH3 compensation points calculated on the basis of the apoplastic bioassay. This suggests that leaf tissue NH4+ concentrations combined with data for the frequency distribution of the corresponding species can be used for

  3. Exciton dynamics in cation-exchanged CdSe/PbSe nanorods: The role of defects

    NASA Astrophysics Data System (ADS)

    Lee, Sooho; Wang, Yimeng; Liu, Yawei; Lee, Dongkyu; Lee, Kangha; Lee, Doh C.; Lian, Tianquan

    2017-09-01

    Cation exchange occurs via defect initiated solid-state diffusion, a process that can lead to defect formations. The effect of such inherent defect formation on carrier dynamics of cation-exchanged heterostructures remains poorly understood. Herein, we report exciton dynamics in type II CdSe/PbSe heterostructure nanorods formed via cation exchange. The majority of electrons in CdSe domains decays in 5 ps due to ultrafast carrier trapping. The defect generated by cation exchange can be healed by annealing the as-synthesized CdSe/PbSe heterostructure nanorods. This study suggests a strategy for improving properties of heteronanostructures prepared by cation exchange for applications in photovoltaics and photocatalysis.

  4. 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..

  5. Laser spectroscopy and dynamics of transient species

    NASA Astrophysics Data System (ADS)

    Clouthier, D. J.

    1994-02-01

    Work was done on sub-Doppler spectroscopy of thioformaldehyde, electronic spectrum of FS2 radical, FTIR spectra of the transient molecule formyl chloride (HCOCl and DCOCl), and high-resolution FTIR spectra of the nu(sub 9) (CH2 wag) and nu(sub 5) (CSO symm. stretch) bands of sulfine (H2CSO), a transient species formed in pyrolysis of dimethyl sulfoxide and oxidation of thioformaldehyde.

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

    PubMed

    Kraus, Robert H S; Kerstens, Hindrik H D; van Hooft, Pim; Megens, Hendrik-Jan; Elmberg, Johan; Tsvey, Arseny; Sartakov, Dmitry; Soloviev, Sergej A; Crooijmans, Richard P M A; Groenen, Martien A M; Ydenberg, Ronald C; Prins, Herbert H T

    2012-04-02

    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. 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. 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 hybridisation rates. Observed

  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. Impact of precipitation dynamics on net ecosystem exchange

    USDA-ARS?s Scientific Manuscript database

    Net ecosystem carbon dioxide (CO2) exchange (NEE) was measured on shortgrass steppe (SGS) vegetation at the USDA Central Plains Experimental Range in northeastern Colorado from 2001-2003. Large year-to-year differences were observed in annual NEE, with > 95% of the net carbon uptake occurring during...

  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. Lability of heavy metal species in aquatic humic substances characterized by ion exchange with cellulose phosphate.

    PubMed

    Rocha, J C; Toscano, I A; Burba, P

    1997-01-01

    Labile metal species in aquatic humic substances (HSs) were characterized by ion exchange on cellulose phosphate (CellPhos) by applying an optimized batch procedure. The HSs investigated were pre-extracted from humic-rich waters by ultrafiltration and a resin XAD 8 procedure. The HS-metal species studied were formed by complexation with Cd(II), Ni(II), Cu(II), Mn(II) and Pb(II) as a function of time and the ratio ions to HSs. The kinetics and reaction order of this exchange process were studied. At the beginning (<3 min), the labile metal fractions are separated relatively quickly. After 3 min, the separation of the metal ions proceeds with uniform half-lives of about 12-14 min, revealing rather slow first-order kinetics. The metal exchange between HSs and CellPhos exhibited the following order of metal lability with the studied HSs: Cu > Pb > Mn > Ni > Cd. The required metal determinations were carried out by atomic absorption spectrometry.

  11. Separation and determination of arsenic species in water by selective exchange and hybrid resins.

    PubMed

    Ben Issa, Nureddin; Rajaković-Ognjanović, Vladana N; Marinković, Aleksandar D; Rajaković, Ljubinka V

    2011-11-07

    A simple and efficient method for separation and determination of inorganic arsenic (iAs) and organic arsenic (oAs) in drinking, natural and wastewater was developed. If arsenic is present in water prevailing forms are inorganic acids of As(III) and As(V). oAs can be found in traces as monomethylarsenic acid, MMA(V), and dimethylarsenic acid, DMAs(V). Three types of resins: a strong base anion exchange (SBAE) and two hybrid (HY) resins: HY-Fe and HY-AgCl, based on the activity of hydrated iron oxides and a silver chloride were investigated. It was found that the sorption processes (ion exchange, adsorption and chemisorptions) of arsenic species on SBAE (ion exchange) and HY resins depend on pH values of water. The quantitative separation of molecular and ionic forms of iAs and oAs was achieved by SBAE and pH adjustment, the molecular form of As(III) that exists in the water at pH <8.0 was not bonded with SBAE, which was convenient for direct determination of As(III) concentration in the effluent. HY-Fe resin retained all arsenic species except DMAs(V), which makes possible direct measurements of this specie in the effluent. HY-AgCl resin retained all iAs which was convenient for direct determination of oAs species concentration in the effluent. The selective bonding of arsenic species on three types of resins makes possible the development of the procedure for measuring and calculation of all arsenic species in water. In order to determine capacity of resins the preliminary investigations were performed in batch system and fixed bed flow system. Resin capacities were calculated according to breakthrough points in a fixed bed flow system which is the first step in designing of solid phase extraction (SPE) module for arsenic speciation separation and determination. Arsenic adsorption behavior in the presence of impurities showed tolerance with the respect to potential interference of anionic compounds commonly found in natural water. Proposed method was established

  12. Anchoring and support system of pulmonary gas-exchange tissue in four bird species.

    PubMed

    Klika, E; Scheuermann, D W; De Groodt-Lasseel, M H; Bazantova, I; Switka, A

    1997-01-01

    Avian air capillaries are delicate structures compared to the mammalian pulmonary alveolus. A transmission and scanning electron microscopic study was carried out on several species of birds with the aim of determining the support structures of the avian gas-exchange mantle. Lung tissue of two bird species belonging to strong flying birds (pigeon and barn owl) and two relatively flightless species (domestic fowl and quail) was subjected to standard processing for transmission and scanning electron microscopy after intratracheal inflation. Twisted profiles of lipoproteinaceous trilaminar substance as specific secretory product of avian squamous respiratory cells can be seen in the cell body and cytoplasmic extensions that are wedged between the blood capillaries, partly surrounding them. The intracytoplasmatically located trilaminar complexes form a three-dimensional intricate spiderweb-like system between the blood capillaries and air capillaries, which presumably function as an anchoring and support structure of the gas-exchange tissue. This system is strengthened by retinacula--pairs of attenuated parallel processes of squamous respiratory cells that project to the airway lumen--expanding and bridging the opposite side of air capillaries. The trilaminar substance is discharged in the form of a 15-nm-thick acellular lining layer which is uniquely adapted to the extremely thin respiratory epithelium. The trilaminar substance arises in the cytoplasm of squamous respiratory cells from profiles of granular and smooth endoplasmic reticulum. The integrity and stability of the gas-exchange tissue is likely to be guaranteed by a specific arrangement of the squamous respiratory cells, in which the trilaminar substance plays a paramount role. This general pattern can be observed in strong flying bird species as in the relatively flightless birds.

  13. 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.

  14. Dynamics and species richness of tropical rain forests.

    PubMed Central

    Phillips, O L; Hall, P; Gentry, A H; Sawyer, S A; Vásquez, R

    1994-01-01

    We present a worldwide analysis of humid tropical forest dynamics and tree species richness. New tree mortality, recruitment, and species richness data include the most dynamic and diverse mature tropical forests known. Twenty-five sites show a strong tendency for the most species-rich forests to be dynamic and aseasonal. Mean annual tree mortality and recruitment-turnover-is the most predictive factor of species richness, implying that small-scale disturbance helps regulate tropical forest diversity. Turnover rates are also closely related to the amount of basal area turnover in mature tropical forests. Therefore the contribution of small-scale disturbance to maintaining tropical forest diversity may ultimately be driven by ecosystem productivity. PMID:11607468

  15. 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.

  16. 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.

  17. A comprehensive molecular dynamics approach to protein retention modeling in ion exchange chromatography.

    PubMed

    Lang, Katharina M H; Kittelmann, Jörg; Dürr, Cathrin; Osberghaus, Anna; Hubbuch, Jürgen

    2015-02-13

    In downstream processing, the underlying adsorption mechanism of biomolecules to adsorbent material are still subject of extensive research. One approach to more mechanistic understanding is simulating this adsorption process and hereby the possibility to identify the parameters with strongest impact. So far this method was applied with all-atom molecular dynamics simulations of two model proteins on one cation exchanger. In this work we developed a molecular dynamics tool to simulate protein-adsorber interaction for various proteins on an anion exchanger and ran gradient elution experiments to relate the simulation results to experimental data. We were able to show that simulation results yield similar results as experimental data regarding retention behavior as well as binding orientation. We could identify arginines in case of cation exchangers and aspartic acids in case of anion exchangers as major contributors to binding.

  18. Water and ions in clays: Unraveling the interlayer/micropore exchange using molecular dynamics

    NASA Astrophysics Data System (ADS)

    Rotenberg, Benjamin; Marry, Virginie; Vuilleumier, Rodolphe; Malikova, Natalie; Simon, Christian; Turq, Pierre

    2007-11-01

    We present the first microscopic description of the exchange of water and ions between clay interlayers and microporosity. A force field based on ab-initio calculations is developed and used in classical molecular dynamics simulations. The latter allow to compute the potential of mean force for the interlayer/micropore exchange for water, Na + and Cs + cations and Cl - anions. For the simulated water content (water bilayer, with interlayer spacing 15.4 Å) and salt concentration in the micropore (0.52 mol dm -3) the exchange is found to be almost not activated for water and cations, whereas the entrance of an anion into the interlayer is strongly unfavorable ( ΔF˜9kT). Calculations of the diffusion tensor in the interlayer and in the micropore complete the study of the exchange dynamics.

  19. 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.

  20. Dynamics of Catalytic Resolution of 2-Lithio-N-Boc-piperidine by Ligand Exchange

    PubMed Central

    Beng, Timothy K.; Tyree, William S.; Parker, Trent; Su, Chicheung; Williard, Paul G.

    2012-01-01

    The dynamics of the racemization, catalytic and stoichiometric dynamic resolution of 2-lithio-N-Boc-piperidine, 7, have been investigated. The kinetic order in TMEDA, for both racemization and resolution of the title compound, and the kinetic order in resolving ligands, have been determined. The catalytic dynamic resolution is 0.5-order in chiral ligand 8, 0.265 order in chiral ligand 10, and second order in TMEDA. The X-ray crystal structure of ligand 10 shows it to be an octamer. Dynamic NMR studies of the resolution process were obtained. Some of the requirements for a successful catalytic dynamic resolution by ligand exchange have been identified. PMID:22967289

  1. 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.

  2. 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.

  3. 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. © 2015 The Protein Society.

  4. 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

  5. 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.

  6. 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.

  7. Comparison of budburst dynamics between species on altitudinal gradient

    NASA Astrophysics Data System (ADS)

    Davi, H.; Gillmann, M.; Ibanez, T.

    2009-04-01

    Phenology of plants is a key ecosystem parameter controlling carbon and water fluxes and also acting on the dynamics of communities. This parameter is highly sensitive to the climate and consequently is often used as a proxy of global change. In this paper, we attempt to analyse the dynamics of budburst every week for seven species (Fagus sylvatica L., Acer opalus Mill , Sorbus aria L., Quercus pubescens Willd. Abies alba Mill., Pinus sylvestris L., Pinus nigra Arnold) in two altitudinal gradients, one in a northern slope and one in a southern slope in the Ventoux mountain. The originality of this work is to assess not only the budburst date but to more precisely analyse the dynamics of budburst and its variation with altitude according to the species. Two important results are highlighted. First, the dynamics of budburst changes according to the species. Three distinct patterns can be drawn, a rapid sigmoid increase for the deciduous species, a short sigmoid increase for the pines and an intermediate curve for silver fir. These dynamics can be slowing down for coniferous when frost arises during the budburst. The second topic is the link between budburst and temperature by analysing respectively the year, the altitudinal and the aspect (north and south) effects. In 2007, budburst occurs earlier for Fagus, Acer, and Abies, it does not change for pines and is delayed for Sorbus. Date of beech budburst is the same between north and south in spite of higher temperature in south. The altitude effect on budburst varies greatly according to species and the year with a weak effect on Fagus and a stronger effect for the others species showing a threshold at 1200 m. By analysing the mean of temperatures at each altitude, we conclude that temperature effect acts differently between years or between altitudes. To conclude, we highlighted the complex effect of temperatures on budburst varying between species and situations.

  8. 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).

  9. Influence of coupling on thermal forces and dynamic friction in plasmas with multiple ion species

    NASA Astrophysics Data System (ADS)

    Kagan, Grigory; Baalrud, Scott D.; Daligault, Jérôme

    2017-07-01

    The recently proposed effective potential theory [Phys. Rev. Lett. 110, 235001 (2013)] is used to investigate the influence of coupling on inter-ion-species diffusion and momentum exchange in multi-component plasmas. Thermo-diffusion and the thermal force are found to diminish rapidly as strong coupling onsets. For the same coupling parameters, the dynamic friction coefficient is found to tend to unity. These results provide an impetus for addressing the role of coupling on diffusive processes in inertial confinement fusion experiments.

  10. 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.

  11. 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

  12. Effect of leaf phenology on canopy exchange processes in temperate tree species

    NASA Astrophysics Data System (ADS)

    Adriaenssens, S.; Staelens, J.; Wuyts, K.; Samson, R.; Boeckx, P. F.; Verheyen, K.

    2011-12-01

    Many forest ecosystems worldwide are exposed to enhanced atmospheric deposition of nitrogen (N) and sulphur (S), which may have adverse effects on forest structure and functioning. Canopy exchange processes, i.e. ion exchange between the water layer covering plant tissues and the underlying apoplast, as well as stomatal or cuticular uptake of gases, can play an important role in determining the impact of air pollution on forest ecosystems and in studying internal nutrient cycling. However, leaf phenology exhibits a large influence on these processes, in particular for deciduous trees where leaf longevity is restricted to one growing season. In a first experiment, 15N-labelled sources were used to investigate the uptake of dissolved (NH4+, NO3-) and gaseous N (NH3) by leaves and twigs at four phenological stages, i.e. the period of leaf development, the fully leafed period, the period of leaf senescence and the leafless period. For this purpose, potted saplings of tree deciduous species, i.e. European beech (Fagus sylvatica L.), pedunculate oak (Quercus robur L.) and common birch (Betula pendula L.), and one coniferous species, Scots pine (Pinus sylvestris L.) were used. Along with the uptake of dissolved N, leaf water storage capacity, leaf wettability and canopy leaching of ions in throughfall water were assessed. In general, dissolved N uptake was highest during leaf senescence, while for gaseous N this was during the fully leafed period. Dissolved NH4+ uptake was significantly correlated with the leaching of base cations (K+, Mg2+ and Ca2+), but only during the growing season. Furthermore, dissolved N uptake was related to leaf wettability and not to leaf water storage capacity. A second experiment assessed the temporal variation of throughfall water along a vertical gradient within the canopy of an adult European beech tree. To analyse temporal trends a generalized additive model was used, which showed that throughfall deposition at all canopy levels followed

  13. 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.

  14. Theorization on ion-exchange equilibria: activity of species in 2-D phases.

    PubMed

    Tamura, Hiroki

    2004-11-01

    Ion-exchange reactions are naturally occurring at soil and sediment/water interphases, determining soil fertility and water quality. These ion-exchange reactions with inorganic and organic exchangers are applied to chemical analysis, recovery of useful ions from low-grade ores (potentially from sea water), water purification including the preparation of "ultrapure" water, production of foods and medicines, therapy, and other uses. It is important to theorize about or to model ion-exchange reactions for quantitative explanations of ion-exchange phenomena and for efficient operation of ion-exchange processes. This paper describes the modeling of ion-exchange equilibria for hydroxyl sites on metal oxides and carboxyl sites in resins with monovalent cations (alkali metal ions), a monovalent anion (nitrate ion), and divalent heavy metal ions. The procedure of modeling is as follows: the stoichiometry and material balance equations of the respective ion-exchange reactions were established based on findings here and by others. The equilibrium conditions were given by the Frumkin equation, where the mass-action relation is modified with lateral interactions between species at the interphase. The model equations were fitted to the measured data and model parameter values were determined by nonlinear regression analysis. The formation of bonds between ions and exchanger sites was evaluated by the equilibrium constant and the suppression of bond formation by electrostatic, geometric, and other lateral interactions was evaluated by the interaction constant. It was established that the properties of ions are determined by the valence, size, and hydration state of the ions. Monovalent ions (anions and cations) react with oxide surface hydroxyl and resin carboxyl sites as hydrated ions and form loose ion-site pairs by a weak electrostatic bond (nonspecific adsorption). However, the lateral interactions are large because of a large polarization of the ion-site pairs. When the

  15. Replica exchange simulations of the three-dimensional Ising spin glass: static and dynamic properties

    NASA Astrophysics Data System (ADS)

    Yucesoy, Burcu; Machta, Jonathan; Katzgraber, Helmut G.

    2012-02-01

    We present the results of a large-scale numerical study of the equilibrium three-dimensional Ising spin glass with Gaussian disorder. Using replica exchange (parallel tempering) Monte Carlo, we measure various static, as well as dynamical quantities, such as the autocorrelation times and round-trip times for the replica exchange Monte Carlo method. The correlation between static and dynamic observables for 5000 disorder realizations (N <=10^3 spins) down to very low temperatures (T 0.2Tc) is examined. Our results show that autocorrelation times are directly correlated with the roughness of the free energy landscape. We also discuss the size dependence of several static quantities.

  16. Jealousy and Trust: Unexplored Dimensions of Social Exchange Dynamics.

    ERIC Educational Resources Information Center

    McDonald, Gerald W.; Osmond, Marie Withers

    Little effort has been made to systematically assess the determinants and consequences of marital jealousy which affect marital, familial and extra-familial expectations, interactions and behavior. A preliminary attempt to rectify this omission provides a conceptual/theoretical perspective on jealousy dynamics in marriage. Marital jealousy, a…

  17. Jealousy and Trust: Unexplored Dimensions of Social Exchange Dynamics.

    ERIC Educational Resources Information Center

    McDonald, Gerald W.; Osmond, Marie Withers

    Little effort has been made to systematically assess the determinants and consequences of marital jealousy which affect marital, familial and extra-familial expectations, interactions and behavior. A preliminary attempt to rectify this omission provides a conceptual/theoretical perspective on jealousy dynamics in marriage. Marital jealousy, a…

  18. Delay driven spatiotemporal chaos in single species population dynamics models.

    PubMed

    Jankovic, Masha; Petrovskii, Sergei; Banerjee, Malay

    2016-08-01

    Questions surrounding the prevalence of complex population dynamics form one of the central themes in ecology. Limit cycles and spatiotemporal chaos are examples that have been widely recognised theoretically, although their importance and applicability to natural populations remains debatable. The ecological processes underlying such dynamics are thought to be numerous, though there seems to be consent as to delayed density dependence being one of the main driving forces. Indeed, time delay is a common feature of many ecological systems and can significantly influence population dynamics. In general, time delays may arise from inter- and intra-specific trophic interactions or population structure, however in the context of single species populations they are linked to more intrinsic biological phenomena such as gestation or resource regeneration. In this paper, we consider theoretically the spatiotemporal dynamics of a single species population using two different mathematical formulations. Firstly, we revisit the diffusive logistic equation in which the per capita growth is a function of some specified delayed argument. We then modify the model by incorporating a spatial convolution which results in a biologically more viable integro-differential model. Using the combination of analytical and numerical techniques, we investigate the effect of time delay on pattern formation. In particular, we show that for sufficiently large values of time delay the system's dynamics are indicative to spatiotemporal chaos. The chaotic dynamics arising in the wake of a travelling population front can be preceded by either a plateau corresponding to dynamical stabilisation of the unstable equilibrium or by periodic oscillations.

  19. 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.

  20. Dynamic species distribution models from categorical survey data.

    PubMed

    Mieszkowska, Nova; Milligan, Gregg; Burrows, Michael T; Freckleton, Rob; Spencer, Matthew

    2013-11-01

    1. Species distribution models are static models for the distribution of a species, based on Hutchinson's niche concept. They make probabilistic predictions about the distribution of a species, but do not have a temporal interpretation. In contrast, density-structured models based on categorical abundance data make it possible to incorporate population dynamics into species distribution modelling. 2. Using dynamic species distribution models, temporal aspects of a species' distribution can be investigated, including the predictability of future abundance categories and the expected persistence times of local populations, and how these may respond to environmental or anthropogenic drivers. 3. We built density-structured models for two intertidal marine invertebrates, the Lusitanian trochid gastropods Phorcus lineatus and Gibbula umbilicalis, based on 9 years of field data from around the United Kingdom. Abundances were recorded on a categorical scale, and stochastic models for year-to-year changes in abundance category were constructed with winter mean sea surface temperature (SST) and wave fetch (a measure of the exposure of a shore) as explanatory variables. 4. Both species were more likely to be present at sites with high SST, but differed in their responses to wave fetch. Phorcus lineatus had more predictable future abundance and longer expected persistence times than G. umbilicalis. This is consistent with the longer lifespan of P. lineatus. 5. Where data from multiple time points are available, dynamic species distribution models of the kind described here have many applications in population and conservation biology. These include allowing for changes over time when combining historical and contemporary data, and predicting how climate change might alter future abundance conditional on current distributions.

  1. Analyzing energy-water exchange dynamics in the Thar desert

    NASA Astrophysics Data System (ADS)

    Raja, P.; Singh, Nilendu; Srinivas, C. V.; Singhal, Mohit; Chauhan, Pankaj; Singh, Maharaj; Sinha, N. K.

    2017-07-01

    Regions of strong land-atmosphere coupling will be more susceptible to the hydrological impacts in the intensifying hydrological cycle. In this study, micrometeorological experiments were performed to examine the land-atmosphere coupling strength over a heat low region (Thar desert, NW India), known to influence the Indian summer monsoon (ISM). Within the vortex of Thar desert heat low, energy-water exchange and coupling behavior were studied for 4 consecutive years (2011-2014) based on sub-hourly measurements of radiative-convective flux, state parameters and sub-surface thermal profiles using lead-lag analysis between various E-W balance components. Results indicated a strong (0.11-0.35) but variable monsoon season (July-September) land-atmosphere coupling events. Coupling strength declined with time, becomes negative beyond 10-day lag. Evapotranspiration (LE) influences rainfall at the monthly time-scale (20-40 days). Highly correlated monthly rainfall and LE anomalies (r = 0.55, P < 0.001) suggested a large precipitation memory linked to the local land surface state. Sensible heating (SH) during March and April are more strongly (r = 0.6-0.7) correlated to ISM rainfall than heating during May or June (r = 0.16-0.36). Analyses show strong and weak couplings among net radiation (Rn)-vapour pressure deficit (VPD), LE-VPD and Rn-LE switching between energy-limited to water-limited conditions. Consistently, +ve and -ve residual energy [(dE) = (Rn - G) - (SH + LE)] were associated with regional wet and dry spells respectively with a lead of 10-40 days. Dew deposition (18.8-37.9 mm) was found an important component in the annual surface water balance. Strong association of variation of LE and rainfall was found during monsoon at local-scale and with regional-scale LE (MERRA 2D) but with a lag which was more prominent at local-scale than at regional-scale. Higher pre-monsoon LE at local-scale as compared to low and monotonous variation in regional-scale LE led to

  2. Energy Exchange Dynamics across L-H transitions in NSTX

    NASA Astrophysics Data System (ADS)

    Diallo, A.; Banerjee, S.; Zweben, S.; Stoltzfus-Dueck, T.

    2016-10-01

    This work is motivated by the need to test L-H transition paradigms (e.g., predator-prey, and ExB flow suppression) and explore possible new L-H transition dynamics. We present analysis of the L-H transition on three sets (NBI, RF, and Ohmic) of NSTX discharges using the gas-puff-imaging diagnostics for high temporal and spatial resolutions. The analysis studies the edge velocities and energy dynamics across the L-H transition using an implementation of the orthogonal decomposition programming for high temporal resolution velocity fields. In the database NSTX discharges, the production term (computed 1 cm inside the separatrix) is negative, pointing to transfer from the DC flows to the fluctuations, even immediately before the L-H transition. This suggests that depletion of turbulent fluctuation energy via transfer to the mean flow may not play a key role in the L-H transition. The thermal free energy is consistently much larger than the kinetic energy produced by the mean poloidal flow across the L-H transitions. These observations are inconsistent with the predator-prey model. The paper will describe the analysis including error estimations. Furthermore, analysis of the radial correlation dynamics across the L-H transition will be discussed. Work supported by U.S. DoE contract #DE-AC02-09CH11466.

  3. 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

  4. 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.

  5. 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.

  6. Exchange anisotropy and the dynamic phase transition in thin ferromagnetic Heisenberg films.

    PubMed

    Jang, Hyunbum; Grimson, Malcolm J; Hall, Carol K

    2003-10-01

    Monte Carlo simulations have been performed to investigate the dependence of the dynamic phase behavior on the bilinear exchange anisotropy of a classical Heisenberg spin system. The system under consideration is a planar thin ferromagnetic film with competing surface fields subject to a pulsed oscillatory external field. The results show that the films exhibit a single discontinuous dynamic phase transition (DPT) as a function of the anisotropy of the bilinear exchange interaction in the Hamiltonian. Furthermore, there is no evidence of stochastic resonance associated with the DPT. These results are in marked contrast to the continuous DPT observed in the same system as a function of temperature and applied field strength for a fixed bilinear exchange anisotropy.

  7. Dynamic Cyclic Thiodepsipeptide Libraries from Thiol-Thioester Exchange

    DTIC Science & Technology

    2010-04-01

    use in a variety of dynamic combinatorial chemistry assays. The kinetic determinants of macrocycle formation and the role of amino acid structure on...were then made in AA1, AA3, and AA4 (Table 1); by design, AA2-AA3-AA4 forms the macrocycle, and AA1 remains exocyclic. Charged amino acids (Lys, Arg...was initially included in AA3 as a turn residue that favors macrocycles. 9 Various amino acids were incorporated into AA4 to study their effect on

  8. Riparian hydraulic gradient and stream-groundwater exchange dynamics in steep headwater valleys

    Treesearch

    T.J. Voltz; M.N. Gooseff; A.S. Ward; K. Singha; M. Fitzgerald; T. Wagener

    2013-01-01

    Patterns of riparian hydraulic gradients and stream-groundwater exchange in headwater catchments provide the hydrologic context for important ecological processes. Although the controls are relatively well understood, their dynamics during periods of hydrologic change is not. We investigate riparian hydraulic gradients over three different time scales in two steep,...

  9. Dynamic diversity of synthetic supramolecular polymers in water as revealed by hydrogen/deuterium exchange

    NASA Astrophysics Data System (ADS)

    Lou, Xianwen; Lafleur, René P. M.; Leenders, Christianus M. A.; Schoenmakers, Sandra M. C.; Matsumoto, Nicholas M.; Baker, Matthew B.; van Dongen, Joost L. J.; Palmans, Anja R. A.; Meijer, E. W.

    2017-05-01

    Numerous self-assembling molecules have been synthesized aiming at mimicking both the structural and dynamic properties found in living systems. Here we show the application of hydrogen/deuterium exchange (HDX) mass spectrometry (MS) to unravel the nanoscale organization and the structural dynamics of synthetic supramolecular polymers in water. We select benzene-1,3,5-tricarboxamide (BTA) derivatives that self-assemble in H2O to illustrate the strength of this technique for supramolecular polymers. The BTA structure has six exchangeable hydrogen atoms and we follow their exchange as a function of time after diluting the H2O solution with a 100-fold excess of D2O. The kinetic H/D exchange profiles reveal that these supramolecular polymers in water are dynamically diverse; a notion that has previously not been observed using other techniques. In addition, we report that small changes in the molecular structure can be used to control the dynamics of synthetic supramolecular polymers in water.

  10. Dynamic diversity of synthetic supramolecular polymers in water as revealed by hydrogen/deuterium exchange.

    PubMed

    Lou, Xianwen; Lafleur, René P M; Leenders, Christianus M A; Schoenmakers, Sandra M C; Matsumoto, Nicholas M; Baker, Matthew B; van Dongen, Joost L J; Palmans, Anja R A; Meijer, E W

    2017-05-15

    Numerous self-assembling molecules have been synthesized aiming at mimicking both the structural and dynamic properties found in living systems. Here we show the application of hydrogen/deuterium exchange (HDX) mass spectrometry (MS) to unravel the nanoscale organization and the structural dynamics of synthetic supramolecular polymers in water. We select benzene-1,3,5-tricarboxamide (BTA) derivatives that self-assemble in H2O to illustrate the strength of this technique for supramolecular polymers. The BTA structure has six exchangeable hydrogen atoms and we follow their exchange as a function of time after diluting the H2O solution with a 100-fold excess of D2O. The kinetic H/D exchange profiles reveal that these supramolecular polymers in water are dynamically diverse; a notion that has previously not been observed using other techniques. In addition, we report that small changes in the molecular structure can be used to control the dynamics of synthetic supramolecular polymers in water.

  11. LCE: Leaf carbon exchange dataset for tropical, temperate, and boreal species of North and Central America.

    PubMed

    Smith, Nicholas G; Dukes, Jeffrey S

    2017-08-20

    Leaf canopy carbon exchange processes, such as photosynthesis and respiration, are substantial components of the global carbon cycle. Climate models base their simulations of photosynthesis and respiration on an empirical understanding of the underlying biochemical processes, and the responses of those processes to environmental drivers. As such, data spanning large spatial scales are needed to evaluate and parameterize these models. Here, we present data on four important biochemical parameters defining leaf carbon exchange processes from 626 individuals of 98 species at 12 North and Central American sites spanning ~53° of latitude. The four parameters are the maximum rate of Rubisco carboxylation (Vcmax ), the maximum rate of electron transport for the regeneration of Ribulose-1,5,-bisphosphate (Jmax ), the maximum rate of phosphoenolpyruvate carboxylase carboxylation (Vpmax ), and leaf dark respiration (Rd ). The raw net photosynthesis by intercellular CO2 (A/Ci ) data used to calculate Vcmax , Jmax , and Vpmax rates are also presented. Data were gathered on the same leaf of each individual (one leaf per individual), allowing for the examination of each parameter relative to others. Additionally, the dataset contains a number of covariates for the plants measured. Covariate data include (a) leaf-level traits (leaf mass, leaf area, leaf nitrogen and carbon content, predawn leaf water potential), (b) plant-level traits (plant height for herbaceous individuals and diameter at breast height for trees), (c) soil moisture at the time of measurement, (d) air temperature from nearby weather stations for the day of measurement and each of the 90 days prior to measurement, and (e) climate data (growing season mean temperature, precipitation, photosynthetically active radiation, vapor pressure deficit, and aridity index). We hope that the data will be useful for obtaining greater understanding of the abiotic and biotic determinants of these important biochemical

  12. Dynamic Exchange of Myosin VI on Endocytic Structures*

    PubMed Central

    Bond, Lisa M.; Arden, Susan D.; Kendrick-Jones, John; Buss, Folma; Sellers, James R.

    2012-01-01

    The actin-based molecular motor myosin VI functions in the endocytic uptake pathway, both during the early stages of clathrin-mediated uptake and in later transport to/from early endosomes. This study uses fluorescence recovery after photobleaching (FRAP) to examine the turnover rate of myosin VI during endocytosis. The results demonstrate that myosin VI turns over dynamically on endocytic structures with a characteristic half-life common to both the large insert isoform of myosin VI on clathrin-coated structures and the no-insert isoform on early endosomes. This half-life is shared by the myosin VI-binding partner Dab2 and is identical for full-length myosin VI and the cargo-binding tail region. The 4-fold slower half-life of an artificially dimerized construct of myosin VI on clathrin-coated structures suggests that wild type myosin VI does not function as a stable dimer, but either as a monomer or in a monomer/dimer equilibrium. Taken together, these FRAP results offer insight into both the basic turnover dynamics and the monomer/dimer nature of myosin VI. PMID:22992744

  13. Energy exchange via multi-species streaming in laser-driven ion acceleration

    NASA Astrophysics Data System (ADS)

    King, M.; Gray, R. J.; Powell, H. W.; Capdessus, R.; McKenna, P.

    2017-01-01

    Due to the complex electron dynamics and multiple ion acceleration mechanisms that can take place in the interaction of an ultra-intense laser pulse with a thin foil, it is possible for multiple charged particle populations to overlap in space with varying momentum distributions. In certain scenarios this can drive streaming instabilities such as the relativistic Buneman instability and the ion-ion acoustic instability. The potential for such instabilities to occur are demonstrated using particle-in-cell simulations. It is shown that if a population of ions can be accelerated such that it can propagate through other slowly expanding ion populations, energy exchange can occur via the ion-ion acoustic instability.

