WorldWideScience

Sample records for large time-scale molecular

  1. Large Deviations for Two-Time-Scale Diffusions, with Delays

    International Nuclear Information System (INIS)

    Kushner, Harold J.

    2010-01-01

    We consider the problem of large deviations for a two-time-scale reflected diffusion process, possibly with delays in the dynamical terms. The Dupuis-Ellis weak convergence approach is used. It is perhaps the most intuitive and simplest for the problems of concern. The results have applications to the problem of approximating optimal controls for two-time-scale systems via use of the averaged equation.

  2. Time scale of diffusion in molecular and cellular biology

    International Nuclear Information System (INIS)

    Holcman, D; Schuss, Z

    2014-01-01

    Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function. (topical review)

  3. Time scale of diffusion in molecular and cellular biology

    Science.gov (United States)

    Holcman, D.; Schuss, Z.

    2014-05-01

    Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function.

  4. Vibration amplitude rule study for rotor under large time scale

    International Nuclear Information System (INIS)

    Yang Xuan; Zuo Jianli; Duan Changcheng

    2014-01-01

    The rotor is an important part of the rotating machinery; its vibration performance is one of the important factors affecting the service life. This paper presents both theoretical analyses and experimental demonstrations of the vibration rule of the rotor under large time scales. The rule can be used for the service life estimation of the rotor. (authors)

  5. Shock compression and flash-heating of molecular adsorbates on the picosecond time scale

    Science.gov (United States)

    Berg, Christopher Michael

    An ultrafast nonlinear coherent laser spectroscopy termed broadband multiplex vibrational sum-frequency generation (SFG) with nonresonant suppression was employed to monitor vibrational transitions of molecular adsorbates on metallic substrates during laser-driven shock compression and flash-heating. Adsorbates were in the form of well-ordered self-assembled monolayers (SAMs) and included molecular explosive simulants, such as nitroaromatics, and long chain-length alkanethiols. Based on reflectance measurements of the metallic substrates, femtosecond flash-heating pulses were capable of producing large-amplitude temperature jumps with DeltaT = 500 K. Laser-driven shock compression of SAMs produced pressures up to 2 GPa, where 1 GPa ≈ 1 x 104 atm. Shock pressures were estimated via comparison with frequency shifts observed in the monolayer vibrational transitions during hydrostatic pressure measurements in a SiC anvil cell. Molecular dynamics during flash-heating and shock loading were probed with vibrational SFG spectroscopy with picosecond temporal resolution and sub-nanometer spatial resolution. Flash-heating studies of 4-nitrobenzenethiolate (NBT) on Au provided insight into effects from hot-electron excitation of the molecular adsorbates at early pump-probe delay times. At longer delay times, effects from the excitation of SAM lattice modes and lower-energy NBT vibrations were shown. In addition, flash-heating studies of alkanethiolates demonstrated chain disordering behaviors as well as interface thermal conductances across the Au-SAM junction, which was of specific interest within the context of molecular electronics. Shock compression studies of molecular explosive simulants, such as 4-nitrobenzoate (NBA), demonstrated the proficiency of this technique to observe shock-induced molecular dynamics, in this case orientational dynamics, on the picosecond time scale. Results validated the utilization of these refined shock loading techniques to probe the shock

  6. Modeling and control of a large nuclear reactor. A three-time-scale approach

    Energy Technology Data Exchange (ETDEWEB)

    Shimjith, S.R. [Indian Institute of Technology Bombay, Mumbai (India); Bhabha Atomic Research Centre, Mumbai (India); Tiwari, A.P. [Bhabha Atomic Research Centre, Mumbai (India); Bandyopadhyay, B. [Indian Institute of Technology Bombay, Mumbai (India). IDP in Systems and Control Engineering

    2013-07-01

    Recent research on Modeling and Control of a Large Nuclear Reactor. Presents a three-time-scale approach. Written by leading experts in the field. Control analysis and design of large nuclear reactors requires a suitable mathematical model representing the steady state and dynamic behavior of the reactor with reasonable accuracy. This task is, however, quite challenging because of several complex dynamic phenomena existing in a reactor. Quite often, the models developed would be of prohibitively large order, non-linear and of complex structure not readily amenable for control studies. Moreover, the existence of simultaneously occurring dynamic variations at different speeds makes the mathematical model susceptible to numerical ill-conditioning, inhibiting direct application of standard control techniques. This monograph introduces a technique for mathematical modeling of large nuclear reactors in the framework of multi-point kinetics, to obtain a comparatively smaller order model in standard state space form thus overcoming these difficulties. It further brings in innovative methods for controller design for systems exhibiting multi-time-scale property, with emphasis on three-time-scale systems.

  7. Molecular dynamics on diffusive time scales from the phase-field-crystal equation.

    Science.gov (United States)

    Chan, Pak Yuen; Goldenfeld, Nigel; Dantzig, Jon

    2009-03-01

    We extend the phase-field-crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of them. By solving the dynamical equation of the model, which is a partial differential equation, we are essentially performing molecular dynamics simulations on diffusive time scales. To illustrate this approach, we calculate the two-point correlation function of a fluid.

  8. Atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

    Science.gov (United States)

    Pabst, Stefan

    2013-04-01

    Time-resolved investigations of ultrafast electronic and molecular dynamics were not possible until recently. The typical time scale of these processes is in the picosecond to attosecond realm. The tremendous technological progress in recent years made it possible to generate ultrashort pulses, which can be used to trigger, to watch, and to control atomic and molecular motion. This tutorial focuses on experimental and theoretical advances which are used to study the dynamics of electrons and molecules in the presence of ultrashort pulses. In the first part, the rotational dynamics of molecules, which happens on picosecond and femtosecond time scales, is reviewed. Well-aligned molecules are particularly suitable for angle-dependent investigations like x-ray diffraction or strong-field ionization experiments. In the second part, the ionization dynamics of atoms is studied. The characteristic time scale lies, here, in the attosecond to few-femtosecond regime. Although a one-particle picture has been successfully applied to many processes, many-body effects do constantly occur. After a broad overview of the main mechanisms and the most common tools in attosecond physics, examples of many-body dynamics in the attosecond world (e.g., in high-harmonic generation and attosecond transient absorption spectroscopy) are discussed.

  9. Modeling and Control of a Large Nuclear Reactor A Three-Time-Scale Approach

    CERN Document Server

    Shimjith, S R; Bandyopadhyay, B

    2013-01-01

    Control analysis and design of large nuclear reactors requires a suitable mathematical model representing the steady state and dynamic behavior of the reactor with reasonable accuracy. This task is, however, quite challenging because of several complex dynamic phenomena existing in a reactor. Quite often, the models developed would be of prohibitively large order, non-linear and of complex structure not readily amenable for control studies. Moreover, the existence of simultaneously occurring dynamic variations at different speeds makes the mathematical model susceptible to numerical ill-conditioning, inhibiting direct application of standard control techniques. This monograph introduces a technique for mathematical modeling of large nuclear reactors in the framework of multi-point kinetics, to obtain a comparatively smaller order model in standard state space form thus overcoming these difficulties. It further brings in innovative methods for controller design for systems exhibiting multi-time-scale property,...

  10. Time-scale effects in the interaction between a large and a small herbivore

    NARCIS (Netherlands)

    Kuijper, D. P. J.; Beek, P.; van Wieren, S.E.; Bakker, J. P.

    2008-01-01

    In the short term, grazing will mainly affect plant biomass and forage quality. However, grazing can affect plant species composition by accelerating or retarding succession at longer time-scales. Few studies concerning interactions among herbivores have taken the change in plant species composition

  11. Boreal Forests Sequester Large Amounts of Mercury over Millennial Time Scales in the Absence of Wildfire.

    Science.gov (United States)

    Giesler, Reiner; Clemmensen, Karina E; Wardle, David A; Klaminder, Jonatan; Bindler, Richard

    2017-03-07

    Alterations in fire activity due to climate change and fire suppression may have profound effects on the balance between storage and release of carbon (C) and associated volatile elements. Stored soil mercury (Hg) is known to volatilize due to wildfires and this could substantially affect the land-air exchange of Hg; conversely the absence of fires and human disturbance may increase the time period over which Hg is sequestered. Here we show for a wildfire chronosequence spanning over more than 5000 years in boreal forest in northern Sweden that belowground inventories of total Hg are strongly related to soil humus C accumulation (R 2 = 0.94, p millennial time scales in the prolonged absence of fire.

  12. New theoretical approaches to atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

    International Nuclear Information System (INIS)

    Pabst, Stefan Ulf

    2013-04-01

    The concept of atoms as the building blocks of matter has existed for over 3000 years. A revolution in the understanding and the description of atoms and molecules has occurred in the last century with the birth of quantum mechanics. After the electronic structure was understood, interest in studying the dynamics of electrons, atoms, and molecules increased. However, time-resolved investigations of these ultrafast processes were not possible until recently. The typical time scale of atomic and molecular processes is in the picosecond to attosecond realm. Tremendous technological progress in recent years makes it possible to generate light pulses on these time scales. With such ultrashort pulses, atomic and molecular dynamics can be triggered, watched, and controlled. Simultaneously, the need rises for theoretical models describing the underlying mechanisms. This doctoral thesis focuses on the development of theoretical models which can be used to study the dynamical behavior of electrons, atoms, and molecules in the presence of ultrashort light pulses. Several examples are discussed illustrating how light pulses can trigger and control electronic, atomic, and molecular motions. In the first part of this work, I focus on the rotational motion of asymmetric molecules, which happens on picosecond and femtosecond time scales. Here, the aim is to align all three axes of the molecule as well as possible. To investigate theoretically alignment dynamics, I developed a program that can describe alignment motion ranging from the impulsive to the adiabatic regime. The asymmetric molecule SO 2 is taken as an example to discuss strategies of optimizing 3D alignment without the presence of an external field (i.e., field-free alignment). Field-free alignment is particularly advantageous because subsequent experiments on the aligned molecule are not perturbed by the aligning light pulse. Wellaligned molecules in the gas phase are suitable for diffraction experiments. From the

  13. New theoretical approaches to atomic and molecular dynamics triggered by ultrashort light pulses on the atto- to picosecond time scale

    Energy Technology Data Exchange (ETDEWEB)

    Pabst, Stefan Ulf

    2013-04-15

    The concept of atoms as the building blocks of matter has existed for over 3000 years. A revolution in the understanding and the description of atoms and molecules has occurred in the last century with the birth of quantum mechanics. After the electronic structure was understood, interest in studying the dynamics of electrons, atoms, and molecules increased. However, time-resolved investigations of these ultrafast processes were not possible until recently. The typical time scale of atomic and molecular processes is in the picosecond to attosecond realm. Tremendous technological progress in recent years makes it possible to generate light pulses on these time scales. With such ultrashort pulses, atomic and molecular dynamics can be triggered, watched, and controlled. Simultaneously, the need rises for theoretical models describing the underlying mechanisms. This doctoral thesis focuses on the development of theoretical models which can be used to study the dynamical behavior of electrons, atoms, and molecules in the presence of ultrashort light pulses. Several examples are discussed illustrating how light pulses can trigger and control electronic, atomic, and molecular motions. In the first part of this work, I focus on the rotational motion of asymmetric molecules, which happens on picosecond and femtosecond time scales. Here, the aim is to align all three axes of the molecule as well as possible. To investigate theoretically alignment dynamics, I developed a program that can describe alignment motion ranging from the impulsive to the adiabatic regime. The asymmetric molecule SO{sub 2} is taken as an example to discuss strategies of optimizing 3D alignment without the presence of an external field (i.e., field-free alignment). Field-free alignment is particularly advantageous because subsequent experiments on the aligned molecule are not perturbed by the aligning light pulse. Wellaligned molecules in the gas phase are suitable for diffraction experiments. From the

  14. Time-scale invariant changes in atmospheric radon concentration and crustal strain prior to a large earthquake

    Directory of Open Access Journals (Sweden)

    Y. Kawada

    2007-01-01

    Full Text Available Prior to large earthquakes (e.g. 1995 Kobe earthquake, Japan, an increase in the atmospheric radon concentration is observed, and this increase in the rate follows a power-law of the time-to-earthquake (time-to-failure. This phenomenon corresponds to the increase in the radon migration in crust and the exhalation into atmosphere. An irreversible thermodynamic model including time-scale invariance clarifies that the increases in the pressure of the advecting radon and permeability (hydraulic conductivity in the crustal rocks are caused by the temporal changes in the power-law of the crustal strain (or cumulative Benioff strain, which is associated with damage evolution such as microcracking or changing porosity. As the result, the radon flux and the atmospheric radon concentration can show a temporal power-law increase. The concentration of atmospheric radon can be used as a proxy for the seismic precursory processes associated with crustal dynamics.

  15. Large volume recycling of oceanic lithosphere over short time scales: geochemical constraints from the Caribbean Large Igneous Province

    Science.gov (United States)

    Hauff, F.; Hoernle, K.; Tilton, G.; Graham, D. W.; Kerr, A. C.

