Science.gov

Sample records for dynamic species exchange

  1. The Dynamics of Multilateral Exchange

    NASA Astrophysics Data System (ADS)

    Hausken, Kjell; Moxnes, John F.

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

  2. The dynamic multimodeling exchange language

    NASA Astrophysics Data System (ADS)

    Lee, Jinho; Fishwick, Paul A.

    2003-09-01

    The web has made it easy to create multimedia content, which is then viewable by the general community at large. By extending multimedia to include the area of modeling, we make it possible to share and process model structures in the same way as the typical web page. For models of the geometric variety, the new X3D (eXtensible 3D) standard will allow sharing and presentation of 3D scene graphs within the web browser. We have created a dynamic model counterpart to X3D, which we call DXL (Dynamics eXchange Language). DXL is low-level XML-based language, comprising blocks, ports, and connectors. We will define how DXL is used for constructing individual level models, as well as multimodels over multiple abstraction layers.

  3. Nonadiabatic exchange dynamics during adiabatic frequency sweeps

    NASA Astrophysics Data System (ADS)

    Barbara, Thomas M.

    2016-04-01

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

  4. 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

  5. Protein dynamics viewed by hydrogen exchange

    PubMed Central

    Skinner, John J; Lim, Woon K; Bédard, Sabrina; Black, Ben E; Englander, S Walter

    2012-01-01

    To examine the relationship between protein structural dynamics and measurable hydrogen exchange (HX) data, the detailed exchange behavior of most of the backbone amide hydrogens of Staphylococcal nuclease was compared with that of their neighbors, with their structural environment, and with other information. Results show that H-bonded hydrogens are protected from exchange, with HX rate effectively zero, even when they are directly adjacent to solvent. The transition to exchange competence requires a dynamic structural excursion that removes H-bond protection and allows exposure to solvent HX catalyst. The detailed data often make clear the nature of the dynamic excursion required. These range from whole molecule unfolding, through smaller cooperative unfolding reactions of secondary structural elements, and down to local fluctuations that involve as little as a single peptide group or side chain or water molecule. The particular motion that dominates the exchange of any hydrogen is the one that allows the fastest HX rate. The motion and the rate it produces are determined by surrounding structure and not by nearness to solvent or the strength of the protecting H-bond itself or its acceptor type (main chain, side chain, structurally bound water). Many of these motions occur over time scales that are appropriate for biochemical function. PMID:22544544

  6. Protein dynamics viewed by hydrogen exchange.

    PubMed

    Skinner, John J; Lim, Woon K; Bédard, Sabrina; Black, Ben E; Englander, S Walter

    2012-07-01

    To examine the relationship between protein structural dynamics and measurable hydrogen exchange (HX) data, the detailed exchange behavior of most of the backbone amide hydrogens of Staphylococcal nuclease was compared with that of their neighbors, with their structural environment, and with other information. Results show that H-bonded hydrogens are protected from exchange, with HX rate effectively zero, even when they are directly adjacent to solvent. The transition to exchange competence requires a dynamic structural excursion that removes H-bond protection and allows exposure to solvent HX catalyst. The detailed data often make clear the nature of the dynamic excursion required. These range from whole molecule unfolding, through smaller cooperative unfolding reactions of secondary structural elements, and down to local fluctuations that involve as little as a single peptide group or side chain or water molecule. The particular motion that dominates the exchange of any hydrogen is the one that allows the fastest HX rate. The motion and the rate it produces are determined by surrounding structure and not by nearness to solvent or the strength of the protecting H-bond itself or its acceptor type (main chain, side chain, structurally bound water). Many of these motions occur over time scales that are appropriate for biochemical function. PMID:22544544

  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. Optimizing replica exchange moves for molecular dynamics.

    PubMed

    Nadler, Walter; Hansmann, Ulrich H E

    2007-11-01

    We sketch the statistical physics framework of the replica exchange technique when applied to molecular dynamics simulations. In particular, we draw attention to generalized move sets that allow a variety of optimizations as well as new applications of the method. PMID:18233794

  9. 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

  10. 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.

  11. Exchange of Standarized Flight Dynamics Data

    NASA Astrophysics Data System (ADS)

    Martin-Mur, T.; Berry, D.; Flores-Amaya, F.; Foliard, J.; Kiehling, R.; Ogawa, M.; Pallascke

    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.

  12. Dynamics of Exchange-Biased Magnetic Vortices

    NASA Astrophysics Data System (ADS)

    Chen, T. Y.; Chan, M. K.; Crowell, P. A.

    2009-03-01

    We have studied magnetization dynamics in micron-sized circular disks composed of ferromagnetic (FM)-antiferromagnetic (AFM) bilayers. The patterned samples of FeMn/NiFe are field-cooled (FC) or zero-field cooled (ZFC) from above the blocking temperature to room temperature. Time-resolved Kerr microscopy measurements show that the vortex gyrotropic mode fluctuates in frequency as the vortex core is displaced by a static in-plane magnetic field. The average gyrotropic frequency and the magnitude of its fluctuations, which are due to pinning of the vortex core, are larger than in single layer FM films. The enhancement of the gyrotropic frequency is largest in the ZFC samples, in which the effective field due to exchange coupling is expected to enhance pinning of the vortex core at the center of the disk. We find, however, that micromagnetic simulations incorporating uniform or vortex-like exchange-bias fields do not explain our results quantitatively. We interpret this discrepancy as a consequence of randomly orientated AFM domains, which are comparable in size to the vortex core. This work was supported by NSF and the Univ. of Minnesota Graduate School.

  13. 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.

  14. 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.

  15. 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

  16. Cooperation and antagonism in information exchange in a growth scenario with two species.

    PubMed

    Burgos, Andrés C; Polani, Daniel

    2016-06-21

    We consider a simple information-theoretic model of communication, in which two species of bacteria have the option of exchanging information about their environment, thereby improving their chances of survival. For this purpose, we model a system consisting of two species whose dynamics in the world are modelled by a bet-hedging strategy. It is well known that such models lend themselves to elegant information-theoretical interpretations by relating their respective long-term growth rate to the information the individual species has about its environment. We are specifically interested in modelling how this dynamics are affected when the species interact cooperatively or in an antagonistic way in a scenario with limited resources. For this purpose, we consider the exchange of environmental information between the two species in the framework of a game. Our results show that a transition from a cooperative to an antagonistic behaviour in a species results as a response to a change in the availability of resources. Species cooperate in abundance of resources, while they behave antagonistically in scarcity. PMID:27071539

  17. 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.

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

    PubMed Central

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

    2012-01-01

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

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

    PubMed

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

    2012-03-01

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

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

    PubMed

    2012-07-01

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

  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. Water exchange dynamics around H3O+ and OH- ions

    NASA Astrophysics Data System (ADS)

    Roy, Santanu; Dang, Liem X.

    2015-05-01

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

  3. 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).

  4. 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.

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

    PubMed Central

    della Sala, Flavio; Kay, Euan R

    2015-01-01

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

  6. 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.

  7. Magnetization dynamics in exchange coupled antiferromagnet spin superfluids

    NASA Astrophysics Data System (ADS)

    Liu, Yizhou; Barlas, Yafis; Yin, Gen; Zang, Jiadong; Lake, Roger

    Antiferromagnets (AFMs) are commonly used as the exchange bias layer in magnetic recording and spintronic devices. Recently, several studies on the spin transfer torque and spin pumping in AFMs reveal much more interesting physics in AFMs. Properties of AFMs such as the ultrafast switching within picoseconds and spin superfluidity demonstrate the potential to build AFM based spintronic devices. Here, we study the magnetization dynamics in an exchange coupled AFM systems. Beginning from the Landau-Lifshitz-Gilbert equation, we derive a Josephson-like equation for the exchange coupled system. We investigate the detailed magnetization dynamics by employing spin injection and spin pumping theory. We also propose a geometry that could be used to measure this magnetization dynamics. This work was supported as part of the Spins and Heat in Nanoscale Electronic Systems (SHINES) an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award #SC0012670.

  8. Species Abundance Patterns in Complex Evolutionary Dynamics

    NASA Astrophysics Data System (ADS)

    Tokita, Kei

    2004-10-01

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

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

    NASA Astrophysics Data System (ADS)

    Rao, Riccardo; Lacoste, David; Esposito, Massimiliano

    2015-12-01

    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.

  10. 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.

  11. Dynamic simulation of shell-and-tube heat exchangers

    SciTech Connect

    Correa, D.J.; Marchetti, J.L.

    1987-01-01

    The transient operation of a multipass shell-and-tube heat exchanger with baffles is described by a multicell dynamic model where every cell represents a specific part of the exchanger. The proposed modeling technique can be used in a digital computer for the dynamic simulation of almost any type of shell-and-tube heat exchanger. The model includes time-dependent inlet conditions for both the cold and the hot streams. Hence, a number of start-up cases can be simulated and, once the system reaches a stationary operating point, a disturbance can be introduced in the inlet temperatures or the flow rates. This particular feature makes the model very useful not only for design purposes but also for transient analysis and control system design.

  12. 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…

  13. 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.

  14. Spin and orbital exchange interactions from Dynamical Mean Field Theory

    NASA Astrophysics Data System (ADS)

    Secchi, A.; Lichtenstein, A. I.; Katsnelson, M. I.

    2016-02-01

    We derive a set of equations expressing the parameters of the magnetic interactions characterizing a strongly correlated electronic system in terms of single-electron Green's functions and self-energies. This allows to establish a mapping between the initial electronic system and a spin model including up to quadratic interactions between the effective spins, with a general interaction (exchange) tensor that accounts for anisotropic exchange, Dzyaloshinskii-Moriya interaction and other symmetric terms such as dipole-dipole interaction. We present the formulas in a format that can be used for computations via Dynamical Mean Field Theory algorithms.