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

    NASA Astrophysics Data System (ADS)

    Ou, Yu-Sheng

    Spintronics is the area of research that aims at utilizing the quantum mechanical spin degree of freedom of electrons in solid-state materials for information processing and data storage application. Since the discovery of the giant magnetoresistance, the field of spintronics has attracted lots of attention for its numerous potential advantages over contemporary electronics, such as less power consumption, high integration density and non-volatility. The realization of a spin battery, defined by the ability to create spin current without associated charge current, has been a long-standing goal in the field of spintronics. The demonstration of pure spin current in ferromagnet/nonmagnetic material hybrid structures by ferromagnetic resonance spin pumping has defined a thrilling direction for this field. As such, this dissertation targets at exploring the spin and magnetization dynamics in ferromagnet/oxide/semiconductor heterostructures (Fe/MgO/GaAs) using time-resolved optical pump-probe spectroscopy with the long-range goal of understanding the fundamentals of FMR-driven spin pumping. Fe/GaAs heterostructures are complex systems that contain multiple spin species, including paramagnetic spins (GaAs electrons), nuclear spins (Ga and As nuclei) and ferromagnetic spins (Fe). Optical pump-probe studies on their interplay have revealed a number of novel phenomena that has not been explored before. As such they will be the major focus of this dissertation. First, I will discuss the effect of interfacial exchange coupling on the GaAs free-carrier spin relaxation. Temperature- and field-dependent spin-resolved pump-probe studies reveal a strong correlation of the electron spin relaxation with carrier freeze-out, in quantitative agreement with a theoretical interpretation that at low temperatures the free-carrier spin lifetime is dominated by inhomogeneity in the local hyperfine field due to carrier localization. Second, we investigate the impact of tunnel barrier thickness

  15. 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.

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

    USGS Publications Warehouse

    Beerens, James M.; 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

  17. Similar cation exchange capacities among bryophyte species refute a presumed mechanism of peatland acidification.

    PubMed

    Soudzilovskaia, N A; Cornelissen, J H C; During, H J; van Logtestijn, R S P; Lang, S I; Aerts, R

    2010-09-01

    Fen-bog succession is accompanied by strong increases of carbon accumulation rates. We tested the prevailing hypothesis that living Sphagna have extraordinarily high cation exchange capacity (CEC) and therefore acidify their environment by exchanging tissue-bound protons for basic cations in soil water. As Sphagnum invasion in a peatland usually coincides with succession from a brown moss-dominated alkaline fen to an acidic bog, the CEC of Sphagna is widely believed to play an important role in this acidification process. However, Sphagnum CEC has never been compared explicitly to that of a wide range of other bryophyte taxa. Whether high CEC directly leads to the ability to acidify the environment in situ also remains to be tested. We screened 20 predominant subarctic bryophyte species, including fen brown mosses and bog Sphagna for CEC, in situ soil water acidification capacity (AC), and peat acid neutralizing capacity (ANC). All these bryophyte species possessed substantial CEC, which was remarkably similar for brown mosses and Sphagna. This refutes the commonly accepted idea of living Sphagnum CEC being responsible for peatland acidification, as Sphagnum's ecological predecessors, brown mosses, can do the same job. Sphagnum AC was several times higher than that of other bryophytes, suggesting that CE (cation exchange) sites of Sphagna in situ are not saturated with basic cations, probably due to the virtual absence of these cations in the bog water. Together, these results suggest that Sphagna can not realize their CEC in bogs, while fen mosses can do so in fens. The fen peat ANC was 65% higher than bog ANC, indicating that acidity released by brown mosses in the CE process was neutralized, maintaining an alkaline environment. We propose two successional pathways indicating boundaries for a fen-bog shift with respect to bryophyte CEC. In neither of them is Sphagnum CE an important factor. We conclude that living Sphagnum CEC does not play any considerable role

  18. Invasion dynamics of competing species with stage-structure.

    PubMed

    Bewick, Sharon; Wang, Guoqing; Younes, Hannah; Li, Bingtuan; Fagan, William F

    2017-08-03

    The spread of an invasive species often results in a decline and subsequent disappearance of native competitors. Several models, primarily based on spatially explicit Lotka-Volterra competition dynamics, have been developed to understand this phenomenon. In general, the goal of these models is to relate fundamental life history traits, for example dispersal ability and competition strength, to the rate of spread of the invasive species, which is also the rate at which the invasive species displaces its native competitor. Stage-structure is often an important determinant of population dynamics, but it has received little attention within the context of Lotka-Volterra invasion models. For many species, behaviors like dispersal and competition depend on life-stage. To describe the processes of invasion in these species, it is important to understand how behaviors that vary as a function of life-stage can impact spread rate. In this paper, we develop a spatially explicit, stage-structured Lotka-Volterra competition model. By comparing spread speed predictions from this model to spread speed predictions from an analogous single-stage model, we are able to determine when stage-structure is important and how stage-dependent behavior can alter the characteristics of an invasion. Copyright © 2017. Published by Elsevier Ltd.

  19. Spatial dynamics of invasion: the geometry of introduced species.

    PubMed

    Korniss, Gyorgy; Caraco, Thomas

    2005-03-07

    Many exotic species combine low probability of establishment at each introduction with rapid population growth once introduction does succeed. To analyse this phenomenon, we note that invaders often cluster spatially when rare, and consequently an introduced exotic's population dynamics should depend on locally structured interactions. Ecological theory for spatially structured invasion relies on deterministic approximations, and determinism does not address the observed uncertainty of the exotic-introduction process. We take a new approach to the population dynamics of invasion and, by extension, to the general question of invasibility in any spatial ecology. We apply the physical theory for nucleation of spatial systems to a lattice-based model of competition between plant species, a resident and an invader, and the analysis reaches conclusions that differ qualitatively from the standard ecological theories. Nucleation theory distinguishes between dynamics of single- and multi-cluster invasion. Low introduction rates and small system size produce single-cluster dynamics, where success or failure of introduction is inherently stochastic. Single-cluster invasion occurs only if the cluster reaches a critical size, typically preceded by a number of failed attempts. For this case, we identify the functional form of the probability distribution of time elapsing until invasion succeeds. Although multi-cluster invasion for sufficiently large systems exhibits spatial averaging and almost-deterministic dynamics of the global densities, an analytical approximation from nucleation theory, known as Avrami's law, describes our simulation results far better than standard ecological approximations.

  20. Relative species abundance of replicator dynamics with sparse interactions

    NASA Astrophysics Data System (ADS)

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-11-01

    A theory of relative species abundance on sparsely-connected networks is presented by investigating the replicator dynamics with symmetric interactions. Sparseness of a network involves difficulty in analyzing the fixed points of the equation, and we avoid this problem by treating large self interaction u, which allows us to construct a perturbative expansion. Based on this perturbation, we find that the nature of the interactions is directly connected to the abundance distribution, and some characteristic behaviors, such as multiple peaks in the abundance distribution and all species coexistence at moderate values of u, are discovered in a wide class of the distribution of the interactions. The all species coexistence collapses at a critical value of u, u c , and this collapsing is regarded as a phase transition. To get more quantitative information, we also construct a non-perturbative theory on random graphs based on techniques of statistical mechanics. The result shows those characteristic behaviors are sustained well even for not large u. For even smaller values of u, extinct species start to appear and the abundance distribution becomes rounded and closer to a standard functional form. Another interesting finding is the non-monotonic behavior of diversity, which quantifies the number of coexisting species, when changing the ratio of mutualistic relations Δ . These results are examined by numerical simulations, which show that our theory is exact for the case without extinct species, but becomes less and less precise as the proportion of extinct species grows.

  1. 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.

  2. 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

  3. 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.

  4. Direct Observation of Nanosecond Water Exchange Dynamics at a Protein Metal Site

    PubMed Central

    Stachura, Monika; Chakraborty, Saumen; Gottberg, Alexander; Ruckthong, Leela; Pecoraro, Vincent L.; Hemmingsen, Lars

    2017-01-01

    Nanosecond ligand exchange dynamics at metal sites within proteins is essential in catalysis, metal ion transport, and regulatory metallobiochemistry. Herein we present direct observation of the exchange dynamics of water at a Cd2+ binding site within two de novo designed metalloprotein constructs using 111mCd perturbed angular correlation (PAC) of γ-rays and 113Cd NMR spectroscopy. The residence time of the Cd2+-bound water molecule is tens of nanoseconds at 20 °C in both proteins. This constitutes the first direct experimental observation of the residence time of Cd2+ coordinated water in any system, including the simple aqua ion. A Leu to Ala amino acid substitution ~10 Å from the Cd2+ site affects both the equilibrium constant and the residence time of water, while, surprisingly, the metal site structure, as probed by PAC spectroscopy, remains essentially unaltered. This implies that remote mutations may affect metal site dynamics, even when structure is conserved. PMID:27973778

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

    PubMed Central

    2013-01-01

    We compare the efficiency of multicanonical and replica exchange molecular dynamics for the sampling of folding/unfolding events in simulations of proteins with end-to-end β-sheet. In Go-model simulations of the 75-residue MNK6, we observe improvement factors of 30 in the number of folding/unfolding events of multicanonical molecular dynamics over replica exchange molecular dynamics. As an application, we use this enhanced sampling to study the folding landscape of the 36-residue DS119 with an all-atom physical force field and implicit solvent. Here, we find that the rate-limiting step is the formation of the central helix that then provides a scaffold for the parallel β-sheet formed by the two chain ends. PMID:24198735

  6. Dynamic metabolic exchange governs a marine algal-bacterial interaction

    PubMed Central

    Segev, Einat; Wyche, Thomas P; Kim, Ki Hyun; Petersen, Jörn; Ellebrandt, Claire; Vlamakis, Hera; Barteneva, Natasha; Paulson, Joseph N; Chai, Liraz; Clardy, Jon; Kolter, Roberto

    2016-01-01

    Emiliania huxleyi is a model coccolithophore micro-alga that generates vast blooms in the ocean. Bacteria are not considered among the major factors influencing coccolithophore physiology. Here we show through a laboratory model system that the bacterium Phaeobacter inhibens, a well-studied member of the Roseobacter group, intimately interacts with E. huxleyi. While attached to the algal cell, bacteria initially promote algal growth but ultimately kill their algal host. Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic acid. Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased by tryptophan, which is exuded from the algal cell. Algal death triggered by bacteria involves activation of pathways unique to oxidative stress response and programmed cell death. Our observations suggest that bacteria greatly influence the physiology and metabolism of E. huxleyi. Coccolithophore-bacteria interactions should be further studied in the environment to determine whether they impact micro-algal population dynamics on a global scale. DOI: http://dx.doi.org/10.7554/eLife.17473.001 PMID:27855786

  7. Dynamic metabolic exchange governs a marine algal-bacterial interaction.

    PubMed

    Segev, Einat; Wyche, Thomas P; Kim, Ki Hyun; Petersen, Jörn; Ellebrandt, Claire; Vlamakis, Hera; Barteneva, Natasha; Paulson, Joseph N; Chai, Liraz; Clardy, Jon; Kolter, Roberto

    2016-11-18

    Emiliania huxleyi is a model coccolithophore micro-alga that generates vast blooms in the ocean. Bacteria are not considered among the major factors influencing coccolithophore physiology. Here we show through a laboratory model system that the bacterium Phaeobacter inhibens, a well-studied member of the Roseobacter group, intimately interacts with E. huxleyi. While attached to the algal cell, bacteria initially promote algal growth but ultimately kill their algal host. Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic acid. Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased by tryptophan, which is exuded from the algal cell. Algal death triggered by bacteria involves activation of pathways unique to oxidative stress response and programmed cell death. Our observations suggest that bacteria greatly influence the physiology and metabolism of E. huxleyi. Coccolithophore-bacteria interactions should be further studied in the environment to determine whether they impact micro-algal population dynamics on a global scale.

  8. A dynamic leaf gas-exchange strategy is conserved in woody ...

    EPA Pesticide Factsheets

    Rising atmospheric [CO2], ca, is expected to affect stomatal regulation of leaf gas-exchange of woody plants, thus influencing energy fluxes as well as carbon (C), water and nutrient cycling of forests. Researchers have reported that stomata regulate leaf gas-exchange around “set points” that include a constant leaf internal [CO2], ci, a constant drawdown in CO2 (ca - ci), and a constant ci/ca. Because these set points can result in drastically different consequences for leaf gas-exchange, it will be essential for the accuracy of Earth systems models that generalizable patterns in leaf gas-exchange responses to ca be identified if any do exist. We hypothesized that the concept of optimal stomatal behavior, exemplified by woody plants shifting along a continuum of these set point strategies, would provide a unifying framework for understanding leaf gas-exchange responses to ca. We analyzed studies reporting C stable isotope ratio (δ13C) or photosynthetic discrimination (∆13C) from woody plant taxa that grew across ca spanning at least 100 ppm for each species investigated. From these data we calculated ci, and in combination with known or estimated ca, leaf gas-exchange regulation strategies were assessed. Overall, our analyses does not support the hypothesis that trees are canalized towards any of the proposed set points, particularly so for a constant ci. Rather, the results are consistent with the hypothesis that stomatal optimization regulates leaf gas

  9. A dynamic leaf gas-exchange strategy is conserved in woody ...

    EPA Pesticide Factsheets

    Rising atmospheric [CO2], ca, is expected to affect stomatal regulation of leaf gas-exchange of woody plants, thus influencing energy fluxes as well as carbon (C), water and nutrient cycling of forests. Researchers have reported that stomata regulate leaf gas-exchange around “set points” that include a constant leaf internal [CO2], ci, a constant drawdown in CO2 (ca - ci), and a constant ci/ca. Because these set points can result in drastically different consequences for leaf gas-exchange, it will be essential for the accuracy of Earth systems models that generalizable patterns in leaf gas-exchange responses to ca be identified if any do exist. We hypothesized that the concept of optimal stomatal behavior, exemplified by woody plants shifting along a continuum of these set point strategies, would provide a unifying framework for understanding leaf gas-exchange responses to ca. We analyzed studies reporting C stable isotope ratio (δ13C) or photosynthetic discrimination (∆13C) from woody plant taxa that grew across ca spanning at least 100 ppm for each species investigated. From these data we calculated ci, and in combination with known or estimated ca, leaf gas-exchange regulation strategies were assessed. Overall, our analyses does not support the hypothesis that trees are canalized towards any of the proposed set points, particularly so for a constant ci. Rather, the results are consistent with the hypothesis that stomatal optimization regulates leaf gas

  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. Spectroscopic, Kinetic, and Dynamic Experiments on Atmospheric Species.

    DTIC Science & Technology

    1985-03-21

    0077 PHYSICAL SCIENCES RESEARCH PAPERS , NO. 668 P D-A 162 691 Spectroscopic, Kinetic, and Dynamic Experiments on Atmospheric Species S. M. MILLER J. I...we observed, in a very limited data base , values similar to those predicted by the theory of Billingsley4 over the range 4 ! v’ :- 12. This result is...the identities of several others. Further investigations will be aided by an improved data base under conditions similar to those in Figure 9, with

  12. Potential Energy Surfaces and Dynamics of High Energy Species

    DTIC Science & Technology

    2009-04-13

    such calculations with dynamics and condensed phase models, and (b) apply these methods to design and evaluate potentially new high energy species. The...IBM SP2 at the Maui High Performance Computation Center, the heat of formation for 1 is predicted to be 456.8 kcallmol. This translates to an l sp...which numerical derivatives become trivially parallel in a coarse-grained sense by having each function evaluation performed on a different node. If

  13. Dynamic Seascapes Predict the Marine Occurrence of an Endangered Species

    NASA Astrophysics Data System (ADS)

    Breece, M.; Fox, D. A.; Dunton, K. J.; Frisk, M. G.; Jordaan, A.; Oliver, M. J.

    2016-12-01

    Landscapes are powerful environmental partitions that index complex biogeochemical processes that drive terrestrial species distributions. However, translating landscapes into seascapes requires that the dynamic nature of the fluid environment be reflected in spatial and temporal boundaries such that seascapes can be used in marine species distribution models and conservation decisions. A seascape product derived from satellite ocean color and sea surface temperature partitioned mid-Atlantic coastal waters on scales commensurate with the Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus coastal migration. The seascapes were then matched with acoustic telemetry records of Atlantic Sturgeon to determine seascape selectivity. To test our model, we used real-time satellite seascape maps to normalize the sampling of an autonomous underwater vehicle that resampled similar geographic regions with time varying seascape classifications. We found that Atlantic Sturgeon exhibited preference for one seascape class over those available in the coastal ocean, indicating selection for environmental properties that co-varied with the dynamic seascape class rather than geographical location. The recent listing of Atlantic Sturgeon as Endangered throughout much of their United States range has highlighted the need for improved understanding of their occurrence in marine waters to reduce interactions with various anthropogenic stressors. Narrow dynamic migration corridors may enable seascapes to be used as a daily decision tool by industry and managers to reduce interactions with this Endangered Species during coastal migrations.

  14. Oxytocin receptor dynamics in the brain across development and species.

    PubMed

    Vaidyanathan, Radhika; Hammock, Elizabeth A D

    2017-02-01

    Oxytocin (OXT) signaling through the OXT receptor plays a significant role in a variety of physiological processes throughout the lifespan. OXT's effects depend on the tissue distribution of the receptor. This tissue specificity is dynamic and changes across development, and also varies with sex, experience, and species. The purpose of this review is to highlight these themes with examples from several life stages and several species. Important knowledge gaps will also be emphasized. Understanding the effective sites of action for OXT via its receptor will help refine hypotheses about the roles of this important neuropeptide in the experience-dependent development and expression of species-typical social behavior. © 2016 Wiley Periodicals, Inc. Develop Neurobiol 77: 143-157, 2017. © 2016 Wiley Periodicals, Inc.

  15. 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. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  16. Dynamics of catalytic resolution of 2-lithio-N-Boc-piperidine by ligand exchange.

    PubMed

    Beng, Timothy K; Tyree, William S; Parker, Trent; Su, Chicheung; Williard, Paul G; Gawley, Robert E

    2012-10-10

    The dynamics of the racemization and catalytic and stoichiometric dynamic resolution of 2-lithio-N-Boc-piperidine (7) have been investigated. The kinetic order in tetramethylethylenediamine (TMEDA) for both racemization and resolution of the title compound and the kinetic orders in two resolving ligands have been determined. The catalytic dynamic resolution is second order in TMEDA and 0.5 and 0.265 order in chiral ligands 8 and 10, respectively. The X-ray crystal structure of ligand 10 shows it to be an octamer. Dynamic NMR studies of the resolution process were carried out. Some of the requirements for a successful catalytic dynamic resolution by ligand exchange have been identified.

  17. Gas exchange of two CAM species of the genus Cissus (vitaceae) differing in morphological features.

    PubMed

    De Santo, A V; Fioretto, A; Bartoli, G; Alfani, A

    1987-01-01

    Pattern and magnitude of stem gas exchange were studied under controlled conditions on two CAM species of the genus Cissus differing in morphological features. In the cactus-like liana Cissus quadrangularis, at water vapour deficit of the air (VPD) lower than 400 mPa Pa(-1) during daytime, under 24/16°C and 27/16°C temperature regime, CO2 uptake occurred during daytime and nighttime but night fixation was responsible for 74 and 77% respectively of the CO2 fixed during the whole diurnal cycle; the contribution of night fixation increased up to 84% at VPD of 590 mPa Pa(-1) under 27/15°C. In Cissus sp., a slightly succulent xerophytic liana with mesophytic deciduous leaves, at 27°C day temperature and VPD of 520-540 mPa Pa(-1), under both 12 and 16°C night temperature, CO2 uptake occurred exclusively during the night; however at lower day temperatures (18-20°C) and lower VPD (169-269 mPa Pa(-1)) substantial CO2 uptake was observed in the light. Transpiration was higher in Cissus sp. than in Cissus quadrangularis under all of the conditions applied; moreover night transpiration in Cissus sp. contributed more to total day transpiration as compared with Cissus quadrangularis. The results support the opinion that the nocturnal gas exchange has a preeminent role in Cissus sp. as compared with Cissus quadrangularis. Indeed under conditions which enhance evaporative demand even well-watered plants of Cissus sp. resort totally to night fixation. In contrast Cissus quadrangularis which shows a larger resistance to water loss and possesses an abundant water storing parenchyma as compared with Cissus sp. resorts totally to night CO2 fixation only under drought stress.

  18. Anti-inflammatory activity of human IgG4 antibodies by dynamic Fab arm exchange.

    PubMed

    van der Neut Kolfschoten, Marijn; Schuurman, Janine; Losen, Mario; Bleeker, Wim K; Martínez-Martínez, Pilar; Vermeulen, Ellen; den Bleker, Tamara H; Wiegman, Luus; Vink, Tom; Aarden, Lucien A; De Baets, Marc H; van de Winkel, Jan G J; Aalberse, Rob C; Parren, Paul W H I

    2007-09-14

    Antibodies play a central role in immunity by forming an interface with the innate immune system and, typically, mediate proinflammatory activity. We describe a novel posttranslational modification that leads to anti-inflammatory activity of antibodies of immunoglobulin G, isotype 4 (IgG4). IgG4 antibodies are dynamic molecules that exchange Fab arms by swapping a heavy chain and attached light chain (half-molecule) with a heavy-light chain pair from another molecule, which results in bispecific antibodies. Mutagenesis studies revealed that the third constant domain is critical for this activity. The impact of IgG4 Fab arm exchange was confirmed in vivo in a rhesus monkey model with experimental autoimmune myasthenia gravis. IgG4 Fab arm exchange is suggested to be an important biological mechanism that provides the basis for the anti-inflammatory activity attributed to IgG4 antibodies.

  19. 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.

  20. Real-time observation of cation exchange kinetics and dynamics at the muscovite-water interface

    NASA Astrophysics Data System (ADS)

    Lee, Sang Soo; Fenter, Paul; Nagy, Kathryn L.; Sturchio, Neil C.

    2017-06-01

    Ion exchange at charged solid-liquid interfaces is central to a broad range of chemical and transport phenomena. Real-time observations of adsorption/desorption at the molecular-scale elucidate exchange reaction pathways. Here we report temporal variation in the distribution of Rb+ species at the muscovite (001)-water interface during exchange with Na+. Time-resolved resonant anomalous X-ray reflectivity measurements at 25 °C reveal that Rb+ desorption occurs over several tens of seconds during which thermodynamically stable inner-sphere Rb+ slowly transforms to a less stable outer-sphere Rb+. In contrast, Rb+ adsorption is about twice as fast, proceeding from Rb+ in the bulk solution to the stable inner-sphere species. The Arrhenius plot of the adsorption/desorption rate constants measured from 9 to 55 °C shows that the pre-exponential factor for desorption is significantly smaller than that for adsorption, indicating that this reduced attempt frequency of cation detachment largely explains the slow cation exchange processes at the interface.

  1. Real-time observation of cation exchange kinetics and dynamics at the muscovite-water interface

    DOE PAGES

    Lee, Sang Soo; Fenter, Paul; Nagy, Kathryn L.; ...

    2017-06-09

    Here, ion exchange at charged solid–liquid interfaces is central to a broad range of chemical and transport phenomena. Real-time observations of adsorption/desorption at the molecular-scale elucidate exchange reaction pathways. Here, we report temporal variation in the distribution of Rb+ species at the muscovite (001)–water interface during exchange with Na+. Time-resolved resonant anomalous X-ray reflectivity measurements reveal that Rb+ desorption occurs over several tens of seconds during which thermodynamically stable inner-sphere Rb+ slowly transforms to less stable outer-sphere Rb+ at 25°C. In contrast, Rb+ adsorption is about twice as fast, proceeding quickly from Rb+ in the bulk solution to the stablemore » inner-sphere species. The Arrhenius plot of the adsorption/desorption rate constants measured from 9 to 55°C shows that the pre-exponential factor for desorption is significantly smaller than for adsorption, indicating that this reduced attempt frequency of cation detachment largely explains the slow cation exchange processes at the interface.« less

  2. 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.

  3. Ion exchange in alginate gels--dynamic behaviour revealed by electron paramagnetic resonance.

    PubMed

    Ionita, Gabriela; Ariciu, Ana Maria; Smith, David K; Chechik, Victor

    2015-12-14

    The formation of alginate gel from low molecular weight alginate and very low molecular weight alginate in the presence of divalent cations was investigated using Electron Paramagnetic Resonance (EPR) spectroscopy. The transition from sol to gel in the presence of divalent cations was monitored by the changes in the dynamics of spin labelled alginate. The immobilisation of the spin labelled alginate in the gel reflects the strength of interaction between the cation and alginate chain. Diffusion experiments showed that both the cation and alginate polyanion in the gel fibres can exchange with molecules in solution. In particular, we showed that dissolved alginate polyanions can replace alginates in the gel fibres, which can hence diffuse through the bulk of the gel. This illustrates the surprisingly highly dynamic nature of these gels and opens up the possibility of preparing multicomponent alginate gels via polyanion exchange process.

  4. Heat transfer enhancement by dynamic corrugated heat exchanger wall: Numerical study

    NASA Astrophysics Data System (ADS)

    Kumar, P.; Schmidmayer, K.; Topin, F.; Miscevic, M.

    2016-09-01

    A new concept of heat exchanger at sub-millimeter scale is proposed for applications in cooling on-board electronics devices, in which the quality of the exchanges between fluid and wall is very critical. In the proposed system, the upper wall of the channel is deformed dynamically to obtain a sinusoidal wave on this surface. The lower wall is exposed to constant heat flux simulating the imprint of an electronic component. A systematic 3-D numerical study in transient regime on the different deformation parameters allowed obtaining both the pumping characteristics and the heat transfer characteristics of the system. It was observed that the dynamic deformation of the wall induces a significant pumping effect. The intensification of the heat transfer is very important even for highly degraded waveforms, although the pumping efficiency is reduced in this case.

  5. Provably authenticated group Diffie-Hellman key exchange - The dynamic case (Extended abstract)

    SciTech Connect

    Bresson, Emmanuel; Chevassut, Olivier; Pointcheval, David

    2001-09-20

    Dynamic group Diffie-Hellman protocols for Authenticated Key Exchange(AKE) are designed to work in scenario in which the group membership is not known in advance but where parties may join and may also leave the multicast group at any given time. While several schemes have been proposed to deal with this scenario no formal treatment for this cryptographic problem has ever been suggested. In this paper, we define a security model for this problem and use it to precisely define Authenticated Key Exchange (AKE) with ''implicit'' authentication as the fundamental goal, and the entity-authentication goal as well. We then define in this model the execution of a protocol modified from a dynamic group Diffie-Hellman scheme offered in the literature and prove its security.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Hybrid dynamics in a species group of swallowtail butterflies.

    PubMed

    Dupuis, J R; Sperling, F A H

    2016-10-01

    Hybrid zones provide unique natural laboratories for studying mechanisms of evolution. But identification and classification of hybrid individuals (F1, F2, backcross, etc.) can be complicated by real population changes over time as well as by use of different marker types, both of which challenge documentation of hybrid dynamics. Here, we use multiple genetic markers (mitochondrial DNA, microsatellites and genomewide single nucleotide polymorphisms) to re-examine population structure in a hybrid zone between two species of swallowtail butterflies in western Canada, Papilio machaon and P. zelicaon. Our aim was to test whether their hybrid dynamics remain the same as found 30 years ago using morphology and allozymes, and we compared different genetic data sets as well as alternative hybrid identification and classification methods. Overall, we found high differentiation between the two parental species, corroborating previous research from the 1980s. We identified fewer hybrid individuals in the main zone of hybridization in recent years, but this finding depended on the genetic markers considered. Comparison of methods with simulated data sets generated from our data showed that single nucleotide polymorphisms were more powerful than microsatellites for both hybrid identification and classification. Moreover, substantial variation among comparisons underlined the value of multiple markers and methods for documenting evolutionarily dynamic systems.

  11. Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials.

    PubMed

    Lu, Jianfeng; Vanden-Eijnden, Eric

    2013-02-28

    Replica exchange molecular dynamics (REMD) becomes more efficient as the frequency of swap between the temperatures is increased. Recently Plattner et al. [J. Chem. Phys. 135, 134111 (2011)] proposed a method to implement infinite swapping REMD in practice. Here we introduce a natural modification of this method that involves molecular dynamics simulations over a mixture potential. This modification is both simple to implement in practice and provides a better, energy based understanding of how to choose the temperatures in REMD to optimize efficiency. It also has implications for generalizations of REMD in which the swaps involve other parameters than the temperature.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Dependence of spectral characteristics on parameters describing CO2 exchange between crop species and the atmosphere

    NASA Astrophysics Data System (ADS)

    Uździcka, Bogna; Stróżecki, Marcin; Urbaniak, Marek; Juszczak, Radosław

    2017-07-01

    The aim of this paper is to demonstrate that spectral vegetation indices are good indicators of parameters describing the intensity of CO2 exchange between crops and the atmosphere. Measurements were conducted over 2011-2013 on plots of an experimental arable station on winter wheat, winter rye, spring barley, and potatoes. CO2 fluxes were measured using the dynamic closed chamber system, while spectral vegetation indices were determined using SKYE multispectral sensors. Based on spectral data collected in 2011 and 2013, various models to estimate net ecosystem productivity and gross ecosystem productivity were developed. These models were then verified based on data collected in 2012. The R2 for the best model based on spectral data ranged from 0.71 to 0.83 and from 0.78 to 0.92, for net ecosystem productivity and gross ecosystem productivity, respectively. Such high R2 values indicate the utility of spectral vegetation indices in estimating CO2 fluxes of crops. The effects of the soil background turned out to be an important factor decreasing the accuracy of the tested models.

  18. Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers.

    PubMed

    Grilli, Jacopo; Romano, Mariacristina; Bassetti, Federico; Cosentino Lagomarsino, Marco

    2014-06-01

    Prokaryotes vary their protein repertoire mainly through horizontal transfer and gene loss. To elucidate the links between these processes and the cross-species gene-family statistics, we perform a large-scale data analysis of the cross-species variability of gene-family abundance (the number of members of the family found on a given genome). We find that abundance fluctuations are related to the rate of horizontal transfers. This is rationalized by a minimal theoretical model, which predicts this link. The families that are not captured by the model show abundance profiles that are markedly peaked around a mean value, possibly because of specific abundance selection. Based on these results, we define an abundance variability index that captures a family's evolutionary behavior (and thus some of its relevant functional properties) purely based on its cross-species abundance fluctuations. Analysis and model, combined, show a quantitative link between cross-species family abundance statistics and horizontal transfer dynamics, which can be used to analyze genome 'flux'. Groups of families with different values of the abundance variability index correspond to genome sub-parts having different plasticity in terms of the level of horizontal exchange allowed by natural selection. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Cross-species gene-family fluctuations reveal the dynamics of horizontal transfers

    PubMed Central

    Grilli, Jacopo; Romano, Mariacristina; Bassetti, Federico; Cosentino Lagomarsino, Marco

    2014-01-01

    Prokaryotes vary their protein repertoire mainly through horizontal transfer and gene loss. To elucidate the links between these processes and the cross-species gene-family statistics, we perform a large-scale data analysis of the cross-species variability of gene-family abundance (the number of members of the family found on a given genome). We find that abundance fluctuations are related to the rate of horizontal transfers. This is rationalized by a minimal theoretical model, which predicts this link. The families that are not captured by the model show abundance profiles that are markedly peaked around a mean value, possibly because of specific abundance selection. Based on these results, we define an abundance variability index that captures a family's evolutionary behavior (and thus some of its relevant functional properties) purely based on its cross-species abundance fluctuations. Analysis and model, combined, show a quantitative link between cross-species family abundance statistics and horizontal transfer dynamics, which can be used to analyze genome ‘flux’. Groups of families with different values of the abundance variability index correspond to genome sub-parts having different plasticity in terms of the level of horizontal exchange allowed by natural selection. PMID:24829449

  20. Hydrogen exchange dynamics of the P22 virion determined by time-resolved Raman spectroscopy. Effects of chromosome packaging on the kinetics of nucleotide exchanges.

    PubMed

    Reilly, K E; Thomas, G J

    1994-08-05

    We describe the application of laser Raman spectroscopy to probe hydrogen isotope exchange dynamics of nucleic acid and protein constituents in a double-stranded DNA virus, the icosahedral bacteriophage P22. The Raman dynamic method employs a dialysis flow cell to control D2O efflux into an H2O solution of the virus sample while the rates of deuterium exchange of protons in the viral nucleic acid and protein molecules are measured spectrophotometrically in real time. The method provides structural and kinetic information about three different and distinct classes of exchangeable protons of the native virion: (1) labile imino (NH) and amino (NH2) protons of the bases which participate in Watson-Crick hydrogen bonding in the packaged genome; (2) pseudolabile purinic (8CH) protons that line the major groove of packaged P22 DNA; and (3) main-chain amide (NH) protons of viral subunits comprising the shell that encapsidates the DNA. The results obtained on P22 demonstrate that interchange of aqueous solvent with the virion interior is rapid and complete. We find that while labile protons of packaged DNA exchange rapidly, most amide protons in capsid subunits are resistant to solvent-catalyzed exchange. Further, stereospecific retardation of exchange is observed for major-groove protons of the packaged P22 genome. The quantitative measurements can be summarized and interpreted as follows. (1) Imino and amino protons of all bases in packaged P22 DNA exchange more rapidly (approximately 2-fold faster) than the corresponding protons in unpackaged P22 DNA. Remarkably, packaging actually accelerates labile imino and amino hydrogen exchanges of the viral DNA, an effect which can be attributed to selective stabilization in the packaged chromosome of a base-pair open state (breathing model). (2) Conversely, purine 8CH exchange rates in packaged P22 DNA are significantly retarded in comparison to those of unpackaged P22 DNA. The observed 8CH exchange retardation effects are

  1. FtsZ Filament Dynamics at Steady State: Subunit Exchange with and without Nucleotide Hydrolysis†

    PubMed Central

    Chen, Yaodong; Erickson, Harold P.