    2000-01-01

    Oceanic flood basalts are poorly understood, short-term expressions of highly increased heat flux and mass flow within the convecting mantle. The uniqueness of the Caribbean Large Igneous Province (CLIP, 92-74 Ma) with respect to other Cretaceous oceanic plateaus is its extensive sub-aerial exposures, providing an excellent basis to investigate the temporal and compositional relationships within a starting plume head. We present major element, trace element and initial Sr-Nd-Pb isotope composition of 40 extrusive rocks from the Caribbean Plateau, including onland sections in Costa Rica, Colombia and Curaçao as well as DSDP Sites in the Central Caribbean. Even though the lavas were erupted over an area of ˜3×10 6 km 2, the majority have strikingly uniform incompatible element patterns (La/Yb=0.96±0.16, n=64 out of 79 samples, 2σ) and initial Nd-Pb isotopic compositions (e.g. 143Nd/ 144Nd in=0.51291±3, ɛNdi=7.3±0.6, 206Pb/ 204Pb in=18.86±0.12, n=54 out of 66, 2σ). Lavas with endmember compositions have only been sampled at the DSDP Sites, Gorgona Island (Colombia) and the 65-60 Ma accreted Quepos and Osa igneous complexes (Costa Rica) of the subsequent hotspot track. Despite the relatively uniform composition of most lavas, linear correlations exist between isotope ratios and between isotope and highly incompatible trace element ratios. The Sr-Nd-Pb isotope and trace element signatures of the chemically enriched lavas are compatible with derivation from recycled oceanic crust, while the depleted lavas are derived from a highly residual source. This source could represent either oceanic lithospheric mantle left after ocean crust formation or gabbros with interlayered ultramafic cumulates of the lower oceanic crust. High 3He/ 4He in olivines of enriched picrites at Quepos are ˜12 times higher than the atmospheric ratio suggesting that the enriched component may have once resided in the lower mantle. Evaluation of the Sm-Nd and U-Pb isotope systematics on

  16. Are characiform fishes Gondwanan in origin? Insights from a time-scaled molecular phylogeny of the Citharinoidei (Ostariophysi: Characiformes.

    Directory of Open Access Journals (Sweden)

    Jairo Arroyave

    Full Text Available Fishes of the order Characiformes are a diverse and economically important teleost clade whose extant members are found exclusively in African and Neotropical freshwaters. Although their transatlantic distribution has been primarily attributed to the Early Cretaceous fragmentation of western Gondwana, vicariance has not been tested with temporal information beyond that contained in their fragmentary fossil record and a recent time-scaled phylogeny focused on the African family Alestidae. Because members of the suborder Citharinoidei constitute the sister lineage to the entire remaining Afro-Neotropical characiform radiation, we inferred a time-calibrated molecular phylogeny of citharinoids using a popular Bayesian approach to molecular dating in order to assess the adequacy of current vicariance hypotheses and shed light on the early biogeographic history of characiform fishes. Given that the only comprehensive phylogenetic treatment of the Citharinoidei has been a morphology-based analysis published over three decades ago, the present study also provided an opportunity to further investigate citharinoid relationships and update the evolutionary framework that has laid the foundations for the current classification of the group. The inferred chronogram is robust to changes in calibration priors and suggests that the origins of citharinoids date back to the Turonian (ca 90 Ma of the Late Cretaceous. Most modern citharinoid genera, however, appear to have originated and diversified much more recently, mainly during the Miocene. By reconciling molecular-clock- with fossil-based estimates for the origins of the Characiformes, our results provide further support for the hypothesis that attributes the disjunct distribution of the order to the opening of the South Atlantic Ocean. The striking overlap in tempo of diversification and biogeographic patterns between citharinoids and the African-endemic family Alestidae suggests that their evolutionary

  17. Internal motion time scales of a small, highly stable and disulfide-rich protein: A 15N, 13C NMR and molecular dynamics study

    International Nuclear Information System (INIS)

    Guenneugues, Marc; Gilquin, Bernard; Wolff, Nicolas; Menez, Andre; Zinn-Justin, Sophie

    1999-01-01

    Motions of the backbone CαHα and threonine CβHβ bonds of toxin α were investigated using natural abundance 13C NMR and molecular dynamics. Measurement of the 13C longitudinal and transverse relaxation rates employed ACCORDION techniques together with coherence selection by pulsed field gradients and sensitivity enhancement through the use of preservation of equivalent pathway, thus allowing a considerable reduction of the required spectrometer time. 13C R1, R2, 1H → 13C NOE were obtained, as well as the variations of R1ρ(90 deg.) as a function of the rf field strength. These data were compared to those recorded by 1H and 15N NMR on a labelled sample of the toxin [Guenneugues et al. (1997) Biochemistry, 36, 16097-16108]. Both sets of data showed that picosecond to nanosecond time scale motions are well correlated to the secondary structure of the protein. This was further reinforced by the analysis of a 1 ns molecular dynamics simulation in water. Several CαHα and threonine CβHβ experimentally exhibit fast motions with a correlation time longer than 500 ps, that cannot be sampled along the simulation. In addition, the backbone exhibits motions on the microsecond to millisecond time scale on more than half of its length. Thus, toxin α, a highly stable protein (Tm=75 deg. C at acidic pH) containing 61 amino acids and 4 disulfides, shows important internal motions on time scales ranging from 0.1-0.5 ps, to 10-100 ps, 1 ns, and about 30 μs to 10 ms

  18. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    Energy Technology Data Exchange (ETDEWEB)

    Bylaska, Eric J., E-mail: Eric.Bylaska@pnnl.gov [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States); Weare, Jonathan Q., E-mail: weare@uchicago.edu [Department of Mathematics, University of Chicago, Chicago, Illinois 60637 (United States); Weare, John H., E-mail: jweare@ucsd.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 (United States)

    2013-08-21

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up

  19. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.

    Science.gov (United States)

    Bylaska, Eric J; Weare, Jonathan Q; Weare, John H

    2013-08-21

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a

  20. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    International Nuclear Information System (INIS)

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-01-01

    Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t i (trajectory positions and velocities x i = (r i , v i )) to time t i+1 (x i+1 ) by x i+1 = f i (x i ), the dynamics problem spanning an interval from t 0 …t M can be transformed into a root finding problem, F(X) = [x i − f(x (i−1 )] i =1,M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H 2 O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a

  1. A molecular genetic time scale demonstrates Cretaceous origins and multiple diversification rate shifts within the order Galliformes (Aves).

    Science.gov (United States)

    Stein, R Will; Brown, Joseph W; Mooers, Arne Ø

    2015-11-01

    The phylogeny of Galliformes (landfowl) has been studied extensively; however, the associated chronologies have been criticized recently due to misplaced or misidentified fossil calibrations. As a consequence, it is unclear whether any crown-group lineages arose in the Cretaceous and survived the Cretaceous-Paleogene (K-Pg; 65.5 Ma) mass extinction. Using Bayesian phylogenetic inference on an alignment spanning 14,539 bp of mitochondrial and nuclear DNA sequence data, four fossil calibrations, and a combination of uncorrelated lognormally distributed relaxed-clock and strict-clock models, we inferred a time-calibrated molecular phylogeny for 225 of the 291 extant Galliform taxa. These analyses suggest that crown Galliformes diversified in the Cretaceous and that three-stem lineages survived the K-Pg mass extinction. Ideally, characterizing the tempo and mode of diversification involves a taxonomically complete phylogenetic hypothesis. We used simple constraint structures to incorporate 66 data-deficient taxa and inferred the first taxon-complete phylogenetic hypothesis for the Galliformes. Diversification analyses conducted on 10,000 timetrees sampled from the posterior distribution of candidate trees show that the evolutionary history of the Galliformes is best explained by a rate-shift model including 1-3 clade-specific increases in diversification rate. We further show that the tempo and mode of diversification in the Galliformes conforms to a three-pulse model, with three-stem lineages arising in the Cretaceous and inter and intrafamilial diversification occurring after the K-Pg mass extinction, in the Paleocene-Eocene (65.5-33.9 Ma) or in association with the Eocene-Oligocene transition (33.9 Ma). Copyright © 2015 Elsevier Inc. All rights reserved.

  2. Time-scale and extent at which large-scale circulation modes determine the wind and solar potential in the Iberian Peninsula

    International Nuclear Information System (INIS)

    Jerez, Sonia; Trigo, Ricardo M

    2013-01-01

    The North Atlantic Oscillation (NAO), the East Atlantic (EA) and the Scandinavian (SCAND) modes are the three main large-scale circulation patterns driving the climate variability of the Iberian Peninsula. This study assesses their influence in terms of solar (photovoltaic) and wind power generation potential (SP and WP) and evaluates their skill as predictors. For that we use a hindcast regional climate simulation to retrieve the primary meteorological variables involved, surface solar radiation and wind speed. First we identify that the maximum influence of the various modes occurs on the interannual variations of the monthly mean SP and WP series, being generally more relevant in winter. Second we find that in this time-scale and season, SP (WP) varies up to 30% (40%) with respect to the mean climatology between years with opposite phases of the modes, although the strength and the spatial distribution of the signals differ from one month to another. Last, the skill of a multi-linear regression model (MLRM), built using the NAO, EA and SCAND indices, to reconstruct the original wintertime monthly series of SP and WP was investigated. The reconstructed series (when the MLRM is calibrated for each month individually) correlate with the original ones up to 0.8 at the interannual time-scale. Besides, when the modeled series for each individual month are merged to construct an October-to-March monthly series, and after removing the annual cycle in order to account for monthly anomalies, these correlate 0.65 (0.55) with the original SP (WP) series in average. These values remain fairly stable when the calibration and reconstruction periods differ, thus supporting up to a point the predictive potential of the method at the time-scale assessed here. (letter)

  3. Time scales of supercooled water and implications for reversible polyamorphism

    Science.gov (United States)

    Limmer, David T.; Chandler, David

    2015-09-01

    Deeply supercooled water exhibits complex dynamics with large density fluctuations, ice coarsening and characteristic time scales extending from picoseconds to milliseconds. Here, we discuss implications of these time scales as they pertain to two-phase coexistence and to molecular simulations of supercooled water. Specifically, we argue that it is possible to discount liquid-liquid criticality because the time scales imply that correlation lengths for such behaviour would be bounded by no more than a few nanometres. Similarly, it is possible to discount two-liquid coexistence because the time scales imply a bounded interfacial free energy that cannot grow in proportion to a macroscopic surface area. From time scales alone, therefore, we see that coexisting domains of differing density in supercooled water can be no more than nanoscale transient fluctuations.

  4. Stability of large-area molecular junctions

    NARCIS (Netherlands)

    Akkerman, Hylke B.; Kronemeijer, Auke J.; Harkema, Jan; van Hal, Paul A.; Smits, Edsger C. P.; de Leeuw, Dago M.; Blom, Paul W. M.

    The stability of molecular junctions is crucial for any application of molecular electronics. Degradation of molecular junctions when exposed to ambient conditions is regularly observed. In this report the stability of large-area molecular junctions under ambient conditions for more than two years

  5. Multiple time scale dynamics

    CERN Document Server

    Kuehn, Christian

    2015-01-01

    This book provides an introduction to dynamical systems with multiple time scales. The approach it takes is to provide an overview of key areas, particularly topics that are less available in the introductory form.  The broad range of topics included makes it accessible for students and researchers new to the field to gain a quick and thorough overview. The first of its kind, this book merges a wide variety of different mathematical techniques into a more unified framework. The book is highly illustrated with many examples and exercises and an extensive bibliography. The target audience of this  book are senior undergraduates, graduate students as well as researchers interested in using the multiple time scale dynamics theory in nonlinear science, either from a theoretical or a mathematical modeling perspective. 

  6. Evaluating cloud processes in large-scale models: Of idealized case studies, parameterization testbeds and single-column modelling on climate time-scales

    Science.gov (United States)

    Neggers, Roel

    2016-04-01

    ), and iii) process-level evaluation at climate time-scales. The advantages and disadvantages of each approach will be identified and discussed, and some thoughts about possible future developments will be given.

  7. Multiple time scale methods in tokamak magnetohydrodynamics

    International Nuclear Information System (INIS)

    Jardin, S.C.

    1984-01-01

    Several methods are discussed for integrating the magnetohydrodynamic (MHD) equations in tokamak systems on other than the fastest time scale. The dynamical grid method for simulating ideal MHD instabilities utilizes a natural nonorthogonal time-dependent coordinate transformation based on the magnetic field lines. The coordinate transformation is chosen to be free of the fast time scale motion itself, and to yield a relatively simple scalar equation for the total pressure, P = p + B 2 /2μ 0 , which can be integrated implicitly to average over the fast time scale oscillations. Two methods are described for the resistive time scale. The zero-mass method uses a reduced set of two-fluid transport equations obtained by expanding in the inverse magnetic Reynolds number, and in the small ratio of perpendicular to parallel mobilities and thermal conductivities. The momentum equation becomes a constraint equation that forces the pressure and magnetic fields and currents to remain in force balance equilibrium as they evolve. The large mass method artificially scales up the ion mass and viscosity, thereby reducing the severe time scale disparity between wavelike and diffusionlike phenomena, but not changing the resistive time scale behavior. Other methods addressing the intermediate time scales are discussed

  8. On the Geologic Time Scale

    NARCIS (Netherlands)

    Gradstein, F.M.; Ogg, J.G.; Hilgen, F.J.