  15. Surface nanobubble nucleation dynamics during water-ethanol exchange

    NASA Astrophysics Data System (ADS)

    Chan, Chon U.; Ohl, Claus-Dieter

    2015-11-01

    Water-ethanol exchange has been a promising nucleation method for surface attached nanobubbles since their discovery. In this process, water and ethanol displace each other sequentially on a substrate. As the gas solubility is 36 times higher in ethanol than water, it was suggested that the exchange process leads to transient supersaturation and is responsible for the nanobubble nucleation. In this work, we visualize the nucleation dynamics by controllably mixing water and ethanol. It depicts the temporal evolution of the conventional exchange in a single field of view, detailing the conditions for surface nanobubble nucleation and the flow field that influences their spatial organization. This technique can also pattern surface nanobubbles with variable size distribution.

  16. Hyporheic exchange controlled by dynamic hydrologic boundary conditions

    NASA Astrophysics Data System (ADS)

    Schmadel, Noah M.; Ward, Adam S.; Lowry, Christopher S.; Malzone, Jonathan M.

    2016-05-01

    The relative roles of dynamic hydrologic forcing and geomorphology as controls on the timescales and magnitudes of stream-aquifer exchange and hyporheic flow paths are unknown but required for management of stream corridors. We developed a comprehensive framework relating diel hydrologic fluctuations to hyporheic exchange in the absence of geomorphic complexity. We simulated groundwater flow through an aquifer bounded by a straight stream and hillslope and under time-varying boundary conditions. We found that diel fluctuations can produce hyporheic flow path lengths and residence times that span orders of magnitude. With these results, hyporheic flow path residence times and lengths can be predicted from the timing and magnitude of diel fluctuations and valley slope. Finally, we demonstrated that dynamic hydrologic boundary conditions can produce spatial and temporal scales of hyporheic flow paths equivalent to those driven by many well-studied geomorphic features, indicating that these controls must be considered together in future efforts of upscaling to stream networks.

  17. Replica exchange molecular dynamics simulations of amyloid peptide aggregation

    NASA Astrophysics Data System (ADS)

    Cecchini, M.; Rao, F.; Seeber, M.; Caflisch, A.

    2004-12-01

    The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the β-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides.

  18. A dynamical structure of high frequency currency exchange market

    NASA Astrophysics Data System (ADS)

    Sazuka, Naoya; Ohira, Toru; Marumo, Kouhei; Shimizu, Tokiko; Takayasu, Misako; Takayasu, Hideki

    2003-06-01

    We analyze tick-by-tick data, the most high frequency data available, of yen-dollar currency exchange rates. We show that a dynamical structure can be observed in binarized data indicating the direction of up and down movement of prices, which is not apparently seen from the price change itself. This result is consistent with our previous study that there exists a conditional probabilistic structure in binarized data. The dynamical and probabilistic structure which we found could indicate that dealers’ decision making is based on a binary strategy, even if they are unconscious of this fact.

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

    PubMed

    Rao, Riccardo; Lacoste, David; Esposito, Massimiliano

    2015-12-28

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

  20. 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.

  1. Error and efficiency of replica exchange molecular dynamics simulations

    PubMed Central

    Rosta, Edina; Hummer, Gerhard

    2009-01-01

    We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977

  2. Error and efficiency of replica exchange molecular dynamics simulations.

    PubMed

    Rosta, Edina; Hummer, Gerhard

    2009-10-28

    We derive simple analytical expressions for the error and computational efficiency of replica exchange molecular dynamics (REMD) simulations (and by analogy replica exchange Monte Carlo simulations). The theory applies to the important case of systems whose dynamics at long times is dominated by the slow interconversion between two metastable states. As a specific example, we consider the folding and unfolding of a protein. The efficiency is defined as the rate with which the error in an estimated equilibrium property, as measured by the variance of the estimator over repeated simulations, decreases with simulation time. For two-state systems, this rate is in general independent of the particular property. Our main result is that, with comparable computational resources used, the relative efficiency of REMD and molecular dynamics (MD) simulations is given by the ratio of the number of transitions between the two states averaged over all replicas at the different temperatures, and the number of transitions at the single temperature of the MD run. This formula applies if replica exchange is frequent, as compared to the transition times. High efficiency of REMD is thus achieved by including replica temperatures in which the frequency of transitions is higher than that at the temperature of interest. In tests of the expressions for the error in the estimator, computational efficiency, and the rate of equilibration we find quantitative agreement with the results both from kinetic models of REMD and from actual all-atom simulations of the folding of a peptide in water. PMID:19894977

  3. 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

  4. G-register exchange dynamics in guanine quadruplexes.

    PubMed

    Harkness, Robert W; Mittermaier, Anthony K

    2016-05-01

    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

  5. 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.

  6. A multi-species exchange model for fully fluctuating polymer field theory simulations

    SciTech Connect

    Düchs, Dominik; Delaney, Kris T.; Fredrickson, Glenn H.

    2014-11-07

    Field-theoretic models have been used extensively to study the phase behavior of inhomogeneous polymer melts and solutions, both in self-consistent mean-field calculations and in numerical simulations of the full theory capturing composition fluctuations. The models commonly used can be grouped into two categories, namely, species models and exchange models. Species models involve integrations of functionals that explicitly depend on fields originating both from species density operators and their conjugate chemical potential fields. In contrast, exchange models retain only linear combinations of the chemical potential fields. In the two-component case, development of exchange models has been instrumental in enabling stable complex Langevin (CL) simulations of the full complex-valued theory. No comparable stable CL approach has yet been established for field theories of the species type. Here, we introduce an extension of the exchange model to an arbitrary number of components, namely, the multi-species exchange (MSE) model, which greatly expands the classes of soft material systems that can be accessed by the complex Langevin simulation technique. We demonstrate the stability and accuracy of the MSE-CL sampling approach using numerical simulations of triblock and tetrablock terpolymer melts, and tetrablock quaterpolymer melts. This method should enable studies of a wide range of fluctuation phenomena in multiblock/multi-species polymer blends and composites.

  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. Optimized explicit-solvent replica exchange molecular dynamics from scratch.

    PubMed

    Nadler, Walter; Hansmann, Ulrich H E

    2008-08-28

    Replica exchange molecular dynamics (REMD) simulations have become an important tool to study proteins and other biological molecules in silico. However, such investigations require considerable, and often prohibitive, numerical effort when the molecules are simulated in explicit solvents. In this communication we show that in this case the cost can be minimized by choosing the number of replicas as N(opt) approximately 1+0.594 radical C ln(Tmax/Tmin), where C is the specific heat, and the temperatures distributed according to Ti(opt) approximately T min(Tmax/Tmin)(i-1)/(N-1). PMID:18671362

  9. Dynamically corrected gates for an exchange-only qubit

    NASA Astrophysics Data System (ADS)

    Hickman, G. T.; Wang, Xin; Kestner, J. P.; Das Sarma, S.

    2013-10-01

    We provide analytical composite pulse sequences that perform dynamical decoupling concurrently with arbitrary rotations for a qubit coded in the spin state of a triple quantum dot. The sequences are designed to respect realistic experimental constraints such as strictly nonnegative couplings. Logical errors and leakage errors are simultaneously corrected. A short pulse sequence is presented to compensate nuclear noise and a longer sequence is presented to simultaneously compensate nuclear and charge noise. The capability developed in this work provides a clear prescription for combatting the relevant sources of noise that currently hinder exchange-only qubit experiments.

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

    NASA Astrophysics Data System (ADS)

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

    2009-12-01

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

  11. Thermostat artifacts in replica exchange molecular dynamics simulations.

    PubMed

    Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard

    2009-01-01

    We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980

  12. Thermostat artifacts in replica exchange molecular dynamics simulations

    PubMed Central

    Rosta, Edina; Buchete, Nicolae-Viorel; Hummer, Gerhard

    2009-01-01

    We explore the effects of thermostats in replica exchange molecular dynamics (REMD) simulations. For thermostats that do not produce a canonical ensemble, REMD simulations are found to distort the configuration-space distributions. For bulk water, we find small deviations of the average potential energies, the buildup of tails in the potential energy distributions, and artificial correlations between the energies at different temperatures. If a solute is present, as in protein folding simulations, its conformational equilibrium can be altered. In REMD simulations of a helix-forming peptide with a weak-coupling (Berendsen) thermostat, we find that the folded state is overpopulated by about 10% at low temperatures, and underpopulated at high temperatures. As a consequence, the enthalpy of folding deviates by almost 3 kcal/mol from the correct value. The reason for this population shift is that non-canonical ensembles with narrowed potential energy fluctuations artificially bias toward replica exchanges between low-energy folded structures at the high temperature and high-energy unfolded structures at the low temperature. We conclude that REMD simulations should only be performed in conjunction with thermostats that produce a canonical ensemble. PMID:20046980

  13. 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.

  14. 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.

  15. Modeling metapopulation dynamics for single species of seabirds

    USGS Publications Warehouse

    Buckley, P.A.; Downer, R.

    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

  16. Dynamics of ligand exchange mechanism at Cu(II) in water: An ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region

    SciTech Connect

    Moin, Syed Tarique; Hofer, Thomas S.; Weiss, Alexander K. H.; Rode, Bernd M.

    2013-07-07

    Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment.