    2009-01-01

    We have measured three aspects of FtsZ filament dynamics at steady state: rates of GTP hydrolysis, subunit exchange between protofilaments, and disassembly induced by dilution or excess GDP. All three reactions were slowed with an increase in the potassium concentration from 100 to 500 mM, via replacement of potassium with rubidium, or with an increase in the magnesium concentration from 5 to 20 mM. Electron microscopy showed that the polymers assembled under the conditions of fastest assembly were predominantly short, one-stranded protofilaments, whereas under conditions of slower dynamics, the protofilaments tended to associate into long, thin bundles. We suggest that exchange of subunits between protofilaments at steady state involves two separate mechanisms: (1) fragmentation or dissociation of subunits from protofilament ends following GTP hydrolysis and (2) reversible association and dissociation of subunits from protofilament ends independent of hydrolysis. Exchange of nucleotides on these recycling subunits could give the appearance of exchange directly into the polymer. Several of our observations suggest that exchange of nucleotide can take place on these recycling subunits, but not directly into the FtsZ polymer. Annealing of protofilaments was demonstrated for the L68W mutant in EDTA buffer but not in Mg buffer, where rapid cycling of subunits may obscure the effect of annealing. We also reinvestigated the nucleotide composition of FtsZ polymers at steady state. We found that the GDP:GTP ratio was 50:50 for concentrations of GTP > 100 μM, significantly higher than the 20:80 ratio previously reported at 20 μM GTP. PMID:19527070

  2. 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.

  3. Structural Insights into Fibrinogen Dynamics Using Amide Hydrogen/Deuterium Exchange Mass Spectrometry

    PubMed Central

    Marsh, James J.; Guan, Henry S.; Li, Sheng; Chiles, Peter G.; Tran, Danny; Morris, Timothy A.

    2013-01-01

    We determined the amide hydrogen/deuterium exchange profile of native human fibrinogen under physiologic conditions. After optimization of the quench and proteolysis conditions, more than 1,200 peptides were identified by mass spectrometry, spanning more than 90% of the constituent Aα, Bβ, and γ chain amino acid sequences. The compact central and distal globular regions of fibrinogen were well protected from deuterium exchange, with the exception of the unfolded amino-terminal segments of the Aα and Bβ chains extending from the central region, and the short γ chain “tail” extending from each distal globular region. The triple-helical coiled-coil regions, which bridge the central region to each distal region, were also well protected with the exception of a moderately fast-exchanging area in the middle of each coiled coil adjacent to the γ chain carbohydrate attachment site. These dynamic regions appear to provide flexibility to the fibrinogen molecule. The γ chain “out loop” contained within each coiled-coil also exchanged rapidly. The αC domain (Aα 392–610) exchanged rapidly, with the exception of a short segment sandwiched between a conserved disulfide linkage in the N-terminal αC subdomain. This latter finding is consistent with a mostly disordered structure for the αC domain in native fibrinogen. Analysis of the dysfibrinogen Bβ 235 Pro/Leu, which exhibits abnormal fibrin structure, revealed enhanced deuterium exchange surrounding the Pro/Leu substitution site as well as in the vicinity of the high affinity calcium binding site and the A knob polymerization pocket within the γC domain. The implication of these changes with respect to fibrin structure is discussed. PMID:23875785

  4. 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.

  5. Dynamics of stem water uptake among isohydric and anisohydric species experiencing a severe drought.

    PubMed

    Yi, Koong; Dragoni, Danilo; Phillips, Richard P; Roman, D Tyler; Novick, Kimberly A

    2017-01-05

    Predicting the impact of drought on forest ecosystem processes requires an understanding of trees' species-specific responses to drought, especially in the Eastern USA, where species composition is highly dynamic due to historical changes in land use and fire regime. Here, we adapted a framework that classifies trees' water-use strategy along the spectrum of isohydric to anisohydric behavior to determine the responses of three canopy-dominant species to drought. We used a collection of leaf-level gas exchange, tree-level sap flux and stand-level eddy covariance data collected in south-central Indiana from 2011 to 2013, which included an unusually severe drought in the summer of 2012. Our goal was to assess how patterns in the radial profile of sap flux and reliance on hydraulic capacitance differed among species of contrasting water-use strategies. In isohydric species (Quercus alba L. and Quercus rubra L.), which included sugar maple (Acer saccharum Marsh.) and tulip poplar (Liriodendron tulipifera L.), we found that the sap flux in the outer xylem experienced dramatic declines during drought, but sap flux at inner xylem was buffered from reductions in water availability. In contrast, for anisohydric oak species, we observed relatively smaller variations in sap flux during drought in both inner and outer xylem, and higher nighttime refilling when compared with isohydric species. This reliance on nocturnal refilling, which occurred coincident with a decoupling between leaf- and tree-level water-use dynamics, suggests that anisohydric species may benefit from a reliance on hydraulic capacitance to mitigate the risk of hydraulic failure associated with maintaining high transpiration rates during drought. In the case of both isohydric and anisohydric species, our work demonstrates that failure to account for shifts in the radial profile of sap flux during drought could introduce substantial bias in estimates of tree water use during both drought and non

  6. The plastoquinol-plastoquinone exchange mechanism in photosystem II: insight from molecular dynamics simulations.

    PubMed

    Zobnina, Veranika; Lambreva, Maya D; Rea, Giuseppina; Campi, Gaetano; Antonacci, Amina; Scognamiglio, Viviana; Giardi, Maria Teresa; Polticelli, Fabio

    2017-01-01

    In the photosystem II (PSII) of oxygenic photosynthetic organisms, the reaction center (RC) core mediates the light-induced electron transfer leading to water splitting and production of reduced plastoquinone molecules. The reduction of plastoquinone to plastoquinol lowers PSII affinity for the latter and leads to its release. However, little is known about the role of protein dynamics in this process. Here, molecular dynamics simulations of the complete PSII complex embedded in a lipid bilayer have been used to investigate the plastoquinol release mechanism. A distinct dynamic behavior of PSII in the presence of plastoquinol is observed which, coupled to changes in charge distribution and electrostatic interactions, causes disruption of the interactions seen in the PSII-plastoquinone complex and leads to the "squeezing out" of plastoquinol from the binding pocket. Displacement of plastoquinol closes the second water channel, recently described in a 2.9 Å resolution PSII structure (Guskov et al. in Nat Struct Mol Biol 16:334-342, 2009), allowing to rule out the proposed "alternating" mechanism of plastoquinol-plastoquinone exchange, while giving support to the "single-channel" one. The performed simulations indicated a pivotal role of D1-Ser264 in modulating the dynamics of the plastoquinone binding pocket and plastoquinol-plastoquinone exchange via its interaction with D1-His252 residue. The effects of the disruption of this hydrogen bond network on the PSII redox reactions were experimentally assessed in the D1 site-directed mutant Ser264Lys.

  7. Spin dynamics of polarization inversion spin exchange at the magic angle in multiple spin systems.

    PubMed

    Gan, Z

    2000-03-01

    Polarization inversion spin exchange at the magic angle (PISEMA) [J. Magn. Reson. A 109, 270 (1994)] is an important experiment in NMR structural characterization of membrane proteins in oriented lipid bilayers. This paper presents a theoretical and experimental study of the spin dynamics in PISEMA to investigate the line-narrowing mechanism. The study focuses on the effect of neighboring protons on the spin exchange of a strongly coupled spin pair. The spin exchange is solved analytically for simple spin systems and is numerically simulated for many-spin systems. The results show that the dipolar couplings from the neighboring protons of a strongly coupled spin pair perturb the spin exchange only in the second order, therefore it has little contribution to the linewidth of PISEMA spectra in comparison to the separated-local-field spectra. The effects from proton resonance offset and the mismatch of the Hartmann-Hahn condition are also discussed along with experimental results using model single-crystal samples.

  8. Nonparametric analysis of nonexponential and multidimensional kinetics. I. Quantifying rate dispersion, rate heterogeneity, and exchange dynamics

    NASA Astrophysics Data System (ADS)

    Berg, Mark A.; Kaur, Harveen

    2017-02-01

    The quantification of nonexponential (dispersed) kinetics has relied on empirical functions, which yield parameters that are neither unique nor easily related to the underlying mechanism. Multidimensional kinetics provide more information on dispersed processes, but a good approach to their analysis is even less clear than for standard, one-dimensional kinetics. This paper is the first in a series that analyzes kinetic data in one or many dimensions with a scheme that is nonparametric: it quantifies nonexponential decays without relying on a specific functional form. The quantities obtained are directly related to properties of the mechanism causing the rate dispersion. Log-moments of decays, which parallel the standard moments of distributions (mean, standard deviation, etc.), are introduced for both one- and multi-dimensional decays. Kinetic spectra are defined to visualize the data. The utility of this approach is demonstrated on a simple, but general, model of dispersed kinetics—a nonexponential homogeneous decay combined with slowly exchanging rate heterogeneity. The first log-moments give a geometric-mean relaxation time. Second log-moments quantify the magnitude of rate dispersion, the fraction of the dispersion due to heterogeneity, and the dynamics of exchange between different rate subensembles. A suitable combination of these moments isolates exchange dynamics from three-dimensional kinetics without contamination by the rate-filtering effects that were identified in a recent paper [M. A. Berg and J. R. Darvin, J. Chem. Phys. 145, 054119 (2016)].

  9. Nonparametric analysis of nonexponential and multidimensional kinetics. I. Quantifying rate dispersion, rate heterogeneity, and exchange dynamics.

    PubMed

    Berg, Mark A; Kaur, Harveen

    2017-02-07

    The quantification of nonexponential (dispersed) kinetics has relied on empirical functions, which yield parameters that are neither unique nor easily related to the underlying mechanism. Multidimensional kinetics provide more information on dispersed processes, but a good approach to their analysis is even less clear than for standard, one-dimensional kinetics. This paper is the first in a series that analyzes kinetic data in one or many dimensions with a scheme that is nonparametric: it quantifies nonexponential decays without relying on a specific functional form. The quantities obtained are directly related to properties of the mechanism causing the rate dispersion. Log-moments of decays, which parallel the standard moments of distributions (mean, standard deviation, etc.), are introduced for both one- and multi-dimensional decays. Kinetic spectra are defined to visualize the data. The utility of this approach is demonstrated on a simple, but general, model of dispersed kinetics-a nonexponential homogeneous decay combined with slowly exchanging rate heterogeneity. The first log-moments give a geometric-mean relaxation time. Second log-moments quantify the magnitude of rate dispersion, the fraction of the dispersion due to heterogeneity, and the dynamics of exchange between different rate subensembles. A suitable combination of these moments isolates exchange dynamics from three-dimensional kinetics without contamination by the rate-filtering effects that were identified in a recent paper [M. A. Berg and J. R. Darvin, J. Chem. Phys. 145, 054119 (2016)].

  10. General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application

    NASA Astrophysics Data System (ADS)

    Nagai, Tetsuro

    2017-01-01

    Replica-exchange molecular dynamics (REMD) has demonstrated its efficiency by combining trajectories of a wide range of temperatures. As an extension of the method, the author formalizes the mass-manipulating replica-exchange molecular dynamics (MMREMD) method that allows for arbitrary mass scaling with respect to temperature and individual particles. The formalism enables the versatile application of mass-scaling approaches to the REMD method. The key change introduced in the novel formalism is the generalized rules for the velocity and momentum scaling after accepted replica-exchange attempts. As an application of this general formalism, the refinement of the viscosity-REMD (V-REMD) method [P. H. Nguyen, J. Chem. Phys. 132, 144109 (2010)] is presented. Numerical results are provided using a pilot system, demonstrating easier and more optimized applicability of the new version of V-REMD as well as the importance of adherence to the generalized velocity scaling rules. With the new formalism, more sound and efficient simulations will be performed.

  11. Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation.

    PubMed

    Xue, Xu; Yongjun, Wang; Zhihong, Li

    2015-01-21

    Riboswitches are cis-acting RNA fragments that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket, representing an inviting new class of biomolecular target for the development of antibiotics. To understand the folding mechanism of SAM-II riboswitch, occurring predominantly in proteobacteria, a 100ns replica-exchange molecular dynamics simulation in explicit solvent is performed. Our results show that this RNA pseudoknot has multiple folding pathways, and various intermediate structures. The resultant riboswitch conformational transition map is well consistent with the recent fluorescence measurement, which confirms the dynamical properties of this pseudoknot. Moreover, a novel transition pathway is predicted. The global folding dynamics is mainly coupled with the helix rather than the loop region. The potential folding pathways of the riboswitch presented here should lead to a deeper understanding of the folding mechanism of the riboswitch, as well as the conformational change of RNA pseudoknot.

  12. 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.

  13. Hydrogen exchange-mass spectrometry measures stapled peptide conformational dynamics and predicts pharmacokinetic properties.

    PubMed

    Shi, Xiangguo Eric; Wales, Thomas E; Elkin, Carl; Kawahata, Noriyuki; Engen, John R; Annis, D Allen

    2013-12-03

    Peptide drugs have traditionally suffered from poor pharmacokinetic properties due to their conformational flexibility and the interaction of proteases with backbone amide bonds. "Stapled Peptides" are cyclized using an all-hydrocarbon cross-linking strategy to reinforce their α-helical conformation, yielding improved protease resistance and drug-like properties. Here we demonstrate that hydrogen exchange-mass spectrometry (HX-MS) effectively probes the conformational dynamics of Stapled Peptides derived from the survivin-borealin protein-protein interface and predicts their susceptibility to proteolytic degradation. In Stapled Peptides, amide exchange was reduced by over five orders-of-magnitude versus the native peptide sequence depending on staple placement. Furthermore, deuteration kinetics correlated directly with rates of proteolysis to reveal the optimal staple placement for improved drug properties.

  14. 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.

  15. Ion exchange chromatography of monoclonal antibodies: effect of resin ligand density on dynamic binding capacity.

    PubMed

    Hardin, Ann Marie; Harinarayan, Chithkala; Malmquist, Gunnar; Axén, Andreas; van Reis, Robert

    2009-05-15

    Dynamic binding capacity (DBC) of a monoclonal antibody on agarose based strong cation exchange resins is determined as a function of resin ligand density, apparent pore size of the base matrix, and protein charge. The maximum DBC is found to be unaffected by resin ligand density, apparent pore size, or protein charge within the tested range. The critical conductivity (conductivity at maximum DBC) is seen to vary with ligand density. It is hypothesized that the maximum DBC is determined by the effective size of the proteins and the proximity to which they can approach one another. Once a certain minimum resin ligand density is supplied, additional ligand is not beneficial in terms of resin capacity. Additional ligand can provide flexibility in designing ion exchange resins for a particular application as the critical conductivity could be matched to the feedstock conductivity and it may also affect the selectivity.

  16. 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.

  17. Ion-exchange of monovalent and bivalent cations with NaA zeolite membranes : a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Murad, S.; Jia, W.; Krishnamurthy, M.

    2004-01-01

    Molecular simulations using the method of molecular dynamics have been carried out to study the dynamics and energetics of ion exchanges between monovalent and bivalent cations in supercritical and subcritical (liquid) electrolyte solutions (here Li+, and Ca++ in aqueous solutions of LiCl and CaCl2) and an ion exchange membrane (NaA zeolite) using direct simulations of up to a nanosecond or more. NaA zeolites are widely used in many commercial ion-exchange processes including detergents. Results show that with appropriate driving forces, such ion exchange processes can be clearly witnessed and investigated using molecular simulations at these timescales, especially for supercritical solutions. An attempt is made to understand the phenomenon of ion exchange at the molecular level. Results have shown that the ion-exchange process is primarily energetically driven and entropic forces do not appear to be playing a significant role in the exchanges observed. For supercritical LiCl solutions, small differences were found between the energy of the Li+ inside and outside the membrane. In contrast, for Na+ there was a considerable energetic advantage in being outside the membrane, making the overall exchange process energetically favourable. In subcritical (liquid) LiCl solutions an exchange was found to be more favourable energetically than supercritical solutions. For Ca++ similar trends were observed, except the differences in the energies were much larger (compared to the corresponding Li+ exchanges), making them more energetically efficient, as has also been observed experimentally. In addition to clarifying the molecular basis for these exchanges, simulations can also potentially be very useful to determine the behaviour (e.g. state dependence, etc.) of hydrodynamic parameters commonly used to characterize ion-exchange processes at a fundamental molecular level, and to determine if the hydrodynamic equations used for ion-exchange processes are applicable to nano

  18. Dynamics and energetics of the mammalian phosphatidylinositol transfer protein phospholipid exchange cycle.

    PubMed

    Grabon, Aby; Orłowski, Adam; Tripathi, Ashutosh; Vuorio, Joni; Javanainen, Matti; Róg, Tomasz; Lönnfors, Max; McDermott, Mark I; Siebert, Garland; Somerharju, Pentti; Vattulainen, Ilpo; Bankaitis, Vytas A

    2017-09-01

    Phosphatidylinositol-transfer proteins (PITPs) regulate phosphoinositide signaling in eukaryotic cells. The defining feature of PITPs is their ability to exchange phosphatidylinositol (PtdIns) molecules between membranes, and this property is central to PITP-mediated regulation of lipid signaling. However, the details of the PITP-mediated lipid exchange cycle remain entirely obscure. Here, all-atom molecular dynamics simulations of the mammalian StART-like PtdIns/phosphatidylcholine (PtdCho) transfer protein PITPα, both on membrane bilayers and in solvated systems, informed downstream biochemical analyses that tested key aspects of the hypotheses generated by the molecular dynamics simulations. These studies provided five key insights into the PITPα lipid exchange cycle: (i) interaction of PITPα with the membrane is spontaneous and mediated by four specific protein substructures; (ii) the ability of PITPα to initiate closure around the PtdCho ligand is accompanied by loss of flexibility of two helix/loop regions, as well as of the C-terminal helix; (iii) the energy barrier of phospholipid extraction from the membrane is lowered by a network of hydrogen bonds between the lipid molecule and PITPα; (iv) the trajectory of PtdIns or PtdCho into and through the lipid-binding pocket is chaperoned by sets of PITPα residues conserved throughout the StART-like PITP family; and (v) conformational transitions in the C-terminal helix have specific functional involvements in PtdIns transfer activity. Taken together, these findings provide the first mechanistic description of key aspects of the PITPα PtdIns/PtdCho exchange cycle and offer a rationale for the high conservation of particular sets of residues across evolutionarily distant members of the metazoan StART-like PITP family. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  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. Redox-dependent dynamics of putidaredoxin characterized by amide proton exchange.

    PubMed Central

    Lyons, T. A.; Ratnaswamy, G.; Pochapsky, T. C.

    1996-01-01

    Multidimensional NMR methods were used to obtain 1H-15N correlations and 15N resonance assignments for amide and side-chain nitrogens of oxidized and reduced putidaredoxin (Pdx), the Fe2S2 ferredoxin, which acts as the physiological reductant of cytochrome P-450cam (CYP101). A model for the solution structure of oxidized Pdx has been determined recently using NMR methods (Pochapsky TC, Ye XM, Ratnaswamy G, Lyons TA, 1994, Biochemistry 33:6424-6432) and redox-dependent 1H NMR spectral features have been described (Pochapsky TC, Ratnaswamy G, Patera A, 1994, Biochemistry 33:6433-6441). 15N assignments were made with NOESY-(1H/15N) HMQC and TOCSY-(1H/15N) HSQC spectra obtained using samples of Pdx uniformly labeled with 15N. Local dynamics in both oxidation states of Pdx were then characterized by comparison of residue-specific amide proton exchange rates, which were measured by a combination of saturation transfer and H2O/D2O exchange methods at pH 6.4 and 7.4 (uncorrected for isotope effects). In general, where exchange rates for a given site exhibit significant oxidation-state dependence, the oxidized protein exchanges more rapidly than the reduced protein. The largest dependence of exchange rate upon oxidation state is found for residues near the metal center and in a region of compact structure that includes the loop-turn Val 74-Ser 82 and the C-terminal residues (Pro 102-Trp 106). The significance of these findings is discussed in light of the considerable dependence of the binding interaction between Pdx and CYP101 upon the oxidation state of Pdx. PMID:8845752

  1. 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.

  2. Capillary electrochromatography using a strong cation-exchange column with a dynamically modified cationic surfactant

    PubMed

    Ye; Zou; Liu; Ni; Zhang

    2000-02-01

    A novel mode of capillary electrochromatography (CEC), called dynamically modified strong cation-exchange CEC (DMSCX-CEC), is described in this paper. A column packed with a strong cation-exchange (SCX) packing material was dynamically modified with a long-chain quaternary ammonium salt, cetyltrimethylammonium bromide (CTAB), which was added to the mobile phase. CTAB ions were adsorbed onto the surface of the SCX packing material, and the resulting hydrophobic layer on this packing was used as the stationary phase. Using the dynamically modified SCX column, neutral solutes were separated with the CEC mode. The highest number of theoretical plates obtained was about 190,000/m, and the relative standard deviations (RSD's) for migration times and capacity factors of alkylbenzenes were less than 1.0% and 2.0% for five consecutive runs, respectively. The effects of CTAB and methanol concentrations and the pH value of the mobile phase on the electroosmotic flow and the separation mechanism were investigated. Excellent simultaneous separation of the basic and neutral solutes in DMSCX-CEC with a high-pH mobile phase was obtained. A mixture containing the acidic, basic, and neutral compounds was well separated in this mode with a low-pH mobile phase; however, peak tailing for basic compounds was observed in this mobile phase.

  3. Characterization of the acidic species of a monoclonal antibody using weak cation exchange chromatography and LC-MS.

    PubMed

    Ponniah, Gomathinayagam; Kita, Adriana; Nowak, Christine; Neill, Alyssa; Kori, Yekaterina; Rajendran, Saravanamoorthy; Liu, Hongcheng

    2015-09-01

    Charge variants, especially acidic charge variants, of recombinant monoclonal antibodies have been challenging to fully characterize despite the fact that several posttranslational modifications have already been identified. The acidic species of a recombinant monoclonal antibody were collected using weak cation exchange (WCX)-10 chromatography and characterized by LC-MS at multiple levels. In this study, methionine oxidation and asparagine deamidation are the only two modifications identified in the acidic species. Incubation of the collected main chromatographic peak with hydrogen peroxide generated acidic species, which confirmed that acidic species were enriched in oxidized antibody. Differences observed between the original acidic species and the oxidization-induced acidic species indicate that different mechanisms are involved in the formation of acidic species. Additionally, acidic species were generated by thermal stress of the collected main peak from the original sample. Thermal stress of the collected main peak in pH 9 buffer or ammonium bicarbonate generated chromatograms that are highly similar to those from the analysis of the original molecule. LC-MS analysis identified oxidation of the same methionine residue and deamidation of the same asparagine in the corresponding acidic fractions generated by thermal stress; however, relatively lower levels of methionine oxidation and higher levels of asparagine deamdiation were observed. The results support the use of stressed conditions to generate low abundance species for detailed characterization of recombinant monoclonal antibody charge variants, but with caution.

  4. Assembly and exchange of intermediate filament proteins of neurons: neurofilaments are dynamic structures

    PubMed Central

    1989-01-01

    We have explored the dynamics of intermediate filament assembly and subunit exchange using fluorescently labeled neurofilament proteins and a fluorescence resonance energy transfer assay. Neurofilaments (NFs) are assembled from three highly phosphorylated proteins with molecular masses of 180 (NF-H), 130 (NF-M), and 66 kD (NF-L) of which NF-L forms the structural core. The core component, NF-L, was stoichiometrically labeled at cysteine 321 with fluorescein, coumarin, or biotin-maleimide to produce assembly-competent fluorescent or biotinylated derivatives, respectively. Using coumarin-labeled NF-L as fluorescence donor and fluorescein-labeled NF-L as the fluorescence acceptor, assembly of NF filaments was induced by rapidly raising the NaCl concentration to 170 mM, and the kinetics was followed by the decrease in the donor fluorescence. Assembly of NF-L subunits into filaments does not require nucleotide binding or hydrolysis but is strongly dependent on ionic strength, pH, and temperature. The critical concentration of NF-L, that concentration that remains unassembled at equilibrium with fully formed filaments, is 38 micrograms/ml or 0.6 microM. Under physiological salt conditions NF-L filaments also undergo extensive subunit exchange. Kinetic analysis and evaluation of several possible mechanisms indicate that subunit exchange is preceded by dissociation of subunits from the filament and generation of a kinetically active pool of soluble subunits. Given the concentration of NF-L found in nerve cells and the possibility of regulating this pool, these results provide the first information that intermediate filaments are dynamic structures and that NF-L within the NF complex is in dynamic equilibrium with a small but kinetically active pool of unassembled NF-L units. PMID:2925792

  5. Exchange bias in (FeNi/IrMn)n multilayer films evaluated by static and dynamic techniques

    NASA Astrophysics Data System (ADS)

    Khanal, Shankar; Diaconu, Andrei; Vargas, Jose M.; Lenormand, Denny R.; Garcia, Carlos; Ross, C. A.; Spinu, Leonard

    2014-06-01

    Exchange bias properties of [FeNi/IrMn]n multilayer films with variable thickness of the ferromagnetic layers and different repetitions n were determined by using static and dynamic measurement techniques. The static magnetic properties were revealed through magnetometry measurements at room temperature following major hysteresis loops and first-order reversal curves protocols. Room temperature x-band ferromagnetic resonance (FMR) and vector network analyser (VNA)-FMR experiments were used to determine dynamically the exchange anisotropy in the FeNi/IrMn multilayers. From the static measurements the exchange anisotropy was determined while dynamic measurements allowed the determination of additional parameters including anisotropy field, saturation magnetization and rotatable anisotropy. The differences between the values of the exchange biased obtained from each technique are discussed.

  6. 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.

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. A system dynamics evaluation model: implementation of health information exchange for public health reporting.

    PubMed

    Merrill, Jacqueline A; Deegan, Michael; Wilson, Rosalind V; Kaushal, Rainu; Fredericks, Kimberly

    2013-06-01

    To evaluate the complex dynamics involved in implementing electronic health information exchange (HIE) for public health reporting at a state health department, and to identify policy implications to inform similar implementations. Qualitative data were collected over 8 months from seven experts at New York State Department of Health who implemented web services and protocols for querying, receipt, and validation of electronic data supplied by regional health information organizations. Extensive project documentation was also collected. During group meetings experts described the implementation process and created reference modes and causal diagrams that the evaluation team used to build a preliminary model. System dynamics modeling techniques were applied iteratively to build causal loop diagrams representing the implementation. The diagrams were validated iteratively by individual experts followed by group review online, and through confirmatory review of documents and artifacts. Three casual loop diagrams captured well-recognized system dynamics: Sliding Goals, Project Rework, and Maturity of Resources. The findings were associated with specific policies that address funding, leadership, ensuring expertise, planning for rework, communication, and timeline management. This evaluation illustrates the value of a qualitative approach to system dynamics modeling. As a tool for strategic thinking on complicated and intense processes, qualitative models can be produced with fewer resources than a full simulation, yet still provide insights that are timely and relevant. System dynamics techniques clarified endogenous and exogenous factors at play in a highly complex technology implementation, which may inform other states engaged in implementing HIE supported by federal Health Information Technology for Economic and Clinical Health (HITECH) legislation.

  12. 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.

  13. 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

  14. Rapid Analysis of Protein Structure and Dynamics by Hydrogen/Deuterium Exchange Mass Spectrometry

    PubMed Central

    Hamuro, Yoshitomo; Coales, Stephen J.; Southern, Mark R.; Nemeth-Cawley, Jennifer F.; Stranz, David D.; Griffin, Patrick R.

    2003-01-01

    An automated approach for the rapid analysis of protein structure has been developed and used to study acid-induced conformational changes in human growth hormone. The labeling approach involves hydrogen/deuterium exchange (H/D-Ex) of protein backbone amide hydrogens with rapid and sensitive detection by mass spectrometry (MS). Briefly, the protein is incubated for defined intervals in a deuterated environment. After rapid quenching of the exchange reaction, the partially deuterated protein is enzymatically digested and the resulting peptide fragments are analyzed by liquid chromatography mass spectrometry (LC-MS). The deuterium buildup curve measured for each fragment yields an average amide exchange rate that reflects the environment of the peptide in the intact protein. Additional analyses allow mapping of the free energy of folding on localized segments along the protein sequence affording unique dynamic and structural information. While amide H/D-Ex coupled with MS is recognized as a powerful technique for studying protein structure and protein–ligand interactions, it has remained a labor-intensive task. The improvements in the amide H/D-Ex methodology described here include solid phase proteolysis, automated liquid handling and sample preparation, and integrated data reduction software that together improve sequence coverage and resolution, while achieving a sample throughput nearly 10-fold higher than the commonly used manual methods. PMID:13678147

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

    PubMed

    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

    2009-06-01

    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 100K which shows 30 Hz linewidths.

  16. 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.

  17. σ and κ mesons as broad dynamical resonances in one-meson-exchange model

    NASA Astrophysics Data System (ADS)

    Hong Xiem, Ngo Thi; Shinmura, Shoji

    2014-09-01

    The existences of broad scalar σ (600) and κ (700) mesons have been discussed intensively in the experimental and theoretical studies on ππ and πK scatterings. By using chiral perturbation model, J. Oller, A. Gómez and J. R. Peláez confirmed the existence of these mesons as dynamical resonances. In meson-exchange models, their existence has not been established yet. In this talk, using the quasi-potential of meson-exchange model and Lippmann-Schwinger equation, we determine the T and S-matrices, from which we could find the positions of poles in physical amplitudes in the complex E-plane. With the full treatment of meson-meson interactions (ππ - πK - πη - ηη and πK - ηK) , for the first time, the existence of the scalar σ (600) and κ (700) mesons are confirmed in one-meson-exchange model. There are two kinds of form factors in our model: the monopole and the Gaussian. Our recent results show that the poles σ and κ appear at around 410 - i 540 MeV and 650 - i 20 MeV for monopole form factors, respectively. For Gaussian form factors, the poles σ and κ, respectively, are at 360 - i 510 MeV and 649 - i 190 MeV.

  18. Seasonal dynamics of tree species specific soil moisture patterns

    NASA Astrophysics Data System (ADS)

    Heidbuechel, I.; Blume, T.; Guntner, A.; Dreibrodt, J.; Simard, S.

    2015-12-01

    Soil moisture patterns in the landscape are largely controlled by soil types (pore size distributions), landscape position and precipitation events. But how strong is the influence of vegetation on patterns within a single soil type? While we would envision a clear difference in soil moisture patterns and responses between for example bare soil, a pasture and a forest, our conceptual images start to become less clear when we compare different forest stands. Do different tree species cause species specific moisture patterns to emerge? Do these patterns change with the seasons? To investigate this question we analyzed data from 15 sensor clusters in the lowlands of north-eastern Germany (within the TERENO observatory) which were instrumented with soil moisture sensors (5 profiles per site), tensiometers, sap flow sensors, throughfall and stemflow gauges. Data has been collected at these sites since May 2014. While the soils under beech trees were more often relatively wet and more often relatively dry, the soils under pine trees showed less variability and more often average soil moisture. These differences could be explained by differences in the complex interactions between throughfall and stemflow on the one hand as well as root water uptake and sap flow patterns on the other hand. Further analysis will explore hydraulic redistribution between soil layers and hydraulic lift of groundwater (using root zone water balance methods and stable water isotope samples that were taken at different depths in the soil, in the groundwater and from the sapwood). The manifestation of tree species differences in soil moisture patterns and dynamics is likely to have implications for groundwater recharge, transit times and hydrologic partitioning within the critical zone.

  19. 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.

  20. Dynamic characteristics of heat exchanger tubes vibrating in a tube support plate inactive mode

    SciTech Connect

    Jendrzejczyk, J.A.

    1984-06-01

    Tubes in shell-and-tube heat exchangers, including nuclear plant steam generators, derive their support from longitudinally positioned tube support plates (TSPs). Typically there is a clearance between the tube and TSP hole. Depending on design and fabrication tolerances, the tube may or may not contract all of the TSPs. Noncontact results in an inactive TSP which can lead to detrimental flow induced tube vibrations under certain conditions dependent on the resulting tube-TSP interaction dynamics and the fluid excitation forces. The purpose of this study is to investigate the tube-TSP interaction dynamics. Results of an experimental study of damping and natural frequency as functions of tube-TSP diametral clearance and TSP thickness are reported. Calculated values of damping ratio and frequency of a tube vibrating within an inactive TSP are also presented together with a comparison of calculated and experimental quantities.

  1. Dynamic characteristics of heat exchanger tubes vibrating in a tube support plate inactive mode

    SciTech Connect

    Jendrzejczyk, J.A.