    2012-01-01

    This report summarizes the international divisions and ages in the Geologic Time Scale, published in 2012 (GTS2012). Since 2004, when GTS2004 was detailed, major developments have taken place that directly bear and have considerable impact on the intricate science of geologic time scaling. Precam

  9. Dynamic inequalities on time scales

    CERN Document Server

    Agarwal, Ravi; Saker, Samir

    2014-01-01

    This is a monograph devoted to recent research and results on dynamic inequalities on time scales. The study of dynamic inequalities on time scales has been covered extensively in the literature in recent years and has now become a major sub-field in pure and applied mathematics. In particular, this book will cover recent results on integral inequalities, including Young's inequality, Jensen's inequality, Holder's inequality, Minkowski's inequality, Steffensen's inequality, Hermite-Hadamard inequality and Čebyšv's inequality. Opial type inequalities on time scales and their extensions with weighted functions, Lyapunov type inequalities, Halanay type inequalities for dynamic equations on time scales, and Wirtinger type inequalities on time scales and their extensions will also be discussed here in detail.

  10. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  11. Pair plasma relaxation time scales.

    Science.gov (United States)

    Aksenov, A G; Ruffini, R; Vereshchagin, G V

    2010-04-01

    By numerically solving the relativistic Boltzmann equations, we compute the time scale for relaxation to thermal equilibrium for an optically thick electron-positron plasma with baryon loading. We focus on the time scales of electromagnetic interactions. The collisional integrals are obtained directly from the corresponding QED matrix elements. Thermalization time scales are computed for a wide range of values of both the total-energy density (over 10 orders of magnitude) and of the baryonic loading parameter (over 6 orders of magnitude). This also allows us to study such interesting limiting cases as the almost purely electron-positron plasma or electron-proton plasma as well as intermediate cases. These results appear to be important both for laboratory experiments aimed at generating optically thick pair plasmas as well as for astrophysical models in which electron-positron pair plasmas play a relevant role.

  12. Large scale molecular simulations of nanotoxicity.

    Science.gov (United States)

    Jimenez-Cruz, Camilo A; Kang, Seung-gu; Zhou, Ruhong

    2014-01-01

    The widespread use of nanomaterials in biomedical applications has been accompanied by an increasing interest in understanding their interactions with tissues, cells, and biomolecules, and in particular, on how they might affect the integrity of cell membranes and proteins. In this mini-review, we present a summary of some of the recent studies on this important subject, especially from the point of view of large scale molecular simulations. The carbon-based nanomaterials and noble metal nanoparticles are the main focus, with additional discussions on quantum dots and other nanoparticles as well. The driving forces for adsorption of fullerenes, carbon nanotubes, and graphene nanosheets onto proteins or cell membranes are found to be mainly hydrophobic interactions and the so-called π-π stacking (between aromatic rings), while for the noble metal nanoparticles the long-range electrostatic interactions play a bigger role. More interestingly, there are also growing evidences showing that nanotoxicity can have implications in de novo design of nanomedicine. For example, the endohedral metallofullerenol Gd@C₈₂(OH)₂₂ is shown to inhibit tumor growth and metastasis by inhibiting enzyme MMP-9, and graphene is illustrated to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using the cytotoxicity of nanoparticles against cancer or bacteria cells. © 2014 Wiley Periodicals, Inc.

  13. Liquidity crises on different time scales

    Science.gov (United States)

    Corradi, Francesco; Zaccaria, Andrea; Pietronero, Luciano

    2015-12-01

    We present an empirical analysis of the microstructure of financial markets and, in particular, of the static and dynamic properties of liquidity. We find that on relatively large time scales (15 min) large price fluctuations are connected to the failure of the subtle mechanism of compensation between the flows of market and limit orders: in other words, the missed revelation of the latent order book breaks the dynamical equilibrium between the flows, triggering the large price jumps. On smaller time scales (30 s), instead, the static depletion of the limit order book is an indicator of an intrinsic fragility of the system, which is related to a strongly nonlinear enhancement of the response. In order to quantify this phenomenon we introduce a measure of the liquidity imbalance present in the book and we show that it is correlated to both the sign and the magnitude of the next price movement. These findings provide a quantitative definition of the effective liquidity, which proves to be strongly dependent on the considered time scales.

  14. Mouse Activity across Time Scales: Fractal Scenarios

    Science.gov (United States)

    Lima, G. Z. dos Santos; Lobão-Soares, B.; do Nascimento, G. C.; França, Arthur S. C.; Muratori, L.; Ribeiro, S.; Corso, G.

    2014-01-01

    In this work we devise a classification of mouse activity patterns based on accelerometer data using Detrended Fluctuation Analysis. We use two characteristic mouse behavioural states as benchmarks in this study: waking in free activity and slow-wave sleep (SWS). In both situations we find roughly the same pattern: for short time intervals we observe high correlation in activity - a typical 1/f complex pattern - while for large time intervals there is anti-correlation. High correlation of short intervals ( to : waking state and to : SWS) is related to highly coordinated muscle activity. In the waking state we associate high correlation both to muscle activity and to mouse stereotyped movements (grooming, waking, etc.). On the other side, the observed anti-correlation over large time scales ( to : waking state and to : SWS) during SWS appears related to a feedback autonomic response. The transition from correlated regime at short scales to an anti-correlated regime at large scales during SWS is given by the respiratory cycle interval, while during the waking state this transition occurs at the time scale corresponding to the duration of the stereotyped mouse movements. Furthermore, we find that the waking state is characterized by longer time scales than SWS and by a softer transition from correlation to anti-correlation. Moreover, this soft transition in the waking state encompass a behavioural time scale window that gives rise to a multifractal pattern. We believe that the observed multifractality in mouse activity is formed by the integration of several stereotyped movements each one with a characteristic time correlation. Finally, we compare scaling properties of body acceleration fluctuation time series during sleep and wake periods for healthy mice. Interestingly, differences between sleep and wake in the scaling exponents are comparable to previous works regarding human heartbeat. Complementarily, the nature of these sleep-wake dynamics could lead to a better

  15. Grid computing in large pharmaceutical molecular modeling.

    Science.gov (United States)

    Claus, Brian L; Johnson, Stephen R

    2008-07-01

    Most major pharmaceutical companies have employed grid computing to expand their compute resources with the intention of minimizing additional financial expenditure. Historically, one of the issues restricting widespread utilization of the grid resources in molecular modeling is the limited set of suitable applications amenable to coarse-grained parallelization. Recent advances in grid infrastructure technology coupled with advances in application research and redesign will enable fine-grained parallel problems, such as quantum mechanics and molecular dynamics, which were previously inaccessible to the grid environment. This will enable new science as well as increase resource flexibility to load balance and schedule existing workloads.

  16. Towards molecular electronics with large-area molecular junctions

    NARCIS (Netherlands)

    Akkerman, HB; Blom, PWM; de Leeuw, DM; de Boer, B

    2006-01-01

    Electronic transport through single molecules has been studied extensively by academic(1-8) and industrial(9,10) research groups. Discrete tunnel junctions, or molecular diodes, have been reported using scanning probes(11,12), break junctions(13,14), metallic crossbars(6) and nanopores(8,15). For

  17. Coulomb explosion of large penetrating molecular clusters

    International Nuclear Information System (INIS)

    Wegner, H.E.; Thieberger, P.

    1981-01-01

    The main purpose of these Coulomb explosion measurements is to determine what kind of structure these and other complex molecules may have and also to determine what other special phenomena may come into play as these complex molecules pass through matter. Although the first preliminary measurements involving the Coulomb explosion of these molecules was reported at this workshop last year, the results are briefly summarized before going on to the more recent measurements obtained with a completely new kind of detector system. This new image intensifier detector system, coupled with a microcomputer, has proven to be a valuable tool in the study of the Coulomb explosion of complex molecules that penetrate matter. In the future, with some additional improvements in the system, and much better statistics for most of the molecules studied to date, it is expected that much new information will be gained about the structure of many kinds of complex molecular ions including the special effects that may be encountered when these fast molecular ions penetrate matter

  18. Challenges in analysing and visualizing large-scale molecular dynamics simulations: domain and defect formation in lung surfactant monolayers

    International Nuclear Information System (INIS)

    Mendez-Villuendas, E; Baoukina, S; Tieleman, D P

    2012-01-01

    Molecular dynamics simulations have rapidly grown in size and complexity, as computers have become more powerful and molecular dynamics software more efficient. Using coarse-grained models like MARTINI system sizes of the order of 50 nm × 50 nm × 50 nm can be simulated on commodity clusters on microsecond time scales. For simulations of biological membranes and monolayers mimicking lung surfactant this enables large-scale transformation and complex mixtures of lipids and proteins. Here we use a simulation of a monolayer with three phospholipid components, cholesterol, lung surfactant proteins, water, and ions on a ten microsecond time scale to illustrate some current challenges in analysis. In the simulation, phase separation occurs followed by formation of a bilayer fold in which lipids and lung surfactant protein form a highly curved structure in the aqueous phase. We use Voronoi analysis to obtain detailed physical properties of the different components and phases, and calculate local mean and Gaussian curvatures of the bilayer fold.

  19. The temperature of large dust grains in molecular clouds

    Science.gov (United States)

    Clark, F. O.; Laureijs, R. J.; Prusti, T.

    1991-01-01

    The temperature of the large dust grains is calculated from three molecular clouds ranging in visual extinction from 2.5 to 8 mag, by comparing maps of either extinction derived from star counts or gas column density derived from molecular observations to I(100). Both techniques show the dust temperature declining into clouds. The two techniques do not agree in absolute scale.

  20. Geologic history of Siletzia, a large igneous province in the Oregon and Washington Coast Range: correlation to the geomagnetic polarity time scale and implications for a long-lived Yellowstone hotspot

    Science.gov (United States)

    Wells, Ray; Bukry, David; Friedman, Richard; Pyle, Douglas; Duncan, Robert; Haeussler, Peter J.; Wooden, Joe

    2014-01-01

    Siletzia is a basaltic Paleocene and Eocene large igneous province in coastal Oregon, Washington, and southern Vancouver Island that was accreted to North America in the early Eocene. New U-Pb magmatic, detrital zircon, and 40Ar/39Ar ages constrained by detailed field mapping, global nannoplankton zones, and magnetic polarities allow correlation of the volcanics with the 2012 geologic time scale. The data show that Siletzia was rapidly erupted 56–49 Ma, during the Chron 25–22 plate reorganization in the northeast Pacific basin. Accretion was completed between 51 and 49 Ma in Oregon, based on CP11 (CP—Coccolith Paleogene zone) coccoliths in strata overlying onlapping continental sediments. Magmatism continued in the northern Oregon Coast Range until ca. 46 Ma with the emplacement of a regional sill complex during or shortly after accretion. Isotopic signatures similar to early Columbia River basalts, the great crustal thickness of Siletzia in Oregon, rapid eruption, and timing of accretion are consistent with offshore formation as an oceanic plateau. Approximately 8 m.y. after accretion, margin parallel extension of the forearc, emplacement of regional dike swarms, and renewed magmatism of the Tillamook episode peaked at 41.6 Ma (CP zone 14a; Chron 19r). We examine the origin of Siletzia and consider the possible role of a long-lived Yellowstone hotspot using the reconstruction in GPlates, an open source plate model. In most hotspot reference frames, the Yellowstone hotspot (YHS) is on or near an inferred northeast-striking Kula-Farallon and/or Resurrection-Farallon ridge between 60 and 50 Ma. In this configuration, the YHS could have provided a 56–49 Ma source on the Farallon plate for Siletzia, which accreted to North America by 50 Ma. A sister plateau, the Eocene basalt basement of the Yakutat terrane, now in Alaska, formed contemporaneously on the adjacent Kula (or Resurrection) plate and accreted to coastal British Columbia at about the same time

  1. Stochastic time scale for the Universe

    International Nuclear Information System (INIS)

    Szydlowski, M.; Golda, Z.

    1986-01-01

    An intrinsic time scale is naturally defined within stochastic gradient dynamical systems. It should be interpreted as a ''relaxation time'' to a local potential minimum after the system has been randomly perturbed. It is shown that for a flat Friedman-like cosmological model this time scale is of order of the age of the Universe. 7 refs. (author)

  2. Some nonlinear dynamic inequalities on time scales

    Indian Academy of Sciences (India)

    In 1988, Stefan Hilger [10] introduced the calculus on time scales which unifies continuous and discrete analysis. Since then many authors have expounded on various aspects of the theory of dynamic equations on time scales. Recently, there has been much research activity concerning the new theory. For example, we ...

  3. Uniform Statistical Convergence on Time Scales

    Directory of Open Access Journals (Sweden)

    Yavuz Altin

    2014-01-01

    Full Text Available We will introduce the concept of m- and (λ,m-uniform density of a set and m- and (λ,m-uniform statistical convergence on an arbitrary time scale. However, we will define m-uniform Cauchy function on a time scale. Furthermore, some relations about these new notions are also obtained.