  17. Two competing species in super-diffusive dynamical regimes

    NASA Astrophysics Data System (ADS)

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

    2010-09-01

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

  18. Modeling dynamic exchange of gaseous elemental mercury at polar sunrise.

    PubMed

    Dastoor, Ashu P; Davignon, Didier; Theys, Nicolas; Van Roozendael, Michel; Steffen, Alexandra; Ariya, Parisa A

    2008-07-15

    At polar sunrise, gaseous elemental mercury (GEM) undergoes an exceptional dynamic exchange in the air and at the snow surface during which GEM can be rapidly removed from the atmosphere (the so-called atmospheric mercury depletion events (AMDEs)) as well as re-emitted from the snow within a few hours to days in the Polar Regions. Although high concentrations of total mercury in snow following AMDEs is well documented, there is very little data available on the redox transformation processes of mercury in the snow and the fluxes of mercury at the air/snow interface. Therefore, the net gain of mercury in the Polar Regions as a result of AMDEs is still an open question. We developed a new version of the global mercury model, GRAHM, which includes for the first time bidirectional surface exchange of GEM in Polar Regions in spring and summer by developing schemes for mercury halogen oxidation, deposition, and re-emission. Also for the first time, GOME satellite data-derived boundary layer concentrations of BrO have been used in a global mercury model for representation of halogen mercury chemistry. Comparison of model simulated and measured atmospheric concentrations of GEM at Alert, Canada, for 3 years (2002-2004) shows the model's capability in simulating the rapid cycling of mercury during and after AMDEs. Brooks et al. (1) measured mercury deposition, reemission, and net surface gain fluxes of mercury at Barrow, AK, during an intensive measurement campaign for a 2 week period in spring (March 25 to April 7, 2003). They reported 1.7, 1.0 +/- 0.2, and 0.7 +/- 0.2 microg m(-2) deposition, re-emission, and net surface gain, respectively. Using the optimal configuration of the model, we estimated 1.8 microg m(-2) deposition, 1.0 microg m(-2) re-emission, and 0.8 microg m(-2) net surface gain of mercury for the same time period at Barrow. The estimated net annual accumulation of mercury within the Arctic Circle north of 66.5 degrees is approximately 174 t with +/-7 t of

  19. Effect of chelate dynamics on water exchange reactions of paramagnetic aminopolycarboxylate complexes.

    PubMed

    Maigut, Joachim; Meier, Roland; Zahl, Achim; van Eldik, Rudi

    2008-07-01

    Because of our interest in evaluating a possible relationship between complex dynamics and water exchange reactivity, we performed (1)H NMR studies on the paramagnetic aminopolycarboxylate complexes Fe (II)-TMDTA and Fe (II)-CyDTA and their diamagnetic analogues Zn (II)-TMDTA and Zn (II)-CyDTA. Whereas a fast Delta-Lambda isomerization was observed for the TMDTA species, no acetate scrambling between in-plane and out-of-plane positions is accessible for any of the CyDTA complexes because the rigid ligand backbone prevents any configurational changes in the chelate system. In variable-temperature (1)H NMR studies, no evidence of spectral coalescence due to nitrogen inversion was found for any of the complexes in the available temperature range. The TMDTA complexes exhibit the known solution behavior of EDTA, whereas the CyDTA complexes adopt static solution structures. Comparing the exchange kinetics of flexible EDTA-type complexes and static CyDTA complexes appears to be a suitable method for evaluating the effect of ligand dynamics on the overall reactivity. In order to assess information concerning the rates and mechanism of water exchange, we performed variable-temperature and -pressure (17)O NMR studies of Ni (II)-CyDTA, Fe (II)-CyDTA, and Mn (II)-CyDTA. For Ni (II)-CyDTA, no significant effects on line widths or chemical shifts were apparent, indicating either the absence of any chemical exchange or the existence of a very small amount of the water-coordinated complex in solution. For [Fe (II)(CyDTA)(H 2O)] (2-) and [Mn (II)(CyDTA)(H 2O)] (2-), exchange rate constant values of (1.1 +/- 0.3) x 10 (6) and (1.4 +/- 0.2) x 10 (8) s (-1), respectively, at 298 K were determined from fits to resonance-shift and line-broadening data. A relationship between chelate dynamics and reactivity seems to be operative, since the CyDTA complexes exhibited significantly slower reactions than their EDTA counterparts. The variable-pressure (17)O NMR measurements for [Mn (II

  20. Dynamic Distortion Correction for Endoscopy Systems with Exchangeable Optics

    NASA Astrophysics Data System (ADS)

    Stehle, Thomas; Hennes, Michael; Gross, Sebastian; Behrens, Alexander; Wulff, Jonas; Aach, Til

    Endoscopic images are strongly affected by lens distortion caused by the use of wide angle lenses. In case of endoscopy systems with exchangeable optics, e.g. in bladder endoscopy or sinus endoscopy, the camera sensor and the optics do not form a rigid system but they can be shifted and rotated with respect to each other during an examination. This flexibility has a major impact on the location of the distortion centre as it is moved along with the optics. In this paper, we describe an algorithm for the dynamic correction of lens distortion in cystoscopy which is based on a one time calibration. For the compensation, we combine a conventional static method for distortion correction with an algorithm to detect the position and the orientation of the elliptic field of view. This enables us to estimate the position of the distortion centre according to the relative movement of camera and optics. Therewith, a distortion correction for arbitrary rotation angles and shifts becomes possible without performing static calibrations for every possible combination of shifts and angles beforehand.

  1. 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.

  2. 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

  3. 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. PMID:15214428

  4. 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.

  5. 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

  6. 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. PMID:16154585

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

    SciTech Connect

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

    2008-12-26

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

  8. 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…

  9. Subzero temperature chromatography for reduced back-exchange and improved dynamic range in amide hydrogen/deuterium exchange mass spectrometry.

    PubMed

    Venable, John D; Okach, Linda; Agarwalla, Sanjay; Brock, Ansgar

    2012-11-01

    Amide hydrogen/deuterium exchange is a commonly used technique for studying the dynamics of proteins and their interactions with other proteins or ligands. When coupled with liquid chromatography and mass spectrometry, hydrogen/deuterium exchange provides several unique advantages over other structural characterization techniques including very high sensitivity, the ability to analyze proteins in complex environments, and a large mass range. A fundamental limitation of the technique arises from the loss of the deuterium label (back-exchange) during the course of the analysis. A method to limit loss of the label during the separation stage of the analysis using subzero temperature reversed-phase chromatography is presented. The approach is facilitated by the use of buffer modifiers that prevent freezing. We evaluated ethylene glycol, dimethyl formamide, formamide, and methanol for their freezing point suppression capabilities, effects on peptide retention, and their compatibilities with electrospray ionization. Ethylene glycol was used extensively because of its good electrospray ionization compatibility; however, formamide has potential to be a superior modifier if detrimental effects on ionization can be overcome. It is demonstrated using suitable buffer modifiers that separations can be performed at temperatures as low as -30 °C with negligible loss of the deuterium label, even during long chromatographic separations. The reduction in back-exchange is shown to increase the dynamic range of hydrogen/deuterium exchange mass spectrometry in terms of mixture complexity and the magnitude with which changes in deuteration level can be quantified. PMID:23025328

  10. 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

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

    PubMed

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

    2016-06-01

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

  12. Richards-like two species population dynamics model.

    PubMed

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

    2014-12-01

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

  13. 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..

  14. 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. PMID:9522895

  15. 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

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

    PubMed

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

    2016-08-01

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

  17. [Parametric control of the yield characteristics and species composition dynamics of algal poly-culture].

    PubMed

    Nefedova, E L; Levinskikh, M A; Sychev, V N

    2006-01-01

    There are several experimental models of biological life support systems (BLSS) designed to incorporate a chlorella pool. These BLSS can be optimized if populated by algal associations that could take up more functions within the closed cycling system than a single alga species. Introduction of a Spirulina and Chlamydomonas poly-culture with differing in gas exchange and biochemical composition resulted in a tighter closure of linkages within the system. The factors determining the size of a species population in intensive continuous poly-cultures are, first and foremost, pH and suspension flow rate. Experimental testing of this supposition brought us to the conclusion that parametric control of alga productivity and species composition dynamics makes it possible to create a steady intensive poly-culture as part of the LSS for humans. Flow rate and pH can be the parameters for control of the Spirulina and Chlamydomonas populations during continuous cultivation of this poly-culture. PMID:17357628

  18. EXCHANGE

    SciTech Connect

    Boltz, J.C.

    1992-09-01

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

  19. 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. PMID:27154920

  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. PMID:23889003

  1. Impact of precipitation dynamics on net ecosystem exchange

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    PubMed

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

    2015-12-01

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

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

    USGS Publications Warehouse

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

    2015-01-01

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

  4. Benchmarking novel approaches for modelling species range dynamics

    PubMed Central

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Wörman, Anders; Morén, Ida; Riml, Joakim

    2016-04-01

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

  6. Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

    PubMed

    Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

    2015-06-01

    Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data. PMID:26575570

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

    PubMed

    Xiao, Yiming; Konermann, Lars

    2015-08-01

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

  8. 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

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

    PubMed

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

    2016-02-01

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

  10. 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.

  11. 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). PMID:25706188

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

    PubMed

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

    2012-07-01

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

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

    PubMed

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

    2010-06-01

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

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

    PubMed Central

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

    2015-01-01

    Dynamic combinatorial chemistry has emerged as a promising tool for the discovery of complex receptors in supramolecular chemistry. At the heart of dynamic combinatorial chemistry are the reversible reactions that enable the exchange of building blocks between library members in dynamic combinatorial libraries (DCLs) ensuring thermodynamic control over the system. If more than one reversible reaction operates in a single dynamic combinatorial library, the complexity of the system increases dramatically, and so does its possible applications. One can imagine two reversible reactions that operate simultaneously or two reversible reactions that operate independently. Both these scenarios have advantages and disadvantages. In this contribution, we show how disulfide exchange and boronic ester transesterification can function simultaneous in dynamic combinatorial libraries under appropriate conditions. We describe the detailed studies necessary to establish suitable reaction conditions and highlight the analytical techniques appropriate to study this type of system. PMID:26378519

  15. 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…

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

    SciTech Connect

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

    1998-12-01

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

  17. 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.

  18. 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.

  19. 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

  20. Exchange explosions: Magnetization dynamics during vortex-antivortex annihilation.

    PubMed

    Hertel, Riccardo; Schneider, Claus M

    2006-10-27

    A magnetic vortex and an antivortex can annihilate, resulting in a homogeneous magnetization. A detailed description of the magnetization dynamics of such annihilation processes is obtained by micromagnetic simulations based on the Landau-Lifshitz-Gilbert equation. We show that, depending on the relative polarization of the vortex-antivortex pair, the annihilation process is either a continuous transformation of the magnetic structure or it involves the propagation of a micromagnetic singularity (Bloch point) causing a burstlike emission of spin waves. These results provide new insight into a fundamental micromagnetic process that has recently been proposed for a controlled generation of spin waves. PMID:17155502

  1. 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.

  2. Dynamics of polymeric brushes: End exchange and bridging kinetics

    NASA Astrophysics Data System (ADS)

    Johner, A.; Joanny, J. F.