    1985-01-01

    Tubes in shell-and-tube heat exchangers, including nuclear plant steam generators, derive their support from longitudinally positioned tube support plates (TSPs). Typically there is a clearance between the tube and TSP hole. Depending on design and fabrication tolerances, the tube may or may not contact all of the TSPs. Noncontact results in an inactive TSP which can lead to detrimental flow induced tube vibrations under certain conditions dependent on the resulting tube-TSP interaction dynamics and the fluid excitation forces. The purpose of this study is to investigate the tube-TSP interaction dynamics. Results of an experimental study of damping and natural frequency as functions of tube-TSP diametral clearance and TSP thickness are reported. Calculated values of damping ratio and frequency of a tube vibrating within an inactive TSP are also presented together with a comparison of calculated and experimetnal quantities.

  2. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    PubMed

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  3. Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

    NASA Astrophysics Data System (ADS)

    Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

    2017-03-01

    Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion...carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

  4. Influence of Fock exchange in combined many-body perturbation and dynamical mean field theory

    NASA Astrophysics Data System (ADS)

    Ayral, Thomas; Biermann, Silke; Werner, Philipp; Boehnke, Lewin

    2017-06-01

    In electronic systems with long-range Coulomb interaction, the nonlocal Fock-exchange term has a band-widening effect. While this effect is included in combined many-body perturbation theory and dynamical mean field theory (DMFT) schemes, it is not taken into account in standard extended DMFT (EDMFT) calculations. Here, we include this instantaneous term in both approaches and investigate its effect on the phase diagram and dynamically screened interaction. We show that the largest deviations between previously presented EDMFT and G W +EDMFT results originate from the nonlocal Fock term, and that the quantitative differences are especially large in the strong-coupling limit. Furthermore, we show that the charge-ordering phase diagram obtained in G W +EDMFT methods for moderate interaction values is very similar to the one predicted by dual-boson methods that include the fermion-boson or four-point vertex.

  5. Replica exchange molecular dynamics simulation of cross-fibrillation of IAPP and PrP106-126.

    PubMed

    Chua, Khi Pin; Chew, Lock Yue; Mu, Yuguang

    2016-08-01

    Aggregation of proteins into amyloid is the central hallmark of a number of protein diseases. Most studies were carried out on the aggregation between proteins of similar species. However, it was observed that some patients with certain protein disease can easily acquire another unrelated protein disease. As such, it is also important to examine aggregation between proteins of different species. Usually aggregation between proteins of the same species can be attributed to the similarity between their respective amino acid sequences. In this article, we were motivated by an experimental study of aggregation between amylin (Islet Amyloid Polypeptide, IAPP) and prion106-126 (PrP106-126) fragment (JACS, 2013, 135, 13582-9). It was found that the two non-homologous peptides can aggregate quickly to form fibrils in the presence of negatively charged lipid bilayer. We attempted to elucidate the molecular mechanism of the early stage of dimerization of these two peptides through extensive replica exchange molecular dynamics simulations. Conformations consisting of various degrees of β-sheets structures, both intra-chain and inter-chain, were found in the simulations. The conformations of the aggregated complex are very diverse, which suggests that the cross-species fibrils formed between the two proteins are highly polymorphic. The driving forces are mainly hydrophobic interactions, including aromatic-aliphatic interactions. The palindromic region of PrP106-126 and SNNFGAIL region of IAPP were found to play important roles in the interaction. Our study sheds insight into the exciting research of protein cross-fibrillation. Proteins 2016; 84:1134-1146. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  6. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. 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

  8. 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

  9. 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.

  10. Considerably Unfolded Transthyretin Monomers Preceed and Exchange with Dynamically Structured Amyloid Protofibrils

    PubMed Central

    Groenning, Minna; Campos, Raul I.; Hirschberg, Daniel; Hammarström, Per; Vestergaard, Bente

    2015-01-01

    Despite numerous studies, a detailed description of the transthyretin (TTR) self-assembly mechanism and fibril structure in TTR amyloidoses remains unresolved. Here, using a combination of primarily small -angle X-ray scattering (SAXS) and hydrogen exchange mass spectrometry (HXMS) analysis, we describe an unexpectedly dynamic TTR protofibril structure which exchanges protomers with highly unfolded monomers in solution. The protofibrils only grow to an approximate final size of 2,900 kDa and a length of 70 nm and a comparative HXMS analysis of native and aggregated samples revealed a much higher average solvent exposure of TTR upon fibrillation. With SAXS, we reveal the continuous presence of a considerably unfolded TTR monomer throughout the fibrillation process, and show that a considerable fraction of the fibrillating protein remains in solution even at a late maturation state. Together, these data reveal that the fibrillar state interchanges with the solution state. Accordingly, we suggest that TTR fibrillation proceeds via addition of considerably unfolded monomers, and the continuous presence of amyloidogenic structures near the protofibril surface offers a plausible explanation for secondary nucleation. We argue that the presence of such dynamic structural equilibria must impact future therapeutic development strategies. PMID:26108284

  11. Characterization of atmosphere-water exchange processes of CO 2 in estuaries using dynamic simulation

    NASA Astrophysics Data System (ADS)

    García-Luque, E.; Forja, J. M.; Gómez-Parra, A.

    2005-12-01

    CO 2 is one of the so-called "greenhouse effect" gases; therefore, its rates of water-atmosphere exchange are very relevant for studies of climate change. Coastal zones (which include estuarine systems) are of special interest in relation to the global carbon cycle. Thus, an estuary simulator, which operates in a dynamic mixing regime, is specifically applied in an initial study of the estuarine dynamic of inorganic carbon, focusing basically on the influence of salinity and pH on the water-atmosphere fluxes of CO 2 in these zones. The simulation has been performed under two assumptions: (i) considering that the system is subjected to a stationary gradient of salinity and (ii) taking into account the effect of the tides, owing to the daily oscillations introduced by this phenomenon in the process of CO 2 transfer between the water and the atmosphere. After analysing the results, it has been observed that a potential source of error exists when choosing the coefficients of gas exchange ( k) for CO 2 studies. Nevertheless, the evolution of CO 2 fluxes along the salinity and pH gradients achieved shows the same trends with those observed in a wide variety of real estuaries described in the related literature.

  12. 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

  13. Improved antibiotic resistance gene cassette for marker exchange mutagenesis in Ralstonia solanacearum and Burkholderia species.

    PubMed

    Um, Hae Young; Chung, Eunsook; Lee, Jai-Heon; Lee, Seon-Woo

    2011-04-01

    Marker exchange mutagenesis is a fundamental approach to understanding gene function at a molecular level in bacteria. New plasmids carrying a kanamycin resistance gene or a trimethoprim resistance gene were constructed to provide antibiotic resistance cassettes for marker exchange mutagenesis in Ralstonia solanacearum and many antibiotic-resistant Burkholderia spp. Insertion sequences present in the flanking sequences of the antibiotic resistance cassette were removed to prevent aberrant gene replacement and polar mutation during mutagenesis in wild-type bacteria. Plasmids provided in this study would be convenient for use in gene cassettes for gene replacement in other Gram-negative bacteria.

  14. Bifurcation theory, adaptive dynamics and dynamic energy budget-structured populations of iteroparous species

    PubMed Central

    Kooi, B. W.; van der Meer, J.

    2010-01-01

    In this paper, we describe a technique to evaluate the evolutionary dynamics of the timing of spawning for iteroparous species. The life cycle of the species consists of three life stages, embryonic, juvenile and adult whereby the transitions of life stages (gametogenesis, birth and maturation) occur at species-specific sizes. The dynamics of the population is studied in a semi-chemostat environment where the inflowing food concentration is periodic (annual). A dynamic energy budget-based continuous-time model is used to describe the uptake of the food, storage in reserves and allocation of the energy to growth, maintenance, development (embryos, juveniles) and reproduction (adults). A discrete-event process is used for modelling reproduction. At a fixed spawning date of the year, the reproduction buffer is emptied and a new cohort is formed by eggs with a fixed size and energy content. The population consists of cohorts: for each year one consisting of individuals with the same age which die after their last reproduction event. The resulting mathematical model is a finite-dimensional set of ordinary differential equations with fixed 1-year periodic boundary conditions yielding a stroboscopic map. We will study the evolutionary development of the population using the adaptive dynamics approach. The trait is the timing of spawning. Pairwise and mutual invasibility plots are calculated using bifurcation analysis of the stroboscopic map. The evolutionary singular strategy value belonging to the evolutionary endpoint for the trait allows for an interpretation of the reproduction strategy of the population. In a case study, parameter values from the literature for the bivalve Macoma balthica are used. PMID:20921055

  15. 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.

  16. 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

  17. Water exchange and permeability properties of the skin in three species of amphibious sea snakes (Laticauda spp.).

    PubMed

    Lillywhite, H B; Menon, J G; Menon, G K; Sheehy, C M; Tu, M C

    2009-06-01

    Evolutionary transitions between different environmental media such as air and water pose special problems with respect to skin permeability because of the dramatic changes in the driving gradients and nature of water exchange processes. Also, during the transitional periods prior to complete adaptation to a new medium, the skin is exposed to two very different sets of environmental conditions. Here, we report new data for transepidermal evaporative water loss (TEWL) and cutaneous resistance to evaporative water loss (R(s)) of sea snakes that are transitional in the sense of being amphibious and semi-terrestrial. We investigated three species of sea kraits (Elapidae: Laticaudinae) that are common to Orchid Island (Lanyu), Taiwan. Generally, R(s) of all three species is lower than that characteristic of terrestrial/xeric species of snakes measured in other taxa. Within Laticauda, R(s) is significantly greater (TEWL lower) in the more terrestrial species and lowest (TEWL highest) in the more aquatic species. Previously reported losses of water from snakes kept in seawater exhibit a reversed trend, with lower rates of loss in the more aquatic species. These data suggest selection for adaptive traits with respect to increasing exposure to the marine environment. Thus, a countergradient of traits is reflected in decreased TEWL in aerial environments and decreased net water efflux in marine environments, acting simultaneously in the three species. The pattern for TEWL correlates with ultrastructural evidence for increased lipogenesis in the stratum corneum of the more terrestrial species. The skin surfaces of all three species are hydrophobic. Species differences in this property possibly explain the pattern for water efflux when these snakes are in seawater, which remains to be investigated.

  18. 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.

  19. Momentum-dependent susceptibilities and magnetic exchange in bcc iron from supercell dynamical mean-field theory calculations

    NASA Astrophysics Data System (ADS)

    Belozerov, A. S.; Katanin, A. A.; Anisimov, V. I.

    2017-08-01

    We analyze the momentum and temperature dependences of the magnetic susceptibilities and magnetic exchange interaction in paramagnetic bcc iron by a combination of density functional theory and dynamical mean-field theory (DFT+DMFT). By considering a general derivation of the orbital-resolved effective model for spin degrees of freedom for Hund's metals, we relate momentum-dependent susceptibilities in the paramagnetic phase to the magnetic exchange. We then calculate nonuniform orbital-resolved susceptibilities at high-symmetry wave vectors by constructing appropriate supercells in the DMFT approach. Extracting the irreducible parts of susceptibilities with respect to Hund's exchange interaction, we determine the corresponding orbital-resolved exchange interactions, which are then interpolated to the whole Brillouin zone. Using the spherical model we estimate the temperature dependence of the resulting exchange between local moments.

  20. 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

  1. Nonadditive effects of leaf litter species diversity on breakdown dynamics in a deteritus-bases stream

    Treesearch

    J.S. Kominoski; C.M. Pringle; B.A. Ball; M.A. Bradford; D.C. Coleman; D.B. Hall; M.D. Hunter

    2007-01-01

    Since species loss is predicted to be nonrandom, it is important to understand the manner in which those species that we anticipate losing interact with other species to affect ecosystem function. We tested whether litter species diversity, measured as richness and composition, affects breakdown dynamics in a detritus-based stream. Using full-factorial analyses of...

  2. Reactive Oxygen Species Regulate Protrusion Efficiency by Controlling Actin Dynamics

    PubMed Central

    Taulet, Nicolas; Delorme-Walker, Violaine D.; DerMardirossian, Céline

    2012-01-01

    Productive protrusions allowing motile cells to sense and migrate toward a chemotactic gradient of reactive oxygen species (ROS) require a tight control of the actin cytoskeleton. However, the mechanisms of how ROS affect cell protrusion and actin dynamics are not well elucidated yet. We show here that ROS induce the formation of a persistent protrusion. In migrating epithelial cells, protrusion of the leading edge requires the precise regulation of the lamellipodium and lamella F-actin networks. Using fluorescent speckle microscopy, we showed that, upon ROS stimulation, the F-actin retrograde flow is enhanced in the lamellipodium. This event coincides with an increase of cofilin activity, free barbed ends formation, Arp2/3 recruitment, and ERK activity at the cell edge. In addition, we observed an acceleration of the F-actin flow in the lamella of ROS-stimulated cells, which correlates with an enhancement of the cell contractility. Thus, this study demonstrates that ROS modulate both the lamellipodium and the lamella networks to control protrusion efficiency. PMID:22876286

  3. Ion-exchange chromatography/electrospray mass spectrometry for the identification of organic and inorganic species in topiramate tablets.

    PubMed

    Xiang, X; Ko, C Y; Guh, H Y

    1996-11-01

    An ion-exchange chromatograph/electrospray ionization mass spectrometer (IC/ESI-MS) was used successfully to identify organic and inorganic species present in topiramate tablets. An ion suppressor is placed between the column and detectors to replace sodium ions in the mobile phase with hydrogen ions supplied by the suppressor. The ensuing combination of the hydrogen ions with the mobile phase hydroxide ions produces water and thus allows simultaneous ion detection by an ion conductivity detector and a mass spectrometer. Analytes, including lactate, glycolate, chloride, formate, sulfate, and oxalate, were unambiguously identified by matching the mass spectra and retention times with those of the authentic compounds. Due to its capability of detecting positive and negative as well as neutral species, ESI-MS provides valuable information which is not available with ion conductivity detection alone. Though the coupling of ion-exchange chromatography to mass spectrometry has been reported previously, this is the first demonstration of IC/ESI-MS for the identification of unknown species in real samples. Finally, with the use of deuterium/carbon-13 labeling and MS/MS techniques, we have confirmed that oxalic acid (HOOC-COOH) is formed from formic acid (HCOOH) at the electrospray interface in the presence of the electric field. This observation not only confirms the identity of an unknown peak, but it also provides new insight into chemistry that can take place during electrospray ionization.

  4. Recent advancements on modelling the exchange flow dynamics through the Turkish Strait System

    NASA Astrophysics Data System (ADS)

    Sannino, Gianmaria; Sözer, Adil; Özsoy, Emin

    2014-05-01

    The system composed by the two narrow Straits, Dardanelles and Bosphorus, and the Marmara Sea is known as the Turkish Straits System (TSS). The scientific questions on the role of the TSS in coupling the adjacent basins of the Mediterranean and Black Seas with highly contrasting properties, in a region of high climatic variability and materials transport depending critically on the cycle of water can only be answered by model predictions of the processes that determine the integral properties of the coupled sub-systems. This can only be achieved if the entire TSS is modeled as a finely resolved integral system that appropriately accounts for the high contrasts in seawater properties, steep topography, hydraulic controls, fine and meso-scale turbulence, nonlinear and non-hydrostatic effects, thermodynamic states and an active free-surface in the fullest extent, based on well represented fluid dynamical principles. In this study the MITgcm is used at very high resolution to study this extreme environment that needs to be represented as a whole and with the full details of its highly contrasting properties. The model domain chosen extends over the entire TSS, including also part of the north-east Aegean Sea at south, and the Black Sea at north of the domain. A non-uniform curvilinear orthogonal grid covers the domain at variable resolution: from less than 50 m in the two Straits up to about 1 Km in the Marmara Sea. To adequately resolve the complex hydraulic dynamics of the TSS, the model grid is made by 100 vertical z-levels. The model is initialized with three different water masses filling the western part of the domain, the Marmara Sea and the eastern side of the domain respectively, with vertical profiles selected from CTD casts obtained during the cruise of the R/V BİLİM of the Institute of Marine Sciences in June-July 2013. With the initial condition specified as lock-exchanges at the two straits, the model is left free to adjust to the expected two

  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.

  6. Recombination-Induced Tag Exchange (RITE) Cassette Series to Monitor Protein Dynamics in Saccharomyces cerevisiae

    PubMed Central

    Terweij, Marit; van Welsem, Tibor; van Deventer, Sjoerd; Verzijlbergen, Kitty F.; Menendez-Benito, Victoria; Ontoso, David; San-Segundo, Pedro; Neefjes, Jacques; van Leeuwen, Fred

    2013-01-01

    Proteins are not static entities. They are highly mobile, and their steady-state levels are achieved by a balance between ongoing synthesis and degradation. The dynamic properties of a protein can have important consequences for its function. For example, when a protein is degraded and replaced by a newly synthesized one, posttranslational modifications are lost and need to be reincorporated in the new molecules. Protein stability and mobility are also relevant for the duplication of macromolecular structures or organelles, which involves coordination of protein inheritance with the synthesis and assembly of newly synthesized proteins. To measure protein dynamics, we recently developed a genetic pulse-chase assay called recombination-induced tag exchange (RITE). RITE has been successfully used in Saccharomyces cerevisiae to measure turnover and inheritance of histone proteins, to study changes in posttranslational modifications on aging proteins, and to visualize the spatiotemporal inheritance of protein complexes and organelles in dividing cells. Here we describe a series of successful RITE cassettes that are designed for biochemical analyses, genomics studies, as well as single cell fluorescence applications. Importantly, the genetic nature and the stability of the tag switch offer the unique possibility to combine RITE with high-throughput screening for protein dynamics mutants and mechanisms. The RITE cassettes are widely applicable, modular by design, and can therefore be easily adapted for use in other cell types or organisms. PMID:23708297

  7. 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.

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

    NASA Astrophysics Data System (ADS)

    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 water column redox conditions and dissolved iron, manganese, and sulfide were measured to monitor sediment redox conditions. Dissolved 238U 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.

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

    PubMed Central

    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

  10. 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.

  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

    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.

  13. Hydrated fractions of cellulosics probed by infrared spectroscopy coupled with dynamics of deuterium exchange.

    PubMed

    Driemeier, Carlos; Mendes, Fernanda M; Ling, Liu Yi

    2015-08-20

    This article presents a novel method to selectively probe the non-crystalline, hydrated fractions of cellulosic biomass. The method is based on time-resolved infrared spectra analyzed to provide information on spectral and dynamical features of deuterium exchange (OH → OD) in D2O atmosphere. We assign deuterium exchange spectral regions (700-3800 cm(-1)) and explore changes due to relative humidity, different cellulosic samples, and infrared polarization. Here, two results are highlighted. First, a wide range of celluloses isolated from plants show remarkable spectral similarities whatever the relative amounts of cellulose and xylan. This result supports an inherent type of hydrated disorder which is mostly insensitive to the molecular identities of the associated polysaccharides. Second, polarized infrared analysis of cotton reveals hydrated cellulose having chains preferentially aligned with those of crystals, while the hydroxyls of hydrated cellulose present much more randomized orientation. Our results provide new insights on molecular and group orientation and on hydrogen bonding in hydrated fractions of cellulosic biomass.

  14. Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method.

    PubMed

    Chen, Changjun; Huang, Yanzhao

    2016-06-30

    Replica Exchange Molecular Dynamics (REMD) method is a powerful sampling tool in molecular simulations. Recently, we made a modification to the standard REMD method. It places some inactive replicas at different temperatures as well as the active replicas. The method completely decouples the number of the active replicas and the number of the temperature levels. In this article, we make a further modification to our previous method. It uses the inactive replicas in a different way. The inactive replicas first sample in their own knowledge-based energy databases and then participate in the replica exchange operations in the REMD simulation. In fact, this method is a hybrid between the standard REMD method and the simulated tempering method. Using different active replicas, one can freely control the calculation quantity and the convergence speed of the simulation. To illustrate the performance of the method, we apply it to some small models. The distribution functions of the replicas in the energy space and temperature space show that the modified REMD method in this work can let the replicas walk freely in both of the two spaces. With the same number of the active replicas, the free energy surface in the simulation converges faster than the standard REMD. © 2016 Wiley Periodicals, Inc.

  15. 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.

  16. Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations.

    PubMed

    Meng, Yilin; Dashti, Danial Sabri; Roitberg, Adrian E

    2011-09-13

    Alchemical free energy calculations play a very important role in the field of molecular modeling. Efforts have been made to improve the accuracy and precision of those calculations. One of the efforts is to employ a Hamiltonian replica exchange molecular dynamics (H-REMD) method to enhance conformational sampling. In this paper, we demonstrated that HREMD method not only improves convergence in alchemical free energy calculations but also can be used to compute free energy differences directly via the Free Energy Perturbation (FEP)algorithm. We show a direct mapping between the H-REMD and the usual FEP equations, which are then used directly to compute free energies. The H-REMD alchemical free energy calculation (Replica exchange Free Energy Perturbation, REFEP) was tested on predicting the pK(a) value of the buried Asp26 in thioredoxin. We compare the results of REFEP with TI and regular FEP simulations. REFEP calculations converged faster than those from TI and regular FEP simulations. The final predicted pK(a) value from the H-REMD simulation was also very accurate, only 0.4 pK(a) unit above the experimental value. Utilizing the REFEP algorithm significantly improves conformational sampling, and this in turn improves the convergence of alchemical free energy simulations.

  17. On the mesoscale dynamics of the Indian/Atlantic interocean exchange.

    NASA Astrophysics Data System (ADS)

    Matano, R. P.; Beier, E. J.

    2002-12-01

    In this presentation we analyze the Indian/Atlantic interocean exchanges in an eddy-permitting numerical simulation of the global ocean circulation. Our analysis focuses in the Cape Basin, a region of the southeastern Atlantic limited to the northwest by the Walvis Ridge and to the south by the subtropical convergence. To quantify the relative importance of the different dynamical mechanisms involved in the interocean exchange we separated the climatological mean circulation from the transients. The analysis indicates that Agulhas eddies not only influence the transient fluxes but also to those associated with the mean circulation (eddy fluxes, for example, supply most of the energy of the Benguela Current). A distinct characteristic of the eddy variability within the Cape Basin is the co-existence of cyclonic and anticyclonic vortices in dipole structures that resemble the heton model of Hogg and Stommel (Deep Sea Research,1985). Anticyclones are surface intensified vortices that, in spite of their baroclinic structure, reach to deep layers. Cyclones, are bottom-intensified vortices with dominant barotropic structure that projects into the upper layer. The propagation of cyclones and anticyclones is strongly affected by the bottom topography. Our analysis shows that the Walvis Ridge and the Vema Seamount block the passage of bottom-intensified cyclones and rectifies the trajectories of the upper-intensified anticyclones. Although most anticyclones are able to escape the basin the deep compensation generated by the ridge generates an energy loss of approximately 30%, and a rectification of the eddy trajectory to a more westward direction.

  18. Computational fluid dynamics simulation of an earth-air heat exchanger for ventilation system

    NASA Astrophysics Data System (ADS)

    Raczkowski, Andrzej; Suchorab, Zbigniew; Czechowska-Kosacka, Aneta

    2017-07-01

    Directive 2010/31/EU (EPBD Recast) obligates European Union members to improve energetic performance of the buildings. One of the crucial standards of energy-saving buildings are the passive houses, which are characterized by annual maximum space heating below 15 kWh/(m2.a) and the use of the specific primary energy for all domestic applications (also heating, hot water production and electricity) below 120 kWh/(m2.a). To achieve this standard there should be applied the solutions based on ground energy acquisition. One of them is the earth-air heat exchanger (EAHC) for ventilation systems. The article presents numerical simulations conducted by solving partial differential equations for three dimensional heat transfer. For the simulations it was applied Computational Fluid Dynamics (CFD) technique. The efficiency of EAHC was considered under different values of external temperature during the winter period (from -24 to -8 °C). Obtained results prove linear correlation with calculations of EAHC according to standards of the Polish National Energy Conservation Agency (NAPE). The slope of regression between outlet temperatures calculated with CFD model and NAPE standards, equals 0.59 which means, that according the CFD model, the efficiency of the exchanger is lower.

  19. Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

    PubMed Central

    Meng, Yilin; Dashti, Danial Sabri; Roitberg, Adrian E.

    2011-01-01

    Alchemical free energy calculations play a very important role in the field of molecular modeling. Efforts have been made to improve the accuracy and precision of those calculations. One of the efforts is to employ a Hamiltonian replica exchange molecular dynamics (H-REMD) method to enhance conformational sampling. In this paper, we demonstrated that HREMD method not only improves convergence in alchemical free energy calculations but also can be used to compute free energy differences directly via the Free Energy Perturbation (FEP)algorithm. We show a direct mapping between the H-REMD and the usual FEP equations, which are then used directly to compute free energies. The H-REMD alchemical free energy calculation (Replica exchange Free Energy Perturbation, REFEP) was tested on predicting the pKa value of the buried Asp26 in thioredoxin. We compare the results of REFEP with TI and regular FEP simulations. REFEP calculations converged faster than those from TI and regular FEP simulations. The final predicted pKa value from the H-REMD simulation was also very accurate, only 0.4 pKa unit above the experimental value. Utilizing the REFEP algorithm significantly improves conformational sampling, and this in turn improves the convergence of alchemical free energy simulations. PMID:22125475

  20. Intensification of heat exchange in a device for gas-dynamic energy separation

    NASA Astrophysics Data System (ADS)

    Leontiev, A. I.; Burtsev, S. A.

    2016-11-01

    The operating efficiency of a gas-dynamic energy-separation device is analyzed, and it is shown that it can be improved if we deposit a regular relief on the wall separating the supersonic and subsonic channels. To decrease the total pressure losses on the side of the supersonic channel, shallow spherical dimples (stampings) are deposited, creating spherical ledges in the subsonic channel because of the small thickness of the wall. The calculation technique is modernized, and modeling is carried out, which shows that by introducing intensified heat exchange, it is possible to improve the efficiency of this device by 1.2-1.4 times in air and in natural gas with a simultaneous decrease in the device size by 20-25%.

  1. Issues associated with modelling of proton exchange membrane fuel cell by computational fluid dynamics

    NASA Astrophysics Data System (ADS)

    Bednarek, Tomasz; Tsotridis, Georgios

    2017-03-01

    The objective of the current study is to highlight possible limitations and difficulties associated with Computational Fluid Dynamics in PEM single fuel cell modelling. It is shown that an appropriate convergence methodology should be applied for steady-state solutions, due to inherent numerical instabilities. A single channel fuel cell model has been taken as numerical example. Results are evaluated for quantitative as well qualitative points of view. The contribution to the polarization curve of the different fuel cell components such as bi-polar plates, gas diffusion layers, catalyst layers and membrane was investigated via their effects on the overpotentials. Furthermore, the potential losses corresponding to reaction kinetics, due to ohmic and mas transport limitations and the effect of the exchange current density and open circuit voltage, were also investigated. It is highlighted that the lack of reliable and robust input data is one of the issues for obtaining accurate results.

  2. Replica-Exchange Molecular Dynamics Simulations of Amyloid Precursor Protein Dimer in Membrane

    NASA Astrophysics Data System (ADS)

    Miyashita, Naoyuki; Sugita, Yuji

    2010-01-01

    Aggregation of amyloid β peptide (Aβ) in the brain is the primary element in the pathogenesis of Alzheimer's disease. Aβ is derived from amyloid precursor protein (APP) in the membrane due to the cleavages by β- and γ-secretases. Here, we predict the transmembrane structures of the wild-type and mutant APP in the biological membrane by replica-exchange molecular dynamics simulations. The simulations illustrate large conformational differences between the wild type and mutant APP fragments in the membrane. Dimerization of the wild type occurs due to the Cα-H⋯O hydrogen bonds at the Gly-XXX-Gly motifs between two APP fragments, whereas the mutant dimer is stabilized by the interactions between hydrophobic side chains. We also observe the downward shift of γ-cleavage site in the mutant APP, which may cause the prohibition of Aβ production.

  3. 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.

  4. Dynamic Characteristics of Ventilatory and Gas Exchange during Sinusoidal Walking in Humans

    PubMed Central

    Fukuoka, Yoshiyuki; Iihoshi, Masaaki; Nazunin, Juhelee Tuba; Abe, Daijiro; Fukuba, Yoshiyuki

    2017-01-01

    Our present study investigated whether the ventilatory and gas exchange responses show different dynamics in response to sinusoidal change in cycle work rate or walking speed even if the metabolic demand was equivalent in both types of exercise. Locomotive parameters (stride length and step frequency), breath-by-breath ventilation (V̇E) and gas exchange (CO2 output (V̇CO2) and O2 uptake (V̇O2)) responses were measured in 10 healthy young participants. The speed of the treadmill was sinusoidally changed between 3 km·h-1 and 6 km·h-1 with various periods (from 10 to 1 min). The amplitude of locomotive parameters against sinusoidal variation showed a constant gain with a small phase shift, being independent of the oscillation periods. In marked contrast, when the periods of the speed oscillations were shortened, the amplitude of V̇E decreased sharply whereas the phase shift of V̇E increased. In comparing walking and cycling at the equivalent metabolic demand, the amplitude of V̇E during sinusoidal walking (SW) was significantly greater than that during sinusoidal cycling (SC), and the phase shift became smaller. The steeper slope of linear regression for the V̇E amplitude ratio to V̇CO2 amplitude ratio was observed during SW than SC. These findings suggested that the greater amplitude and smaller phase shift of ventilatory dynamics were not equivalent between SW and SC even if the metabolic demand was equivalent between both exercises. Such phenomenon would be derived from central command in proportion to locomotor muscle recruitment (feedforward) and muscle afferent feedback. PMID:28076413

  5. Exchanges of genomic domains between poliovirus and other cocirculating species C enteroviruses reveal a high degree of plasticity

    PubMed Central

    Bessaud, Maël; Joffret, Marie-Line; Blondel, Bruno; Delpeyroux, Francis

    2016-01-01

    The attenuated Sabin strains contained in the oral poliomyelitis vaccine are genetically unstable, and their circulation in poorly immunized populations can lead to the emergence of pathogenic circulating vaccine-derived polioviruses (cVDPVs). The recombinant nature of most cVDPV genomes and the preferential presence of genomic sequences from certain cocirculating non-polio enteroviruses of species C (EV-Cs) raise questions about the permissiveness of genetic exchanges between EV-Cs and the phenotypic impact of such exchanges. We investigated whether functional constraints limited genetic exchanges between Sabin strains and other EV-Cs. We bypassed the natural recombination events by constructing 29 genomes containing a Sabin 2 capsid-encoding sequence and other sequences from Sabin 2 or from non-polio EV-Cs. Most genomes were functional. All recombinant viruses replicated similarly in vitro, but recombination modulated plaque size and temperature sensitivity. All viruses with a 5′UTR from Sabin 2 were attenuated in mice, whereas almost all viruses with a non-polio 5′UTR caused disease. These data highlight the striking conservation of functional compatibility between different genetic domains of cocirculating EV-Cs. This aspect is only one of the requirements for the generation of recombinant cVDPVs in natural conditions, but it may facilitate the generation of viable intertypic recombinants with diverse phenotypic features, including pathogenicity. PMID:27958320

  6. Transient computation fluid dynamics modeling of a single proton exchange membrane fuel cell with serpentine channel

    NASA Astrophysics Data System (ADS)

    Hu, Guilin; Fan, Jianren

    The proton exchange membrane fuel cell (PEMFC) has become a promising candidate for the power source of electrical vehicles because of its low pollution, low noise and especially fast startup and transient responses at low temperatures. A transient, three-dimensional, non-isothermal and single-phase mathematical model based on computation fluid dynamics has been developed to describe the transient process and the dynamic characteristics of a PEMFC with a serpentine fluid channel. The effects of water phase change and heat transfer, as well as electrochemical kinetics and multicomponent transport on the cell performance are taken into account simultaneously in this comprehensive model. The developed model was employed to simulate a single laboratory-scale PEMFC with an electrode area about 20 cm 2. The dynamic behavior of the characteristic parameters such as reactant concentration, pressure loss, temperature on the membrane surface of cathode side and current density during start-up process were computed and are discussed in detail. Furthermore, transient responses of the fuel cell characteristics during step changes and sinusoidal changes in the stoichiometric flow ratio of the cathode inlet stream, cathode inlet stream humidity and cell voltage are also studied and analyzed and interesting undershoot/overshoot behavior of some variables was found. It was also found that the startup and transient response time of a PEM fuel cell is of the order of a second, which is similar to the simulation results predicted by most models. The result is an important guide for the optimization of PEMFC designs and dynamic operation.

  7. Thermodynamic and kinetic stability of the Josephin Domain closed arrangement: evidences from replica exchange molecular dynamics.