  4. Time Scale in Least Square Method

    Directory of Open Access Journals (Sweden)

    Özgür Yeniay

    2014-01-01

    Full Text Available Study of dynamic equations in time scale is a new area in mathematics. Time scale tries to build a bridge between real numbers and integers. Two derivatives in time scale have been introduced and called as delta and nabla derivative. Delta derivative concept is defined as forward direction, and nabla derivative concept is defined as backward direction. Within the scope of this study, we consider the method of obtaining parameters of regression equation of integer values through time scale. Therefore, we implemented least squares method according to derivative definition of time scale and obtained coefficients related to the model. Here, there exist two coefficients originating from forward and backward jump operators relevant to the same model, which are different from each other. Occurrence of such a situation is equal to total number of values of vertical deviation between regression equations and observation values of forward and backward jump operators divided by two. We also estimated coefficients for the model using ordinary least squares method. As a result, we made an introduction to least squares method on time scale. We think that time scale theory would be a new vision in least square especially when assumptions of linear regression are violated.

  5. Hardy type inequalities on time scales

    CERN Document Server

    Agarwal, Ravi P; Saker, Samir H

    2016-01-01

    The book is devoted to dynamic inequalities of Hardy type and extensions and generalizations via convexity on a time scale T. In particular, the book contains the time scale versions of classical Hardy type inequalities, Hardy and Littlewood type inequalities, Hardy-Knopp type inequalities via convexity, Copson type inequalities, Copson-Beesack type inequalities, Liendeler type inequalities, Levinson type inequalities and Pachpatte type inequalities, Bennett type inequalities, Chan type inequalities, and Hardy type inequalities with two different weight functions. These dynamic inequalities contain the classical continuous and discrete inequalities as special cases when T = R and T = N and can be extended to different types of inequalities on different time scales such as T = hN, h > 0, T = qN for q > 1, etc.In this book the authors followed the history and development of these inequalities. Each section in self-contained and one can see the relationship between the time scale versions of the inequalities and...

  6. Steffensen's Integral Inequality on Time Scales

    Directory of Open Access Journals (Sweden)

    Ozkan Umut Mutlu

    2007-01-01

    Full Text Available We establish generalizations of Steffensen's integral inequality on time scales via the diamond- dynamic integral, which is defined as a linear combination of the delta and nabla integrals.

  7. Wind power impacts and electricity storage - a time scale perspective

    DEFF Research Database (Denmark)

    Hedegaard, Karsten; Meibom, Peter

    2012-01-01

    Integrating large amounts of wind power in energy systems poses balancing challenges due to the variable and only partly predictable nature of wind. The challenges cover different time scales from intra-hour, intra-day/day-ahead to several days and seasonal level. Along with flexible electricity...... demand options, various electricity storage technologies are being discussed as candidates for contributing to large-scale wind power integration and these also differ in terms of the time scales at which they can operate. In this paper, using the case of Western Denmark in 2025 with an expected 57% wind...... power penetration, wind power impacts on different time scales are analysed. Results show consecutive negative and high net load period lengths indicating a significant potential for flexibility measures capable of charging/activating demand and discharging/inactivating demand in periods of 1 h to one...

  8. Large-scale conformational changes of Trypanosoma cruzi proline racemase predicted by accelerated molecular dynamics simulation.

    Directory of Open Access Journals (Sweden)

    César Augusto F de Oliveira

    2011-10-01

    Full Text Available Chagas' disease, caused by the protozoan parasite Trypanosoma cruzi (T. cruzi, is a life-threatening illness affecting 11-18 million people. Currently available treatments are limited, with unacceptable efficacy and safety profiles. Recent studies have revealed an essential T. cruzi proline racemase enzyme (TcPR as an attractive candidate for improved chemotherapeutic intervention. Conformational changes associated with substrate binding to TcPR are believed to expose critical residues that elicit a host mitogenic B-cell response, a process contributing to parasite persistence and immune system evasion. Characterization of the conformational states of TcPR requires access to long-time-scale motions that are currently inaccessible by standard molecular dynamics simulations. Here we describe advanced accelerated molecular dynamics that extend the effective simulation time and capture large-scale motions of functional relevance. Conservation and fragment mapping analyses identified potential conformational epitopes located in the vicinity of newly identified transient binding pockets. The newly identified open TcPR conformations revealed by this study along with knowledge of the closed to open interconversion mechanism advances our understanding of TcPR function. The results and the strategy adopted in this work constitute an important step toward the rationalization of the molecular basis behind the mitogenic B-cell response of TcPR and provide new insights for future structure-based drug discovery.

  9. Development of the Fragment Molecular Orbital Method for Calculating Nonlocal Excitations in Large Molecular Systems.

    Science.gov (United States)

    Fujita, Takatoshi; Mochizuki, Yuji

    2018-04-19

    We developed the fragment-based method for calculating nonlocal excitations in large molecular systems. This method is based on the multilayer fragment molecular orbital method and the configuration interaction single (CIS) wave function using localized molecular orbitals. The excited-state wave function for the whole system is described as a superposition of configuration state functions (CSFs) for intrafragment excitations and for interfragment charge-transfer excitations. The formulation and calculations of singlet excited-state Hamiltonian matrix elements in the fragment CSFs are presented in detail. The efficient approximation schemes for calculating the matrix elements are also presented. The computational efficiency and the accuracy were evaluated using the molecular dimers and molecular aggregates. We confirmed that absolute errors of 50 meV (relative to the conventional calculations) are achievable for the molecular systems in their equilibrium geometries. The perturbative electron correlation correction to the CIS excitation energies is also demonstrated. The present theory can compute a large number of excited states in large molecular systems; in addition, it allows for the systematic derivation of a model exciton Hamiltonian. These features are useful for studying excited-state dynamics in condensed molecular systems based on the ab initio electronic structure theory.

  10. JY1 time scale: a new Kalman-filter time scale designed at NIST

    International Nuclear Information System (INIS)

    Yao, Jian; Parker, Thomas E; Levine, Judah

    2017-01-01

    We report on a new Kalman-filter hydrogen-maser time scale (i.e. JY1 time scale) designed at the National Institute of Standards and Technology (NIST). The JY1 time scale is composed of a few hydrogen masers and a commercial Cs clock. The Cs clock is used as a reference clock to ease operations with existing data. Unlike other time scales, the JY1 time scale uses three basic time-scale equations, instead of only one equation. Also, this time scale can detect a clock error (i.e. time error, frequency error, or frequency drift error) automatically. These features make the JY1 time scale stiff and less likely to be affected by an abnormal clock. Tests show that the JY1 time scale deviates from the UTC by less than  ±5 ns for ∼100 d, when the time scale is initially aligned to the UTC and then is completely free running. Once the time scale is steered to a Cs fountain, it can maintain the time with little error even if the Cs fountain stops working for tens of days. This can be helpful when we do not have a continuously operated fountain or when the continuously operated fountain accidentally stops, or when optical clocks run occasionally. (paper)

  11. Molecular computational elements encode large populations of small objects

    Science.gov (United States)

    Prasanna de Silva, A.; James, Mark R.; McKinney, Bernadine O. F.; Pears, David A.; Weir, Sheenagh M.

    2006-10-01

    Since the introduction of molecular computation, experimental molecular computational elements have grown to encompass small-scale integration, arithmetic and games, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size (about 1nm) and large `on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100μm) used for synthesis of combinatorial libraries. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a `wash and watch' protocol. Our focus on converting molecular science into technology concerning analog sensors, turns to digital logic devices in the present work.

  12. Decoding the Mobility and Time Scales of Protein Loops.

    Science.gov (United States)

    Gu, Yina; Li, Da-Wei; Brüschweiler, Rafael

    2015-03-10

    The flexible nature of protein loops and the time scales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. In order to obtain a predictive understanding of the dynamic properties of loops, 500 ns molecular dynamics (MD) computer simulations of 38 different proteins were performed and validated using NMR chemical shifts. A total of 169 loops were analyzed and classified into three types, namely fast loops with correlation times Web server (http://spin.ccic.ohio-state.edu/index.php/loop). The results demonstrate that loop dynamics with their time scales can be predicted rapidly with reasonable accuracy, which will allow the screening of average protein structures to help better understand the various roles loops can play in the context of protein-protein interactions and binding.

  13. Large-Area, Ensemble Molecular Electronics: Motivation and Challenges.

    Science.gov (United States)

    Vilan, Ayelet; Aswal, Dinesh; Cahen, David

    2017-03-08

    We review charge transport across molecular monolayers, which is central to molecular electronics (MolEl), using large-area junctions (NmJ). We strive to provide a wide conceptual overview of three main subtopics. First, a broad introduction places NmJ in perspective to related fields of research and to single-molecule junctions (1mJ) in addition to a brief historical account. As charge transport presents an ultrasensitive probe for the electronic perfection of interfaces, in the second part ways to form both the monolayer and the contacts are described to construct reliable, defect-free interfaces. The last part is dedicated to understanding and analyses of current-voltage (I-V) traces across molecular junctions. Notwithstanding the original motivation of MolEl, I-V traces are often not very sensitive to molecular details and then provide a poor probe for chemical information. Instead, we focus on how to analyze the net electrical performance of molecular junctions, from a functional device perspective. Finally, we point to creation of a built-in electric field as a key to achieve functionality, including nonlinear current-voltage characteristics that originate in the molecules or their contacts to the electrodes. This review is complemented by a another review that covers metal-molecule-semiconductor junctions and their unique hybrid effects.

  14. Multivariable dynamic calculus on time scales

    CERN Document Server

    Bohner, Martin

    2016-01-01

    This book offers the reader an overview of recent developments of multivariable dynamic calculus on time scales, taking readers beyond the traditional calculus texts. Covering topics from parameter-dependent integrals to partial differentiation on time scales, the book’s nine pedagogically oriented chapters provide a pathway to this active area of research that will appeal to students and researchers in mathematics and the physical sciences. The authors present a clear and well-organized treatment of the concept behind the mathematics and solution techniques, including many practical examples and exercises.

  15. The Second Noether Theorem on Time Scales

    Directory of Open Access Journals (Sweden)

    Agnieszka B. Malinowska

    2013-01-01

    Full Text Available We extend the second Noether theorem to variational problems on time scales. As corollaries we obtain the classical second Noether theorem, the second Noether theorem for the h-calculus and the second Noether theorem for the q-calculus.

  16. Some Nonlinear Dynamic Inequalities on Time Scales

    Indian Academy of Sciences (India)

    The aim of this paper is to investigate some nonlinear dynamic inequalities on time scales, which provide explicit bounds on unknown functions. The inequalities given here unify and extend some inequalities in (B G Pachpatte, On some new inequalities related to a certain inequality arising in the theory of differential ...

  17. Special Issue on Time Scale Algorithms

    Science.gov (United States)

    2008-01-01

    unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 IOP PUBLISHING METROLOGIA Metrologia 45 (2008) doi:10.1088/0026-1394/45/6/E01...special issue of Metrologia presents selected papers from the Fifth International Time Scale Algorithm Symposium (VITSAS), including some of the...scientists, and hosted by the Real Instituto y Observatorio de la Armada (ROA) in San Fernando, Spain, whose staff further enhanced their nation’s high

  18. Current relaxation time scales in toroidal plasmas

    International Nuclear Information System (INIS)

    Mikkelsen, D.R.

    1987-02-01

    An approximate normal mode analysis of plasma current diffusion in tokamaks is presented. The work is based on numerical solutions of the current diffusion equation in cylindrical geometry. Eigenvalues and eigenfunctions are shown for a broad range of plasma conductivity profile shapes. Three classes of solutions are considered which correspond to three types of tokamak operation. Convenient approximations to the three lowest eigenvalues in each class are presented and simple formulae for the current relaxation time scales are given

  19. Time scales in tidal disruption events

    Directory of Open Access Journals (Sweden)

    Krolik J.

    2012-12-01

    Full Text Available We explore the temporal structure of tidal disruption events pointing out the corresponding transitions in the lightcurves of the thermal accretion disk and of the jet emerging from such events. The hydrodynamic time scale of the disrupted star is the minimal time scale of building up the accretion disk and the jet and it sets a limit on the rise time. This suggest that Swift J1644+57, that shows several flares with a rise time as short as a few hundred seconds could not have arisen from a tidal disruption of a main sequence star whose hydrodynamic time is a few hours. The disrupted object must have been a white dwarf. A second important time scale is the Eddington time in which the accretion rate changes form super to sub Eddington. It is possible that such a transition was observed in the light curve of Swift J2058+05. If correct this provides interesting constraints on the parameters of the system.

  20. Modelling financial markets with agents competing on different time scales and with different amount of information

    Science.gov (United States)

    Wohlmuth, Johannes; Andersen, Jørgen Vitting

    2006-05-01

    We use agent-based models to study the competition among investors who use trading strategies with different amount of information and with different time scales. We find that mixing agents that trade on the same time scale but with different amount of information has a stabilizing impact on the large and extreme fluctuations of the market. Traders with the most information are found to be more likely to arbitrage traders who use less information in the decision making. On the other hand, introducing investors who act on two different time scales has a destabilizing effect on the large and extreme price movements, increasing the volatility of the market. Closeness in time scale used in the decision making is found to facilitate the creation of local trends. The larger the overlap in commonly shared information the more the traders in a mixed system with different time scales are found to profit from the presence of traders acting at another time scale than themselves.

  1. LARGE-SCALE TOPOLOGICAL PROPERTIES OF MOLECULAR NETWORKS.

    Energy Technology Data Exchange (ETDEWEB)

    MASLOV,S.SNEPPEN,K.