    1993-01-01

    We study some dynamical aspects of grafted polymer layers in a solvent. The structure of the brush is described in a θ solvent by the self-consistent mean field theory and in a good solvent using scaling laws. The Rouse-Zimm model including hydrodynamic interactions is used for the dynamic properties. A given chain end explores the entire thickness of a free grafted layer in a time Te proportional to the cube of the thickness. The exploration time is much larger than the Rouse time that characterizes the relaxation of the fluctuations of the chains conformations. In a θ-solvent we give a detailed study of the relaxation of the density of a few labeled chain ends towards its equilibrium value. The bridging kinetics between a grafting plate and a plate adsorbing the free ends is also discussed. When adsorption proceeds, an exclusion zone grows in the vicinity of the adsorbing plate. To cross the exclusion zone and adsorb, a chain end must overcome an energy barrier. The typical adsorption time is the first passage time through this barrier. Except in the very late stages where the fraction of chains η forming bridges saturates at its equilibrium value, the energy barrier against adsorption increases as a power law of η and the bridging fraction increases very slowly (logarithmically) with time. Both weak bridging where only a small fraction of chains form bridges and total bridging where all the chains form bridges are studied.

  3. Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics.

    PubMed

    Sanbonmatsu, K Y; García, A E

    2002-02-01

    Replica exchange molecular dynamics (MD) simulations of Met-enkephalin in explicit solvent reveal helical and nonhelical structures. Four predominant structures of Met-enkephalin are sampled with comparable probabilities (two helical and two nonhelical). The energy barriers between these configurations are low, suggesting that Met-enkephalin switches easily between configurations. This is consistent with the requirement that Met-enkephalin be sufficiently flexible to bind to several different receptors. Replica exchange simulations of 32 ns are shown to sample approximately five times more configurational space than constant temperature MD simulations of the same duration. The energy landscape for the replica exchange simulation is presented. A detailed study of replica trajectories demonstrates that the significant increases in temperature provided by the replica exchange technique enable transitions from nonhelical to helical structures that would otherwise be prevented by kinetic trapping. Met-enkephalin (Type Entrez Proteins; Value A61445; Service Entrez Proteins). PMID:11807951

  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. Probing ultrafast photo-induced dynamics of the exchange energy in a Heisenberg antiferromagnet

    NASA Astrophysics Data System (ADS)

    Batignani, G.; Bossini, D.; di Palo, N.; Ferrante, C.; Pontecorvo, E.; Cerullo, G.; Kimel, A.; Scopigno, T.

    2015-08-01

    Manipulating the macroscopic phases of solids using ultrashort light pulses has resulted in spectacular phenomena, including metal-insulator transitions, superconductivity and subpicosecond modification of magnetic order. The development of this research area strongly depends on the understanding and optical control of fundamental interactions in condensed matter, in particular the exchange interaction. However, disentangling the timescales relevant for the contributions of the exchange interaction and spin dynamics to the exchange energy, Eex, is a challenge. Here, we introduce femtosecond stimulated Raman scattering to unravel the ultrafast photo-induced dynamics of magnetic excitations at the edge of the Brillouin zone. We find that femtosecond laser excitation of the antiferromagnet KNiF3 triggers a spectral shift of the two-magnon line, the energy of which is proportional to Eex. By unravelling the photo-induced modification of the two-magnon line frequency from a dominating nonlinear optical effect, we find that Eex is increased by the electromagnetic stimulus.

  6. 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

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

    PubMed

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

    2016-05-01

    Dynamic exchanges between dissolved organic matter (DOM) and particulate organic matter (POM) plays a critical role in organic carbon cycling in coastal and inland aquatic ecosystems, interactions with aquatic organisms, mobility and bioavailability of pollutants, among many other ecological and geochemical phenomena. Although DOM-POM exchange processes have been widely studied from different aspects, little to no effort has been made to date to provide a comprehensive, mechanistic, and micro-spatial schema for understanding various exchange processes occurring in different aquatic ecosystems in a unified way. The phenomena occurring between DOM and POM were explained here with the homogeneous and heterogeneous mechanisms. In the homogeneous mechanism, the participating components are only organic matter (OM) constituents themselves with aggregation and dissolution involved, whereas OM is associated with other components such as minerals and particulate colloids in the heterogeneous counterpart. Besides the generally concerned processes of aggregation/dissolution and adsorption/desorption, other ecological factors such as sunlight and organisms can also participate in DOM-POM exchanges through altering the chemical nature of OM. Despite the limitation of current analytical technologies, many unknown and/or unquantified processes need to be identified to unravel the complicated exchanges of OM between its dissolved and particulate states. Based on the review of several previous mathematical models, we proposed a unified conceptual model to describe all major dynamic exchange mechanisms on the basis of exergy theory. More knowledge of dynamic DOM-POM exchanges is warranted to overcome the potential problems arising from a simple division of OM into dissolved versus particulate states and to further develop more sophisticated mathematic models. PMID:26881732

  8. 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.

  9. 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

  10. 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., III; 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.

  11. 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.

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

    NASA Astrophysics Data System (ADS)

    Lin, Zhixiong; van Gunsteren, Wilfred F.

    2015-07-01

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

  13. Asymmetry in the static and dynamic magnetic properties of a weak exchange spring trilayer

    NASA Astrophysics Data System (ADS)

    Gubbiotti, G.; Carlotti, G.; Weston, J.; Zangari, G.; Crew, D. C.; Stamps, R. L.

    2005-02-01

    Experimental results and theoretical calculations are presented for the static and dynamic magnetic properties of a weak exchange-spring symmetric FeTaN/FeSm/FeTaN trilayer. Static properties were investigated by means of alternating gradient field and magneto-optic Kerr effect magnetometries. The frequencies of three spin wave modes were measured by inelastic light scattering from long wavelength thermal spin waves. The combined analysis of spin wave frequencies and magnetometry data provides a consistent set of exchange, anisotropy and film thickness parameters.

  14. 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.

  15. 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.

  16. 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

  17. [A comparative study of external respiration, gas exchange and circulation during static and dynamic muscular loads].

    PubMed

    Bubeev, Iu A; Khomenko, M N; Poliukhovich, V V; Remizov, Iu I

    1995-01-01

    Indices of external breathing, gas exchange, and circulation were studied during bicycle ergometry and static ergometry of 19 healthy male volunteers which were stopped at critical levels of heart rate, arterial pressure, ECG or subjective fatigue. The bicycle workload maximum averaged 210 Watts, the static ergometric, 224 kg/s. Both types of exercises were characterized by unidirectional shifting of the external breathing and gas exchange indices; however, they were less pronounced at static loads. Arterial pressure and resistance of the peripheral vessels were the only indices of the array the dynamics of which complied with and even exceeded that during bicycling. In contrast to the dynamic muscular load, the maximal dynamics of gas exchange and external breathing during static ergometric workload was observed in the rehabilitation period following restoration of muscle blood flow; this must be taken into account in interpretation of test results. It is concluded that high information virtues of the static ergometric test in the context of predicting aerobatic load tolerance, and similarity of dynamics in the period of rehabilitation hold much promise for using the tests with static muscular loading in aviation and space medicine. PMID:8664858

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

    PubMed

    Gudmundson, Sara; Eklöf, Anna; Wennergren, Uno

    2015-08-01

    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

  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. PMID:27523073

  20. Probing the dynamic regulation of peripheral membrane proteins using hydrogen deuterium exchange-MS (HDX-MS).

    PubMed

    Vadas, Oscar; Burke, John E

    2015-10-01

    Many cellular signalling events are controlled by the selective recruitment of protein complexes to membranes. Determining the molecular basis for how lipid signalling complexes are recruited, assembled and regulated on specific membrane compartments has remained challenging due to the difficulty of working in conditions mimicking native biological membrane environments. Enzyme recruitment to membranes is controlled by a variety of regulatory mechanisms, including binding to specific lipid species, protein-protein interactions, membrane curvature, as well as post-translational modifications. A powerful tool to study the regulation of membrane signalling enzymes and complexes is hydrogen deuterium exchange-MS (HDX-MS), a technique that allows for the interrogation of protein dynamics upon membrane binding and recruitment. This review will highlight the theory and development of HDX-MS and its application to examine the molecular basis of lipid signalling enzymes, specifically the regulation and activation of phosphoinositide 3-kinases (PI3Ks). PMID:26517882

  1. Dynamics of heat, water, and soluble gas exchange in the human airways: 1. A model study.

    PubMed

    Tsu, M E; Babb, A L; Ralph, D D; Hlastala, M P

    1988-01-01

    In order to provide a means for analysis of heat, water, and soluble gas exchange with the airways during tidal ventilation, a one dimensional theoretical model describing heat and water exchange in the respiratory airways has been extended to include soluble gas exchange with the airway mucosa and water exchange with the mucous layer lining the airways. Not only do heat, water, and gas exchange occur simultaneously, but they also interact. Heating and cooling of the airway surface and mucous lining affects both evaporative water and soluble gas exchange. Water evaporation provides a major source of heat exchange. The model-predicted mean airway temperature profiles agree well with literature data for both oral and nasal breathing validating that part of the model. With model parameters giving the best fit to experimental data, the model shows: (a) substantial heat recovery in the upper airways, (b) minimal respiratory heat and water loss, and (c) low average mucous temperatures and maximal increases in mucous thickness. For resting breathing of room air, heat and water conservation appear to be more important than conditioning efficiency. End-tidal expired partial pressures of very soluble gases eliminated by the lungs are predicted to be lower than the alveolar partial pressures due to the absorption of the expired gases by the airway mucosa. The model may be usable for design of experiments to examine mechanisms associated with the local hydration and dehydration dynamics of the mucosal surface, control of bronchial perfusion, triggering of asthma, mucociliary clearance and deposition of inhaled pollutant gases. PMID:3228218

  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. 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

  4. 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.

  5. Changes in ecosystem structure related to the type and extent of woody cover alter carbon dynamics and surface energy exchange in central Texas ecosystems.

    NASA Astrophysics Data System (ADS)

    Litvak, M. E.; Heilman, J.; McInnes, K.; Owens, K.; Kjelgaard, J.; Thijs, A.