    PubMed

    Grasso, Gianvito; Tuszynski, Jack A; Morbiducci, Umberto; Licandro, Ginevra; Danani, Andrea; Deriu, Marco A

    2017-01-19

    Molecular phenomena driving pathological aggregation in neurodegenerative diseases are not completely understood yet. Peculiar is the case of Spinocerebellar Ataxia 3 (SCA3) where the conformational properties of the AT-3 N-terminal region, also called Josephin Domain (JD), play a key role in the first step of aggregation, having the JD an amyloidogenic propensity itself. For this reason, unraveling the intimate relationship between JD structural features and aggregation tendency may lead to a step forward in understanding the pathology and rationally design a cure. In this connection, computational modeling has demonstrated to be helpful in exploring the protein molecular dynamics and mechanism of action. Conformational dynamics of the JD is here finely investigated by replica exchange molecular dynamics simulations able to sample the microsecond time scale and to provide both a thermodynamic and kinetic description of the protein conformational changes. Accessible structural conformations of the JD have been identified in: open, intermediate and closed like arrangement. Data indicated the closed JD arrangement as the most likely protein arrangement. The protein transition from closed toward intermediate/open states was characterized by a rate constant higher than 700 ns. This result also explains the inability of classical molecular dynamics to explore transitions from closed to open JD configuration on a time scale of hundreds of nanoseconds. This work provides the first kinetic estimation of the JD transition pathway from open-like to closed-like arrangement and vice-versa, indicating the closed-like arrangement as the most likely configuration for a JD in water environment. More widely, the importance of our results is also underscored considering that the ability to provide a kinetic description of the protein conformational changes is a scientific challenge for both experimental and theoretical approaches to date. This article was reviewed by Oliviero

  8. Implications of Airflow Dynamics and Soft-Tissue Reconstructions for the Heat Exchange Potential of Dinosaur Nasal Passages

    NASA Astrophysics Data System (ADS)

    Bourke, Jason Michael

    This study seeks to restore the internal anatomy within the nasal passages of dinosaurs via the use of comparative anatomical methods along with computational fluid dynamic simulations. Nasal airway descriptions and airflow simulations are described for extant birds, crocodylians, and lizards. These descriptions served as a baseline for airflow within the nasal passages of diapsids. The presence of shared airflow and soft-tissue properties found in the nasal passages of extant diapsids, were used to restore soft tissues within the airways of dinosaurs under the assumption that biologically unfeasible airflow patterns (e.g., lack of air movement in olfactory recess) can serve as signals for missing soft tissues. This methodology was tested on several dinosaur taxa. Restored airways in some taxa revealed the potential presence and likely shape of nasal turbinates. Heat transfer efficiency was tested in two dinosaur species with elaborated nasal passages. Results of that analysis revealed that dinosaur noses were efficient heat exchangers that likely played an integral role in maintaining cephalic thermoregulation. Brain cooling via nasal expansion appears to have been necessary for dinosaurs to have achieved their immense body sizes without overheating their brains.

  9. 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. No claim to original US Government works New Phytologist © 2014 New Phytologist Trust.

  10. 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.

  11. The impact of ten years at -20°C on gas exchange in five lichen species.

    PubMed

    Larson, D W

    1989-01-01

    Rates of net CO2 exchange in five sympatric species of Umbilicaria were measured after 10 years at-20°C. During that time, the lichens had been at either a high (saturated) or a low (air-dry) water content. The results showed an immediate, return to normal rates of gas exchange for air-dried then frozen U.vellea. Rates returned to normal for air-dried U. deusta within four days. The three other species studied, U. mammulata, U. papulosa and U. muhlenbergii showed intermediate responses. Water saturated then frozen thalli of U. vellea were irreparably damaged after 10 years; even fungal respiration was severely impaired. In U. mammulata, U. papulosa and U. muhlenbergii, photosynthesis was eliminated but fungal respiration rates were not influenced. In contrast to this, water saturated then frozen thalli of U. deusta showed a nearly equal photosynthetic capacity to the original rates following 10 years at -20°C. In all cases the magnitude of the effect of the long-term subzero treatment correlated well with the known distribution patterns of the lichens in the field.

  12. Dynamic Covalent Chemistry of Aldehyde Enamines: Bi(III) - and Sc(III) -Catalysis of Amine-Enamine Exchange.

    PubMed

    Zhang, Yang; Xie, Sheng; Yan, Mingdi; Ramström, Olof

    2017-09-04

    The dynamic exchange of enamines from secondary amines and enolizable aldehydes has been demonstrated in organic solvents. The enamine exchange with amines was efficiently catalyzed by Bi(OTf)3 and Sc(OTf)3 (2 mol %) and the equilibria (60 mm) could be attained within hours at room temperature. The formed dynamic covalent systems displayed high stabilities in basic environment with <2 % by-product formation within one week after complete equilibration. This study expands the scope of dynamic C-N bonds from imine chemistry to enamines, enabling further dynamic methodologies in exploration of this important class of structures in systems chemistry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Dynamics of radiocesium exchange and interstratification in anhydrous clay interlayers: Bridging the atom and single crystal scales

    NASA Astrophysics Data System (ADS)

    Lammers, L. N.; Pestana, L. R.; Schaettle, K. B.; Head-Gordon, T.

    2016-12-01

    High structural charge clay minerals govern the transport and retention of radiocesium in soils and clay-rich geologic repositories. Cation exchange capacities in these phases are typically assumed to be limited to fast-exchanging basal and high-affinity edge sites, while ions in anhydrous interlayers, usually K+, are considered non-exchangeable. However, recent high resolution imaging and spectroscopic studies have demonstrated that Cs ions can in fact exchange with interlayer K without the formation of a hydrated intermediate.1,2 These exchange reactions result in sharp exchange fronts wherein K+ ions are completely replaced by Cs+ at the exchange interface, and the rate of exchange varies from layer to layer, resulting in the formation of interstratified structures (i.e., randomly alternating layers of exchanged and pristine interlayers). Currently, this process cannot be explained by any known exchange mechanism, and consequently, no kinetic expressions are available to account for this phenomenon in models of subsurface radiocesium fate and transport. We present a mesoscale model for direct exchange in anhydrous clay interlayers that is based on the kinetics of single ion migration events. Single atom migration kinetics derived from density functional theory (DFT) calculations are used as inputs to kinetic Monte Carlo (kMC) simulations, which capture the collective dynamics of the exchange process over length- and timescales relevant for implementation in reactive transport models. Potential energy surfaces derived from DFT demonstrate that exchange of Cs+ for K+ in anhydrous interlayers lowers the energy barrier to K ion migration by 145 kJ/mol, leading to a positive feedback mechanism that generates atomically sharp exchange fronts. Our work demonstrates the application of "coarse-graining" techniques to develop models for processes with characteristic length- and timescales not accessible by direct atomistic simulation. 1 Okumura T. et al. (2014) Direct

  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. 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.

  16. The dynamics of stock exchange based on the formalism of weak continuous quantum measurement

    NASA Astrophysics Data System (ADS)

    Melnyk, S.; Tuluzov, I.

    2010-07-01

    The problem of measurement in economic models and the possibility of their quantum-mechanical description are considered. It is revealed that the apparent paradox of such a description is associated with a priori requirement of conformity of the model to all the alternatives of free choice of the observer. The measurement of the state of a trader on a stock exchange is formally defined as his responses to the proposals of sale at a fixed price. It is shown that an analogue of Bell's inequalities for this measurement model is violated at the most general assumptions related to the strategy of the trader and requires a quantum-mechanical description of the dynamics of his condition. In the framework of the theory of weak continuous quantum measurements, the equation of stock price dynamics and the quantum-mechanical generalization of the F. Black and M. Scholes model for pricing options are obtained. The fundamental distinctions between the obtained model and the classical one are discussed.

  17. Implementation of Dynamic Extensible Adaptive Locally Exchangeable Measures (IDEALEM) v 0.1

    SciTech Connect

    Sim, Alex; Lee, Dongeun; Wu, K. John

    2016-03-04

    Handling large streaming data is essential for various applications such as network traffic analysis, social networks, energy cost trends, and environment modeling. However, it is in general intractable to store, compute, search, and retrieve large streaming data. This software addresses a fundamental issue, which is to reduce the size of large streaming data and still obtain accurate statistical analysis. As an example, when a high-speed network such as 100 Gbps network is monitored, the collected measurement data rapidly grows so that polynomial time algorithms (e.g., Gaussian processes) become intractable. One possible solution to reduce the storage of vast amounts of measured data is to store a random sample, such as one out of 1000 network packets. However, such static sampling methods (linear sampling) have drawbacks: (1) it is not scalable for high-rate streaming data, and (2) there is no guarantee of reflecting the underlying distribution. In this software, we implemented a dynamic sampling algorithm, based on the recent technology from the relational dynamic bayesian online locally exchangeable measures, that reduces the storage of data records in a large scale, and still provides accurate analysis of large streaming data. The software can be used for both online and offline data records.

  18. Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery

    PubMed Central

    Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

    2017-01-01

    Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level. PMID:28272396

  19. 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.

  20. Novel dynamic flux chamber for measuring air-surface exchange of Hg(o) from soils.

    PubMed

    Lin, Che-Jen; Zhu, Wei; Li, Xianchang; Feng, Xinbin; Sommar, Jonas; Shang, Lihai

    2012-08-21

    Quantifying the air-surface exchange of Hg(o) from soils is critical to understanding the cycling of mercury in different environmental compartments. Dynamic flux chambers (DFCs) have been widely employed for Hg(o) flux measurement over soils. However, DFCs of different sizes, shapes, and sampling flow rates yield distinct measured fluxes for a soil substrate under identical environmental conditions. In this study, we performed an integrated modeling, laboratory and field study to design a DFC capable of producing a steady and uniform air flow over a flat surface. The new DFC was fabricated using polycarbonate sheets. The internal velocity field was experimentally verified against model predictions using both theoretical and computational fluid dynamics techniques, suggesting fully developed flow with velocity profiles in excellent agreement with model results. Laboratory flux measurements demonstrated that the new design improves data reproducibility as compared to a conventional DFC, and reproduces the model-predicted flux trend with increasing sampling flow. A mathematical relationship between the sampling flow rate and surface friction velocity, a variable commonly parametrized in atmospheric models, was developed for field application. For the first time, the internal shear property of a DFC can be precisely controlled using the sampling flow rate, and the flux under atmospheric condition can be inferred from the measured flux and surface shear property. The demonstrated methodology potentially bridges the gap in measured fluxes obtained by the DFC method and the micrometeorological methods.

  1. Ultrafast fluxional exchange dynamics in electrolyte solvation sheath of lithium ion battery.

    PubMed

    Lee, Kyung-Koo; Park, Kwanghee; Lee, Hochan; Noh, Yohan; Kossowska, Dorota; Kwak, Kyungwon; Cho, Minhaeng

    2017-03-08

    Lithium cation is the charge carrier in lithium-ion battery. Electrolyte solution in lithium-ion battery is usually based on mixed solvents consisting of polar carbonates with different aliphatic chains. Despite various experimental evidences indicating that lithium ion forms a rigid and stable solvation sheath through electrostatic interactions with polar carbonates, both the lithium solvation structure and more importantly fluctuation dynamics and functional role of carbonate solvent molecules have not been fully elucidated yet with femtosecond vibrational spectroscopic methods. Here we investigate the ultrafast carbonate solvent exchange dynamics around lithium ions in electrolyte solutions with coherent two-dimensional infrared spectroscopy and find that the time constants of the formation and dissociation of lithium-ion···carbonate complex in solvation sheaths are on a picosecond timescale. We anticipate that such ultrafast microscopic fluxional processes in lithium-solvent complexes could provide an important clue to understanding macroscopic mobility of lithium cation in lithium-ion battery on a molecular level.

  2. Complement proteins bind to nanoparticle protein corona and undergo dynamic exchange in vivo

    NASA Astrophysics Data System (ADS)

    Chen, Fangfang; Wang, Guankui; Griffin, James I.; Brenneman, Barbara; Banda, Nirmal K.; Holers, V. Michael; Backos, Donald S.; Wu, Linping; Moghimi, Seyed Moein; Simberg, Dmitri

    2017-05-01

    When nanoparticles are intravenously injected into the body, complement proteins deposit on the surface of nanoparticles in a process called opsonization. These proteins prime the particle for removal by immune cells and may contribute toward infusion-related adverse effects such as allergic responses. The ways complement proteins assemble on nanoparticles have remained unclear. Here, we show that dextran-coated superparamagnetic iron oxide core-shell nanoworms incubated in human serum and plasma are rapidly opsonized with the third complement component (C3) via the alternative pathway. Serum and plasma proteins bound to the nanoworms are mostly intercalated into the nanoworm shell. We show that C3 covalently binds to these absorbed proteins rather than the dextran shell and the protein-bound C3 undergoes dynamic exchange in vitro. Surface-bound proteins accelerate the assembly of the complement components of the alternative pathway on the nanoworm surface. When nanoworms pre-coated with human plasma were injected into mice, C3 and other adsorbed proteins undergo rapid loss. Our results provide important insight into dynamics of protein adsorption and complement opsonization of nanomedicines.

  3. Size-dependent Melting Behavior of Iron Nanoparticles by Replica Exchange Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Shu, Qiang; Yang, Yang; Zhai, Yingteng; Sun, Deyan; Xiang, Hongjun; Gong, Xingao

    2013-03-01

    Due to the finite size effect, nanoparticles own unique physical, chemical, and magnetic properties. Comparing with the bulk materials, the large surface/volume ratio of nanoparticles could lead to more complicate atomic and electronic behavior, thus the thermodynamical properties can be also very rich. In the last a few decades, as one of the fundamental problems in the nano science, the melting behavior of nanoparticles had been widely investigated by numerous experimental and theoretical studies. Using replica-exchange molecular dynamics method (REMD), we have investigated the size dependence of the melting behavior of iron nanoparticles. Comparing to the conventional molecular dynamics (MD), the REMD method is found to be very efficient to determine the melting point, by avoiding the superheating and undercooling phenomena. With accurate determination of the melting point, we find that the melting temperature does not follow linearly with the inverse of size. By incorporating the size dependent thickness of surface liquid layer which is observed in our simulation, we propose a revised liquid skin melting model to describe the size dependent melting temperature. Special Funds for Major State Basic Research, NSFC, MOE, Shanghai Municipality

  4. Carbon dioxide exchange characteristics of C4 Hawaiian Euphorbia species native to diverse habitats.

    PubMed

    Pearcy, Robert W; Osteryoung, Katherine; Randall, David

    1982-12-01

    The characteristics of the photosynthetic apparatus of 11 Hawaiian Euphorbia species, all of which possess C4 photosynthesis but range from arid habitat, drought-deciduous shrubs to mesic or wet forest evergreen trees and shrubs, were investigated under uniform greenhouse conditions. Nine species exhibited CO2 response curves typical of C4 plants, but differed markedly in photosynthetic capacity. Light-saturated CO2 uptake rates ranged from 48 to 52 μmol m(-2) s(-1) in arid habitat species to 18 to 20 μmol m(-2) s(-1) in mesic and wet forest species. Two possessed unusual CO2 response curves in which photosynthesis was not saturated above intercellular CO2 pressures [p(CO2)] of 10 to 15 Pa, as typically occurs in C4 plants.Both leaf (g'1) and mesophyll (g'm) conductances to CO2 varied widely between species. At an atmospheric p(CO2) of 32 Pa, g'1 regulated intercellular p(CO2) at 12-15 Pa in most species, which supported nearly maximum CO2 uptake rates, but did not result in excessive transpiration. Intercellular p(CO2) was higher in the two species with unusual CO2 response curves. This was especially apparent in E. remyi, which is native to a bog habitat. The regulation of g'1 and intercellular p(CO2) yielded high photosynthetic water use efficiencies (P/E) in the species with typical CO2 response curves, whereas P/E was much lower in E. remyi.Photosynthetic capacity was closely related to leaf nitrogen content, whereas correlations with leaf morphological characteristics and leaf cell surface area were not significant. Thus, differences in photosynthetic capacity may be determined primarily by investment in the biochemical components of the photosynthetic apparatus rather than by differences in diffusion limitations. The lower photosynthetic capacities in the wet habitat species may reflect the lower light availability. However, other factors, such as reduced nutrient availability, may also be important.

  5. 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

  6. 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. © 2014 John Wiley & Sons Ltd/CNRS.

  7. Spatial-temporal population dynamics across species range: from centre to margin

    Treesearch

    Qinfeng Guo; Mark Taper; Michele Schoenberger; J. Brandle

    2005-01-01

    Understanding the boundaries of species'rangs and the variations in population dynamics from the centre to margin of a species' range is critical. This study simulated spatial-tamporal 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...

  8. Loss of foundation species: consequences for the structure and dynamics of forested ecosystems

    Treesearch

    Aaron M. Ellison; Michael S. Bank; Barton D. Clinton; Elizabeth A. Colburn; Katherine Elliott; Chelcy Rae Ford; David R. Foster; Brian D. Kloeppel; Jennifer D. Knoepp; Gary M. Lovett; Jacqueline Mohan; David A. Orwig; Nicholas L. Rodenhouse; William V. Sobczak; Kristina A. Stinson; Jeffrey K. Stone; Christopher M. Swan; Jill Thompson; Betsy Von Holle; Jackson R. Webster

    2005-01-01

    In many forested ecosystems, the architecture and functional ecology of certain tree species define forest structure and their species-specific traits control ecosystem dynamics. Such foundation tree species are declining throughout the world due to introductions and outbreaks of pests and pathogens, selective removal of individual taxa, and over-harvesting. Through a...

  9. Quantifying hyporheic exchange dynamics in a highly regulated large river reach

    NASA Astrophysics Data System (ADS)

    Zhou, T.; Bao, J.; Huang, M.; Hou, Z.; Arntzen, E.; Mackley, R.; Harding, S.; Crump, A.; Xu, Y.; Song, X.; Chen, X.; Stegen, J.; Hammond, G. E.; Thorne, P. D.; Zachara, J. M.

    2016-12-01

    Hyporheic exchange is an important mechanism taking place in riverbanks and riverbed sediments, where the river water and shallow groundwater mix and interact with each other. The direction and magnitude of hyporheic flux that penetrates the river bed and residence time of river water in the hyporheic zone are critical for biogeochemical processes such as carbon and nitrogen cycling, and biodegradation of organic contaminants. Hyporheic flux can be quantified using many direct and indirect measurements as well as analytical and numerical modeling tools. However, in a relatively large river, these methods can be limited by the accessibility, spatial constraints, complexity of geomorphologic features and subsurface properties, and computational power. In rivers regulated by hydroelectric dams, quantifying hyporheic fluxes becomes more challenging due to frequent hydropeaking events created by dam operations. In this study, we developed and validated methods that combined field measurements and numerical modeling for estimating hyporheic fluxes across the river bed in a 7-km long reach of the highly regulated Columbia River. The reach has a minimum width of about 800 meters and variations in river stage within a day could be up to two meters due to the upstream dam operations. In shallow water along the shoreline, vertical thermal profiles measured by self-recording thermistors were combined with time series of hydraulic gradient derived from river stage and water level at in-land wells to estimate the hyporheic flux rate. For the deep section, a high resolution computational fluid dynamics (CFD) modeling framework was developed to characterize the spatial distribution of flux rates at the river bed and the residence time of hyporheic flow at different river flow conditions. Our modeling results show that the rates of hyporheic exchange and residence time are controlled by (1) hydrostatic pressure induced by river stage fluctuations, and (2) hydrodynamic drivers

  10. Dynamics of Human Telomerase Holoenzyme Assembly and Subunit Exchange across the Cell Cycle.

    PubMed

    Vogan, Jacob M; Collins, Kathleen

    2015-08-28

    Human telomerase acts on telomeres during the genome synthesis phase of the cell cycle, accompanied by its concentration in Cajal bodies and transient colocalization with telomeres. Whether the regulation of human telomerase holoenzyme assembly contributes to the cell cycle restriction of telomerase function is unknown. We investigated the steady-state levels, assembly, and exchange dynamics of human telomerase subunits with quantitative in vivo cross-linking and other methods. We determined the physical association of telomerase subunits in cells blocked or progressing through the cell cycle as synchronized by multiple protocols. The total level of human telomerase RNA (hTR) was invariant across the cell cycle. In vivo snapshots of telomerase holoenzyme composition established that hTR remains bound to human telomerase reverse transcriptase (hTERT) throughout all phases of the cell cycle, and subunit competition assays suggested that hTERT-hTR interaction is not readily exchangeable. In contrast, the telomerase holoenzyme Cajal body-associated protein, TCAB1, was released from hTR in mitotic cells coincident with TCAB1 delocalization from Cajal bodies. This telomerase holoenzyme disassembly was reversible with cell cycle progression without any change in total TCAB1 protein level. Consistent with differential cell cycle regulation of hTERT-hTR and TCAB1-hTR protein-RNA interactions, overexpression of hTERT or TCAB1 had limited if any influence on hTR assembly of the other subunit. Overall, these findings revealed a cell cycle regulation that disables human telomerase association with telomeres while preserving the co-folded hTERT-hTR ribonucleoprotein catalytic core. Studies here, integrated with previous work, led to a unifying model for telomerase subunit assembly and trafficking in human cells.

  11. Molecular exchange dynamics in partially filled microscale and nanoscale pores of silica glasses studied by field-cycling nuclear magnetic resonance relaxometry

    NASA Astrophysics Data System (ADS)

    Mattea, C.; Kimmich, R.; Ardelean, I.; Wonorahardjo, S.; Farrher, G.

    2004-12-01

    Nuclear magnetic spin-lattice relaxation experiments have been performed in partially filled porous glasses with wetting and nonwetting fluids. The frequency dependence of the spin-lattice relaxation rate in Vycor (4 nm pores) and VitraPOR #5 (1 μm pores) silica glasses was studied as a function of the filling degree with the aid of field-cycling NMR relaxometry. The species of primary interest were water ("polar") and cyclohexane ("nonpolar"). Spin-lattice relaxation was examined in the frequency range from 1 kHz to 400 MHz with the aid of a field-cycling NMR relaxometer and an ordinary 400 MHz NMR spectrometer. Three different mobility states of the fluid molecules are distinguished: The adsorbed state at the pore walls, the bulklike liquid phase, and the vapor phase. The adsorbate spin-lattice relaxation rate is dominated by the "reorientation mediated by translational displacements" (RMTD) mechanism taking place at the adsorbate/matrix interface at frequencies low enough to neglect rotational diffusion of the molecules. The experimental data are analyzed in terms of molecular exchange between the different mobility states. Judged from the dependence of the spin-lattice relaxation rates on the filling degree, limits for slow and fast exchange (relative to the RMTD time scale) can be distinguished and identified. It is concluded that water always shows the features of slow exchange irrespective of the investigated pore sizes and filling degrees. This is in contrast to cyclohexane which is subject to slow exchange in micrometer pores, whereas fast exchange occurs in nanoscopic pores. The latter case implies that the vapor phase contributes to molecular dynamics in this case at low filling degrees while it is negligible otherwise.

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

    Treesearch

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

    2017-01-01

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

  13. Predicting the dynamics of local adaptation in invasive species

    USDA-ARS?s Scientific Manuscript database

    An invasive plant species may restrict its spread to only one habitat, or, after some time, may continue to spread into a different, secondary, habitat. The question of whether evolution is required for an invasive species to spread from one habitat to another is currently hotly debated. In order fo...

  14. Transience after disturbance: Obligate species recovery dynamics depend on disturbance duration.

    PubMed

    Singer, Alexander; Johst, Karin

    2017-06-01

    After a disturbance event, population recovery becomes an important species response that drives ecosystem dynamics. Yet, it is unclear how interspecific interactions impact species recovery from a disturbance and which role the disturbance duration (pulse or press) plays. Here, we analytically derive conditions that govern the transient recovery dynamics from disturbance of a host and its obligately dependent partner in a two-species metapopulation model. We find that, after disturbance, species recovery dynamics depend on the species' role (i.e. host or obligately dependent species) as well as the duration of disturbance. Host recovery starts immediately after the disturbance. In contrast, for obligate species, recovery depends on disturbance duration. After press disturbance, which allows dynamics to equilibrate during disturbance, obligate species immediately start to recover. Yet, after pulse disturbance, obligate species continue declining although their hosts have already begun to increase. Effectively, obligate species recovery is delayed until a necessary host threshold occupancy is reached. Obligates' delayed recovery arises solely from interspecific interactions independent of dispersal limitations, which contests previous explanations. Delayed recovery exerts a two-fold negative effect, because populations continue declining to even smaller population sizes and the phase of increased risk from demographic stochastic extinction in small populations is prolonged. We argue that delayed recovery and its determinants -species interactions and disturbance duration - have to be considered in biodiversity management. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Severe population collapses and species extinctions in multihost epidemic dynamics

    NASA Astrophysics Data System (ADS)

    Maslov, Sergei; Sneppen, Kim

    2017-08-01

    Most infectious diseases, including more than half of known human pathogens, are not restricted to just one host, yet much of the mathematical modeling of infections has been limited to a single species. We investigate consequences of a single epidemic propagating in multiple species and compare and contrast it with the endemic steady state of the disease. We use the two-species susceptible-infected-recovered model to calculate the severity of postepidemic collapses in populations of two-host species as a function of their initial population sizes, the times individuals remain infectious, and the matrix of infection rates. We derive the criteria for a very large, extinction-level, population collapse in one or both of the species. The main conclusion of our study is that a single epidemic could drive a species with high mortality rate to local or even global extinction provided that it is coinfected with an abundant species. Such collapse-driven extinctions depend on factors different than those in the endemic steady state of the disease.

  16. Intertypic modular exchanges of genomic segments by homologous recombination at universally conserved segments in human adenovirus species D.

    PubMed

    Gonzalez, Gabriel; Koyanagi, Kanako O; Aoki, Koki; Kitaichi, Nobuyoshi; Ohno, Shigeaki; Kaneko, Hisatoshi; Ishida, Susumu; Watanabe, Hidemi

    2014-08-15

    Human adenovirus species D (HAdV-D), which is composed of clinically and epidemiologically important pathogens worldwide, contains more taxonomic "types" than any other species of the genus Mastadenovirus, although the mechanisms accounting for the high level of diversity remain to be disclosed. Recent studies of known and new types of HAdV-D have indicated that intertypic recombination between distant types contributes to the increasing diversity of the species. However, such findings raise the question as to how homologous recombination events occur between diversified types since homologous recombination is suppressed as nucleotide sequences diverge. In order to address this question, we investigated the distribution of the recombination boundaries in comparison with the landscape of intergenomic sequence conservation assessed according to the synonymous substitution rate (dS). The results revealed that specific genomic segments are conserved between even the most distantly related genomes; we call these segments "universally conserved segments" (UCSs). These findings suggest that UCSs facilitate homologous recombination, resulting in intergenomic segmental exchanges of UCS-flanking genomic regions as recombination modules. With the aid of such a mechanism, the haploid genomes of HAdV-Ds may have been reshuffled, resulting in chimeric genomes out of diversified repertoires in the HAdV-D population analogous to the MHC region reshuffled via crossing over in vertebrates. In addition, some HAdVs with chimeric genomes may have had the opportunity to avoid host immune responses thereby causing epidemics. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Nuclear magnetic resonance spectra for l > 1 spins in dynamically heterogeneous systems with chemical exchange among environments.

    PubMed

    Zhang, H; Bryant, R G

    1995-06-01

    Nuclear magnetic resonance spectra for nuclei with spin l > 1 are considered in cases in which the observed nucleus may sample a rotationally immobilized and an isotropic environment that are coupled by a chemical exchange process. Spectra are simulated for the central (1/2, -1/2) transition for a 3/2 nucleus as a function of the concentrations of the two environments and as a function of the exchange rate between them. It is shown that a crucial feature determining the shape of the observable spectra is the spatial extent or the local order in the immobilized phase. In the case for which all rotationally immobilized sites sampled by the exchanging nucleus are identically oriented but where there is a distribution of these microdomain orientations with respect to the magnetic field direction, a powder pattern for the central transition is observed that carries whatever dynamic information may be derived from it. In the fast exchange limit, the width of the powder pattern scales inversely with the concentration of the isotropic environment as usual. In the intermediate exchange regimes, a complex line shape results that may mask the anisotropic character of the spectrum. In the slow exchange limit, superposition of the spectral contributions results; however, if the isotropic environment concentration is significantly larger than the anisotropic environment concentration, the anisotropic contribution is very difficult to detect because of the dynamic range problem and the possibly large difference in the effective line widths. In the case for which the exchanging nucleus samples a considerable distribution of rotationally immobilized site orientations, the anisotropic character of the spectrum is lost and a super-Lorentzian line shape results. These effects are demonstrated experimentally by 35Cl nuclear magnetic resonance spectra obtained on a lamellar liquid crystal that is modified with the addition of a thiolmercurate to provide a site of large quadrupole

  18. Dynamic relationship between Japanese Yen exchange rates and market anxiety: A new perspective based on MF-DCCA

    NASA Astrophysics Data System (ADS)

    Lu, Xinsheng; Sun, Xinxin; Ge, Jintian

    2017-05-01

    This paper investigates the dynamic relationship between Japanese Yen exchange rates and market anxiety during the period from January 5, 1998 to April 18, 2016. A quantitative technique of multifractal detrended cross-correlation analysis (MF-DCCA) is used to explore the multifractal features of the cross-correlations between USD/JPY, AUD/JPY exchange rates and the market anxiety gauge VIX. The investigation shows that the causal relationship between Japanese Yen exchange rates and VIX are bidirectional in general, and the cross-correlations between the two sets of time series are multifractal. Strong evidence suggests that the cross-correlation exponents tend to exhibit different volatility patterns in response to diverse external shocks such as financial distress and widening in interest rate spread, suggesting that the cross-correlated behavior between Japanese Yen exchange rates and VIX are susceptible to economic uncertainties and risks. In addition, the performances of two market anxiety gauges, the VIX and the TED spread, are compared and the sources of multifractality are also traced. Thus, this paper contributes to the literature by shedding light on the unique driving forces of the Yen exchange rate fluctuations in the international foreign exchange market.

  19. Time-resolved magnetization dynamics in crystalline ferromagnets and exchange-biased systems

    NASA Astrophysics Data System (ADS)

    Engebretson, David Michael

    Time-resolved ferromagnetic resonance (FMR) measurements are performed using a pump-probe technique with a non-optical pump to observe precession and relaxation of the magnetization in epitaxial magnetic thin films at temperatures down to 5 K. Spatial localization achieved through use of an optical probe allows a direct measurement of spin relaxation, reducing the effects of inhomogeneous dephasing relative to probes of larger areas, while the use of low fields allows a study of dynamics throughout the entire magnetization reversal process. The reversal mechanism of FexCo1-x is probed as a function of cubic and uniaxial anisotropy strengths, using FMR as a direct probe of the free energy surface. A coherent rotation model describes the reversal for fields up through 700 Oe, failing only for fields near 105 Oe applied along the GaAs [01 1¯] direction where nucleation of nearly perpendicular domains is observed. Measurements of the Gilbert damping parameter alpha indicate that it is smaller for fields applied along the [01 1¯] direction than for fields along [011] or [010]. Dynamic interactions between local moments and itinerant carriers are examined in the diluted magnetic semiconductor Ga1-xMn xAs. Holes and local moments are found to precess together on timescales greater than 50 ps. Although previous experiments by other groups have observed a change in the magnetization due to introduction of photoexcited carriers, our measurements indicate no dynamical change in magnetization due to additional optically pumped carriers. The Gilbert damping parameter alpha is observed to increase more than twofold as temperature is raised from 20 K to the Curie temperature, although the decay time remains nearly independent of temperature over this range. Exchange-biased Fe/FeF2 is found to exhibit temperature-dependent anisotropy above its Neel temperature (78 K), while the anisotropy of structurally similar Fe/MnF2 remains independent of temperature above TN = 67 K. Dynamic

  20. Determination of mercurial species in fish by inductively coupled plasma mass spectrometry with anion exchange chromatographic separation.

    PubMed

    Chen, Xiaopan; Han, Chao; Cheng, Heyong; Liu, Jinhua; Xu, Zigang; Yin, Xuefeng

    2013-09-24

    This work demonstrated the feasibility of mercury speciation analysis by anion exchange chromatographic separation with inductively coupled plasma mass spectrometry detection. For the first time, by complexing with the mobile phase containing 3-mercapto-1-propanesulfonate into negatively charged complexes, fast separation of inorganic mercury (Hg(2+)), monomethylmercury (MeHg), ethylmercury (EtHg) and phenylmercury (PhHg) was achieved within 5 min on a 12.5-mm strong anion exchange column. The detection limits for Hg(2+), MeHg, EtHg and PhHg were 0.008, 0.024, 0.029 and 0.034 μg L(-1), respectively. The relative standard deviations of peak height and peak area (5.0 μg L(-1) for each Hg species) were all below 3%. The determined contents of Hg(2+), MeHg and total Hg in a certified reference material of fish tissue by the proposed method were in good accordance with the certified values with satisfactory recoveries. The relative errors for determining MeHg and total mercury were -2.4% and -1.2%, respectively, with an acceptable range for spike recoveries of 94-101%. Mercury speciation in 11 fish samples were then analyzed after the pretreated procedure. The mercury contents in all fish samples analyzed were found compliant with the criteria of the National Standards of China.

  1. 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

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

    PubMed

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

    2009-09-01

    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 (V(cmax)) and electron transport (J(max)) - differ between species. This study explored whether a general pattern of changes in V(cmax), J(max), and a standardized soil moisture response accounted for carbon dioxide exchange of deciduous trees throughout the growing season. The model MAESTRA was used to examine V(cmax) and J(max) 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 V(cmax) and J(max) 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. 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 V(cmax) and J(max), and a standardized response to soil moisture was sufficient to parameterize carbon dioxide exchange for large-scale evaluations. Simplification in parameterization of the seasonal pattern of leaf biochemical activity and soil moisture response of deciduous forest species is demonstrated. This

  3. Gas exchange and low temperature resistance in two tropical high mountain tree species from the Venezuelan Andes

    NASA Astrophysics Data System (ADS)

    Cavieres, Lohengrin A.; Rada, Fermín; Azócar, Aura; García-Núñez, Carlos; Cabrera, Hernán M.