    2003-11-17

    Bio-molecular networks lack the top-down design. Instead, selective forces of biological evolution shape them from raw material provided by random events such as gene duplications and single gene mutations. As a result individual connections in these networks are characterized by a large degree of randomness. One may wonder which connectivity patterns are indeed random, while which arose due to the network growth, evolution, and/or its fundamental design principles and limitations? Here we introduce a general method allowing one to construct a random null-model version of a given network while preserving the desired set of its low-level topological features, such as, e.g., the number of neighbors of individual nodes, the average level of modularity, preferential connections between particular groups of nodes, etc. Such a null-model network can then be used to detect and quantify the non-random topological patterns present in large networks. In particular, we measured correlations between degrees of interacting nodes in protein interaction and regulatory networks in yeast. It was found that in both these networks, links between highly connected proteins are systematically suppressed. This effect decreases the likelihood of cross-talk between different functional modules of the cell, and increases the overall robustness of a network by localizing effects of deleterious perturbations. It also teaches us about the overall computational architecture of such networks and points at the origin of large differences in the number of neighbors of individual nodes.

  2. uncertain dynamic systems on time scales

    Directory of Open Access Journals (Sweden)

    V. Lakshmikantham

    1995-01-01

    Full Text Available A basic feedback control problem is that of obtaining some desired stability property from a system which contains uncertainties due to unknown inputs into the system. Despite such imperfect knowledge in the selected mathematical model, we often seek to devise controllers that will steer the system in a certain required fashion. Various classes of controllers whose design is based on the method of Lyapunov are known for both discrete [4], [10], [15], and continuous [3–9], [11] models described by difference and differential equations, respectively. Recently, a theory for what is known as dynamic systems on time scales has been built which incorporates both continuous and discrete times, namely, time as an arbitrary closed sets of reals, and allows us to handle both systems simultaneously [1], [2], [12], [13]. This theory permits one to get some insight into and better understanding of the subtle differences between discrete and continuous systems. We shall, in this paper, utilize the framework of the theory of dynamic systems on time scales to investigate the stability properties of conditionally invariant sets which are then applied to discuss controlled systems with uncertain elements. For the notion of conditionally invariant set and its stability properties, see [14]. Our results offer a new approach to the problem in question.

  3. Lightweight computational steering of very large scale molecular dynamics simulations

    International Nuclear Information System (INIS)

    Beazley, D.M.

    1996-01-01

    We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages

  4. Approximate method for stochastic chemical kinetics with two-time scales by chemical Langevin equations

    International Nuclear Information System (INIS)

    Wu, Fuke; Tian, Tianhai; Rawlings, James B.; Yin, George

    2016-01-01

    The frequently used reduction technique is based on the chemical master equation for stochastic chemical kinetics with two-time scales, which yields the modified stochastic simulation algorithm (SSA). For the chemical reaction processes involving a large number of molecular species and reactions, the collection of slow reactions may still include a large number of molecular species and reactions. Consequently, the SSA is still computationally expensive. Because the chemical Langevin equations (CLEs) can effectively work for a large number of molecular species and reactions, this paper develops a reduction method based on the CLE by the stochastic averaging principle developed in the work of Khasminskii and Yin [SIAM J. Appl. Math. 56, 1766–1793 (1996); ibid. 56, 1794–1819 (1996)] to average out the fast-reacting variables. This reduction method leads to a limit averaging system, which is an approximation of the slow reactions. Because in the stochastic chemical kinetics, the CLE is seen as the approximation of the SSA, the limit averaging system can be treated as the approximation of the slow reactions. As an application, we examine the reduction of computation complexity for the gene regulatory networks with two-time scales driven by intrinsic noise. For linear and nonlinear protein production functions, the simulations show that the sample average (expectation) of the limit averaging system is close to that of the slow-reaction process based on the SSA. It demonstrates that the limit averaging system is an efficient approximation of the slow-reaction process in the sense of the weak convergence.

  5. Decay of surface nanostructures via long-time-scale dynamics

    International Nuclear Information System (INIS)

    Voter, A.F.; Stanciu, N.

    1998-01-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have developed a new approach for extending the time scale of molecular dynamics simulations. For infrequent-event systems, the category that includes most diffusive events in the solid phase, this hyperdynamics method can extend the simulation time by a few orders of magnitude compared to direct molecular dynamics. The trajectory is run on a potential surface that has been biased to raise the energy in the potential basins without affecting the transition state region. The method is described and applied to surface and bulk diffusion processes, achieving microsecond and millisecond simulation times. The authors have also developed a new parallel computing method that is efficient for small system sizes. The combination of the hyperdynamics with this parallel replica dynamics looks promising as a general materials simulation tool

  6. Time-Scale Invariant Audio Data Embedding

    Directory of Open Access Journals (Sweden)

    Mansour Mohamed F

    2003-01-01

    Full Text Available We propose a novel algorithm for high-quality data embedding in audio. The algorithm is based on changing the relative length of the middle segment between two successive maximum and minimum peaks to embed data. Spline interpolation is used to change the lengths. To ensure smooth monotonic behavior between peaks, a hybrid orthogonal and nonorthogonal wavelet decomposition is used prior to data embedding. The possible data embedding rates are between 20 and 30 bps. However, for practical purposes, we use repetition codes, and the effective embedding data rate is around 5 bps. The algorithm is invariant after time-scale modification, time shift, and time cropping. It gives high-quality output and is robust to mp3 compression.

  7. Diffusion time scales and accretion in the sun

    International Nuclear Information System (INIS)

    Michaud, G.

    1977-01-01

    It is thought that surface abundances in the Sun could be due largely to accretion either of comets or grains, and it has been suggested that if surface convection zones were smaller than is usually indicated by model calculations, accretion would be especially important. Unless the zone immediately below the surface convection zone is sufficiently stable for diffusion to be important, other transport processes, such as turbulence and meridional circulation, more efficient than diffusion, will tend to homogenise the Sun. Diffusion is the slowest of the transport processes and will become important when other transport processes become inoperative. Using diffusion theory the minimum mass of the convection zone can be determined in order that transport processes at the bottom of the zone are not to influence abundances in the convection zone. If diffusion time scales are shorter than the life of the star (Sun) diffusion will modify the abundances in the convection zone. The mass in the convection zone for which diffusion time scales are equal to the life of the star on the main sequence then determines the minimum mass in the convection zone that justifies neglect of transport processes at the bottom of the convection zone. It is calculated here that, for the Sun, this mass is between 3 x 10 -3 and 10 -2 solar mass, and a general explosion is derived for the diffusion time scale as a function of the mass of the convection zone. (U.K.)

  8. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    Energy Technology Data Exchange (ETDEWEB)

    Kashiwagi, H [Institute for Molecular Science, Okazaki, Aichi (Japan)

    1982-06-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience.

  9. Large-scale theoretical calculations in molecular science - design of a large computer system for molecular science and necessary conditions for future computers

    International Nuclear Information System (INIS)

    Kashiwagi, H.

    1982-01-01

    A large computer system was designed and established for molecular science under the leadership of molecular scientists. Features of the computer system are an automated operation system and an open self-service system. Large-scale theoretical calculations have been performed to solve many problems in molecular science, using the computer system. Necessary conditions for future computers are discussed on the basis of this experience. (orig.)

  10. Large, cold, and unusual molecular cloud in Monoceros

    International Nuclear Information System (INIS)

    Maddalena, R.J.; Thaddeus, P.; and Columbia University)

    1985-01-01

    Observations of the J = 1 → 0 rotational transition of CO near the galactic plane in Monoceros (lroughly-equal216 0 ) reveal a molecular cloud with unusually low peak CO temperatures (T/sub R/ -1 ) typical of much warmer clouds. At the assumed distance of 3 kpc, the cloud is large (250 x 100 pc), has a mass of 7-11 x 10 5 M/sub sun/, and is well removed from the galactic midplane (130 pc). Except for a possible H II region, all the signs of star formation usually shown by clouds of comparable mass are missing. The cloud, unlike cloud complexes of similar size, is a single, continuous object that apparently has not been torn apart by star formation. Clouds with such properties are rare in the Galaxy; only one or two similar objects have been found. We discuss the possibility that the cloud is young and not yet forming stars but will evolve into a typical cloud complex once star formation begins

  11. A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

    Science.gov (United States)

    Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Kunaseth, Manaschai; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Ohmura, Satoshi; Rajak, Pankaj; Shimamura, Kohei; Vashishta, Priya

    2014-05-01

    are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales.

  12. A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

    International Nuclear Information System (INIS)

    Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya; Kunaseth, Manaschai; Ohmura, Satoshi; Shimamura, Kohei

    2014-01-01

    techniques are employed for efficiently calculating the long-range exact exchange correction and excited-state forces. The NAQMD trajectories are analyzed to extract the rates of various excitonic processes, which are then used in KMC simulation to study the dynamics of the global exciton flow network. This has allowed the study of large-scale photoexcitation dynamics in 6400-atom amorphous molecular solid, reaching the experimental time scales

  13. Multiple time-scale methods in particle simulations of plasmas

    International Nuclear Information System (INIS)

    Cohen, B.I.

    1985-01-01

    This paper surveys recent advances in the application of multiple time-scale methods to particle simulation of collective phenomena in plasmas. These methods dramatically improve the efficiency of simulating low-frequency kinetic behavior by allowing the use of a large timestep, while retaining accuracy. The numerical schemes surveyed provide selective damping of unwanted high-frequency waves and preserve numerical stability in a variety of physics models: electrostatic, magneto-inductive, Darwin and fully electromagnetic. The paper reviews hybrid simulation models, the implicitmoment-equation method, the direct implicit method, orbit averaging, and subcycling

  14. EDITORIAL: Special issue on time scale algorithms

    Science.gov (United States)

    Matsakis, Demetrios; Tavella, Patrizia

    2008-12-01

    This special issue of Metrologia presents selected papers from the Fifth International Time Scale Algorithm Symposium (VITSAS), including some of the tutorials presented on the first day. The symposium was attended by 76 persons, from every continent except Antarctica, by students as well as senior scientists, and hosted by the Real Instituto y Observatorio de la Armada (ROA) in San Fernando, Spain, whose staff further enhanced their nation's high reputation for hospitality. Although a timescale can be simply defined as a weighted average of clocks, whose purpose is to measure time better than any individual clock, timescale theory has long been and continues to be a vibrant field of research that has both followed and helped to create advances in the art of timekeeping. There is no perfect timescale algorithm, because every one embodies a compromise involving user needs. Some users wish to generate a constant frequency, perhaps not necessarily one that is well-defined with respect to the definition of a second. Other users might want a clock which is as close to UTC or a particular reference clock as possible, or perhaps wish to minimize the maximum variation from that standard. In contrast to the steered timescales that would be required by those users, other users may need free-running timescales, which are independent of external information. While no algorithm can meet all these needs, every algorithm can benefit from some form of tuning. The optimal tuning, and even the optimal algorithm, can depend on the noise characteristics of the frequency standards, or of their comparison systems, the most precise and accurate of which are currently Two Way Satellite Time and Frequency Transfer (TWSTFT) and GPS carrier phase time transfer. The interest in time scale algorithms and its associated statistical methodology began around 40 years ago when the Allan variance appeared and when the metrological institutions started realizing ensemble atomic time using more than

  15. Atomistic simulations of graphite etching at realistic time scales.

    Science.gov (United States)

    Aussems, D U B; Bal, K M; Morgan, T W; van de Sanden, M C M; Neyts, E C

    2017-10-01

    Hydrogen-graphite interactions are relevant to a wide variety of applications, ranging from astrophysics to fusion devices and nano-electronics. In order to shed light on these interactions, atomistic simulation using Molecular Dynamics (MD) has been shown to be an invaluable tool. It suffers, however, from severe time-scale limitations. In this work we apply the recently developed Collective Variable-Driven Hyperdynamics (CVHD) method to hydrogen etching of graphite for varying inter-impact times up to a realistic value of 1 ms, which corresponds to a flux of ∼10 20 m -2 s -1 . The results show that the erosion yield, hydrogen surface coverage and species distribution are significantly affected by the time between impacts. This can be explained by the higher probability of C-C bond breaking due to the prolonged exposure to thermal stress and the subsequent transition from ion- to thermal-induced etching. This latter regime of thermal-induced etching - chemical erosion - is here accessed for the first time using atomistic simulations. In conclusion, this study demonstrates that accounting for long time-scales significantly affects ion bombardment simulations and should not be neglected in a wide range of conditions, in contrast to what is typically assumed.

  16. The length and time scales of water's glass transitions

    Science.gov (United States)

    Limmer, David T.

    2014-06-01

    Using a general model for the equilibrium dynamics of supercooled liquids, I compute from molecular properties the emergent length and time scales that govern the nonequilibrium relaxation behavior of amorphous ice prepared by rapid cooling. Upon cooling, the liquid water falls out of equilibrium whereby the temperature dependence of its relaxation time is predicted to change from super-Arrhenius to Arrhenius. A consequence of this crossover is that the location of the apparent glass transition temperature depends logarithmically on cooling rate. Accompanying vitrification is the emergence of a dynamical length-scale, the size of which depends on the cooling rate and varies between angstroms and tens of nanometers. While this protocol dependence clarifies a number of previous experimental observations for amorphous ice, the arguments are general and can be extended to other glass forming liquids.