    2006-12-01

    Rangeland ecosystems account for almost two thirds the total land area in Texas. Over the past century, heavy livestock grazing and fire suppression coupled with changes in climate have facilitated the expansion of woody species into rangelands throughout the state. Based in part on the assumption that woody species use more water than their herbaceous counterparts, land managers have used a variety of techniques to reduce tree and shrub abundance to combat the loss of forage for cattle. As a result, the structure of rangelands in Texas is complex, characterized by woody vegetation that is patchy in distribution, and continually changing between grassland, savanna and woodland. Despite the large areal extent of Texas rangelands, very little is known about how the observed changes in ecosystem structure impact carbon cycle dynamics and surface energy exchange. To reduce these uncertainties, we explored explicit relationships between structure and function in these ecosystems by comparing tower-based measurements of carbon and water vapor exchange made simultaneously from July 2004-Dec 2005 across three representative land covers in central Texas: open grassland, savanna with 30% Ashe juniper and honey mesquite cover, and closed canopy woodland. Here we report our findings on what impact the type and pattern of woody plant cover has on biological controls and patterns of carbon sequestration, evapotranspiration, and sensitivity to precipitation pulses. Monthly measurements of leaf level gas exchange, soil respiration rates, herbaceous net ecosystem exchange, and sap flow measurements on dominant woody species were used to augment eddy covariance estimates of ecosystem-atmosphere exchange. The addition of woody species significantly increased carbon sequestration in these ecosystems. Net ecosystem production from July 05-Jun 05 in the grassland, savanna and forest ecosystems was -14 g C m-2, -413 g C m-2, -450 g C m-2, respectively. Evapotranspiration was less

  6. 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.

  7. Hydrogen-deuterium exchange mass spectrometry for investigation of backbone dynamics of oxidized and reduced cytochrome P450cam.

    PubMed

    Hamuro, Yoshitomo; Molnar, Kathleen S; Coales, Stephen J; OuYang, Bo; Simorellis, Alana K; Pochapsky, Thomas C

    2008-02-01

    Backbone dynamics of the camphor monoxygenase cytochrome P450(cam) (CYP101) as a function of oxidation/ligation state of the heme iron were investigated via hydrogen/deuterium exchange (H/D exchange) as monitored by mass spectrometry. Main chain amide NH hydrogens can exchange readily with solvent and the rate of this exchange depends upon, among other things, dynamic fluctuations in local structural elements. A fluxional region of the polypeptide will exchange more quickly with solvent than one that is more constrained. In most regions of the enzyme, exchange rates were similar between oxidized high-spin camphor-bound and reduced camphor- and CO-bound CYP101 (CYP-S and CYP-S-CO, respectively). However, in regions of the protein that have previously been implicated in substrate access by structural and molecular dynamics investigations, the reduced enzyme shows significantly slower exchange rates than the oxidized CYP-S. This observation corresponds to increased flexibility of the oxidized enzyme relative to the reduced form. Structural features previously found to be perturbed in CYP-S-CO upon binding of the biologically relevant effector and reductant putidaredoxin (Pdx) as determined by nuclear magnetic resonance are also more protected from exchange in the reduced state. To our knowledge, this study represents the first experimental investigation of backbone dynamics within the P450 family using this methodology. PMID:18023482

  8. Molecular dynamics simulations of transducin: interdomain and front to back communication in activation and nucleotide exchange.

    PubMed

    Ceruso, Marc A; Periole, Xavier; Weinstein, Harel

    2004-04-30

    The dynamic events that underlie the nucleotide exchange process for the Galpha subunit of transducin (Galpha(t)) were studied with nanosecond time-scale molecular dynamics simulations. The modeled systems include the active and inactive forms of the wild-type Galpha(t) and three of its mutants (GDP-bound form only): F332A, A322S, and Q326A that are known to exhibit various degrees of enhancement of their basal and receptor-catalyzed rates of nucleotide exchange (150-fold, 70-fold and WT-like, respectively). The results of these computational experiments reveal a number of nucleotide-dependent structural and dynamic changes (involving the alpha(B)-alpha(C) loop, the inter-domain orientation of the helical and GTPase domains and the alpha(5) helix) that were not observed in the various crystal structures of Galpha(t). Notably, the results show the existence of a front to back communication device (involving the beta(2)-beta(3) hairpin, the alpha(1) helix and the alpha(5) helix), strategically located near all elements susceptible to be involved in receptor-mediated activation/nucleotide exchange. The wild-type simulations suggest that the dynamic interplay between the elements of this device would be critical for the activation of the Galpha(t) subunit. This inference is confirmed by the results of the computational experiments on the mutants that show that even in their GDP-bound forms, the A322S and F332A mutants acquire an "active-like" structure and dynamics phenotype. The same is not true for the Q326A mutant whose structural and dynamic properties remain similar to those of the GDP-bound WT. Taken together the results suggest a nucleotide exchange mechanism, analogous to that found in the Arf family GTPases, in which a partially activated state, achievable from a receptor-mediated action of the front to back communication device either by displacement of the C-terminal alpha(5) helix, of the N-terminal alpha(N) helix, or of the Gbetagamma subunit, could

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

    NASA Astrophysics Data System (ADS)

    Voltz, Thomas; Gooseff, Michael; Ward, Adam S.; Singha, Kamini; Fitzgerald, Michael; Wagener, Thorsten

    2013-06-01

    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, forested, headwater catchments in Oregon (WS01 and WS03) to determine the potential controls of reach-scale valley slope and cross-sectional valley geometry. Groundwater and stream stage data collected at high spatial and temporal resolutions over a period encompassing a 1.25 year storm and subsequent seasonal baseflow recession indicate that hydraulic gradients in both riparian aquifers exhibit strong persistence of down-valley dominance. Responses to rainfall do not support the simple conceptual models of increased riparian hydraulic gradient toward streams. Hydraulic gradient response in WS01 to both the seasonal baseflow recession and the storm suggested the potential for increased stream-groundwater exchange, but there was less evidence for this in WS03. Results from four constant-rate tracer injections in each stream showed a high baseline level of exchange overall, and both a slight seasonal increase (WS01) and slight decrease (WS03) in the riparian intrusion of tracer-labeled stream water as stream discharge receded. These results indicate that steep headwater valley floors host extensive stream water exchange and very little change in the water table gradients over 3 orders of magnitude of stream discharge.

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

    PubMed

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

    1992-10-15

    A procedure has been developed for measuring 147Pm in bioassay samples, based on the separation and preconcentration of 147Pm from the urine matrix by adsorption onto a conventional cation-exchange column with final separation and purification by HPLC using dynamic ion-exchange chromatography. The concentration of 147Pm is determined by collecting the appropriate HPLC fraction and measuring the 147Pm by liquid scintillation counting. The limit of detection is 0.1 Bq (3 fg) 147Pm based on a 500-mL sample of urine and a counting time of 30 min with a background of 100 cpm. Ten samples can be processed in 1.5-2 days. PMID:1466450

  11. 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.

  12. Tree Species Specific Soil Moisture Patterns and Dynamics

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    Land use has a major influence on the hydrologic processes that take place in soils. Soil compaction on pastures for example leads to infiltration patterns that differ considerably from the ones observable in forests. It is not clear, however, how different forest stands influence soil infiltration and soil moisture distributions. Factors that that vary amongst different stands and potentially affect soil moisture processes in forests are, amongst others, canopy density, throughfall patterns, the intensity and frequency of stem flow, litter type, root distributions and rooting depth. To investigate how different tree species influence the way soils partition, store and conduct incoming precipitation we selected 15 locations under different tree stands within the TERENO observatory in north-east Germany. The forest stands under investigation were mature oak, young pine, mature pine, young beech and mature beech. At each location we installed 30 FDR soil moisture sensors grouped into five depth profiles (monitoring soil moisture from 10 cm to 200 cm) and 5 additional near surface sensors. The profile locations within each forest stand covered most of the anticipated variability by ranging from minimum to maximum distance to the trees including locations under more and less dense canopy. Supplementary to the FDR sensors, throughfall measurements, tensiometers and groundwater data were available to observe dynamics of tree water availability, water fluxes within the soils and percolation towards the groundwater. To identify patterns in space and time we referred to the statistical methods of wavelet analysis and temporal stability analysis. Finally, we tried to link the results from these analyses to specific hydrologic processes at the different locations.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  14. pH-replica exchange molecular dynamics in proteins using a discrete protonation method.

    PubMed

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

    2012-08-01

    Protonation equilibria in biological molecules modulates structure, dynamics, and function. A pH-replica exchange molecular dynamics (pH-REMD) method is described here to improve the coupling between conformational and protonation sampling. Under a Hamiltonian replica exchange setup, conformations are swapped between two neighboring replicas, which themselves are at different pHs. The method has been validated on a series of biological systems. We applied pH-REMD to a series of model compounds, to an terminally charged ADFDA pentapeptide, and to a heptapeptide derived from the ovomucoid third domain (OMTKY3). In all of those systems, the predicted pK(a) by pH-REMD is very close to the experimental value and almost identical to the ones obtained by constant pH molecular dynamics (CpH MD). The method presented here, pH-REMD, has the advantage of faster convergence properties due to enhanced sampling of both conformation and protonation spaces. PMID:22694266

  15. 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.

  16. 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. PMID:27153477

  17. Flow dynamics of ash deposition in heat-exchanger tube banks

    SciTech Connect

    Shaffer, F.; Ekmann, J.; Mathur, M.

    1991-01-01

    The objective of this project is to generate experimental data to describe flow fields in heat-exchanger tube banks. One of the main applications of this data is in the evaluation of computational fluid dynamics (CFD) models which are an important part of an ash deposition model. The CFD models under evaluation include a large eddy simulation (LES) being developed by Textron Inc. under DOE-PETC funding and the CLEW code developed at the University of California at Berkeley. Various CFD modeling approaches, e.g., implementation of a transition-to-turbulence and modified wall functions, are also being tested using the PHOENICS code.

  18. Flow dynamics of ash deposition in heat-exchanger tube banks

    SciTech Connect

    Shaffer, F.; Ekmann, J.; Mathur, M.