    2000-05-01

    Temperature may determine altitudinal tree distribution in different ways: affecting survival through freezing temperatures or by a negative carbon balance produced by lower photosynthetic rates. We studied gas exchange and supercooling capacity in a timberline and a treeline species ( Podocarpus oleifolius and Espeletia neriifolia, respectively) in order to determine if their altitudinal limits are related to carbon balance, freezing temperature damage, or both. Leaf gas exchange, leaf temperature-net photosynthesis curves and leaf temperature at which ice formation occurred were measured at two sites along an altitudinal gradient. Mean CO 2 assimilation rates for E. neriifolia were 3.4 and 1.3 μmol·m -2·s -1, at 2 400 and 3 200 m, respectively. Mean night respiration was 2.2 and 0.9 μmol·m -2·s -1 for this species at 2 400 and 3 200 m, respectively. Mean assimilation rates for P. oleifolius were 3.8 and 2.2 μmol·m -2·s -1 at 2 550 and 3 200 m, respectively. Night respiration was 0.8 μmol·m -2·s -1 for both altitudes. E. neriifolia showed similar optimum temperatures for photosynthesis at both altitudes, while a decrease was observed in P. oleifolius.E. neriifolia and P. oleifolius presented supercooling capacities of -6.5 and -3.0 °C, respectively. For E. neriifolia, freezing resistance mechanisms are sufficient to reach higher altitudes; however, other environmental factors such as cloudiness may be affecting its carbon balance. P. oleifolius does not reach higher elevations because it does not have the freezing resistance mechanisms.

  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. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.

    PubMed

    Chebaro, Yassmine; Dong, Xiao; Laghaei, Rozita; Derreumaux, Philippe; Mousseau, Normand

    2009-01-08

    Current approaches aimed at determining the free energy surface of all-atom medium-size proteins in explicit solvent are slow and are not sufficient to converge to equilibrium properties. To ensure a proper sampling of the configurational space, it is preferable to use reduced representations such as implicit solvent and/or coarse-grained protein models, which are much lighter computationally. Each model must be verified, however, to ensure that it can recover experimental structures and thermodynamics. Here we test the coarse-grained implicit solvent OPEP model with replica exchange molecular dynamics (REMD) on six peptides ranging in length from 10 to 28 residues: two alanine-based peptides, the second beta-hairpin from protein G, the Trp-cage and zinc-finger motif, and a dimer of a coiled coil peptide. We show that REMD-OPEP recovers the proper thermodynamics of the systems studied, with accurate structural description of the beta-hairpin and Trp-cage peptides (within 1-2 A from experiments). The light computational burden of REMD-OPEP, which enables us to generate many hundred nanoseconds at each temperature and fully assess convergence to equilibrium ensemble, opens the door to the determination of the free energy surface of larger proteins and assemblies.

  6. 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.

  7. Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data.

    PubMed

    Gu, Yina; Hansen, Alexandar L; Peng, Yu; Brüschweiler, Rafael

    2016-02-24

    Functional motions of (15)N-labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R1ρ and CPMG-type experiments. CEST also simultaneously reports on site-specific R1 and R2 parameters. It is shown here how CEST-derived R1 and R2 relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a "lean" version of the model-free approach S(2) order parameters can be determined that match those from the standard model-free approach applied to (15)N R1, R2 , and {(1)H}-(15)N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond-to-millisecond timescales.

  8. 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.

  9. 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.

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

    PubMed

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

    2005-08-15

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    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.

  12. Nonconservative kinetic exchange model of opinion dynamics with randomness and bounded confidence.

    PubMed

    Sen, Parongama

    2012-07-01

    The concept of a bounded confidence level is incorporated in a nonconservative kinetic exchange model of opinion dynamics model where opinions have continuous values ∈[-1,1]. The characteristics of the unrestricted model, which has one parameter λ representing conviction, undergo drastic changes with the introduction of bounded confidence parametrized by δ. Three distinct regions are identified in the phase diagram in the δ-λ plane and the evidences of a first order phase transition for δ ≥ 0.3 are presented. A neutral state with all opinions equal to zero occurs for λ ≤ λ(c1) ≃ 2/3, independent of δ, while for λ(c(1)) ≤ λ ≤ λ(c(2))(δ), an ordered region is seen to exist where opinions of only one sign prevail. At λ(c(2))(δ), a transition to a disordered state is observed, where individual opinions of both signs coexist and move closer to the extreme values (±1) as λ is increased. For confidence level δ < 0.3, the ordered phase exists for a narrow range of λ only. The line δ = 0 is apparently a line of discontinuity, and this limit is discussed in some detail.

  13. Replica exchange molecular dynamics study of the truncated amyloid beta (11-40) trimer in solution.

    PubMed

    Ngo, Son Tung; Hung, Huynh Minh; Truong, Duc Toan; Nguyen, Minh Tho

    2017-01-18

    Amyloid beta (Aβ) oligomers are neurotoxic compounds that destroy the brain of Alzheimer's disease patients. Recent studies indicated that the trimer is one of the most cytotoxic forms of low molecular weight Aβ oligomers. As there was limited information about the structure of the Aβ trimer, either by experiment or by computation, we determined in this work the structure of the 3Aβ11-40 oligomer for the first time using the temperature replica exchange molecular dynamics simulations in the presence of an explicit solvent. More than 20.0 μs of MD simulations were performed. The probability of the β-content and random coil structure of the solvated trimer amounts to 42 ± 6 and 49 ± 7% which is in good agreement with experiments. Intermolecular interactions in central hydrophobic cores play a key role in stabilizing the oligomer. Intermolecular polar contacts between D23 and residues 24-29 replace the salt bridge D23-K28 to secure the loop region. The hydrophilic region of the N-terminus is maintained by the intermolecular polar crossing contacts H13A-Q15B and H13B-Q15C. The difference in the free energy of binding between the constituting monomers and the others amounts to -36 ± 8 kcal mol(-1). The collision cross section of the representative structures of the trimer was computed to be 1330 ± 47 Å(2), which is in good agreement with previous experiments.

  14. 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.

  15. A whole-plant chamber system for parallel gas exchange measurements of Arabidopsis and other herbaceous species.

    PubMed

    Kölling, Katharina; George, Gavin M; Künzli, Roland; Flütsch, Patrick; Zeeman, Samuel C

    2015-01-01

    Photosynthetic assimilation of carbon is a defining feature of the plant kingdom. The fixation of large amounts of carbon dioxide supports the synthesis of carbohydrates, which make up the bulk of plant biomass. Exact measurements of carbon assimilation rates are therefore crucial due to their impact on the plants metabolism, growth and reproductive success. Commercially available single-leaf cuvettes allow the detailed analysis of many photosynthetic parameters, including gas exchange, of a selected leaf area. However, these cuvettes can be difficult to use with small herbaceous plants such as Arabidopsis thaliana or plants having delicate or textured leaves. Furthermore, data from single leaves can be difficult to scale-up for a plant shoot with a complex architecture and tissues in different physiological states. Therefore, we constructed a versatile system-EGES-1-to simultaneously measure gas exchange in the whole shoots of multiple individual plants. Our system was designed to be able record data continuously over several days. The EGES-1 system yielded comparable measurements for eight plants for up to 6 days in stable, physiologically realistic conditions. The chambers seals have negligible permeability to carbon dioxide and the system is designed so as to detect any bulk-flow air leaks. We show that the system can be used to monitor plant responses to changing environmental conditions, such as changes in illumination or stress treatments, and to compare plants with phenotypically severe mutations. By incorporating interchangeable lids, the system could be used to measure photosynthetic gas exchange in several genera such as Arabidopsis, Nicotiana, Pisum, Lotus and Mesembryanthemum. EGES-1 can be introduced into a variety of growth facilities and measure gas exchange in the shoots diverse plant species grown in different growth media. It is ideal for comparing photosynthetic carbon assimilation of wild-type and mutant plants and/or plants undergoing

  16. A dynamic species modeling approach to assess climate change impacts on California tree species

    NASA Astrophysics Data System (ADS)

    Ries, L. P.; Hannah, L.; Thorne, J.; Seo, C.; Davis, F.

    2007-12-01

    Global climate change during the 21st century is anticipated to have consequences on potential niche viability for woody plant species. Previous research on modeling bioclimatic envelopes has allowed us to predict where to find species assemblages under future climate scenarios and hence predict loss or gain of specific habitats. However, species may not identically respond to climate change. This could result in species disassembling and disagreement between predicted potential niches and realized niches. Therefore, it is critical to examine potential niche shifts at the species level. We used a spatially explicit demographic model to predict shifts in tree species of the northern Sierra Nevada mountains in the context of competition with neighboring plant functional types as well as disturbance (i.e. fire) under various climate change scenarios. Additionally, we incorporated a dispersal model to account for intermediary dispersal strategies. In particular, we were interested in modeling Pinus species found in the "checkerboard" region of the northern Sierra Nevada. These populations are of novel interest due to their disparate management strategies (private vs. public landownership). Our findings have important implications for the assessment of the impact of climate change on these high elevation Montane species.

  17. Species coexistence in a neutral dynamics with environmental noise.

    PubMed

    Hidalgo, Jorge; Suweis, Samir; Maritan, Amos

    2017-01-21

    Environmental fluctuations have important consequences in the organization of ecological communities, and understanding how such a variability influences the biodiversity of an ecosystem is a major question in ecology. In this paper, we analyze the case of two species competing for the resources within the framework of the neutral theory in the presence of environmental noise, devoting special attention on how such a variability modulates species fitness. The environment is dichotomous and stochastically alternates between periods favoring one of the species while disfavoring the other one, preserving neutrality on the long term. We study two different scenarios: in the first one species fitness varies linearly with the environment, and in the second one the effective fitness is re-scaled by the total fitness of the individuals competing for the same resource. We find that, in the former case environmental fluctuations always reduce the time of species coexistence, whereas such a time can be enhanced or reduced in the latter case, depending on the correlation time of the environment. This phenomenon can be understood as a direct consequence of Chesson's storage effect.

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

    PubMed

    Gudmundson, Sara; Eklöf, Anna; Wennergren, Uno

    2015-08-07

    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. © 2015 The Author(s).

  19. Replica exchange molecular dynamics simulations provide insight into substrate recognition by small heat shock proteins.

    PubMed

    Patel, Sunita; Vierling, Elizabeth; Tama, Florence

    2014-06-17

    The small heat shock proteins (sHSPs) are a virtually ubiquitous and diverse group of molecular chaperones that can bind and protect unfolding proteins from irreversible aggregation. It has been suggested that intrinsic disorder of the N-terminal arm (NTA) of sHSPs is important for substrate recognition. To investigate conformations of the NTA that could recognize substrates we performed replica exchange molecular dynamics simulations. Behavior at normal and stress temperatures of the dimeric building blocks of dodecameric HSPs from wheat (Ta16.9) and pea (Ps18.1) were compared because they display high sequence similarity, but Ps18.1 is more efficient in binding specific substrates. In our simulations, the NTAs of the dimer are flexible and dynamic; however, rather than exhibiting highly extended conformations they retain considerable α-helical character and contacts with the conserved α-crystallin domain (ACD). Network analysis and clustering methods reveal that there are two major conformational forms designated either "open" or "closed" based on the relative position of the two NTAs and their hydrophobic solvent accessible surface area. The equilibrium constant for the closed to open transition is significantly different for Ta16.9 and Ps18.1, with the latter showing more open conformations at elevated temperature correlated with its more effective chaperone activity. In addition, the Ps18.1 NTAs have more hydrophobic solvent accessible surface than those of Ta16.9. NTA hydrophobic patches are comparable in size to the area buried in many protein-protein interactions, which would enable sHSPs to bind early unfolding intermediates. Reduced interactions of the Ps18.1 NTAs with each other and with the ACD contribute to the differences in dynamics and hydrophobic surface area of the two sHSPs. These data support a major role for the conformational equilibrium of the NTA in substrate binding and indicate features of the NTA that contribute to sHSP chaperone

  20. Environmental and canopy control of leaf level gas exchange of two evergreen tree species in a semiarid rangeland.

    NASA Astrophysics Data System (ADS)

    Bendevis, M. A.; Owens, M.; Heilman, J.; McInnes, K.

    2006-05-01

    Ashe juniper (Juniperus asheii) and plateau live oak (Quercus virginiana var fusiformis) have encroached into the historical grasslands of the Edwards Plateau of central Texas. The increased tree density may impact local water budgets because the area is the recharge zone for the Edwards Aquifer, the drinking water source for large municipalities like Austin and San Antonio. On the other hand, the trees have the capability of sequestering a greater amount of carbon than the historic grasslands. This study is a part of a larger NIGEC project examining the energy fluxes of the Oak-Juniper ecosystem. Four trees of each species were permanently marked and sampled with a leaf-level gas exchange system every 5 to 6 weeks throughout an entire year. Each tree was sampled on the northwest and southeast sides of the canopy, and at each location both sun-lit and shaded leaves were sampled. Averaged (± SE) over the entire year, live oak had significantly greater carbon assimilation rates than Ashe juniper (13.12 ± 0.6 vs. 6.47 ± 0.4 µmol CO2/m2/s, respectively). Oak trees exhibited a greater seasonal flux in carbon assimilation than juniper. Carbon assimilation was least in October 2005 for both species (2.47 and 6.46 µmol CO2/m2/s for juniper and oak, respectively) and greatest in November 2004 for juniper (13.02 µmol CO2/m2/s) and in April 2005 for oak (21.64 µmol CO2/m2/s). Sun-lit leaves also had a consistently greater assimilation rate (P<0.01) Transpirational water loss followed the same pattern with seasonal differences (P<0.0001) and canopy level (P<0.01) as critical factors. Xylem water potentials varied significantly by tree species and the month of observation. Juniper trees were initially less water stressed than the oak trees, but when precipitation was low near the end of the observation period the juniper trees showed a much larger increase in water stress. This was reflected in the higher transpiration and photosynthetic rates observed for oak trees

  1. 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.

  2. Methane exchange at the peatland forest floor - automatic chamber system exposes the dynamics of small fluxes

    NASA Astrophysics Data System (ADS)

    Korkiakoski, Mika; Tuovinen, Juha-Pekka; Aurela, Mika; Koskinen, Markku; Minkkinen, Kari; Ojanen, Paavo; Penttilä, Timo; Rainne, Juuso; Laurila, Tuomas; Lohila, Annalea

    2017-04-01

    We measured methane (CH4) exchange rates with automatic chambers at the forest floor of a nutrient-rich drained peatland in 2011-2013. The fen, located in southern Finland, was drained for forestry in 1969 and the tree stand is now a mixture of Scots pine, Norway spruce, and pubescent birch. Our measurement system consisted of six transparent chambers and stainless steel frames, positioned on a number of different field and moss layer compositions. Gas concentrations were measured with an online cavity ring-down spectroscopy gas analyzer. Fluxes were calculated with both linear and exponential regression. The use of linear regression resulted in systematically smaller CH4 fluxes by 10-45 % as compared to exponential regression. However, the use of exponential regression with small fluxes ( < 2.5 µg CH4 m-2 h-1) typically resulted in anomalously large absolute fluxes and high hour-to-hour deviations. Therefore, we recommend that fluxes are initially calculated with linear regression to determine the threshold for low fluxes and that higher fluxes are then recalculated using exponential regression. The exponential flux was clearly affected by the length of the fitting period when this period was < 190 s, but stabilized with longer periods. Thus, we also recommend the use of a fitting period of several minutes to stabilize the results and decrease the flux detection limit. There were clear seasonal dynamics in the CH4 flux: the forest floor acted as a CH4 sink particularly from early summer until the end of the year, while in late winter the flux was very small and fluctuated around zero. However, the magnitude of fluxes was relatively small throughout the year, ranging mainly from -130 to +100 µg CH4 m-2 h-1. CH4 emission peaks were observed occasionally, mostly in summer during heavy rainfall events. Diurnal variation, showing a lower CH4 uptake rate during the daytime, was observed in all of the chambers, mainly in the summer and late spring, particularly

  3. Solution dynamics of the trp repressor: a study of amide proton exchange by T1 relaxation.

    PubMed

    Gryk, M R; Finucane, M D; Zheng, Z; Jardetzky, O

    1995-03-10

    The amide proton exchange rates of Escherichia coli trp repressor have been measured through their effects on the longitudinal relaxation rates of the amide protons. Three types of exchange regimes have been observed: (1) slow exchange (on a minute/hour time-scale), measurable by isotope exchange, but not by relaxation techniques in the core of the molecule; (2) relatively rapid exchange, with the rates on a T1 relaxation time-scale (seconds) in the DNA-binding region and (3) very fast exchange at the N and C termini. The results have been analyzed in terms of the two-site exchange model originally proposed by Linderstrøm-Lang, and of a three-site extension of the model. The values of the intrinsic exchange rates calculated using the two-state model agree with the values expected from the studies of Englander and co-workers for the very fast case of the chain terminals, but disagree with the literature values by two orders of magnitude in the intermediate case found in the DNA-binding region. The implication of these findings is that the "open" state of the two-state model in the DNA-binding region is not completely open and has an intrinsic exchange rate different from that of a random coil peptide. Alternatively, if the literature values of the intrinsic exchange rates are assumed to apply to the open states in all parts of the repressor molecule, two "closed" helical states have to be postulated, in slow exchange with each other, with only one of them in rapid exchange with the open state and hence with the solvent. Kinetically, the two models are indistinguishable.

  4. 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.

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

    PubMed

    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

    2015-04-02

    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 - 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.

  6. Timetree of Aselloidea reveals species diversification dynamics in groundwater.

    PubMed

    Morvan, Claire; Malard, Florian; Paradis, Emmanuel; Lefébure, Tristan; Konecny-Dupré, Lara; Douady, Christophe J

    2013-07-01

    A key challenge for biologists is to document and explain global patterns of diversification in a wide range of environments. Here, we explore patterns of continental-scale diversification in a groundwater species-rich clade, the superfamily Aselloidea (Pancrustacea: Isopoda). Our analyses supported a constant diversification rate during most of the course of Aselloidea evolution, until 4-15 Ma when diversification rates started to decrease. This constant accumulation of lineages challenges the view that groundwater species diversification in temperate regions might have been primarily driven by major changes in physical environment leading to the extinction of surface populations and subsequent synchronous isolation of multiple groundwater populations. Rather than acting synchronously over broad geographic regions, factors causing extinction of surface populations and subsequent reproductive isolation of groundwater populations may act in a local and asynchronous manner, thereby resulting in a constant speciation rate over time. Our phylogeny also revealed several cases of parapatric distributions among closely related surface-water and groundwater species suggesting that species diversification could also arise from a process of disruptive selection along the surface-subterranean environmental gradient. Our results call for re-evaluating the spatial scale and timing of factors causing diversification events in groundwater.

  7. Dynamic variation in sapwood specific conductivity in six woody species

    Treesearch

    Jean-Christophe Domec; Frederick C. Meinzer; Barbara Lachenbruch; Johann Housset

    2008-01-01

    Our goals were to quantify how non-embolism inducing pressure gradients influence trunk sapwood specific conductivity (ks) and to compare the impacts of constant and varying pressure gradients on ks with KCl and H20 as the perfusion solutions. We studied six woody species (three conifers and three...

  8. Static and dynamic quenching of luminescent species in polymer media.

    PubMed

    Hartmann, P; Leiner, M J; Lippitsch, M E

    1994-12-01

    A method developed for quantitative determination of static and dynamic contributions to luminescence quenching is applied to Ru(II) complexes in polymer matrices (silica gel and polystyrene), quenched by oxygen. This method is based on both intensity and lifetime quenching experiments. The curvature of intensity Stern-Volmer plots is related to the results.

  9. Elucidation of molecular dynamics of invasive species of rice

    USDA-ARS?s Scientific Manuscript database

    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...

  10. An enhanced vector-free allele exchange (VFAE) mutagenesis protocol for genome editing in a wide range of bacterial species.

    PubMed

    Gomaa, Ahmed E; Zhang, Chen; Yang, Zhimin; Shang, Liguo; Jiang, Shijie; Deng, Zhiping; Zhan, Yuhua; Lu, Wei; Lin, Min; Yan, Yongliang

    2017-12-01

    Vector-free allele exchange (VFAE) is a newly developed protocol for genome editing in Pseudomonas species. Although several parameters have been determined to optimize the procedures for obtaining a stable and high-frequency mutation, numerous false-positive clones still appear on the plate, which increases the difficulty of finding the desired mutants. It has also not been established whether this protocol can be used for genome editing in other bacterial species. In the current study, the protocol was modified to dramatically decrease the occurrence of false-positive colonies using Pseudomonas stutzeri A1501 as a model strain. This improvement was reached by increasing the occurrence of circular-DNA cassettes of the correct size. Furthermore, the enhanced protocol was used to construct mutants in both the gram-negative Escherichia coli BL21 and gram-positive Bacillus subtilis 168 strains. The protocol works well in both strains, yielding ideal results with a low percentage of false-positive colonies. In summary, the enhanced VFAE mutagenesis protocol is a potential tool for use in bacterial genome editing.

  11. 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

    2012-04-06

    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.

  12. Canopy CO2 exchange of two neotropical tree species exhibiting constitutive and facultative CAM photosynthesis, Clusia rosea and Clusia cylindrica

    PubMed Central

    Winter, Klaus; Garcia, Milton; Holtum, Joseph A. M.

    2009-01-01

    Photon flux density (PFD) and water availability, the daily and seasonal factors that vary most in tropical environments, were examined to see how they influenced expression of crassulacean acid metabolism (CAM) in 3-year-old Clusia shrubs native to Panama. Instead of the commonly used single-leaf approach, diel CO2 exchange was measured for whole individual canopies of plants in large soil containers inside a naturally illuminated 8.8 m3 chamber. In well-watered C. rosea, a mainly constitutive CAM species, nocturnally fixed CO2 contributed about 50% to 24 h carbon gain on sunny days but the contribution decreased to zero following overcast days. Nonetheless, CO2 fixation in the light responded in such a way that 24 h carbon gain was largely conserved across the range of daily PFDs. The response of C. rosea to drought was similarly buffered. A facultative component of CAM expression led to reversible increases in nocturnal carbon gain that offset drought-induced reductions of CO2 fixation in the light. Clusia cylindrica was a C3 plant when well-watered but exhibited CAM when subjected to water stress. The induction of CAM was fully reversible upon rewatering. C. cylindrica joins C. pratensis as the most unambiguous facultative CAM species reported in the genus Clusia. PMID:19487388

  13. 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.

  14. Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

    PubMed

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

    2009-03-10

    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.

  15. 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

  16. 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.

  17. Can gas exchange dynamics predict non-structural carbohydrate use under drought stress?

    NASA Astrophysics Data System (ADS)

    Kannenberg, S.; Phillips, R.

    2016-12-01

    A recent conceptual framework for understanding tree drought responses characterizes species along a continuum from isohydry to anisohydry, with theory predicting that isohydric and anisohydric trees should display different carbon (C) allocation patterns under drought conditions. We tested the hypothesis that the trade-offs inherent in the isohydry-anisohydry framework (i.e., C starvation vs. hydraulic failure) necessitate different allocation patterns to non-structural carbohydrates (NSCs), growth, and respiration. Specifically, we hypothesized that isohydric trees would decrease NSC stores and growth in the face of reduced incoming photoassimilate, whereas anisohydric trees would maintain assimilation, growth, and NSC pools due to decreased demand for stored metabolic C and enhanced osmoregulatory needs. To test this, we subjected saplings of Liriodendron tulipifera (an isohydric tree) and Quercus alba (an anisohydric tree) to a six week drought in the greenhouse, and measured assimilation, leaf water potential (midday and predawn), growth, leaf dark respiration and NSCs (both sugars and starch in aboveground and belowground tissues) in control and droughted plants. Overall, we confirmed that the isohydric and anisohydric species used NSCs differently during drought. In most tissues, both species had similar responses of NSCs to drought: starch NSCs were maintained or decreased while sugar NSCs tended to increase. Stem NSCs were a notable exception, as L. tulipifera decreased total NSC to almost zero while NSCs in Q. alba remained constant. This depletion of stem NSC in L. tulipifera was offset by increases in other tissues, however, resulting in no net change to total NSC during the drought. In contrast, Q. alba increased total NSC. Interestingly, Q. alba also decreased assimilation and growth, indicating a potential trade-off between NSC and biomass allocation. Our results show that NSCs in different tissues may have contrasting uses as storage or

  18. Ab initio molecular dynamics investigation of structural, dynamic and spectroscopic aspects of Se(vi) species in the aqueous environment.

    PubMed

    Borah, Sangkha; Padma Kumar, P

    2016-06-07

    Microscopic investigation of solvation of selenic acid (H2SeO4) in the aqueous environment has been carried out using the Car-Parrinello molecular dynamics simulation technique. The species deprotonates to HSeO4(-) in a few picoseconds owing to its low pKa1 value of -3.0. A dynamic equilibrium between HSeO4(-) and SeO4(2-), is observed in qualitative agreement with the reported pKa2 value of 1.70. The governing deprotonation mechanism and the structural and dynamic evolutions of the system, particularly the nature of hydrogen bonding, their strengths and lifetimes are investigated comprehensively. A comparison of the vibrational spectra of the species recorded in the gas phase and in the aqueous environment provides further insights on the nature of the interaction between the solute species and water. The results are in good agreement with the available experimental data and other recent computational studies.

  19. 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

  20. Dynamics of stem water uptake among isohydric and anisohydric species experiencing a severe drought

    Treesearch

    Koong Yi; Danilo Dragoni; Richard P. Phillips; Daniel Tyler Roman; Kimberly A. Novick

    2017-01-01

    Predicting the impact of drought on forest ecosystem processes requires an understanding of trees' species-specific responses to drought, especially in the Eastern USA, where species composition is highly dynamic due to historical changes in land use and fire regime. Here, we adapted a framework that classifies trees' water-use strategy along the spectrum of...

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

    Treesearch

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

    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 species (Barred Owl,...

  2. 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.

  3. Orientational ordering and dynamics of the hydrate and exchangeable hydrogen atoms in crystalline crambin.

    PubMed

    Usha, M G; Wittebort, R J

    1989-08-20

    Deuterium nuclear magnetic resonance studies of crambin crystals grown from deuterated solvent (2H2O/CH3CH2O2H or H2O/C2H3CH2OH) are reported. The extent to which the hydrate and exchangeable hydrogen atoms are dynamically disordered are then determined from the size of the residual deuterium quadrupole couplings, qcc. Rapid molecular reorientation (tau c-1 greater than 10(5) s-1) reduces the magnitude of the quadrupole coupling from its static value (216 kHz for solid water). We find that the room temperature spectrum of crambin is dominated by two features: a sharp line with very small residual quadrupolar coupling less than 3 kHz, and a broad pattern with a quadrupolar coupling in the range 185 to 195 kHz. The former is indicative of very nearly isotropically reorienting deuterons, whereas the latter is somewhat narrower than that observed for the amide deuterons of poly-gamma-benzyl-L-glutamate and thus indicative of deuterons that are almost but not completely stationary. By considering the nuclear magnetic resonance spectrum intensities along with the amino acid sequence, X-ray structure and the manner in which quadrupole couplings are reduced by dynamics, we conclude that the nuclear magnetic resonance signal from most of the water molecules of hydration are contained in the sharp line, i.e. reorient nearly isotropically in the crystalline protein. Unlike bulk water, which freezes abruptly in the manner of a phase transition, the water of hydration in crambin has a broad freezing range from 180 to 250K, as evidenced by the decreasing intensity of the sharp line that disappears at 180K. At temperatures between 150 and 200K, a typical hydrate molecule reorients at a rate comparable to the quadrupole coupling, 10(4) s-1 to 10(5) s-1, a process that occurs in hexagonal ice in the range of 240 to 270K. At 140K, the hydrate is stationary, tau c-1 less than 10(3) s-1. Studies of the protein crystallized from solvent deuterated only at the non-exchangeable methyl

  4. Inflationary preheating dynamics with two-species condensates

    NASA Astrophysics Data System (ADS)

    Zache, T. V.; Kasper, V.; Berges, J.

    2017-06-01

    We investigate both analytically and numerically a two-component ultracold atom system in one spatial dimension. The model features a tachyonic instability, which incorporates characteristic aspects of the mechanisms for particle production in early universe inflaton models. We establish a direct correspondence between measurable macroscopic growth rates for occupation numbers of the ultracold Bose gas and the underlying microscopic processes in terms of Feynman loop diagrams. We analyze several existing ultracold atom setups featuring dynamical instabilities and propose optimized protocols for their experimental realization. We demonstrate that relevant dynamical processes can be enhanced using a seeding procedure for unstable modes and clarify the role of initial quantum fluctuations and the generation of a nonlinear secondary stage for the amplification of modes.

  5. Dynamics of Electronically Excited Species in Gaseous and Condensed Phase

    DTIC Science & Technology

    1989-12-01

    1987). 3 D. McQuarrie , " Statistical Mechanics " (Harper and Row, 1976). 4. C. Chabalowsky, J. 0. Jensen, D. R. Yariony, and B. H. Lengsfield Ill, J. Chem...initio, lattice dynamical, and statistical mechanical approaches, helium has long attracted many researchers because it constitutes a fundamental system...modelling MTGLE parameters for realistic quenching studies (e.g., in He-He* matrix studies). This involves certain approximate statistical mechanical

  6. Boundary layers at a dynamic interface: Air-sea exchange of heat and mass

    NASA Astrophysics Data System (ADS)

    Szeri, Andrew J.

    2017-04-01

    Exchange of mass or heat across a turbulent liquid-gas interface is a problem of critical interest, especially in air-sea transfer of natural and anthropogenic gases involved in the study of climate. The goal in this research area is to determine the gas flux from air to sea or vice versa. For sparingly soluble nonreactive gases, this is controlled by liquid phase turbulent velocity fluctuations that act on the thin species concentration boundary layer on the liquid side of the interface. If the fluctuations in surface-normal velocity w' and gas concentration c' are known, then it is possible to determine the turbulent contribution to the gas flux. However, there is no suitable fundamental direct approach in the general case where neither w' nor c' can be easily measured. A new approach is presented to deduce key aspects about the near-surface turbulent motions from measurements that can be taken by an infrared (IR) camera. An equation is derived with inputs being the surface temperature and heat flux, and a solution method developed for the surface-normal strain experienced over time by boundary layers at the interface. Because the thermal and concentration boundary layers experience the same near-surface fluid motions, the solution for the surface-normal strain determines the gas flux or gas transfer velocity. Examples illustrate the approach in the cases of complete surface renewal, partial surface renewal, and insolation. The prospects for use of the approach in flows characterized by sheared interfaces or rapid boundary layer straining are explored.

  7. Prion versus doppel protein misfolding: new insights from replica-exchange molecular dynamics simulations.

    PubMed

    Baillod, Pascal; Garrec, Julian; Tavernelli, Ivano; Rothlisberger, Ursula

    2013-11-26

    The doppel (Dpl) and prion (PrP) proteins share a very similar fold (three helices and two short β-strands), while they differ significantly in sequence (only 25% homologous) and in disease-related β-rich conformations that occur for PrP only. In a previous study [Baillod, P., et al. (2012) Biochemistry 51, 9891-9899], we investigated the misfolding and rare, β-rich folds of monomeric PrP with replica-exchange molecular dynamics (REMD) simulations. In the work presented here, we perform analogous simulations for Dpl with the aim of comparing the two systems and characterizing possible specificities of PrP for misfolding and amyloidogenesis. Our extensive simulations, which allow us to overcome high energy barriers via the REMD approach, sample several β-rich folds, some of which are stable at room temperature, for both proteins. Per residue secondary structure propensities reveal that novel β-sheets of Dpl and PrP are formed by amino acids belonging to the helices that are the least stable in the respective native structure, H1 for Dpl and H2 and H3 for PrP, in agreement with experimental data. Using a specific clustering method that allows discrimination against different β-strand arrangements, seven β-rich folds could be characterized for PrP and five for Dpl, which are clearly distinct and share only one single similar fold. A major difference between the two proteins is found in the free energy barriers leading to misfolded structures: they are approximately 3 times higher for Dpl than for PrP. This suggests that the difference in amyloidogenic behavior between PrP and Dpl might be due to kinetic reasons.

  8. Structural Insights of Glucan Phosphatase Dynamics using Amide Hydrogen/Deuterium Exchange Mass Spectrometry

    PubMed Central

    Hsu, Simon; Kim, Youngjun; Li, Sheng; Durrant, Eric S.; Pace, Rachel M.; Woods, Virgil L.; Gentry, Matthew S.