  17. The length and time scales of water's glass transitions.

    Science.gov (United States)

    Limmer, David T

    2014-06-07

    Using a general model for the equilibrium dynamics of supercooled liquids, I compute from molecular properties the emergent length and time scales that govern the nonequilibrium relaxation behavior of amorphous ice prepared by rapid cooling. Upon cooling, the liquid water falls out of equilibrium whereby the temperature dependence of its relaxation time is predicted to change from super-Arrhenius to Arrhenius. A consequence of this crossover is that the location of the apparent glass transition temperature depends logarithmically on cooling rate. Accompanying vitrification is the emergence of a dynamical length-scale, the size of which depends on the cooling rate and varies between angstroms and tens of nanometers. While this protocol dependence clarifies a number of previous experimental observations for amorphous ice, the arguments are general and can be extended to other glass forming liquids.

  18. On the strong influence of molecular interactions over large distances

    Science.gov (United States)

    Pfennig, Andreas

    2018-03-01

    Molecular-dynamics simulations of liquid water show deterministic chaos, i.e. an intentionally introduced molecular position shift of an individual molecule increases exponentially by a factor of 10 in 0.23 ps. This is a Lyaponov instability. As soon as it reaches molecular scale, the direction of the resulting shift in molecular motions is unpredictable. The influence of any individual distant particle on an observed molecule will be minute, but the effect will quickly increase to molecular scale and beyond due to this exponential growth. Consequently, any individual particle in the universe will affect the behavior of any molecule within at most 33 ps after the interaction reaches it. A larger distance of the faraway particle does not decrease the influence on an observed molecule, but the effect reaches molecular scale only some ps later. Thus in evaluating the interactions, nearby and faraway molecules have to be equally accounted for. The consequences of this quickly reacting network of interactions on universal scale are fundamental. Even in a strictly deterministic view, molecular behavior is principally unpredictable, and thus has to be regarded random. Corresponding statements apply for any particles interacting. This result leads to a fundamental rethinking of the structure of interactions of molecules and particles as well as the behavior of reality.

  19. Almost Automorphic Functions on the Quantum Time Scale and Applications

    Directory of Open Access Journals (Sweden)

    Yongkun Li

    2017-01-01

    Full Text Available We first propose two types of concepts of almost automorphic functions on the quantum time scale. Secondly, we study some basic properties of almost automorphic functions on the quantum time scale. Then, we introduce a transformation between functions defined on the quantum time scale and functions defined on the set of generalized integer numbers; by using this transformation we give equivalent definitions of almost automorphic functions on the quantum time scale; following the idea of the transformation, we also give a concept of almost automorphic functions on more general time scales that can unify the concepts of almost automorphic functions on almost periodic time scales and on the quantum time scale. Finally, as an application of our results, we establish the existence of almost automorphic solutions of linear and semilinear dynamic equations on the quantum time scale.

  20. Thermodynamic Stability of Structure H Hydrates Based on the Molecular Properties of Large Guest Molecules

    OpenAIRE

    Tezuka, Kyoichi; Taguchi, Tatsuhiko; Alavi, Saman; Sum, Amadeu K.; Ohmura, Ryo

    2012-01-01

    This paper report analyses of thermodynamic stability of structure-H clathrate hydrates formed with methane and large guest molecules in terms of their gas phase molecular sizes and molar masses for the selection of a large guest molecule providing better hydrate stability. We investigated the correlation among the gas phase molecular sizes, the molar masses of large molecule guest substances, and the equilibrium pressures. The results suggest that there exists a molecular-size value for the ...

  1. A Quaternary Geomagnetic Instability Time Scale

    Science.gov (United States)

    Singer, B. S.

    2013-12-01

    Reversals and excursions of Earth's geomagnetic field create marker horizons that are readily detected in sedimentary and volcanic rocks worldwide. An accurate and precise chronology of these geomagnetic field instabilities is fundamental to understanding several aspects of Quaternary climate, dynamo processes, and surface processes. For example, stratigraphic correlation between marine sediment and polar ice records of climate change across the cryospheres benefits from a highly resolved record of reversals and excursions. The temporal patterns of dynamo behavior may reflect physical interactions between the molten outer core and the solid inner core or lowermost mantle. These interactions may control reversal frequency and shape the weak magnetic fields that arise during successive dynamo instabilities. Moreover, weakening of the axial dipole during reversals and excursions enhances the production of cosmogenic isotopes that are used in sediment and ice core stratigraphy and surface exposure dating. The Geomagnetic Instability Time Scale (GITS) is based on the direct dating of transitional polarity states recorded by lava flows using the 40Ar/39Ar method, in parallel with astrochronologic age models of marine sediments in which O isotope and magnetic records have been obtained. A review of data from Quaternary lava flows and sediments yields a GITS comprising 10 polarity reversals and 27 excursions during the past 2.6 million years. Nine of the ten reversals bounding chrons and subchrons are associated with 40Ar/39Ar ages of transitionally-magnetized lava flows. The tenth, the Guass-Matuyama chron boundary, is tightly bracketed by 40Ar/39Ar dated ash deposits. Of the 27 well-documented excursions, 14 occurred during the Matuyama chron and 13 during the Brunhes chron; 19 have been dated directly using the 40Ar/39Ar method on transitionally-magnetized volcanic rocks and form the backbone of the GITS. Excursions are clearly not the rare phenomena once thought

  2. Revealing less derived nature of cartilaginous fish genomes with their evolutionary time scale inferred with nuclear genes.

    Directory of Open Access Journals (Sweden)

    Adina J Renz

    Full Text Available Cartilaginous fishes, divided into Holocephali (chimaeras and Elasmoblanchii (sharks, rays and skates, occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.

  3. A Bayesian method for construction of Markov models to describe dynamics on various time-scales.

    Science.gov (United States)

    Rains, Emily K; Andersen, Hans C

    2010-10-14

    The dynamics of many biological processes of interest, such as the folding of a protein, are slow and complicated enough that a single molecular dynamics simulation trajectory of the entire process is difficult to obtain in any reasonable amount of time. Moreover, one such simulation may not be sufficient to develop an understanding of the mechanism of the process, and multiple simulations may be necessary. One approach to circumvent this computational barrier is the use of Markov state models. These models are useful because they can be constructed using data from a large number of shorter simulations instead of a single long simulation. This paper presents a new Bayesian method for the construction of Markov models from simulation data. A Markov model is specified by (τ,P,T), where τ is the mesoscopic time step, P is a partition of configuration space into mesostates, and T is an N(P)×N(P) transition rate matrix for transitions between the mesostates in one mesoscopic time step, where N(P) is the number of mesostates in P. The method presented here is different from previous Bayesian methods in several ways. (1) The method uses Bayesian analysis to determine the partition as well as the transition probabilities. (2) The method allows the construction of a Markov model for any chosen mesoscopic time-scale τ. (3) It constructs Markov models for which the diagonal elements of T are all equal to or greater than 0.5. Such a model will be called a "consistent mesoscopic Markov model" (CMMM). Such models have important advantages for providing an understanding of the dynamics on a mesoscopic time-scale. The Bayesian method uses simulation data to find a posterior probability distribution for (P,T) for any chosen τ. This distribution can be regarded as the Bayesian probability that the kinetics observed in the atomistic simulation data on the mesoscopic time-scale τ was generated by the CMMM specified by (P,T). An optimization algorithm is used to find the most

  4. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

    Science.gov (United States)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  5. Quantum universe on extremely small space-time scales

    International Nuclear Information System (INIS)

    Kuzmichev, V.E.; Kuzmichev, V.V.

    2010-01-01

    The semiclassical approach to the quantum geometrodynamical model is used for the description of the properties of the Universe on extremely small space-time scales. Under this approach, the matter in the Universe has two components of the quantum nature which behave as antigravitating fluids. The first component does not vanish in the limit h → 0 and can be associated with dark energy. The second component is described by an extremely rigid equation of state and goes to zero after the transition to large spacetime scales. On small space-time scales, this quantum correction turns out to be significant. It determines the geometry of the Universe near the initial cosmological singularity point. This geometry is conformal to a unit four-sphere embedded in a five-dimensional Euclidean flat space. During the consequent expansion of the Universe, when reaching the post-Planck era, the geometry of the Universe changes into that conformal to a unit four-hyperboloid in a five-dimensional Lorentzsignatured flat space. This agrees with the hypothesis about the possible change of geometry after the origin of the expanding Universe from the region near the initial singularity point. The origin of the Universe can be interpreted as a quantum transition of the system from a region in the phase space forbidden for the classical motion, but where a trajectory in imaginary time exists, into a region, where the equations of motion have the solution which describes the evolution of the Universe in real time. Near the boundary between two regions, from the side of real time, the Universe undergoes almost an exponential expansion which passes smoothly into the expansion under the action of radiation dominating over matter which is described by the standard cosmological model.

  6. Time-scale invariances in preseismic electromagnetic radiation, magnetization and damage evolution of rocks

    Directory of Open Access Journals (Sweden)

    Y. Kawada

    2007-10-01

    Full Text Available We investigate the time-scale invariant changes in electromagnetic and mechanical energy releases prior to a rock failure or a large earthquake. The energy release processes are caused by damage evolutions such as crack propagation, motion of charged dislocation, area-enlargement of sheared asperities and repetitive creep-rate changes. Damage mechanics can be used to represent the time-scale invariant evolutions of both brittle and plastic damages. Irreversible thermodynamics applied to the damage mechanics reveals that the damage evolution produces the variations in charge, dipole and electromagnetic signals in addition to mechanical energy release, and yields the time-scale invariant patterns of Benioff electromagnetic radiation and cumulative Benioff strain-release. The irreversible thermodynamic framework of damage mechanics is also applicable to the seismo-magnetic effect, and the time-scale invariance is recognized in the remanent magnetization change associated with damage evolution prior to a rock failure.

  7. Bounds of Certain Dynamic Inequalities on Time Scales

    Directory of Open Access Journals (Sweden)

    Deepak B. Pachpatte

    2014-10-01

    Full Text Available In this paper we study explicit bounds of certain dynamic integral inequalities on time scales. These estimates give the bounds on unknown functions which can be used in studying the qualitative aspects of certain dynamic equations. Using these inequalities we prove the uniqueness of some partial integro-differential equations on time scales.

  8. Temperature dependence of fluctuation time scales in spin glasses

    DEFF Research Database (Denmark)

    Kenning, Gregory G.; Bowen, J.; Sibani, Paolo

    2010-01-01

    Using a series of fast cooling protocols we have probed aging effects in the spin glass state as a function of temperature. Analyzing the logarithmic decay found at very long time scales within a simple phenomenological barrier model, leads to the extraction of the fluctuation time scale of the s...

  9. Modeling ramp compression experiments using large-scale molecular dynamics simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

    2011-10-01

    Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

  10. Bridging time scales in cellular decision making with a stochastic bistable switch

    Directory of Open Access Journals (Sweden)

    Waldherr Steffen

    2010-08-01

    Full Text Available Abstract Background Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. Some of these transformations act over a very long time scale on the cell population level, up to the entire lifespan of the organism. Results In this work, we aim at linking cellular decisions taking place on a time scale of years to decades with the biochemical dynamics in signal transduction and gene regulation, occuring on a time scale of minutes to hours. We show that a stochastic bistable switch forms a viable biochemical mechanism to implement decision processes on long time scales. As a case study, the mechanism is applied to model the initiation of follicle growth in mammalian ovaries, where the physiological time scale of follicle pool depletion is on the order of the organism's lifespan. We construct a simple mathematical model for this process based on experimental evidence for the involved genetic mechanisms. Conclusions Despite the underlying stochasticity, the proposed mechanism turns out to yield reliable behavior in large populations of cells subject to the considered decision process. Our model explains how the physiological time constant may emerge from the intrinsic stochasticity of the underlying gene regulatory network. Apart from ovarian follicles, the proposed mechanism may also be of relevance for other physiological systems where cells take binary decisions over a long time scale.

  11. Neural Computations in a Dynamical System with Multiple Time Scales.

    Science.gov (United States)

    Mi, Yuanyuan; Lin, Xiaohan; Wu, Si

    2016-01-01

    Neural systems display rich short-term dynamics at various levels, e.g., spike-frequency adaptation (SFA) at the single-neuron level, and short-term facilitation (STF) and depression (STD) at the synapse level. These dynamical features typically cover a broad range of time scales and exhibit large diversity in different brain regions. It remains unclear what is the computational benefit for the brain to have such variability in short-term dynamics. In this study, we propose that the brain can exploit such dynamical features to implement multiple seemingly contradictory computations in a single neural circuit. To demonstrate this idea, we use continuous attractor neural network (CANN) as a working model and include STF, SFA and STD with increasing time constants in its dynamics. Three computational tasks are considered, which are persistent activity, adaptation, and anticipative tracking. These tasks require conflicting neural mechanisms, and hence cannot be implemented by a single dynamical feature or any combination with similar time constants. However, with properly coordinated STF, SFA and STD, we show that the network is able to implement the three computational tasks concurrently. We hope this study will shed light on the understanding of how the brain orchestrates its rich dynamics at various levels to realize diverse cognitive functions.