    1991-12-31

    The objective of this project is to generate experimental data to describe flow fields in heat-exchanger tube banks. One of the main applications of this data is in the evaluation of computational fluid dynamics (CFD) models which are an important part of an ash deposition model. The CFD models under evaluation include a large eddy simulation (LES) being developed by Textron Inc. under DOE-PETC funding and the CLEW code developed at the University of California at Berkeley. Various CFD modeling approaches, e.g., implementation of a transition-to-turbulence and modified wall functions, are also being tested using the PHOENICS code.

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

    SciTech Connect

    Zhuchenko, S. V.

    2014-11-12

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

  20. 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. PMID:25451529

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

    NASA Astrophysics Data System (ADS)

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

    2010-07-01

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

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

    PubMed

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

    2014-12-01

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

  3. 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.

  4. 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.

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

    PubMed

    Duster, A; Garza, C; Lin, H

    2016-01-01

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

  6. 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

  7. 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.

  8. Predicting the dynamics of local adaptation in invasive species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  9. Genetic exchange leading to self-assembling RNA species upon encapsulation in artificial protocells.

    PubMed

    Zenisek, Sergio-Francis M; Hayden, Eric J; Lehman, Niles

    2007-01-01

    The encapsulation of information-bearing macromolecules inside protocells is a critical step in scenarios for the origins of life on the Earth as well as for the construction of artificial living systems. For these protocells to emulate life, they must be able to transmit genetic information to other cells. We have used a water-in-oil emulsion system to simulate the compartmentalization of catalytic RNA molecules. By exploiting RNA-directed recombination reactions previously developed in our laboratory, including a ribozyme self-assembly pathway, we demonstrate that it is possible for information to be exchanged among protocells. This can happen either indirectly by the passage of divalent cations through the inter-protocellular medium (oil), or by the direct interaction of two or more protocells that allows RNA molecules to be exchanged. The degree of agitation affects the ability of such exchange. The consequences of these results include the implications that prototypical living systems can transmit information among compartments, and that the environment can regulate the extent of this crosstalk. PMID:17567246

  10. 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

  11. Reconstructing the Most Probable Folding Transition Path from Replica Exchange Molecular Dynamics Simulations.

    PubMed

    Jimenez-Cruz, Camilo Andres; Garcia, Angel E

    2013-08-13

    The characterization of transition pathways between long-lived states, and the identification of the corresponding transition state ensembles are useful tools in the study of rare events such as protein folding. In this work we demonstrate how the most probable transition path between metastable states can be recovered from replica exchange molecular dynamic simulation data by using the dynamic string method. The local drift vector in collective variables is determined via short continuous trajectories between replica exchanges at a given temperature, and points along the string are updated based on this drift vector to produce reaction pathways between the folded and unfolded state. The method is applied to a designed beta hairpin-forming peptide to obtain information on the folding mechanism and transition state using different sets of collective variables at various temperatures. Two main folding pathways differing in the order of events are found and discussed, and the relative free energy differences for each path estimated. Finally, the structures near the transition state are found and described. PMID:26584126

  12. 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

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

    PubMed

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

    2016-07-28

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

  14. 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.

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

    PubMed

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

    2016-03-01

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

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

    PubMed

    Fels, Daniel

    2016-01-01

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

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

    PubMed Central

    2016-01-01

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

  18. Active colonization dynamics and diversity patterns are influenced by dendritic network connectivity and species interactions

    PubMed Central

    Seymour, Mathew; Altermatt, Florian

    2014-01-01

    Habitat network connectivity influences colonization dynamics, species invasions, and biodiversity patterns. Recent theoretical work suggests dendritic networks, such as those found in rivers, alter expectations regarding colonization and dispersal dynamics compared with other network types. As many native and non-native species are spreading along river networks, this may have important ecological implications. However, experimental studies testing the effects of network structure on colonization and diversity patterns are scarce. Up to now, experimental studies have only considered networks where sites are connected with small corridors, or dispersal was experimentally controlled, which eliminates possible effects of species interactions on colonization dynamics. Here, we tested the effect of network connectivity and species interactions on colonization dynamics using continuous linear and dendritic (i.e., river-like) networks, which allow for active dispersal. We used a set of six protist species and one rotifer species in linear and dendritic microcosm networks. At the start of the experiment, we introduced species, either singularly or as a community within the networks. Species subsequently actively colonized the networks. We periodically measured densities of species throughout the networks over 2 weeks to track community dynamics, colonization, and diversity patterns. We found that colonization of dendritic networks was faster compared with colonization of linear networks, which resulted in higher local mean species richness in dendritic networks. Initially, community similarity was also greater in dendritic networks compared with linear networks, but this effect vanished over time. The presence of species interactions increased community evenness over time, compared with extrapolations from single-species setups. Our experimental findings confirm previous theoretical work and show that network connectivity, species-specific dispersal ability, and species

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

    PubMed

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

    2016-07-20

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

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

    PubMed

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

    2016-06-13

    Interaction of (2-diphenylphosphoryl-3-iodo-4-methoxy-phenyl) methanol with NaH in DMF at ambient temperature results in the generation of benzyne intermediates that can be trapped by furan or DMF. Trapping with DMF forms 3-(dimethylaminomethyl)-2-hydroxy-6-methoxybenzaldehyde demonstrating the simultaneous exchange of three functionalities in a single step. The presence of the alkoxy substituent adjacent to iodine is critical for high regioselectivity addition of DMF. The corresponding bromide or triflate can be used in place of the iodide with equal efficiency. This methodology was used to synthesize the reported structure of gigasol and leading to a structural reassignment of this biscoumarin natural product. PMID:27144945

  1. Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange.

    PubMed

    Lee, Michael S; Olson, Mark A

    2010-08-10

    Computer simulations are increasingly being used to predict thermodynamic observables for folding small proteins. Key to continued progress in this area is the development of algorithms that accelerate conformational sampling. Temperature-based replica exchange (ReX) is a commonly used protocol whereby simulations at several temperatures are simultaneously performed and temperatures are exchanged between simulations via a Metropolis criterion. Another method, self-guided Langevin dynamics (SGLD), expedites conformational sampling by accelerating low-frequency, large-scale motions through the addition of an ad hoc momentum memory term. In this work, we combined these two complementary techniques and compared the results against conventional ReX formulations of molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage mini-protein. All simulations were performed with CHARMM using the PARAM22+CMAP force field and the generalized Born molecular volume implicit solvent model. While SGLD-ReX does not fold up the protein significantly faster than the two conventional ReX approaches, there is some evidence that the method improves sampling convergence by reducing topological folding barriers between energetically similar near-native states. Unlike MD-ReX and LD-ReX, SGLD-ReX predicts melting temperatures, heat capacity curves, and folding free energies that are closer in agreement to the experimental observations. However, this favorable result may be due to distortions of the relative free energies of the folded and unfolded conformational basins caused by the ad hoc force term in the SGLD model. PMID:26613500

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

    NASA Astrophysics Data System (ADS)

    Wang, Xuan; Guo, Kun; Lu, Xiaolin

    2016-07-01

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

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

    PubMed

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

    2016-01-01

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

  4. 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

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

    PubMed

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

    2016-05-11

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

  6. 1H and 23Na MAS NMR spectroscopy of cationic species in CO2 selective alkaline earth metal porous silicoaluminophosphates prepared via liquid and solid state ion exchange

    NASA Astrophysics Data System (ADS)

    Arévalo-Hidalgo, Ana G.; Dugar, Sneha; Fu, Riqiang; Hernández-Maldonado, Arturo J.

    2012-07-01

    The location of extraframework cations in Sr2+ and Ba2+ ion-exchanged SAPO-34 was estimated by means of 1H and 23Na MAS NMR spectroscopy and spectral deconvolution. Incorporation of the alkaline earth metal cations onto the SAPO framework was achieved via liquid state ion exchange, coupled partial detemplation/solid-state ion exchange, and combination of both techniques. MAS NMR revealed that the level of ion exchange was limited by the presence of protons and sodium cations near hexagonal prisms (site SI), which are relatively difficult to exchange with the alkaline earth metal due to steric and charge repulsion criteria. In addition, the presence of ammonium cations in the supercages facilitated the exchange of otherwise tenacious hydrogen as corroborated by unit cell compositional data as well as enhanced CO2 adsorption at low partial pressures. The extraframework ammonium species were produced from partial detemplation of the structure-directing agent employed for the SAPO-34 synthesis, tetraethylammonium.

  7. 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

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

    PubMed Central

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

    2013-01-01

    Objective 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. Materials and methods 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. Results 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. Discussion 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. Conclusions 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. PMID:23292910

  9. Correlating structure, dynamics, and function in transmembrane segment VII of the Na+/H+ exchanger isoform 1.

    PubMed

    Reddy, Tyler; Li, Xiuju; Fliegel, Larry; Sykes, Brian D; Rainey, Jan K

    2010-02-01

    We place (15)N nuclear magnetic resonance relaxation analysis and functional mutagenesis studies in the context of our previous structural and mutagenesis work to correlate structure, dynamics and function for the seventh transmembrane segment of the human Na(+)/H(+) exchanger isoform 1. Although G261-S263 was previously identified as an interruption point in the helical structure of this isolated transmembrane peptide in dodecylphosphocholine micelles, and rapid conformational exchange was implicated in the NOE measurements, the six (15)N labelled residues examined in this study all have similar dynamics on the ps-ns time scale. A mathematical model incorporating chemical exchange is the best fit for residues G261, L264, and A268. This implies that a segment of residues from G261 to A268 samples different conformations on the mus-ms time scale. Chemical exchange on an intermediate time scale is consistent with an alternating-access cycle where E262 is bent away from the cytosol during proton translocation by the exchanger. The functional importance of chemical exchange at G261-A268 is corroborated by the abrogated activity of the full-length exchanger with the bulky and restricting Ile substitutions F260I, G261I, E262I, S263I, and A268I. PMID:19595986

  10. 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.

  11. 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

  12. 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.

  13. 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.

  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. PMID:27059441

  15. 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.

  16. 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.