    2009-01-01

    Laforin and Starch Excess 4 (SEX4) are founding members of a class of phosphatases that dephosphorylate phosphoglucans. Each protein contains a carbohydrate binding module (CBM) and a dual specificity phosphatase (DSP) domain. The gene encoding laforin is mutated in a fatal neurodegenerative disease called Lafora disease (LD). In the absence of laforin function, insoluble glucans accumulate that are hyperphosphorylated and exhibit sparse branching. It is hypothesized that these accumulations trigger the neurodegeneration and premature death of LD patients. We recently demonstrated that laforin removes phosphate from phosphoglucans and hypothesized that this function inhibits insoluble glucan accumulation. Loss of SEX4 function in plants yields a similar cellular phenotype; cells accumulate an excess amount of insoluble, hyperphosphorylated glucans. While multiple groups have shown that these phosphatases dephosphorylate phosphoglucans, there is no structure of a glucan phosphatase and little is known about the mechanism whereby they perform this action. We utilized hydrogen-deuterium exchange mass spectrometry (DXMS) and structural modeling to probe the conformational and structural dynamics of the glucan phosphatase SEX4. We found that the enzyme does not undergo a global conformational change upon glucan binding, but instead undergoes minimal rearrangement upon binding. The CBM undergoes increased protection from deuteration when bound to glucans, confirming its role in glucan binding. More interestingly, we identified structural components of the DSP that also undergo increased protection from deuteration upon glucan addition. To determine the position of these regions, we generated a homology model of the SEX4 DSP. The homology model shows that all of these regions are adjacent the DSP active site. Therefore, our results suggest that these regions of the DSP participate in presenting the phosphoglucan to the active site and provide the first structural analysis

  9. Dynamic Structural Changes During Complement C3 Activation Analyzed by Hydrogen/Deuterium Exchange Mass Spectrometry

    PubMed Central

    Schuster, Michael C.; Ricklin, Daniel; Papp, Krisztián; Molnar, Kathleen S.; Coales, Stephen J.; Hamuro, Yoshitomo; Sfyroera, Georgia; Chen, Hui; Winters, Michael S.; Lambris, John D.

    2008-01-01

    Proteolytic cleavage of component C3 to C3b is a central step in the activation of complement. Whereas C3 is largely biologically inactive, C3b is directly involved in various complement activities. While the recently described crystal structures of C3 and C3b provide a molecular basis of complement activation, they do not reflect the dynamic changes that occur in solution. In addition, the available C3b structures diverge in some important aspects. Here we have utilized hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) to investigate relative changes in the solution-phase structures of C3 and C3b. By combining two forms of mass spectrometry we could maximize the primary sequence coverage of C3b and demonstrate the feasibility of this method for large plasma proteins. While the majority of the 82 peptides that could be followed over time showed only minor alterations in HDX, we observed clear changes in solvent accessibility for 16 peptides, primarily in the α-chain (α’NT, MG6-8, CUB, TED, C345C domains). Most of these peptides could be directly linked to the structural transitions visible in the crystal structures and revealed additional information about the probability of the structural variants of C3b. In addition, a discontinuous cluster of seven peptides in the MG3, MG6, LNK and α’NT domains showed a decreased accessibility after activation to C3b. Although no gross conformational changes are detected in the crystal structure, this area may reflect a structurally flexible region in solution that contributes to C3 activation and function. PMID:18456336

  10. 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

  11. 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

  12. Influence of intergranular exchange coupling on the magnetization dynamics of CoCrPt:SiO{sub 2} granular media

    SciTech Connect

    Brandt, R.; Schmidt, H.; Tibus, S.; Springer, F.; Fassbender, J.; Rohrmann, H.; Albrecht, M.

    2012-08-01

    We investigate the effect of Co{sup +} irradiation on the magnetization dynamics of CoCrPt:SiO{sub 2} granular media. Increasing irradiation levels reduce the saturation magnetization and effective anisotropy, which decrease the intrinsic magnetization precession frequency. Furthermore, increasing intergranular exchange coupling results in a qualitative change in the behavior of the magnetic material from a collection of individual grains to a homogeneous thin film, as evidenced in both the switching behavior and dynamics. The frequency change cannot be explained by single crystal macrospin modeling, and can only be reproduced by the inclusion of the dipolar effects and anisotropy distribution inherent in a granular medium.

  13. 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

  14. Replica-exchange molecular dynamics simulation of basic fibroblast growth factor adsorption on hydroxyapatite.

    PubMed

    Liao, Chenyi; Zhou, Jian

    2014-06-05

    The adsorption of basic fibroblast growth factor (bFGF) on the hydroxyapatite (001) surface was investigated by a combination of replica-exchange molecular dynamics (REMD) and conventional molecular dynamics (CMD) methods. In CMD, the protein cannot readily cross the surface water layer, whereas in REMD, the protein can cross the adsorption barrier from the surface water layer and go through weak, medium, then strong adsorption states with three energetically preferred configurations: heparin-binding-up (HP-up), heparin-binding-middle (HP-middle), and heparin-binding-down (HP-down). The HP-middle orientation, with the strongest adsorption energy (-1149 ± 40 kJ·mol(-1)), has the largest adsorption population (52.1-52.6%) and exhibits the largest conformational charge (RMSD of 0.26 ± 0.01 nm) among the three orientations. The HP-down and HP-up orientations, with smaller adsorption energies of -1022 ± 55 and -894 ± 70 kJ·mol(-1), respectively, have smaller adsorption populations of 27.4-27.7% and 19.7-20.5% and present smaller RMSD values of 0.21 ± 0.01 and 0.19 ± 0.01 nm, respectively. The convergent distribution indicates that nearly half of the population (in the HP-middle orientation) will support both FGF/FGFR and DGR-integrin signaling and another half (in the HP-up and HP-down orientations) will support DGR-integrin signaling. The major population (~80%) has the protein dipole directed outward. In the strong adsorption state, there are usually 2 to 3 basic residues that form the anchoring interactions of 210-332 kJ·mol(-1) per residue or that are accompanied by an acidic residue with an adsorption energy of ~207 kJ·mol(-1). Together, the major bound residues form a triangle or a quadrilateral on the surface and stabilize the adsorption geometrically, which indicates topologic matching between the protein and HAP surfaces.

  15. Stochastic population dynamics and life-history variation in marine fish species.

    PubMed

    Bjørkvoll, Eirin; Grøtan, Vidar; Aanes, Sondre; Sæther, Bernt-Erik; Engen, Steinar; Aanes, Ronny

    2012-09-01

    We examined whether differences in life-history characteristics can explain interspecific variation in stochastic population dynamics in nine marine fish species living in the Barents Sea system. After observation errors in population estimates were accounted for, temporal variability in natural mortality rate, annual recruitment, and population growth rate was negatively related to generation time. Mean natural mortality rate, annual recruitment, and population growth rate were lower in long-lived species than in short-lived species. Thus, important species-specific characteristics of the population dynamics were related to the species position along the slow-fast continuum of life-history variation. These relationships were further associated with interspecific differences in ecology: species at the fast end were mainly pelagic, with short generation times and high natural mortality, annual recruitment, and population growth rates, and also showed high temporal variability in those demographic traits. In contrast, species at the slow end were long-lived, deepwater species with low rates and reduced temporal variability in the same demographic traits. These interspecific relationships show that the life-history characteristics of a species can predict basic features of interspecific variation in population dynamical characteristics of marine fish, which should have implications for the choice of harvest strategy to facilitate sustainable yields.

  16. Determination of inorganic arsenic species in natural waters--benefits of separation and preconcentration on ion exchange and hybrid resins.

    PubMed

    Ben Issa, Nureddin; Rajaković-Ognjanović, Vladana N; Jovanović, Branislava M; Rajaković, Ljubinka V

    2010-07-19

    A simple method for the separation and determination of inorganic arsenic (iAs) species in natural and drinking water was developed. Procedures for sample preparation, separation of As(III) and As(V) species and preconcentration of the total iAs on fixed bed columns were defined. Two resins, a strong base anion exchange (SBAE) resin and a hybrid (HY) resin were utilized. The inductively-coupled plasma-mass spectrometry method was applied as the analytical method for the determination of the arsenic concentration in water. The governing factors for the ion exchange/sorption of arsenic on resins in a batch and a fixed bed flow system were analyzed and compared. Acidity of the water, which plays an important role in the control of the ionic or molecular forms of arsenic species, was beneficial for the separation; by adjusting the pH values to less than 8.00, the SBAE resin separated As(V) from As(III) in water by retaining As(V) and allowing As(III) to pass through. The sorption activity of the hydrated iron oxide particles integrated into the HY resin was beneficial for bonding of all iAs species over a wide range of pH values from 5.00 to 11.00. The resin capacities were calculated according to the breakthrough points in a fixed bed flow system. At pH 7.50, the SBAE resin bound more than 370 microg g(-1) of As(V) while the HY resin bound more than 4150 microg g(-1) of As(III) and more than 3500 microg g(-1) of As(V). The high capacities and selectivity of the resins were considered as advantageous for the development and application of two procedures, one for the separation and determination of As(III) (with SBAE) and the other for the preconcentration and determination of the total arsenic (with HY resin). Methods were established through basic analytical procedures (with external standards, certified reference materials and the standard addition method) and by the parallel analysis of some samples using the atomic absorption spectrometry-hydride generation

  17. Temperature- and body mass-related variation in cyclic gas exchange characteristics and metabolic rate of seven weevil species: Broader implications.

    PubMed

    Klok, C J; Chown, S L

    2005-07-01

    The influence of temperature on metabolic rate and characteristics of the gas exchange patterns of flightless, sub-Antarctic Ectemnorhinus-group species from Heard and Marion islands was investigated. All of the species showed cyclic gas exchange with no Flutter period, indicating that these species are not characterized by discontinuous gas exchange cycles. Metabolic rate estimates were substantially lower in this study than in a previous one of a subset of the species, demonstrating that open-system respirometry methods provide more representative estimates of standard metabolic rate than do many closed-system methods. We recommend that the latter, and especially constant-pressure methods, either be abandoned for estimates of standard metabolic rate in insects, or have their outputs subject to careful scrutiny, given the wide availability of the former. V(.)CO(2) increase with an increase in temperature (range: 0-15 degrees C) was modulated by an increase in cycle frequency, but typically not by an increase in burst volume. Previous investigations of temperature-related changes in cyclic gas exchange (both cyclic and discontinuous) in several other insect species were therefore substantiated. Interspecific mass-scaling of metabolic rate (ca. 0.466-0.573, excluding and including phylogenetic non-independence, respectively) produced an exponent lower than 0.75 (but not distinguishable from it or from 0.67). The increase of metabolic rate with mass was modulated by an increase in burst volume and not by a change in cycle frequency, in keeping with investigations of species showing discontinuous gas exchange. These findings are discussed in the context of the emerging macrophysiological metabolic theory of ecology.

  18. Dynamic variation in sapwood specific conductivity in six woody species.

    PubMed

    Domec, Jean-Christophe; Meinzer, Frederick C; Lachenbruch, Barbara; Housset, Johann

    2007-10-01

    Our goals were to quantify how non-embolism-inducing pressure gradients influence trunk sapwood specific conductivity (k(s)) and to compare the impacts of constant and varying pressure gradients on k(s) with KCl and H2O as the perfusion solutions. We studied six woody species (three conifers and three angiosperms) which varied in pit membrane structure, pit size and frequency of axial water transport across pits (long versus short conduits). Both stepwise ("steady") and nonlinear continuous ("non-steady") decreases in the pressure gradient led to decreased k(s) in all species but white oak (Quercus garryana Dougl. ex Hook), a ring-porous and long-vesseled angiosperm. In one diffuse-porous angiosperm (red alder, Alnus rubra Bong.) and two conifers (western red cedar, Thuja plicata Donn. ex D. Don, and Douglas-fir, Pseudotsuga menziesii (Mirb.) Franco), k(s) was 10-30% higher under steady pressure gradients than under non-steady pressure gradients, and a decrease in the pressure gradient from 0.15 to 0.01 MPa m(-1) caused a 20-42% decrease in k(s). In another diffuse-porous angiosperm (maple, Acer macrophyllum Pursh) and in a third coniferous species (western hemlock, Tsuga heterophylla (Raf.) Sarg), there was no difference between k(s) measured under steady and non-steady pressure gradients. With the exception of western red cedar, a conifer with simple pit membranes, the differences in k(s) between low and high pressure gradients tended to be lower in the conifers than in the diffuse-porous angiosperms. In Douglas-fir, western red cedar and the diffuse-porous angiosperms, k(s) was higher when measured with KCl than with H2O. In white oak, there were no differences in k(s) whether measured under steady or non-steady pressure gradients, or when xylem was perfused with KCl or H2O. The species differences in the behavior of k(s) suggest that elasticity of the pit membrane was the main factor causing k(s) to be disproportionate to the pressure gradient and to the

  19. 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.

  20. 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

  1. 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.

  2. Relaxation dynamics and coherent energy exchange in coupled vibration-cavity polaritons (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Simpkins, Blake S.; Fears, Kenan P.; Dressick, Walter J.; Dunkelberger, Adam D.; Spann, Bryan T.; Owrutsky, Jeffrey C.

    2016-09-01

    Coherent coupling between an optical transition and confined optical mode have been investigated for electronic-state transitions, however, only very recently have vibrational transitions been considered. Here, we demonstrate both static and dynamic results for vibrational bands strongly coupled to optical cavities. We experimentally and numerically describe strong coupling between a Fabry-Pérot cavity and carbonyl stretch ( 1730 cm 1) in poly-methylmethacrylate and provide evidence that the mixed-states are immune to inhomogeneous broadening. We investigate strong and weak coupling regimes through examination of cavities loaded with varying concentrations of a urethane monomer. Rabi splittings are in excellent agreement with an analytical description using no fitting parameters. Ultrafast pump-probe measurements reveal transient absorption signals over a frequency range well-separated from the vibrational band, as well as drastically modified relaxation rates. We speculate these modified kinetics are a consequence of the energy proximity between the vibration-cavity polariton modes and excited state transitions and that polaritons offer an alternative relaxation path for vibrational excitations. Varying the polariton energies by angle-tuning yields transient results consistent with this hypothesis. Furthermore, Rabi oscillations, or quantum beats, are observed at early times and we see evidence that these coherent vibration-cavity polariton excitations impact excited state population through cavity losses. Together, these results indicate that cavity coupling may be used to influence both excitation and relaxation rates of vibrations. Opening the field of polaritonic coupling to vibrational species promises to be a rich arena amenable to a wide variety of infrared-active bonds that can be studied in steady state and dynamically.

  3. Detection of the dynamic magnetic behavior of the antiferromagnet in exchange-coupled NiFe/IrMn bilayers.

    PubMed

    Spizzo, F; Tamisari, M; Bonfiglioli, E; Del Bianco, L

    2013-09-25

    The magnetothermal behavior of antiferromagnetic IrMn layers of different thickness (3, 6, 10 nm) has been studied by exploiting the exchange coupling with a ferromagnetic 5 nm-thick NiFe layer. A procedure has been devised for the measurement of the magnetization of the NiFe/IrMn bilayers as a function of temperature and time at different values of an external magnetic field, Hinv, antiparallel to the unidirectional exchange anisotropy. This analysis allows one to probe the effective distribution of anisotropy energy barriers of the antiferromagnetic phase, as sensed by the ferromagnetic layer. Two magnetic regimes have been distinguished. At temperature T < 100 K, the interfacial IrMn spins are frozen in a glassy state and are collectively involved in the exchange coupling with the NiFe spins. At T ∼ 100 K the collective state breaks up; thus, above this temperature, only the interfacial IrMn spins which are tightly polarized by the IrMn nanograins, forming the bulk of the layer, are effectively involved in the exchange coupling mechanism. Due to that, for T > 100 K the exchange coupling is ruled by the anisotropy energy barriers of the bulk IrMn nanograins, namely by the layer thickness. The thermal evolution of the exchange field and of the coercivity in the three samples is coherently explained in the framework of this description of the dynamic magnetic behavior of the IrMn phase.

  4. Quantifying Hyporheic Exchanges in a Large Scale River Reach Using Coupled 3-D Surface and Subsurface Computational Fluid Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Bao, J.; Zhou, T.; Huang, M.; Hou, Z.; Perkins, W. A.; Harding, S.; Hammond, G. E.; Ren, H.; Thorne, P. D.; Suffield, S. R.; Zachara, J. M.

    2016-12-01

    Hyporheic exchange between river water and groundwater is an important mechanism for biogeochemical processes, such as carbon and nitrogen cycling, and biodegradation of organic contaminants, in the subsurface interaction zone. The relationship between river flow conditions and hyporheic exchanges therefore is of great interests to hydrologists, biogeochemists, and ecologists. However, quantifying relative influences of hydrostatic and hydrodynamic drivers on hyporheic exchanges is very challenging in large rivers due to accessibility and spatial coverage of measurements, and computational tools available for numerical experiments. In this study, we aim to demonstrate that a high resolution computational fluid dynamics (CFD) model that couples surface and subsurface flow and transport can be used to simulate hyporheic exchanges and the residence time of river water in the hypothetic zone. Base on the assumption that the hyporheic exchange does not affect the surface water flow condition due to its small magnitude compared to the velocity of river water, we developed a one way coupled surface and subsurface water flow model in a commercial CFD software STAR-CCM+, that connects the Reynolds-averaged Navier-Stokes (RANS) equation solver with a realizable two-layer turbulence model, a two-layer all y+ wall treatment, and the volume of fluid (VOF) method for tracking the free water-air interface as well as porous media flow in the subsurface domain. The model is applied to a 7-km long section of the Columbia River and validated against measurements from the acoustic Doppler current profiler (ADCP) in the surface water and hyporheic fluxes derived from a set of temperature profilers installed across the riverbed. The validated model is then employed to systematically investigate how hyporheic exchanges influenced by 1) riverbed properties such as the permeability and thickness of the alluvial layer; 2) surface water hydrodynamics due to channel geomorphological settings

  5. Dynamics of metal-humate complexation equilibria as revealed by isotope exchange studies - a matter of concentration and time

    NASA Astrophysics Data System (ADS)

    Lippold, Holger; Eidner, Sascha; Kumke, Michael U.; Lippmann-Pipke, Johanna

    2017-01-01

    Complexation with dissolved humic matter can be crucial in controlling the mobility of toxic or radioactive contaminant metals. For speciation and transport modelling, a dynamic equilibrium process is commonly assumed, where association and dissociation run permanently. This is, however, questionable in view of reported observations of a growing resistance to dissociation over time. In this study, the isotope exchange principle was employed to gain direct insight into the dynamics of the complexation equilibrium, including kinetic inertisation phenomena. Terbium(III), an analogue of trivalent actinides, was used as a representative of higher-valent metals. Isotherms of binding to (flocculated) humic acid, determined by means of 160Tb as a radiotracer, were found to be identical regardless of whether the radioisotope was introduced together with the bulk of stable 159Tb or subsequently after pre-equilibration for up to 3 months. Consequently, there is a permanent exchange of free and humic-bound Tb since all available binding sites are occupied in the plateau region of the isotherm. The existence of a dynamic equilibrium was thus evidenced. There was no indication of an inertisation under these experimental conditions. If the small amount of 160Tb was introduced prior to saturation with 159Tb, the expected partial desorption of 160Tb occurred at much lower rates than observed for the equilibration process in the reverse procedure. In addition, the rates decreased with time of pre-equilibration. Inertisation phenomena are thus confined to the stronger sites of humic molecules (occupied at low metal concentrations). Analysing the time-dependent course of isotope exchange according to first-order kinetics indicated that up to 3 years are needed to attain equilibrium. Since, however, metal-humic interaction remains reversible, exchange of metals between humic carriers and mineral surfaces cannot be neglected on the long time scale to be considered in predictive

  6. 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…

  7. 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…

  8. Dynamic approaches of mixed species biofilm formation using modern technologies.

    PubMed

    Doiron, Kim; Linossier, Isabelle; Fay, Fabienne; Yong, Julius; Abd Wahid, Effendy; Hadjiev, Dimitre; Bourgougnon, Nathalie

    2012-07-01

    Bacteria and diatoms exist in sessile communities and develop as biofilm on all surfaces in aqueous environments. The interaction between these microorganisms in biofilm was investigated with a bacterial genus Pseudoalteromonas sp. (strain 3J6) and two benthic diatoms Amphora coffeaeformis and Cylindrotheca closterium. Each biofilm was grown for 22 days. Images from the confocal microscopy show a difference of adhesion between Pseudoalteromonas 3J6 and diatoms. Indeed, a stronger adhesion is found with C. closterium suggesting cohabitation between Pseudoalteromonas 3J6 and C. closterium compared at an adaptation for bacteria and A. coffeaeformis. The cellular attachment and the growth evolution in biofilm formation depend on each species of diatoms in the biofilm. Behaviour of microalgae in presence of bacteria demonstrates the complexity of the marine biofilm.

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

  10. 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.

  11. The effect of water exchange on bacterioplankton depletion and inorganic nutrient dynamics in coral reef cavities

    NASA Astrophysics Data System (ADS)

    van Duyl, F. C.; Scheffers, S. R.; Thomas, F. I. M.; Driscoll, M.

    2006-03-01

    We studied the effect of water exchange on the depletion (or accumulation) of bacterioplankton, dissolved organic matter and inorganic nutrients in small open framework cavities (50-70 l) at 15 m depth on the coral reef along Curaçao, Netherlands Antilles. The bacterioplankton removal rate in cavities increased with increasing water exchange rates up to a threshold of 0.0045 s-1, reaching values of 50-100 mg C m-2 total interior cavity surface area (CSA) per day. Beyond the threshold, bacterioplankton removal dropped. The cryptic community is apparently adapted to the average water exchange in these cavities (0.0041 s-1). Dissolved inorganic nitrogen (DIN), nitrate + nitrite (NO x ) in particular, accumulated in cavity water and the accumulation decreased with increasing water exchange. Net NO x effluxes exceeded net DIN effluxes from cavities (average efflux rate of 1.9 mmol NO x vs. 0.8 mmol DIN m-2 interior CSA per day). The difference is ascribed to net ammonium losses (NH4) in cavities at reef concentrations >0.025 μM NH4, possibly due to enhanced nitrification. Dissolved inorganic phosphate accumulated in cavities, but was not related to water exchange. The cryptic biota in cavities depend on water exchange for optimization of consumption of bacterioplankton and removal of inorganic nitrogen. Coral cavities are an evident sink of bacterioplankton and a source of NO x and PO{4/3-}.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25672998

  15. Structure and thermodynamics of amylin dimer studied by Hamiltonian-temperature replica exchange molecular dynamics simulations.

    PubMed

    Laghaei, Rozita; Mousseau, Normand; Wei, Guanghong

    2011-03-31

    The loss of the insulin-producing β-cells in the pancreatic islets of Langerhans, responsible for type-II diabetes, is associated with islet amyloid deposits. The main component of these deposits is the amyloid fibrils formed by the 37-residue human islet amyloid polypeptide (hIAPP also known as amylin). Although the fibrils are well characterized by cross β structure, the structure of the transient oligomers formed in the early stage of aggregation remains elusive. In this study, we apply the Hamiltonian-temperature replica exchange molecular dynamics to characterize the structure and thermodynamics of a full-length hIAPP dimer in both the presence and the absence of the Cys2-Cys7 disulfide bond. We compare these results with those obtained on the monomeric and dimeric forms of rat IAPP (rIAPP) with a disulfide bridge which differ from the hIAPP by 6 amino acids in the C-terminal region, but it is unable to form fibrils. Using a coarse-grained protein force field (OPEP-the Optimized Potential for Efficient peptide structure Prediction) running for a total of 10-28 μs per system studied, we show that sequences sample α-helical structure in the N-terminal region but that the length of this secondary element is shorter and less stable for the chains without the disulfide bridge (residues 5-16 for hIAPP with the bridge vs 10-16 for hIAPP without the bridge). This α-helix is known to be an important transient stage in the formation of oligomers. In the C-terminal, the amyloidogenic region of hIAPP, β-strands are seen for residues 17-26 and 30-35. On the contrary, no significant β-sheet content in the C-terminal is observed for either the monomeric or the dimeric rIAPP. These numerical results are fully consistent with recent experimental findings that the N-terminal residues are not part of the fibril by forming α-helical structure but rather play a significant role in stabilizing the amyloidogenic region available for the fibrillation.

  16. Dynamic exchange via spin currents in acoustic and optical modes of ferromagnetic resonance in spin-valve structures

    NASA Astrophysics Data System (ADS)

    Timopheev, A. A.; Pogorelov, Yu. G.; Cardoso, S.; Freitas, P. P.; Kakazei, G. N.; Sobolev, N. A.

    2014-04-01

    Two ferromagnetic (FM) layers magnetically decoupled by a thick, normal metal spacer layer can be dynamically coupled via spin currents emitted by the spin pump and absorbed through the spin-torque effects at the neighboring interfaces. A decrease of damping in both layers due to a partial compensation of the angular momentum leakage in each layer was previously observed at the coincidence of the two FM resonances. In the case of nonzero magnetic coupling, such a dynamic exchange will depend on the mutual precession of the magnetic moments in the layers. A difference in the linewidth of the resonance peaks is expected for the acoustic and optical regimes of precession. However, the interlayer coupling (IC) hybridizes the resonance responses of the layers and therefore can also change their linewidths. The interplay between the two mechanisms has never been considered before. In the present work, the joint influence of the hybridization and nonlocal damping on the linewidth has been studied in weakly coupled NiFe/CoFe/Cu/CoFe/MnIr spin-valve multilayers. It has been found that the dynamic exchange by spin currents is different in the optical and acoustic modes, and this difference is dependent on the IC strength. In contrast to the acoustic precession mode, the dynamic exchange in the optical mode works as an additional damping source. A simulation in the framework of the Landau-Lifshitz-Gilbert formalism for two FM layers coupled magnetically and by spin currents has been done to separate the effects of the nonlocal damping from the resonance modes hybridization. In our samples, both mechanisms bring about linewidth changes of the same order of magnitude but lead to a distinctly different angular behavior. The obtained results are relevant for a broad class of coupled magnetic multilayers with ballistic regime of the spin transport.

  17. Modeling CO and N2 adsorption at Cr surface species of Phillips catalyst by hybrid density functionals: effect of Hartree-Fock exchange percentage.

    PubMed

    Damin, Alessandro; Vitillo, Jenny G; Ricchiardi, Gabriele; Bordiga, Silvia; Lamberti, Carlo; Groppo, Elena; Zecchina, Adriano

    2009-12-31

    In this article, we present a computational study of the structure and vibrational properties of the species formed by the interaction between Cr sites of Phillips catalyst and probe molecules (CO, N(2)). The vibrational properties of these surface species, intensively investigated in the past, form a very rich and ideal set of experimental data to test computational approaches. By adopting the X(4)Si(2)O(3)Cr (X = H, OH, F) cluster as a simplified model of the ([triple bond]SiO)(2)Cr(II) species present at the surface of the real catalyst, we found that the B3LYP hybrid functional (containing 20% of Hartree-Fock exchange), when applied to this model, is unable to reproduce with reasonable accuracy the currently available experimental data (principally coming from IR spectroscopy). Better agreement is obtained when the percentage of Hartree-Fock exchange is increased (up to 35-40%).

  18. Modeling CO and N2 Adsorption at Cr Surface Species of Phillips Catalyst by Hybrid Density Functionals: Effect of Hartree-Fock Exchange Percentage

    NASA Astrophysics Data System (ADS)

    Damin, Alessandro; Vitillo, Jenny G.; Ricchiardi, Gabriele; Bordiga, Silvia; Lamberti, Carlo; Groppo, Elena; Zecchina, Adriano

    2009-07-01

    In this article, we present a computational study of the structure and vibrational properties of the species formed by the interaction between Cr sites of Phillips catalyst and probe molecules (CO, N2). The vibrational properties of these surface species, intensively investigated in the past, form a very rich and ideal set of experimental data to test computational approaches. By adopting the X4Si2O3Cr (X = H, OH, F) cluster as a simplified model of the (≡SiO)2Cr(II) species present at the surface of the real catalyst, we found that the B3LYP hybrid functional (containing 20% of Hartree-Fock exchange), when applied to this model, is unable to reproduce with reasonable accuracy the currently available experimental data (principally coming from IR spectroscopy). Better agreement is obtained when the percentage of Hartree-Fock exchange is increased (up to 35-40%).

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

    NASA Astrophysics Data System (ADS)

    Ma, Q. L.; Iihama, S.; Zhang, X. M.; Miyazaki, T.; Mizukami, S.

    2015-11-01

    The laser-induced spin dynamics of FeCo in perpendicularly magnetized L10-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.

  20. 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.

  1. Capillary liquid chromatography using a hydrophilic/cation-exchange monolithic column with a dynamically modified cationic surfactant.

    PubMed

    Lin, Jian; Lin, Jia; Lin, Xucong; Xie, Zenghong

    2009-11-06

    A novel form of reversed-phase liquid chromatography (RPLC) by the dynamically modified hydrophilic interaction monolithic column has been described in this paper. A porous poly(SPMA-co-PETA) monolith with strong cation-exchange (SCX) was prepared and the resulting monolith showed a typical hydrophilic interaction chromatography (HILIC) mechanism at higher organic solvent content (ACN%>50%). The good selectivity for neutral, basic and acidic polar analytes was observed in the HILIC mode. In order to increase the hydrophobic interaction, the monolith with SCX was dynamically modified with a long-chain quaternary ammonium salt, cetyltrimethylammonium bromide (CTAB), which was added to the mobile phase. CTAB ions were adsorbed onto the surface of the SCX monolithic material, and the resulting hydrophobic layer was used as the stationary phase. Using the dynamically modified SCX monolithic column, neutral, basic and acidic hydrophobic analytes were well separated with the RPLC mode.

  2. 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.

  3. Dynamic nuclear-polarization studies of paramagnetic species in solution

    SciTech Connect

    Glad, W.E.

    1982-07-01

    Dynamic Nuclear Polarization (DNP) was used to measure the electron spin lattice relaxation times, T/sub 1/, of transition metal ions in aqueous solution. Saturation which is induced in the electron spin system is transferred to the solvent proton spins by dipole-dipole interactions. The change in the polarization of the proton spins is much larger than it is in the electron spins. The change in proton polarization is easily measured by proton Nuclear Magnetic Resonance (NMR). In one experimental arrangement the sample solution was continuously flowed through a microwave cavity to the NMR coil. The NMR was observed with a continuous wave NMR spectrometer. In a second arrangement the whole sample tube was moved from within the microwave cavity to the NMR coil in less than 40 ms by a blast of compressed air. The NMR was then observed with a pulse-Fourier-transform spectrometer. With the second arrangement a mean-square microwave magnetic field at the sample of more than 10 G/sup 2/ is obtainable with 14 W of microwave power. Measurements of DNP at 9 GHz were made on aqueous solutions of VO/sup 2 +/, Mn/sup 2 +/, Cr(CN)/sub 6//sup 3 -/, Cu/sup 2 +/ and Cu(ethylenediamine)/sub 2/(H/sub 2/0)/sub 2//sup 2 +/ ions from 3 to 60/sup 0/C. It was also possible to observe DNP on resolved proton resonances from mixed water-acetonitrile solutions of VO/sup 2 +/ and Cr(CN)/sub 6//sup 3 -/ ions.

  4. Analysis of Postfire Vegetation Dynamics of Mediterranean Shrub Species Based on Terrestrial and NDVI Data

    NASA Astrophysics Data System (ADS)

    Hernández-Clemente, Rocío; Navarro Cerrillo, R. M.; Hernández-Bermejo, J. E.; Escuin Royo, S.; Kasimis, N. A.

    2009-05-01

    The present study offers an analysis of regeneration patterns and diversity dynamics after a wildfire, which occurred in 1993 and affected about 7000 ha in southern Spain. The aim of the work was to analyze the rule in the succession of shrub species after fire, relating it to the changes registered in the Normalized Difference Vegetation Index (NDVI). Fractional vegetation cover was recorded from permanent plots in 2000 and 2005. NDVI data related to each time were obtained from Landsat images. Both data sets, from fieldwork and remote sensing, were analyzed through statistical and quantitative analyses and then correlated. Results have permitted the description of the change in plant cover and species composition on a global and plot scale. It can be affirmed that, from the seventh to the twelfth year after the fire, the floristic composition within the burned area remained unchanged at a global level. However, on a smaller scale (plot level), the major shrub species, Ulex parviflorus, Rosmarinus officinalis, and Cistus clusii, underwent significant changes. The regeneration dynamics established by these species conditioned plant species composition and, consequently, diversity indexes such as Shannon (H) and Simpson (D). The changes recorded in the NDVI values corresponding to the surveyed plots were highly correlated with those found in the regrowth of the main species. Areas dominated by U. parviflorus in a senile phase were related to a decrease in NDVI values and an increase in the number of species. This result describes the successional dynamics; the dryness of the main colonizer shrub species is allowing the regrowth and re-establishment of other species. Within the study area, NDVI shows sensitivity to postfire plant cover changes and indirectly expresses the diversity dynamics.