  12. An extended Halanay inequality of integral type on time scales

    Directory of Open Access Journals (Sweden)

    Boqun Ou

    2015-07-01

    Full Text Available In this paper, we obtain a Halanay-type inequality of integral type on time scales which improves and extends some earlier results for both the continuous and discrete cases. Several illustrative examples are also given.

  13. Multiple dynamical time-scales in networks with hierarchically

    Indian Academy of Sciences (India)

    Modular networks; hierarchical organization; synchronization. ... we show that such a topological structure gives rise to characteristic time-scale separation ... This suggests a possible functional role of such mesoscopic organization principle in ...

  14. Some New Inequalities of Opial's Type on Time Scales

    Directory of Open Access Journals (Sweden)

    Samir H. Saker

    2012-01-01

    Full Text Available We will prove some new dynamic inequalities of Opial's type on time scales. The results not only extend some results in the literature but also improve some of them. Some continuous and discrete inequalities are derived from the main results as special cases. The results can be applied on the study of distribution of generalized zeros of half-linear dynamic equations on time scales.

  15. SUPERGIANT SHELLS AND MOLECULAR CLOUD FORMATION IN THE LARGE MAGELLANIC CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Dawson, J. R.; Dickey, John M. [School of Mathematics and Physics, University of Tasmania, Sandy Bay Campus, Churchill Avenue, Sandy Bay, TAS 7005 (Australia); McClure-Griffiths, N. M. [Australia Telescope National Facility, CSIRO Astronomy and Space Science, Marsfield NSW 2122 (Australia); Wong, T. [Astronomy Department, University of Illinois, Urbana, IL 61801 (United States); Hughes, A. [Max-Planck-Institut fuer Astronomie, Koenigstuhl 17, D-69117, Heidelberg (Germany); Fukui, Y. [Department of Physics and Astrophysics, Nagoya University, Chikusa-ku, Nagoya (Japan); Kawamura, A., E-mail: joanne.dawson@utas.edu.au [National Astronomical Observatory of Japan, Tokyo 181-8588 (Japan)

    2013-01-20

    We investigate the influence of large-scale stellar feedback on the formation of molecular clouds in the Large Magellanic Cloud (LMC). Examining the relationship between H I and {sup 12}CO(J = 1-0) in supergiant shells (SGSs), we find that the molecular fraction in the total volume occupied by SGSs is not enhanced with respect to the rest of the LMC disk. However, the majority of objects ({approx}70% by mass) are more molecular than their local surroundings, implying that the presence of a supergiant shell does on average have a positive effect on the molecular gas fraction. Averaged over the full SGS sample, our results suggest that {approx}12%-25% of the molecular mass in supergiant shell systems was formed as a direct result of the stellar feedback that created the shells. This corresponds to {approx}4%-11% of the total molecular mass of the galaxy. These figures are an approximate lower limit to the total contribution of stellar feedback to molecular cloud formation in the LMC, and constitute one of the first quantitative measurements of feedback-triggered molecular cloud formation in a galactic system.

  16. Soil moisture memory at sub-monthly time scales

    Science.gov (United States)

    Mccoll, K. A.; Entekhabi, D.

    2017-12-01

    For soil moisture-climate feedbacks to occur, the soil moisture storage must have `memory' of past atmospheric anomalies. Quantifying soil moisture memory is, therefore, essential for mapping and characterizing land-atmosphere interactions globally. Most previous studies estimate soil moisture memory using metrics based on the autocorrelation function of the soil moisture time series (e.g., the e-folding autocorrelation time scale). This approach was first justified by Delworth and Manabe (1988) on the assumption that monthly soil moisture time series can be modelled as red noise. While this is a reasonable model for monthly soil moisture averages, at sub-monthly scales, the model is insufficient due to the highly non-Gaussian behavior of the precipitation forcing. Recent studies have shown that significant soil moisture-climate feedbacks appear to occur at sub-monthly time scales. Therefore, alternative metrics are required for defining and estimating soil moisture memory at these shorter time scales. In this study, we introduce metrics, based on the positive and negative increments of the soil moisture time series, that can be used to estimate soil moisture memory at sub-monthly time scales. The positive increments metric corresponds to a rapid drainage time scale. The negative increments metric represents a slower drying time scale that is most relevant to the study of land-atmosphere interactions. We show that autocorrelation-based metrics mix the two time scales, confounding physical interpretation. The new metrics are used to estimate soil moisture memory at sub-monthly scales from in-situ and satellite observations of soil moisture. Reference: Delworth, Thomas L., and Syukuro Manabe. "The Influence of Potential Evaporation on the Variabilities of Simulated Soil Wetness and Climate." Journal of Climate 1, no. 5 (May 1, 1988): 523-47. doi:10.1175/1520-0442(1988)0012.0.CO;2.

  17. Mountain erosion over 10 yr, 10 k.y., and 10 m.y. time scales

    Science.gov (United States)

    James W. Kirchner; Robert C. Finkel; Clifford S. Riebe; Darryl E. Granger; James L. Clayton; John G. King; Walter F. Megahan

    2001-01-01

    We used cosmogenic 10Be to measure erosion rates over 10 k.y. time scales at 32 Idaho mountain catchments, ranging from small experimental watersheds (0.2 km2) to large river basins (35 000 km2). These long-term sediment yields are, on average, 17 times higher than stream sediment fluxes measured over...

  18. Arctic energy budget in relation to sea ice variability on monthly-to-annual time scales

    NARCIS (Netherlands)

    Krikken, F.; Hazeleger, W.

    2015-01-01

    The large decrease in Arctic sea ice in recent years has triggered a strong interest in Arctic sea ice predictions on seasonal-to-decadal time scales. Hence, it is important to understand physical processes that provide enhanced predictability beyond persistence of sea ice anomalies. This study

  19. Mixing and flushing time scales in the Azhikode Estuary, southwest coast of India

    Digital Repository Service at National Institute of Oceanography (India)

    Revichandran, C.; Pylee, A.

    Flushing time scales of the Azhikode Estuary, Kerala, India showed pronounced dry season and wet season signals as well as large inter-annual variation. Cumulative flushing time of the estuary varies from 4.8 tide cycles in April to 1.22 tide cycles...

  20. Phospholipids composition and molecular species of large yellow croaker ( Pseudosciaena crocea ) roe

    DEFF Research Database (Denmark)

    Liang, Peng; Li, Ruifen; Sun, He

    2018-01-01

    The research aims to study phospholipids (PL) classes and molecular species of large yellow croaker (Pseudosciaena crocea) roe. Both gas chromatographymass spectroscopy (GC-MS) and high-performance liquid chromatography with evaporative light-scattering detection (HPLC-ELSD) were utilized to anal......-Q-TOF-MS). A total of 92 PLs molecular species was identified, including 49 PCs, 13 PEs, 10 phosphatidic acids (PAs), 13 phosphatidylserines (PSs), 3 phosphatidylglycerols (PGs), 2 sphingomyelins (SMs), and 2 PIs of the P. crocea roe....

  1. Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics

    Science.gov (United States)

    Sinitskiy, Anton V.; Pande, Vijay S.

    2018-01-01

    Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD) trajectory from the set of trajectories used to build the MSM. A rule of thumb claiming that the slowest implicit time scale captured by an MSM should be comparable by the order of magnitude to the aggregate duration of all MD trajectories used to build this MSM has been known in the field. However, this rule has never been formally proved. In this work, we present analytical results for the slowest time scale in several types of MSMs, supporting the above rule. We conclude that the slowest implicit time scale equals the product of the aggregate sampling and four factors that quantify: (1) how much statistics on the conformational transitions corresponding to the longest implicit time scale is available, (2) how good the sampling of the destination Markov state is, (3) the gain in statistics from using a sliding window for counting transitions between Markov states, and (4) a bias in the estimate of the implicit time scale arising from finite sampling of the conformational transitions. We demonstrate that in many practically important cases all these four factors are on the order of unity, and we analyze possible scenarios that could lead to their significant deviation from unity. Overall, we provide for the first time analytical results on the slowest time scales captured by MSMs. These results can guide further practical applications of MSMs to biomolecular dynamics and allow for higher computational efficiency of simulations.

  2. Superconducting fluctuations and characteristic time scales in amorphous WSi

    Science.gov (United States)

    Zhang, Xiaofu; Lita, Adriana E.; Sidorova, Mariia; Verma, Varun B.; Wang, Qiang; Nam, Sae Woo; Semenov, Alexei; Schilling, Andreas

    2018-05-01

    We study magnitudes and temperature dependencies of the electron-electron and electron-phonon interaction times which play the dominant role in the formation and relaxation of photon-induced hotspots in two-dimensional amorphous WSi films. The time constants are obtained through magnetoconductance measurements in a perpendicular magnetic field in the superconducting fluctuation regime and through time-resolved photoresponse to optical pulses. The excess magnetoconductivity is interpreted in terms of the weak-localization effect and superconducting fluctuations. Aslamazov-Larkin and Maki-Thompson superconducting fluctuations alone fail to reproduce the magnetic field dependence in the relatively high magnetic field range when the temperature is rather close to Tc because the suppression of the electronic density of states due to the formation of short-lifetime Cooper pairs needs to be considered. The time scale τi of inelastic scattering is ascribed to a combination of electron-electron (τe -e) and electron-phonon (τe -p h) interaction times, and a characteristic electron-fluctuation time (τe -f l) , which makes it possible to extract their magnitudes and temperature dependencies from the measured τi. The ratio of phonon-electron (τp h -e) and electron-phonon interaction times is obtained via measurements of the optical photoresponse of WSi microbridges. Relatively large τe -p h/τp h -e and τe -p h/τe -e ratios ensure that in WSi the photon energy is more efficiently confined in the electron subsystem than in other materials commonly used in the technology of superconducting nanowire single-photon detectors (SNSPDs). We discuss the impact of interaction times on the hotspot dynamics and compare relevant metrics of SNSPDs from different materials.

  3. Fractional dynamic calculus and fractional dynamic equations on time scales

    CERN Document Server

    Georgiev, Svetlin G

    2018-01-01

    Pedagogically organized, this monograph introduces fractional calculus and fractional dynamic equations on time scales in relation to mathematical physics applications and problems. Beginning with the definitions of forward and backward jump operators, the book builds from Stefan Hilger’s basic theories on time scales and examines recent developments within the field of fractional calculus and fractional equations. Useful tools are provided for solving differential and integral equations as well as various problems involving special functions of mathematical physics and their extensions and generalizations in one and more variables. Much discussion is devoted to Riemann-Liouville fractional dynamic equations and Caputo fractional dynamic equations.  Intended for use in the field and designed for students without an extensive mathematical background, this book is suitable for graduate courses and researchers looking for an introduction to fractional dynamic calculus and equations on time scales. .

  4. Time scales of tunneling decay of a localized state

    International Nuclear Information System (INIS)

    Ban, Yue; Muga, J. G.; Sherman, E. Ya.; Buettiker, M.

    2010-01-01

    Motivated by recent time-domain experiments on ultrafast atom ionization, we analyze the transients and time scales that characterize, aside from the relatively long lifetime, the decay of a localized state by tunneling. While the tunneling starts immediately, some time is required for the outgoing flux to develop. This short-term behavior depends strongly on the initial state. For the initial state, tightly localized so that the initial transients are dominated by over-the-barrier motion, the time scale for flux propagation through the barrier is close to the Buettiker-Landauer traversal time. Then a quasistationary, slow-decay process follows, which sets ideal conditions for observing diffraction in time at longer times and distances. To define operationally a tunneling time at the barrier edge, we extrapolate backward the propagation of the wave packet that escaped from the potential. This extrapolated time is considerably longer than the time scale of the flux and density buildup at the barrier edge.

  5. Hydrodynamic time scales for intense laser-heated clusters

    International Nuclear Information System (INIS)

    Parra, Enrique; Alexeev, Ilya; Fan, Jingyun; Kim, Kiong Y.; McNaught, Stuart J.; Milchberg, Howard M.