  17. A High-Resolution Modeling Study of the Bosphorus Strait Dynamics and Exchange Flows

    NASA Astrophysics Data System (ADS)

    Sözer, Adil; Sannino, Gianmaria; Özsoy, Emin

    2013-04-01

    An all-time modelling challenge aims to establish a sound understanding of the high energy environment of the Turkish Straits System, relating to inter-basin water and material transports and their influence on the sensitive ecosystems of the adjacent seas. As a first step in this direction, well resolved, high level, physically representative predictive models of the Bosphorus Strait exchange flow hydrodynamics are developed, adequately representing its complex topography, hydraulic controls, dissipative hydraulic jumps, mixing and turbulence mechanisms, with the application of appropriate basin boundary and initial conditions and judiciously selected numerical and physical model options. Both the ROMS and MITgcm models are used and compared for performance. Idealized and real case model results successfully reproduce observed flow features. The unique maximal exchange regime of the Bosphorus Strait, with hydraulic controls are demonstrated, although frictional effects, especially of the highly irregular lateral boundaries, are found to be extremely important, associated with mixing and entrainment and nonlinear dynamics determining the two-way fluxes as a function of sea-level changes across the strait. The intercomparison of ROMS and MITgcm results are extremely satisfactory in the basic elements of the flow, except for some small differences.

  18. 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. PMID:25965468

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

    PubMed

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

    2016-02-01

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

  20. 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. PMID:25412472

  1. Is parasitoid acceptance of different host species dynamic?

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. Elucidation of molecular dynamics of invasive species of rice

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

    Paulson, Elisabeth; Griffin, Christopher

    2016-08-01

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

  4. 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

  5. Evaluation of Enhanced Sampling Provided by Accelerated Molecular Dynamics with Hamiltonian Replica Exchange Methods

    PubMed Central

    2015-01-01

    Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency. PMID:24625009

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

    PubMed

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

    2006-09-01

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

  7. 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.

  8. 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.

  9. 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.

  10. Proton dynamics in sulfonated ionic salt composites: Alternative membrane materials for proton exchange membrane fuel cells

    NASA Astrophysics Data System (ADS)

    De Almeida, N. E.; Goward, G. R.

    2014-12-01

    Hydrated Nafion, the most prevalent proton exchange membrane utilizes a vehicular mechanism for proton conduction. However, there is an increasing need for such membranes to perform under anhydrous conditions, at high temperatures, which would employ a structural transport mechanism for proton conductivity. Here, several solid-acids are characterized, both as pristine salts, and as polymer composites. Materials of interest include benzimidazolium methanesulfonate (BMSA), imidazolium methanesulfonate (IMSA), and imidazolium trifluoromethanesulfate (IFMS). The proton dynamics of these solid acids are characterized as pure salts, and as composites, embedded into porous Teflon, by solid state NMR. It was determined that spin lattice (T1) relaxation of the composites are systematically lower than that of the pure salt, indicating that local dynamics are enhanced in the composites. Spin-spin relaxation (T2∗) was measured as a function of temperature to determine the activation energy for local mobility for each salt and composite. The activation energy for local proton mobility in each salt decreased after being inserted into porous Teflon. Finally, the long-range ion transport was characterized using impedance spectroscopy. The IFMS-Teflon composite possessed the lowest activation energy for local proton mobility, the highest thermal stability, and the most favorable proton conductivity, among the investigated materials.

  11. 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

  12. 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

  13. 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.

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

    PubMed

    Chamachi, Neharika G; Chakrabarty, Suman

    2016-08-01

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

  15. 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.

  16. Reactive oxygen species and energy machinery: an integrated dynamic model.

    PubMed

    Korla, Kalyani

    2016-08-01

    The role of several important reactive oxygen species (ROS) on the Krebs cycle, the electron transport chain (ETC) and the two important shuttles has been modelled. Major part of the ROS is produced during oxygen reduction in the ETC, which has been kinetically simulated, and the changes in the final concentrations of several important metabolites were found. The simulation is based on chemical kinetics equation, and the associated set of differential equations was solved by the ordinary differential equation package in Octave. The validity of the model is checked by comparing the experimental results available in the literature with the simulations when a part of the ETC is blocked (80%) in the script. The present approach is versatile and flexible and has potential applications in various simulations. It is easy to study the change in concentrations of various metabolites when a particular enzyme or pathway is blocked (say by a drug). The Octave script is presented in the text. PMID:26309069

  17. 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

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

    PubMed

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

    2012-04-01

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

  19. 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

  20. 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

  1. 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. PMID:25672998

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

    NASA Astrophysics Data System (ADS)

    Aggarwal, Neha; Bhattacherjee, Aranya B.

    2014-01-01

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed

    Gruba, Piotr; Mulder, Jan

    2015-04-01

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

  5. Leaf gas exchange in Espeletia schultzii Wedd, a giant caulescent rosette species, along an altitudinal gradient in the Venezuelan Andes

    NASA Astrophysics Data System (ADS)

    Rada, Fermin; Azocar, Aura; Gonzalez, Juan; Briceño, Benito

    1998-02-01

    Gas exchange studies along low altitudinal gradients (0-2 500 metres above sea level) suggest an increase in plant CO 2 assimilation with increasing altitude. The question arises however, will this hold true for higher altitudinal ranges? The purpose of this work was to characterize carbon and water relationships in Espeletia schultzii along an extreme altitudinal gradient. Gas exchange characteristics under field conditions during wet and dry seasons were documented for Espeletia schultzii, a giant caulescent rosette species, along an altitudinal gradient (2 950, 3 550 and 4 200 m) in the Venezuelan Andes. Significant differences in CO 2 assimilation rates between seasons were found for all studied sites. Low assimilation rates obtained during the dry season were a consequence of: low leaf conductances to counteract low leaf water potentials and/or high vapour pressure differences between leaf and air, and to high leaf temperatures measured during the dry season. Important differences in A/P i curve parameters were obtained between wet and dry seasons. A decrease in A max was observed for the two lower populations, while a similar value was obtained for both wet and dry seasons at the higher altitude. A decrease in the relation P i/P a and an increase in stomatal limitation and leaf temperature were measured from wet to dry season. There was a differentiation in CO 2 assimilation with increasing altitude. At 2 950 m, maximum rates were above 5 μmol · m -2 · s -1, at 3 550 m 3 μmol · m -2 · s -1, while at 4 200 m maximum CO 2 assimilation rate was below 3 μmol ·m -2 · s -1. This decrease may be explained by: an increase in leaf pubescence, lower leaf conductances and/or lower leaf nitrogen content at higher altitude.

  6. 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.

  7. 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

  8. 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

  9. 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. PMID:26574422

  10. Gas-Substrate Heat Exchange During Cold-Gas Dynamic Spraying

    NASA Astrophysics Data System (ADS)

    McDonald, A. G.; Ryabinin, A. N.; Irissou, E.; Legoux, J.-G.

    2013-03-01

    In this study, the temperature distribution of the surfaces of several substrates under an impinging gas jet from a cold spray nozzle was determined. A low-pressure cold-gas dynamic spraying unit was used to generate a jet of hot compressed nitrogen that impinged upon flat substrates. Computer codes based on a finite differences method were used to solve a simplified 2D temperature distribution equation for the substrate to produce nondimensional relationships between the surface temperature and the radius of the impinging fluid jet, the axial velocity of the cold spray nozzle, the substrate thickness, and the heating time. It was found that a single profile of the transient nondimensional maximum surface temperature could be used to estimate the dimensional maximum surface temperature, regardless of the value of the compressed gas temperature. It was found further that, as the thermal conductance of the substrate increased, the maximum surface temperature of the substrate beneath the gas jet decreased. Heat exchange between the substrate and the compressed gas jet during motion of the nozzle to produce heat conduction within the substrate was characterized by the nondimensional Peclét number. It was found that lower Peclét numbers produced higher temperatures within the substrate. The close agreement of the numerical results with the experimental results suggests that the nondimensionalized results may be applied to a wide range of conditions and materials.

  11. 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.

  12. Conformation study of ɛ-cyclodextrin: Replica exchange molecular dynamics simulations.

    PubMed

    Khuntawee, Wasinee; Rungrotmongkol, Thanyada; Wolschann, Peter; Pongsawasdi, Piamsook; Kungwan, Nawee; Okumura, Hisashi; Hannongbua, Supot

    2016-05-01

    There is growing interest in large-ring cyclodextrins (LR-CDs) which are known to be good host molecules for larger ligands. The isolation of a defined size LR-CD is an essential prerequisite for studying their structural properties. Unfortunately the purification procedure of these substances turned out to be very laborious. Finally the problem could be circumvented by a theoretical consideration: the highly advantageous replica exchange molecular dynamics (REMD) simulation (particularly suitable for studies of conformational changes) offers an ideal approach for studying the conformational change of ɛ-cyclodextrin (CD10), a smaller representative of LR-CDs. Three carbohydrate force fields and three solvent models were tested. The conformational behavior of CD10 was analyzed in terms of the flip (turn) of the glucose subunits within the macrocyclic ring. In addition a ranking of conformations with various numbers of turns was preformed. Our findings might be also helpful in the temperature controlled synthesis of LR-CDs as well as other experimental conditions, in particular for the host-guest reaction. PMID:26877001

  13. Dynamics of a magnetic dimer with exchange, dipolar, and Dzyalozhinski-Moriya interaction

    NASA Astrophysics Data System (ADS)

    Franco, A. F.; Martinez, J. M.; Déjardin, J. L.; Kachkachi, H.

    2011-10-01

    We investigate the dynamics of a magnetic system consisting of two magnetic moments coupled by either the exchange, dipole-dipole, or Dzyalozhinski-Moriya interaction. We compare the switching mechanisms and switching rates as induced by the three couplings. For each coupling and each configuration of the two anisotropy axes, we describe the switching modes and, using the kinetic theory of Langer, we provide (semi-)analytical expressions for the switching rate. We then compare the three interactions with regard to their efficiency in the reversal of the net magnetic moment of the dimer. We also investigate how the energy barriers vary with the coupling. For the dipole-dipole interaction we find that the energy barrier may either increase or decrease with the coupling depending on whether the latter is weak or strong. Finally, upon comparing the various switching rates, we find that the dipole-dipole coupling leads to the slowest magnetic dimer, as far as the switching of its net magnetic moment is concerned.