  5. Analysis of postfire vegetation dynamics of Mediterranean shrub species based on terrestrial and NDVI data.

    PubMed

    Hernández-Clemente, Rocío; Cerrillo, R M Navarro; Hernández-Bermejo, J E; Royo, S Escuin; Kasimis, N A

    2009-05-01

    The present study offers an analysis of regeneration patterns and diversity dynamics after a wildfire, which occurred in 1993 and affected about 7000 ha in southern Spain. The aim of the work was to analyze the rule in the succession of shrub species after fire, relating it to the changes registered in the Normalized Difference Vegetation Index (NDVI). Fractional vegetation cover was recorded from permanent plots in 2000 and 2005. NDVI data related to each time were obtained from Landsat images. Both data sets, from fieldwork and remote sensing, were analyzed through statistical and quantitative analyses and then correlated. Results have permitted the description of the change in plant cover and species composition on a global and plot scale. It can be affirmed that, from the seventh to the twelfth year after the fire, the floristic composition within the burned area remained unchanged at a global level. However, on a smaller scale (plot level), the major shrub species, Ulex parviflorus, Rosmarinus officinalis, and Cistus clusii, underwent significant changes. The regeneration dynamics established by these species conditioned plant species composition and, consequently, diversity indexes such as Shannon (H) and Simpson (D). The changes recorded in the NDVI values corresponding to the surveyed plots were highly correlated with those found in the regrowth of the main species. Areas dominated by U. parviflorus in a senile phase were related to a decrease in NDVI values and an increase in the number of species. This result describes the successional dynamics; the dryness of the main colonizer shrub species is allowing the regrowth and re-establishment of other species. Within the study area, NDVI shows sensitivity to postfire plant cover changes and indirectly expresses the diversity dynamics.

  6. Low Dynamics, High Longevity and Persistence of Sessile Structural Species Dwelling on Mediterranean Coralligenous Outcrops

    PubMed Central

    Teixidó, Núria; Garrabou, Joaquim; Harmelin, Jean-George

    2011-01-01

    There is still limited understanding of the processes underlying benthic species dynamics in marine coastal habitats, which are of disproportionate importance in terms of productivity and biodiversity. The life-history traits of long-lived benthic species in these habitats are particularly poorly documented. In this study, we assessed decadal patterns of population dynamics for ten sponge and anthozoan species that play key structural roles in coralligenous outcrops (∼25 m depth) in two areas of the NW Mediterranean Sea. This study was based on examination of a unique long-term photographic series, which allowed analysis of population dynamics over extensive spatial and time spans for the very first time. Specifically, 671 individuals were censused annually over periods of 25-, 15-, and 5-years. This long-term study quantitatively revealed a common life-history pattern among the ten studied species, despite the fact they present different growth forms. Low mortality rates (3.4% yr−1 for all species combined) and infrequent recruitment events (mean value of 3.1±0.5 SE recruits yr−1) provided only a very small fraction of the new colonies required to maintain population sizes. Overall, annual mortality and recruitment rates did not differ significantly among years; however, some species displayed important mortality events and recruitment pulses, indicating variability among species. Based on the growth rates of these 10 species, we projected their longevity and, obtained a mean estimated age of 25–200 years. Finally, the low to moderate turnover rates (mean value 0.80% yr−1) observed among the coralligenous species were in agreement with their low dynamics and persistence. These results offer solid baseline data and reveal that these habitats are among the most vulnerable to the current increases of anthropogenic disturbances. PMID:21887308

  7. Hydrogen-bonding structure and dynamics of aqueous carbonate species from car-parrinello molecular dynamics simulations.

    PubMed

    Kumar, P Padma; Kalinichev, Andrey G; Kirkpatrick, R James

    2009-01-22

    A comprehensive Car-Parrinello molecular dynamics (CP-MD) study of aqueous solutions of carbonic acid (H(2)CO(3)), bicarbonate (HCO(3)(-)), carbonate (CO(3)(2-)), and carbon dioxide (CO(2)) provides new quantitative insight into the structural and dynamic aspects of the hydrogen-bonding environments for these important aqueous species and their effects on the structure, H-bonding, and dynamical behavior of the surrounding water molecules. The hydration structures of the different carbonate species depend on their ability to accept and donate H-bonds with H(2)O. The H-bonds donated by the C-O-H sites of the carbonate species to water molecules are generally stronger and longer-lived than those accepted by these sites from water molecules. The structural relaxation among the water molecules is dominated by diffusional (translational) motion of H(2)O, whereas the H-bond reorganization is dominated by the librational motion of the water molecules and the carbonate species. The rates of structural relaxation of the H(2)O molecules and the rates of H-bond reorganization among them are slower in systems containing carbonate species, consistent with previous studies of simple salt solutions. The strengths and lifetimes of H-bonds involving the carbonate species positively correlate with the total negative charge on the species. H-bond donation from H(2)O to CO(2) is weak, but the presence of CO(2) noticeably affects the structure and structural relaxation of the surrounding H-bonding network leading to generally stronger H-bonds and slower relaxation rates, the behavior typical of a hydrophobic solute.

  8. Probing RNA dynamics via longitudinal exchange and CPMG relaxation dispersion NMR spectroscopy using a sensitive 13C-methyl label.

    PubMed

    Kloiber, Karin; Spitzer, Romana; Tollinger, Martin; Konrat, Robert; Kreutz, Christoph

    2011-05-01

    The refolding kinetics of bistable RNA sequences were studied in unperturbed equilibrium via (13)C exchange NMR spectroscopy. For this purpose a straightforward labeling technique was elaborated using a 2'-(13)C-methoxy uridine modification, which was prepared by a two-step synthesis and introduced into RNA using standard protocols. Using (13)C longitudinal exchange NMR spectroscopy the refolding kinetics of a 20 nt bistable RNA were characterized at temperatures between 298 and 310K, yielding the enthalpy and entropy differences between the conformers at equilibrium and the activation energy of the refolding process. The kinetics of a more stable 32 nt bistable RNA could be analyzed by the same approach at elevated temperatures, i.e. at 314 and 316 K. Finally, the dynamics of a multi-stable RNA able to fold into two hairpin- and a pseudo-knotted conformation was studied by (13)C relaxation dispersion NMR spectroscopy.

  9. Transmission dynamics of a zoonotic pathogen within and between wildlife host species.

    PubMed Central

    Begon, M; Hazel, S M; Baxby, D; Bown, K; Cavanagh, R; Chantrey, J; Jones, T; Bennett, M

    1999-01-01

    The transmission dynamics of the cowpox virus infection have been quantified in two mixed populations of bank voles (Clethrionomys glareolus) and wood mice (Apodemus sylvaticus), through analyses of detailed time-series of the numbers of susceptible, infectious and newly infected individuals. The cowpox virus is a zoonosis which circulates in these rodent hosts and has been shown to have an adverse effect on reproductive output. The transmission dynamics within species is best described as frequency dependent rather than density dependent, contrary to the 'mass action' assumption of most previous studies, both theoretical and empirical. Estimation of a transmission coefficient for each species in each population also allows annual and seasonal variations in transmission dynamics to be investigated through an analysis of regression residuals. Transmission between host species is found to be negligible despite their close cohabitation. The consequences of this for the combining ability of hosts as zoonotic reservoirs, and for apparent competition between hosts, are discussed. PMID:10584336

  10. Hydrogen/deuterium exchange-mass spectrometry: a powerful tool for probing protein structure, dynamics and interactions.

    PubMed

    Tsutsui, Yuko; Wintrode, Patrick L

    2007-01-01

    Knowledge of the structure and dynamics of proteins and protein assemblies is critical both for understanding the molecular basis of physiological and patho-physiological processes and for guiding drug design. While X-ray crystallography and nuclear magnetic resonance spectroscopy are both excellent techniques for this purpose, both suffer from limitations, including the requirement for high quality crystals and large amounts of material. Recently, hydrogen/deuterium exchange measured using mass spectrometry (HXMS) has emerged as a powerful new tool for the study of protein structure, dynamics and interactions in solution. HXMS exploits the fact that backbone amide hydrogens can exchange with deuterium when a protein is incubated in D(2)O, and that the rate of the exchange process is highly dependent on the local structural environment. Several features of HXMS make it an especially attractive approach, including small sample requirements and the ability to study extremely large protein assemblies that are not amenable to other techniques. Here, we provide an overview of HXMS and describe several recent applications to problems of medical interest. After reviewing the molecular basis of the H/D exchange process, the different steps of the HXMS experiment--labeling, rapid proteolysis, fragment separation and mass measurement--are described, followed by a discussion of data analysis methods. Finally, we describe recent results on the application of HXMS to 1) mapping drug/inhibitor binding sites and detecting drug induced conformational changes, 2) studying viral capsid structure and assembly, and 3) characterizing the structure of pathological protein conformations, specifically amyloid fibrils.

  11. Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents

    PubMed Central

    King, John T.; Arthur, Evan J.; Brooks, Charles L.; Kubarych, Kevin J.

    2012-01-01

    The thermodynamic driving forces for protein folding, association and function are often determined by protein-water interactions. With a novel covalently bound labeling approach, we have used sensitive vibrational probes, site-selectively conjugated to two lysozyme variants–in conjunction with ultrafast two-dimensional infrared (2D-IR) spectroscopy–to investigate directly the protein-water interface. By probing alternatively a topologically flat, rigid domain and a flexible domain, we find direct experimental evidence for spatially heterogeneous hydration dynamics. The hydration environment around globular proteins can vary from exhibiting bulk-like hydration dynamics to dynamically constrained water, which results from stifled hydrogen bond switching dynamics near extended hydrophobic surfaces. Furthermore, we leverage preferential solvation exchange to demonstrate that the liberation of dynamically constrained water is a sufficient driving force for protein-surface association reactions. These results provide an intuitive picture of the dynamic aspects of hydrophobic hydration of proteins, illustrating an essential function of water in biological processes. PMID:22530969

  12. Continuous probabilistic approach to species dynamics in Hubbell's zero-sum local community

    NASA Astrophysics Data System (ADS)

    Babak, Petro

    2006-08-01

    In this paper a continuous probabilistic approach formulated using Kolmogorov-Fokker-Planck forward and backward models is applied to Hubbell’s zero-sum neutral theory for species dynamics in local community. Using this technique the probability density of species abundance, distribution of the first passage time to extinction or fixation and probability of extinction are defined. The resulting values for the distribution of the first passage time to extinction are verified by the simulation study of Hubbell’s zero-sum neutral model for the local community. Based on the sensitivity analysis for the continuous probabilistic models, the realistic classification of local communities subject to their diversity and species dynamics is proposed with respect to the immigration probability, the species metacommunity relative abundance, and the size of local community.

  13. The dynamical analogy between microbial growth on mixtures of substrates and population growth of competing species.

    PubMed

    Narang, A

    1998-07-05

    There is a similarity between the metabolic dynamics of a microbial species growing on a mixture of two substrates and the dynamics of growth of two competing populations. Specifically, the enzymes catalyzing the uptake and catabolism of substrates exhibit phenomena analogous to extinction and coexistence."Extinction" of the enzymes associated with one of the substrates results in sequential utilization of the substrates (diauxie) (Monod, 1942). "Coexistence" of the enzymes associated with the substrates results in simultaneous utilization of the substrates (Egli, 1995). Here, we formulate a simple model that shows the basis for this dynamical similarity: The equations describing the evolution of the enzyme levels are dynamical analogs of the Lotka-Volterra model for two competing species. The analogy suggests ways of capturing the experimentally observed preculture-dependent growth patterns, i.e., growth patterns that vary depending on the physiological state of the preculture.

  14. 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

  15. 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.

  16. 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.

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

    DOE PAGES

    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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  19. Analysis of protein conformation and dynamics by hydrogen/deuterium exchange MS.

    PubMed

    Engen, John R

    2009-10-01

    Understanding as much as possible about proteins in the shortest amount of time has long been a goal of hydrogen exchange (HX) MS. Recent technological advances have led to improvements in the technique, but has this goal yet been achieved? (To listen to a podcast about this Feature, please go to the Analytical Chemistry Web site at pubs.acs.org/journal/ancham.).

  20. 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…

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Exchange interaction-driven dynamic nuclear polarization in Mn-doped InGaAs/GaAs quantum dots

    NASA Astrophysics Data System (ADS)

    Krebs, O.; Baudin, E.; Lemaître, A.

    2016-11-01

    We investigated optical spin orientation and dynamic nuclear polarization (DNP) in individual self-assembled InGaAs/GaAs quantum dots (QDs) doped by a single Mn atom, a magnetic impurity providing a neutral acceptor A0 with an effective spin J =1 . We find that the spin of an electron photocreated in such a quantum dot can be efficiently oriented by a quasiresonant circularly polarized excitation. For the electron spin levels which are made quasidegenerate by a magnetic field compensating the exchange interaction Δe with A0, there is however a full depolarization due the anisotropic part of the exchange. Still, in most studied QDs, the spin polarized photoelectrons give rise to a pronounced DNP which grows with a longitudinal magnetic field until a critical field where it abruptly vanishes. For some QDs, several replica of such DNP sequence are observed at different magnetic fields. This striking behavior is qualitatively discussed as a consequence of different exchange interactions experienced by the electron, driving the DNP rate via the energy cost of electron-nucleus spin flip-flops.

  6. 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.

  7. Emergence of a dynamic resource partitioning based on the coevolution of phenotypic plasticity in sympatric species.

    PubMed

    Suzuki, Reiji; Arita, Takaya

    2014-07-07

    This paper investigates the coevolutionary dynamics of the phenotypic plasticity in the context of overlap avoidance behaviors of shared niches in sympatric species. Especially, we consider whether and how a differentiation of phenotypic plasticity can emerge under the assumption that there are no initial asymmetric relationships among coevolving species. We construct a minimal model where several different species participate in a partitioning of their shared niches, and evolve their behavioral plasticity to avoid an overlap of their niche use. By conducting evolutionary experiments with various conditions of the number of species and niches, we show that the two different types of asymmetric distributions of phenotypic plasticity emerge depending on the settings of the degree of congestion of the shared niches. In both cases, all species tended to obtain the similar amount of fitness regardless of such differences in their plasticity. We also show that the emerged distributions are coevolutionarily stable in general. Copyright © 2014 Elsevier Ltd. All rights reserved.

  8. Species-specific dynamic responses of gut bacteria to a mammalian glycan.

    PubMed

    Raghavan, Varsha; Groisman, Eduardo A

    2015-05-01

    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. 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 regulate the same genes

  9. 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

  10. 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.

  11. Effect of Taiwan mutation (D7H) on structures of amyloid-β peptides: replica exchange molecular dynamics study.

    PubMed

    Truong, Phan Minh; Viet, Man Hoang; Nguyen, Phuong H; Hu, Chin-Kun; Li, Mai Suan

    2014-07-31

    Recent experiments have shown that the Taiwan mutation (D7H) slows the fibril formation of amyloid peptides Aβ40 and Aβ42. Motivated by this finding, we have studied the influence of D7H mutation on structures of Aβ peptide monomers using the replica exchange molecular dynamics simulations with OPLS force field and implicit water model. Our study reveals that the mechanism behind modulation of aggregation rates is associated with decrease of β-content and dynamics of the salt bridge D23-K28. Estimating the bending free energy of this salt bridge, we have found that, in agreement with the experiments, the fibril formation rate of both peptides Aβ40 and Aβ42 is reduced about two times by mutation.

  12. Dynamics of the β2-adrenergic G-protein coupled receptor revealed by hydrogen-deuterium exchange

    PubMed Central

    Zhang, Xi; Chien, Ellen Y.T.; Chalmers, Michael J.; Pascal, Bruce D.; Gatchalian, Jovylyn; Stevens, Raymond C.; Griffin, Patrick R.

    2010-01-01

    To examine the molecular details of ligand activation of G-protein coupled receptor (GPCRs), emphasis has been placed on structure determination of these receptors with stabilizing ligands. Here we present the methodology for receptor dynamics characterization of the GPCR human β2 adrenergic receptor bound to the inverse agonist carazolol using the technique of amide hydrogen/deuterium exchange coupled with mass spectrometry (HDX MS). The HDX MS profile of receptor bound to carazolol is consistent with thermal parameter observations in the crystal structure and provides additional information in highly dynamic regions of the receptor and chemical modifications demonstrating the highly complementary nature of the techniques. Following optimization of HDX experimental conditions for this membrane protein, better than 89% sequence coverage was obtained for the receptor. The methodology presented paves the way for future analysis of β2AR bound to pharmacologically distinct ligands as well as analysis of other GPCR family members. PMID:20058880

  13. Dynamic and steady-state responses of inorganic nitrogen pools and NH(3) exchange in leaves of Lolium perenne and Bromus erectus to changes in root nitrogen supply.

    PubMed

    Mattsson, Marie; Schjoerring, Jan K

    2002-02-01

    Short- and long-term responses of inorganic N pools and plant-atmosphere NH(3) exchange to changes in external N supply were investigated in 11-week-old plants of two grass species, Lolium perenne and Bromus erectus, characteristic of N-rich and N-poor grassland ecosystems, respectively. A switch of root N source from NO(-)(3)to NH(4)(+) caused within 3 h a 3- to 6-fold increase in leaf apoplastic NH(4)(+) concentration and a simultaneous decrease in apoplastic pH of about 0.4 pH units in both species. The concentration of total extractable leaf tissue NH(4)(+) also increased two to three times within 3 h after the switch. Removal of exogenous NH(4)(+) caused the apoplastic NH(4)(+) concentration to decline back to the original level within 24 h, whereas the leaf tissue NH(4)(+)concentration decreased more slowly and did not reach the original level in 48 h. After growing for 5 weeks with a steady-state supply of NO(-)(3)or NH(4)(+), L. perenne were in all cases larger, contained more N, and utilized the absorbed N more efficiently for growth than B. erectus, whereas the two species behaved oppositely with respect to tissue concentrations of NO(-)(3), NH(4)(+), and total N. Ammonia compensation points were higher for B. erectus than for L. perenne and were in both species higher for NH(4)(+)- than for NO(-)(3)-grown plants. Steady-state levels of apoplastic NH(4)(+), tissue NH(4)(+), and NH(3) emission were significantly correlated. It is concluded that leaf apoplastic NH(4)(+) is a highly dynamic pool, closely reflecting changes in the external N supply. This rapid response may constitute a signaling system coordinating leaf N metabolism with the actual N uptake by the roots and the external N availability.

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

    PubMed

    De Simone, Alfonso; Derreumaux, Philippe

    2010-04-28

    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 micros show that low molecular weight oligomers in explicit solvent consist of beta-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 beta-barrel assemblies in the early aggregation steps of amyloid-forming systems. Our findings are discussed in terms of oligomers cytotoxicity.

  16. Application of Elemental Fingerprinting to Evaluate the Dynamics of Larval Exchange

    DTIC Science & Technology

    2001-09-30

    more recently, by Laser Ablation (LA)-ICP MS. Three species have been targeted: Mytilus galloprovincialis (Bay mussel), M. californianus (California... galloprovincialis and M. californianus have not been considered separately. To confirm identifications, Mytilus soft parts are being identified to species by...based on site, species, and size. Overall, the ability to distinguish small (,000 ppb Ca) Mytilus individuals from among Mission Bay, San

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. Flush Development Dynamics in First-Year Nursery-Grown Seedlings of Eight Oak Species

    Treesearch

    Shi-Jean S. Sung; Paul P. Kormanik; Stanley J. Zarnoch

    2004-01-01

    Two experiments were conducted to follow flush development dynamics exhibited by various oak species. In experiment I, southern red oak acorns were sown in mid-March 2001 at Whitehall Nursery (Athens, GA). In experiment II, acorns of black oak, cherrybark oak, Nuttall oak, Shumard oak, southern red oak, swamp chestnut oak, white oak, and willow oak were sown in...

  3. Variational iteration method for solving the population dynamics model of two species

    NASA Astrophysics Data System (ADS)

    Dwi Yuliyanto, Benedictus; Mungkasi, Sudi

    2017-01-01

    This paper applies the variational iteration method for solving systems of nonlinear ordinary differential equations. The model under consideration in this work is the population dynamics model of two species. Our results show that the variational iteration method provides formulas to approximate the exact solution at every time value with a very cheap computation.

  4. The dynamic pipeline: hydraulic capacitance and xylem hydraulic safety in four tall conifer species

    Treesearch

    Katherine A. McCulloh; Daniel M. Johnson; Frederick C. Meinzer; David R. Woodruff

    2013-01-01

    Recent work has suggested that plants differ in their relative reliance on structural avoidance of embolism versus maintenance of the xylem water column through dynamic traits such as capacitance, but we still know little about how and why species differ along this continuum. It is even less clear how or if different parts of a plant vary along this spectrum. Here we...

  5. A review of the regeneration dynamics of North American boreal forest tree species

    Treesearch

    D. F. Greene; John C. Zasada; L. Sirois; D. Kneeshaw; H. Morin; I. Charron; M. J. Simard

    1999-01-01

    In this review, we focus on the biotic parameters that are crucial to an understanding of the recruitment dynamics of North American boreal tree species following natural (fire, budworm infestation, windthrow) or human-induced (clearcut, partial cut) disturbances. The parameters we emphasize are (i) the production of seeds and asexual stems (both of...

  6. Capturing the transient species at the electrode-electrolyte interface by in situ dynamic molecular imaging.

    PubMed

    Yu, Jiachao; Zhou, Yufan; Hua, Xin; Liu, Songqin; Zhu, Zihua; Yu, Xiao-Ying

    2016-09-21

    In situ time-resolved identification of interfacial transient reaction species were captured using imaging mass spectrometry, leading to the discovery of more complex elementary electrode reactions and providing an unprecedented understanding of the reaction mechanism on the electrode surface and solid-electrolyte interface using dynamic molecular imaging.

  7. Dynamics of acorn production by five species of Southern Appalachian oaks

    Treesearch

    Cathryn H. Greenberg; Bernard R. Parresol

    2002-01-01

    The management implications of fluctuations in acorn crop size underscore the need to better understand their patterns, causal factors, and predictability (both within a year and long term). Acorn yield has a demonstrable influence on the population dynamics of many wildlife species, both game (Eiler et al. 1989, Wentworth et al. 1992) and nongame (Hannon et al. 1987,...

  8. 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

  9. 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

  10. 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

  11. Measuring dynamics in weakly structured regions of proteins using microfluidics-enabled subsecond H/D exchange mass spectrometry.

    PubMed

    Rob, Tamanna; Liuni, Peter; Gill, Preet Kamal; Zhu, Shaolong; Balachandran, Naresh; Berti, Paul J; Wilson, Derek J

    2012-04-17

    This work introduces an integrated microfluidic device for measuring rapid H/D exchange (HDX) in proteins. By monitoring backbone amide HDX on the millisecond to low second time scale, we are able to characterize conformational dynamics in weakly structured regions, such as loops and molten globule-like domains that are inaccessible in conventional HDX experiments. The device accommodates the entire MS-based HDX workflow on a single chip with residence times sufficiently small (ca. 8 s) that back-exchange is negligible (≤5%), even without cooling. Components include an adjustable position capillary mixer providing a variable-time labeling pulse, a static mixer for HDX quenching, a proteolytic microreactor for rapid protein digestion, and on-chip electrospray ionization (ESI). In the present work, we characterize device performance using three model systems, each illustrating a different application of 'time-resolved' HDX. Ubiquitin is used to illustrate a crude, high throughput structural analysis based on a single subsecond HDX time-point. In experiments using cytochrome c, we distinguish dynamic behavior in loops, establishing a link between flexibility and interactions with the heme prosthetic group. Finally, we localize an unusually high 'burst-phase' of HDX in the large tetrameric enzyme DAHP synthase to a 'molten globule-like' region surrounding the active site.

  12. Exchange coupling and anisotropy effects on the low temperature magnetization dynamics in rare-earth dioxolene complexes

    NASA Astrophysics Data System (ADS)

    Amjad, Asma; Poneti, Giordano; Sottini, Silvia; Dei, Andrea; Sorace, Lorenzo

    The prelude of relevant magnetic coupling in f-element based complexes is actively pursued to improve the single-molecule magnetic features. However, a quantitative analysis of magnetic properties of exchange-coupled anisotropic rare-earth based complexes is often hampered owing to the comparable magnitude of the crystal field with the magnetic coupling. In this study, we investigated the properties of complexes containing different ligands with comparable molecular structures and ligand field strengths. Comparative low-temperature magnetic and EPR study of homologous LnIIISemiquinonate (LnSQ) and LnIIITropolonate (LnTrp) complexes, where Ln = Dy, Tb is investigated. Single-crystal EPR revealed that the direct exchange coupling in DySQ resulted in a highly anisotropic pseudo-triplet state. An out-of-phase susceptibility signal was observed for TbTrp only in the presence of an external magnetic field. Furthermore, the dynamics revealed slow relaxation of magnetization in the DySQ at low temperature which upon comparative study with the dynamics of the related DyTrp revealed a not so simple dependence on the crystal field effects of the coordination sphere of the lanthanide.

  13. State-to-state quantum dynamics of the H + HBr reaction: competition between the abstraction and exchange reactions.

    PubMed

    Xie, Changjian; Jiang, Bin; Xie, Daiqian

    2011-05-14

    Quantum state-to-state dynamics for the H + HBr(υ(i) = 0, j(i) =0) reaction was studied on an accurate ab intio potential energy surface for the electronic ground state of BrH(2). Both the H + HBr → H(2) + Br abstraction reaction and the H' + HBr → H'Br + H exchange reaction were investigated up to a collision energy of 2.0 eV. It was found that the abstraction channel is dominant at lower collision energies, while the exchange channel becomes dominant at higher collision energies. The total integral cross section of the abstraction reaction at a collision energy of 1.6 eV was found to be 1.37 Å(2), which is larger than a recent quantum mechanical result (1.06 Å(2)) and still significantly smaller than the experimental value (3 ± 1 Å(2)). Meanwhile, similar to the previous theoretical study, our calculations also predicted much hotter product rotational state distributions than those from the experimental study. This suggests that further experimental investigations are highly desirable to elucidate the dynamic properties of the title reactions.

  14. 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

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

    PubMed

    Yasuhara, Moriaki; Hunt, Gene; Cronin, Thomas M; Okahashi, Hisayo

    2009-12-22

    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.

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

    PubMed Central

    Yasuhara, Moriaki; Hunt, Gene; Cronin, Thomas M.; Okahashi, Hisayo

    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. PMID:20018702

  17. 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.

  18. 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.

  19. 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.

  20. Computer fluid dynamics (CFD) study of a plate heat exchanger working with nanofluids

    NASA Astrophysics Data System (ADS)

    Stan, Liviu-Constantin; Cǎlimǎnescu, Ioan

    2016-12-01

    The industry fosters many types of heat exchangers such double pipe or plate heat exchangers (HX), but lately the plate HX are gaining the high ground in many applications. Such a plate HX is made out of serial plate modules packed together allowing the warm and cold fluids to pass through and exchange the heat. The paper is demonstrating the functioning of a medium sized plate HX functioning with 10% Al2O3 and water nanofluids flowing in both cold and warm sides of the HX. The influence of the nanofluid properties will be investigated as impact upon the outlet temperature of the fluid leaving the HX. Using the RSM methodology. The main conclusion of this study is that there is a balance between the nanofluids increased conductivity and their increased viscosity. The nanofluids are working well for those applications where the flow is not impeded by narrow fluid passages where the bigger influence of the viscosity is actually worsening the heat transfer conditions instead of increasing it, since the influence of viscosity in that kind of applications is three time bigger. A nanofluid conductivity threshold was also detected over which the nanofluids say with 15$ or 20% alumina content is useless for the overall heat transfer conditions.

  1. 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.

  2. Common species link global ecosystems to climate change: dynamical evidence in the planktonic fossil record.

    PubMed

    Hannisdal, Bjarte; Haaga, Kristian Agasøster; Reitan, Trond; Diego, David; Liow, Lee Hsiang

    2017-07-12

    Common species shape the world around us, and changes in their commonness signify large-scale shifts in ecosystem structure and function. However, our understanding of long-term ecosystem response to environmental forcing in the deep past is centred on species richness, neglecting the disproportional impact of common species. Here, we use common and widespread species of planktonic foraminifera in deep-sea sediments to track changes in observed global occupancy (proportion of sampled sites at which a species is present and observed) through the turbulent climatic history of the last 65 Myr. Our approach is sensitive to relative changes in global abundance of the species set and robust to factors that bias richness estimators. Using three independent methods for detecting causality, we show that the observed global occupancy of planktonic foraminifera has been dynamically coupled to past oceanographic changes captured in deep-ocean temperature reconstructions. The causal inference does not imply a direct mechanism, but is consistent with an indirect, time-delayed causal linkage. Given the strong quantitative evidence that a dynamical coupling exists, we hypothesize that mixotrophy (symbiont hosting) may be an ecological factor linking the global abundance of planktonic foraminifera to long-term climate changes via the relative extent of oligotrophic oceans. © 2017 The Authors.

  3. 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.

  4. Responses of gas exchange to reversible changes in whole-plant transpiration rate in two conifer species.

    PubMed

    Warren, C R; Livingston, N J; Turpin, D H

    2003-08-01

    This study examined the autonomy of branches with respect to the control of transpiration (E) in Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) and western red cedar (Thuja plicata Donn) seedlings. Experiments were conducted on whole seedlings in a gas exchange system with a dual-cuvette that permitted independent manipulation and measurement of E in the upper and lower cuvettes. The value of E in one cuvette was manipulated by varying vapor pressure deficit (D) between 2.2 and 0.2 kPa, whereas D in the other cuvette was held at 2.2 kPa. Reducing D, while increasing stomatal conductance (gs), resulted in an overall decrease in E. In western red cedar, this decrease was almost threefold, and in Douglas-fir, approximately fourfold. In well-watered western red cedar, a reduction of whole-plant E by 46% (brought about by reducing D in the upper cuvette) resulted in a 12% increase in gs, a 12% increase in E and a 7% increase in net assimilation (A) of untreated foliage in the lower cuvette. Responses of gs, E and A of untreated foliage were similar irrespective of whether foliage was at the top or bottom of the seedling. When D in the treatment cuvette was restored to 2.2 kPa, gs, E and A of foliage in the untreated cuvette returned to pretreatment values. In contrast, in well-watered Douglas-fir, there was almost no change in gs, E or A of untreated foliage in one cuvette when D in the other cuvette was reduced, causing a 52% reduction in whole-plant E. However, similar manipulations on drought-stressed Douglas-fir led to 7-19% increases in gs, E and A of untreated foliage. In well-watered western red cedar, daytime leaf water potential (Psil) was maintained near -0.9 MPa over a wide range of D, whereas Psil of Douglas-fir decreased from -1.2 to -1.5 MPa as D increased. The tighter (isohydric) regulation of Psil in western red cedar may partly explain its greater stomatal response to D and variation in whole-plant E compared with Douglas-fir. In response to a

  5. The Presence of Fast-Exchanging Proton Species in Aqueous Solutions of paraCEST Agents Can Impact Rate Constants Measured for Slower Exchanging Species When Fitting CEST Spectra to the Bloch Equations

    PubMed Central

    2015-01-01

    LnDOTA-tetraamide complexes typically exist in solution as a mixture of square-antiprismatic (SAP) and twisted square-antiprismatic (TSAP) coordination isomers. In most cases, the SAP isomer, which is preferred for CEST imaging, predominates, and the presence of the minor TSAP isomer is assumed to have little influence on quantitative measures of the water-exchange rate constant for the SAP isomer. Here, we sought to confirm the validity of this assumption by mixing two chelates with different SAP and TSAP isomer populations while measuring the water-exchange rate constant of the SAP isomer. The results show that an increase in the population of the TSAP isomer in solution results in as much as a 30% overestimation of the water-exchange rate constant for the SAP isomer when CEST spectra are fit to the Bloch equations. This effect was shown to be significant only when the TSAP isomer population exceeded 50%. PMID:25210979

  6. 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.

  7. 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.

  8. 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

  9. 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. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. Effect of root feeding by Diaprepes abbreviatus (Coleoptera: Curculionidae) larvae on leaf gas exchange and growth of three ornamental tree species.

    PubMed

    Diaz, Alex P; Mannion, Catharine; Schaffer, Bruce

    2006-06-01

    Diaprepes abbreviatus L. (Coleoptera: Curculionidae), feeds on a variety of ornamental plants grown in southern Florida. Studies were conducted to evaluate the effects of root feeding by D. abbreviatus larvae on leaf gas exchange and growth of three ornamental tree species commonly grown in southern Florida that are known hosts of this weevil: green buttonwood, Conocarpus erectus L.; live oak, Quercus virginiana Mill.; and pygmy date palm, Phoenix roebelenii O'Brien. These hosts were grown in containers and infested with weevil larvae. Net CO2 assimilation, transpiration, and stomatal conductance of CO, were measured monthly. Leaf, stem, and root fresh and dry weights of each species also were determined. In one of two tests, larval root feeding significantly reduced net CO2 assimilation, transpiration, and stomatal conductance of CO2 of infested green buttonwood trees. Leaf gas exchange of live oak was not affected by larval infestation. In addition to testing cumulative effects of multiple infestations of larvae, the effects of incremental infestations on leaf gas exchange and fresh and dry weights also were tested for each plant species. Net CO2 assimilation, transpiration, stomatal conductance of CO2, and dry weights of green buttonwood were reduced as a result of larval root feeding, whereas there was no effect of incremental larval infestations on leaf gas exchange of live oak or pygmy date palm within the experimental time frame. There was no effect of incremental larval infestations on dry weights of live oak, but leaf, stem, and dry root weight of pygmy date palm were lower for infested plants than for noninfested plants. Overall, green buttonwood was more susceptible to larval root feeding damage than either live oak or pygmy date palm.

  11. 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