  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. 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. PMID:26319376

  16. 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. PMID:15907926

  17. 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.

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

    PubMed

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

    2015-07-01

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

  19. 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

  20. Language evolution and population dynamics in a system of two interacting species

    NASA Astrophysics Data System (ADS)

    Kosmidis, Kosmas; Halley, John M.; Argyrakis, Panos

    2005-08-01

    We use Monte Carlo simulations and assumptions from evolutionary game theory in order to study the evolution of words and the population dynamics of a system made of two interacting species which initially speak two different languages. The species are characterized by their identity, vocabulary, and have different initial fitness, i.e. reproduction capability. We investigate how different initial fitness affects the vocabulary of the species or the population dynamics by leading to a permanent populational advantage. We further find that the spatial distributions of the species may cause the system to exhibit pattern formation or segregation. We show that an initial fitness advantage, even though very quickly balanced, leads to better spatial arrangement and enhances survival probabilities of the species. In most cases the system will arrive at a final state where both languages coexist. However, in cases where one species greatly outnumbers the other in population and fitness, then only one species survives with its “final” language having a slightly richer vocabulary than its initial language. Thus, our results offer an explanation for the existence and origin of synonyms in spoken languages.

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

    PubMed

    Sadovsky, Michael; Senashova, Mariya

    2016-04-01

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

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

    PubMed

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

    2015-01-01

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

  3. 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.

  4. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Hansen, Gretchen J A; Carey, Cayelan C

    2015-01-01

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

  7. 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

  8. The dynamics of hyporheic exchange flows during storm events in a strongly gaining urban river.

    NASA Astrophysics Data System (ADS)

    Cuthbert, Mark O.; Durand, V.; Aller, M.-F.; Greswell, R. G.; Rivett, M. O.; Mackay, R.

    2010-05-01

    There is little published research to date investigating the transient nature of hyporheic exchange flows in strongly gaining rivers. Furthermore, there is a paucity of research describing high temporal frequency river bed water quality variations. This paper addresses both of these research gaps by presenting pressure, electrical conductivity (EC) and temperature data at high temporal frequency (5 minute resolution) collected from within riverbed sediments, the river channel and from the deeper groundwater system, of a well characterised reach of the urban River Tame, Birmingham, UK. The following conclusions have been reached based on data analysis, analytical modelling, and variably saturated numerical flow and transport modelling: • During storm events, flow reversals observed in the recorded pressure data can lead to substantial changes in EC (>20% in some cases) in the river bed down to depths of greater than 30 cm over periods of tens of hours. • A variable, but significant, proportion of the ‘bank storage' volume during a given storm event comes from the ‘backing up' of groundwater that would have been discharged to the river in the absence of the fluctuating river stage. Thus an important control on the extent and dynamics of the reversal is the storage capacity of the riverbank and bed which can be variable and heavily modified in the urban environment. • Return flows may occur along distinct flowlines in comparison with the path taken by the infiltrating water due to the changing geometry of flows through the storm event. Thus, discharging groundwater may be caused to spiral with each storm event, increasing the dispersion of solutes/contaminants. The magnitude of the exchange flows, and the degree of spiralling is likely to increase with distance away from the centre of the river channel. • Gas is present within the river bed in quantities up to around 14% by volume, and to at least 0.8 m depth below river bed. Given the indications from

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

    SciTech Connect

    Fort, J.A.

    1995-07-01

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

  10. Dynamic response of surface water-groundwater exchange to currents, tides, and waves in a shallow estuary

    NASA Astrophysics Data System (ADS)

    Sawyer, Audrey H.; Shi, Fengyan; Kirby, James T.; Michael, Holly A.

    2013-04-01

    In shallow, fetch-limited estuaries, variations in current and wave energy promote heterogeneous surface water-groundwater mixing (benthic exchange), which influences biogeochemical activity. Here, we characterize heterogeneity in benthic exchange within the subtidal zone of the Delaware Inland Bays by linking hydrodynamic circulation models with mathematical solutions for benthic exchange forced by current-bedform interactions, tides, and waves. Benthic fluxes oscillate over tidal cycles as fluctuating water depths alter fluid interactions with the bed. Maximum current-driven fluxes (~1-10 cm/d) occur in channels with strong tidal currents. Maximum wave-driven fluxes (~1-10 cm/d) occur in downwind shoals. During high-energy storms, simulated wave pumping rates increase by orders of magnitude, demonstrating the importance of storms in solute transfer through the benthic layer. Under moderate wind conditions (~5 m/s), integrated benthic exchange rates due to wave, current, and tidal pumping are each ~1-10 m3/s, on the order of fluid contributions from runoff and fresh groundwater discharge to the estuary. Benthic exchange is thus a significant and dynamic component of an estuary's fluid budget that may influence estuarine geochemistry and ecology.

  11. 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

  12. Study of the aggregation mechanism of polyglutamine peptides using replica exchange molecular dynamics simulations.

    PubMed

    Nakano, Miki; Ebina, Kuniyoshi; Tanaka, Shigenori

    2013-04-01

    Polyglutamine (polyQ, a peptide) with an abnormal repeat length is the causative agent of polyQ diseases, such as Huntington's disease. Although glutamine is a polar residue, polyQ peptides form insoluble aggregates in water, and the mechanism for this aggregation is still unclear. To elucidate the detailed mechanism for the nucleation and aggregation of polyQ peptides, replica exchange molecular dynamics simulations were performed for monomers and dimers of polyQ peptides with several chain lengths. Furthermore, to determine how the aggregation mechanism of polyQ differs from those of other peptides, we compared the results for polyQ with those of polyasparagine and polyleucine. The energy barrier between the monomeric and dimeric states of polyQ was found to be relatively low, and it was observed that polyQ dimers strongly favor the formation of antiparallel β-sheet structures. We also found a characteristic behavior of the monomeric polyQ peptide: a turn at the eighth residue is always present, even when the chain length is varied. We previously showed that a structure including more than two sets of β-turns is stable, so a long monomeric polyQ chain can act as an aggregation nucleus by forming several pairs of antiparallel β-sheet structures within a single chain. Since the aggregation of polyQ peptides has some features in common with an amyloid fibril, our results shed light on the mechanism for the aggregation of polyQ peptides as well as the mechanism for the formation of general amyloid fibrils, which cause the onset of amyloid diseases. PMID:23288093

  13. 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

  14. Influence of intergranular exchange coupling on the magnetization dynamics of CoCrPt:SiO2 granular media

    NASA Astrophysics Data System (ADS)

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

    2012-08-01

    We investigate the effect of Co+ irradiation on the magnetization dynamics of CoCrPt:SiO2 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.

  15. 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.

  16. 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.

  17. 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. PMID:24549938

  18. 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. PMID:23326549

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

    PubMed

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

    2016-03-01

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

  20. Dynamics of ion exchange between self-assembled redox polyelectrolyte multilayer modified electrode and liquid electrolyte.

    PubMed

    Grumelli, Doris E; Garay, Fernando; Barbero, Cesar A; Calvo, Ernesto J

    2006-08-10

    A probe beam deflection (PBD) study of ion exchange between an electroactive polymer poly(allylamine)-bipyridyl-pyridine osmium complex film and liquid electrolyte is reported. The PBD measurements were made simultaneously to chronoamperometric oxidation-reduction cycles, to be able to detect kinetic effects in the ion exchange. Layer-by-layer (LbL) self-assembled redox polyelectrolyte films with osmium bipyridyl complex covalently attached to poly(allylamine) (PAH-Os) and poly(styrene sulfonate) (PSS) have been built by alternate electrostatic adsorption from soluble polyelectrolytes. The ionic exchange during initial conditioning of the film ("break-in") undergoing oxidation-reduction cycles and recovery after equilibration in the reduced state have shown an exchange of anions and cations with time lag between them. The effect of the nature of cation on the ionic exchange has been investigated with dilute HCl, LiCl, NaCl, and CsCl electrolytes. The ratio of anion to cation exchanged at the film-electrolyte interface has a strong dependence on the nature of charge in the topmost layer, that is, when negatively charged PSS is the capping layer, a larger proportion of cation exchange is observed. This demonstrates that the electrical potential distribution at the redox polyelectrolyte multilayer (PEM)/electrolyte interface determines the ionic flux in response to charge injection in the film. PMID:16884254

  1. 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

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

    NASA Astrophysics Data System (ADS)

    Vallade, M.; Houchmandzadeh, B.

    2006-11-01

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

  3. Reconstruction of food conditions for Northeast Atlantic bivalve species based on Dynamic Energy Budgets

    NASA Astrophysics Data System (ADS)

    Freitas, Vânia; Cardoso, Joana F. M. F.; Santos, Sílvia; Campos, Joana; Drent, Jan; Saraiva, Sofia; Witte, Johannes IJ.; Kooijman, Sebastiaan A. L. M.; Van der Veer, Henk W.

    2009-08-01

    Required assimilated energy to support observed growth was reconstructed for four common bivalve species ( Mya arenaria, Cerastoderma edule, Mytilus edulis and Macoma balthica) from various Northeast Atlantic coastal areas, along the species distributional range. The approach applied was based on the Dynamic Energy Budget (DEB) theory whereby observed growth patterns in the field, in combination with prevailing temperatures, were used to reconstruct the average food intake experienced in the field scaled to the maximum possible. For all species, results suggest food limitation over the range of locations. In general, reconstructed food intake indicated better conditions for C. edule compared to the other species, while M. edulis presented the lowest food conditions in all the areas. Despite the indications for a latitudinal trend in primary production, no clear pattern or relationship between reconstructed food conditions and latitude was observed suggesting that any trend may be overruled by local conditions.

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

    NASA Astrophysics Data System (ADS)

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

    2011-03-01

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

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

    PubMed

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-02-01

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

  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. 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-}.

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

    USGS Publications Warehouse

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

    2014-01-01

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

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

    SciTech Connect

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

    2008-12-31

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