    2003-01-01

    Measurements are presented of x-ray (>1.5 keV) and extreme ultraviolet (EUV, λ equal to 2-44 nm) emission from argon clusters irradiated with constant-energy (50 mJ), variable-width laser pulses ranging from 100 fs to 10 ns. The results for clusters can be understood in terms of two time scales: a short time scale for optimal resonant absorption at the critical-density layer in the expanding plasma, and a longer time scale for the plasma to drop below critical density. We present a one-dimensional hydrodynamic model of the intense laser-cluster interaction in which the laser field is treated self-consistently. We find that nonuniform expansion of the heated material results in long-time resonance of the laser field at the critical-density plasma layer. These simulations explain the dependence of generation efficiency on laser pulse width

  6. Computational challenges of large-scale, long-time, first-principles molecular dynamics

    International Nuclear Information System (INIS)

    Kent, P R C

    2008-01-01

    Plane wave density functional calculations have traditionally been able to use the largest available supercomputing resources. We analyze the scalability of modern projector-augmented wave implementations to identify the challenges in performing molecular dynamics calculations of large systems containing many thousands of electrons. Benchmark calculations on the Cray XT4 demonstrate that global linear-algebra operations are the primary reason for limited parallel scalability. Plane-wave related operations can be made sufficiently scalable. Improving parallel linear-algebra performance is an essential step to reaching longer timescales in future large-scale molecular dynamics calculations

  7. Nonlinear triple-point problems on time scales

    Directory of Open Access Journals (Sweden)

    Douglas R. Anderson

    2004-04-01

    Full Text Available We establish the existence of multiple positive solutions to the nonlinear second-order triple-point boundary-value problem on time scales, $$displaylines{ u^{Delta abla}(t+h(tf(t,u(t=0, cr u(a=alpha u(b+delta u^Delta(a,quad eta u(c+gamma u^Delta(c=0 }$$ for $tin[a,c]subsetmathbb{T}$, where $mathbb{T}$ is a time scale, $eta, gamma, deltage 0$ with $Beta+gamma>0$, $0

  8. Dynamics symmetries of Hamiltonian system on time scales

    Energy Technology Data Exchange (ETDEWEB)

    Peng, Keke, E-mail: pengkeke88@126.com; Luo, Yiping, E-mail: zjstulyp@126.com [Department of Physics, Zhejiang Sci-Tech University, Hangzhou 310018 (China)

    2014-04-15

    In this paper, the dynamics symmetries of Hamiltonian system on time scales are studied. We study the symmetries and quantities based on the calculation of variation and Lie transformation group. Particular focus lies in: the Noether symmetry leads to the Noether conserved quantity and the Lie symmetry leads to the Noether conserved quantity if the infinitesimal transformations satisfy the structure equation. As the new application of result, at end of the article, we give a simple example of Noether symmetry and Lie symmetry on time scales.

  9. Molecular device computer: point of departure for large scale cellular automata

    Energy Technology Data Exchange (ETDEWEB)

    Carter, F L

    1984-01-01

    Switching is possible at the molecular size level because of the conformational changes that occur. Three of the most promising switching mechanisms include electron tunnelling in short periodic arrays, soliton switching and soliton valving. Assuming a 3-d architecture and molecular dimensions, memory and switching elements with densities of 10/sup 15/ to 10 /sup 18/ elements per cc are possible. The active elements are connected together conceptionally with molecular wires like polysulfur nitride (sn)/sub x/ and polyacetylene (ch)/sub x/. Simple cellular automata involving soliton propagation in conjugated systems would include soliton valves and cyclic configurations of valves. In the latter, soliton propagation becomes isomorphous with group operations giving rise to possible non-binary finite-state machines. The development of a molecular electron device (MED) synthetic capability in combination with the above devices would suggest that large 3-d arrays of parallel processors will be possible with automata, biological, and crystallographic implications. 41 references.

  10. Cognitive componets of speech at different time scales

    DEFF Research Database (Denmark)

    Feng, Ling; Hansen, Lars Kai

    2007-01-01

    Cognitive component analysis (COCA) is defined as unsupervised grouping of data leading to a group structure well aligned with that resulting from human cognitive activity. We focus here on speech at different time scales looking for possible hidden ‘cognitive structure’. Statistical regularities...

  11. Multiple time scales of adaptation in auditory cortex neurons.

    Science.gov (United States)

    Ulanovsky, Nachum; Las, Liora; Farkas, Dina; Nelken, Israel

    2004-11-17

    Neurons in primary auditory cortex (A1) of cats show strong stimulus-specific adaptation (SSA). In probabilistic settings, in which one stimulus is common and another is rare, responses to common sounds adapt more strongly than responses to rare sounds. This SSA could be a correlate of auditory sensory memory at the level of single A1 neurons. Here we studied adaptation in A1 neurons, using three different probabilistic designs. We showed that SSA has several time scales concurrently, spanning many orders of magnitude, from hundreds of milliseconds to tens of seconds. Similar time scales are known for the auditory memory span of humans, as measured both psychophysically and using evoked potentials. A simple model, with linear dependence on both short-term and long-term stimulus history, provided a good fit to A1 responses. Auditory thalamus neurons did not show SSA, and their responses were poorly fitted by the same model. In addition, SSA increased the proportion of failures in the responses of A1 neurons to the adapting stimulus. Finally, SSA caused a bias in the neuronal responses to unbiased stimuli, enhancing the responses to eccentric stimuli. Therefore, we propose that a major function of SSA in A1 neurons is to encode auditory sensory memory on multiple time scales. This SSA might play a role in stream segregation and in binding of auditory objects over many time scales, a property that is crucial for processing of natural auditory scenes in cats and of speech and music in humans.

  12. Russian national time scale long-term stability

    Science.gov (United States)

    Alshina, A. P.; Gaigerov, B. A.; Koshelyaevsky, N. B.; Pushkin, S. B.

    1994-05-01

    The Institute of Metrology for Time and Space NPO 'VNIIFTRI' generates the National Time Scale (NTS) of Russia -- one of the most stable time scales in the world. Its striking feature is that it is based on a free ensemble of H-masers only. During last two years the estimations of NTS longterm stability based only on H-maser intercomparison data gives a flicker floor of about (2 to 3) x 10(exp -15) for averaging times from 1 day to 1 month. Perhaps the most significant feature for a time laboratory is an extremely low possible frequency drift -- it is too difficult to estimate it reliably. The other estimations, free from possible inside the ensemble correlation phenomena, are available based on the time comparison of NTS relative to the stable enough time scale of outer laboratories. The data on NTS comparison relative to the time scale of secondary time and frequency standards at Golitzino and Irkutsk in Russia and relative to NIST, PTB and USNO using GLONASS and GPS time transfer links gives stability estimations which are close to that based on H-maser intercomparisons.

  13. THE DETECTION OF A HOT MOLECULAR CORE IN THE LARGE MAGELLANIC CLOUD WITH ALMA

    International Nuclear Information System (INIS)

    Shimonishi, Takashi; Onaka, Takashi; Kawamura, Akiko; Aikawa, Yuri

    2016-01-01

    We report the first detection of a hot molecular core outside our Galaxy based on radio observations with ALMA toward a high-mass young stellar object (YSO) in a nearby low metallicity galaxy, the Large Magellanic Cloud (LMC). Molecular emission lines of CO, C 17 O, HCO + , H 13 CO + , H 2 CO, NO, SiO, H 2 CS, 33 SO, 32 SO 2 , 34 SO 2 , and 33 SO 2 are detected from a compact region (∼0.1 pc) associated with a high-mass YSO, ST11. The temperature of molecular gas is estimated to be higher than 100 K based on rotation diagram analysis of SO 2 and 34 SO 2 lines. The compact source size, warm gas temperature, high density, and rich molecular lines around a high-mass protostar suggest that ST11 is associated with a hot molecular core. We find that the molecular abundances of the LMC hot core are significantly different from those of Galactic hot cores. The abundances of CH 3 OH, H 2 CO, and HNCO are remarkably lower compared to Galactic hot cores by at least 1–3 orders of magnitude. We suggest that these abundances are characterized by the deficiency of molecules whose formation requires the hydrogenation of CO on grain surfaces. In contrast, NO shows a high abundance in ST11 despite the notably low abundance of nitrogen in the LMC. A multitude of SO 2 and its isotopologue line detections in ST11 imply that SO 2 can be a key molecular tracer of hot core chemistry in metal-poor environments. Furthermore, we find molecular outflows around the hot core, which is the second detection of an extragalactic protostellar outflow. In this paper, we discuss the physical and chemical characteristics of a hot molecular core in the low metallicity environment.

  14. mmpdb: An Open-Source Matched Molecular Pair Platform for Large Multiproperty Data Sets.

    Science.gov (United States)

    Dalke, Andrew; Hert, Jérôme; Kramer, Christian

    2018-05-29

    Matched molecular pair analysis (MMPA) enables the automated and systematic compilation of medicinal chemistry rules from compound/property data sets. Here we present mmpdb, an open-source matched molecular pair (MMP) platform to create, compile, store, retrieve, and use MMP rules. mmpdb is suitable for the large data sets typically found in pharmaceutical and agrochemical companies and provides new algorithms for fragment canonicalization and stereochemistry handling. The platform is written in Python and based on the RDKit toolkit. It is freely available from https://github.com/rdkit/mmpdb .

  15. Modelling Protein Dynamics on the Microsecond Time Scale

    DEFF Research Database (Denmark)

    Siuda, Iwona Anna

    Recent years have shown an increase in coarse-grained (CG) molecular dynamics simulations, providing structural and dynamic details of large proteins and enabling studies of self-assembly of biological materials. It is not easy to acquire such data experimentally, and access is also still limited...... in atomistic simulations. During her PhD studies, Iwona Siuda used MARTINI CG models to study the dynamics of different globular and membrane proteins. In several cases, the MARTINI model was sufficient to study conformational changes of small, purely alpha-helical proteins. However, in studies of larger......ELNEDIN was therefore proposed as part of the work. Iwona Siuda’s results from the CG simulations had biological implications that provide insights into possible mechanisms of the periplasmic leucine-binding protein, the sarco(endo)plasmic reticulum calcium pump, and several proteins from the saposin-like proteins...

  16. HMC algorithm with multiple time scale integration and mass preconditioning

    Science.gov (United States)

    Urbach, C.; Jansen, K.; Shindler, A.; Wenger, U.

    2006-01-01

    We present a variant of the HMC algorithm with mass preconditioning (Hasenbusch acceleration) and multiple time scale integration. We have tested this variant for standard Wilson fermions at β=5.6 and at pion masses ranging from 380 to 680 MeV. We show that in this situation its performance is comparable to the recently proposed HMC variant with domain decomposition as preconditioner. We give an update of the "Berlin Wall" figure, comparing the performance of our variant of the HMC algorithm to other published performance data. Advantages of the HMC algorithm with mass preconditioning and multiple time scale integration are that it is straightforward to implement and can be used in combination with a wide variety of lattice Dirac operators.

  17. Nonlinear MHD dynamics of tokamak plasmas on multiple time scales

    International Nuclear Information System (INIS)

    Kruger, S.E.; Schnack, D.D.; Brennan, D.P.; Gianakon, T.A.; Sovinec, C.R.

    2003-01-01

    Two types of numerical, nonlinear simulations using the NIMROD code are presented. In the first simulation, we model the disruption occurring in DIII-D discharge 87009 as an ideal MHD instability driven unstable by neutral-beam heating. The mode grows faster than exponential, but on a time scale that is a hybrid of the heating rate and the ideal MHD growth rate as predicted by analytic theory. The second type of simulations, which occur on a much longer time scale, focus on the seeding of tearing modes by sawteeth. Pressure effects play a role both in the exterior region solutions and in the neoclassical drive terms. The results of both simulations are reviewed and their implications for experimental analysis is discussed. (author)

  18. Human learning: Power laws or multiple characteristic time scales?

    Directory of Open Access Journals (Sweden)

    Gottfried Mayer-Kress

    2006-09-01

    Full Text Available The central proposal of A. Newell and Rosenbloom (1981 was that the power law is the ubiquitous law of learning. This proposition is discussed in the context of the key factors that led to the acceptance of the power law as the function of learning. We then outline the principles of an epigenetic landscape framework for considering the role of the characteristic time scales of learning and an approach to system identification of the processes of performance dynamics. In this view, the change of performance over time is the product of a superposition of characteristic exponential time scales that reflect the influence of different processes. This theoretical approach can reproduce the traditional power law of practice – within the experimental resolution of performance data sets - but we hypothesize that this function may prove to be a special and perhaps idealized case of learning.

  19. The fission time scale measured with an atomic clock

    NARCIS (Netherlands)

    Kravchuk, VL; Wilschut, HW; Hunyadi, M; Kopecky, S; Lohner, H; Rogachevskiy, A; Siemssen, RH; Krasznahorkay, A; Hamilton, JH; Ramayya, AV; Carter, HK

    2003-01-01

    We present a new direct method of measuring the fission absolute time scale using an atomic clock based on the lifetime of a vacancy in the atomic K-shell. We studied the reaction Ne-20 + Th-232 -> O-16 + U-236* at 30 MeV/u. The excitation energy of about 115 MeV in such a reaction is in the range

  20. Microsecond time-scale kinetics of transient biochemical reactions

    NARCIS (Netherlands)

    Mitic, S.; Strampraad, M.J.F.; Hagen, W.R.; de Vries, S.

    2017-01-01

    To afford mechanistic studies in enzyme kinetics and protein folding in the microsecond time domain we have developed a continuous-flow microsecond time-scale mixing instrument with an unprecedented dead-time of 3.8 ± 0.3 μs. The instrument employs a micro-mixer with a mixing time of 2.7 μs

  1. Time scale controversy: Accurate orbital calibration of the early Paleogene

    Science.gov (United States)

    Roehl, U.; Westerhold, T.; Laskar, J.

    2012-12-01

    Timing is crucial to understanding the causes and consequences of events in Earth history. The calibration of geological time relies heavily on the accuracy of radioisotopic and astronomical dating. Uncertainties in the computations of Earth's orbital parameters and in radioisotopic dating have hampered the construction of a reliable astronomically calibrated time scale beyond 40 Ma. Attempts to construct a robust astronomically tuned time scale for the early Paleogene by integrating radioisotopic and astronomical dating are only partially consistent. Here, using the new La2010 and La2011 orbital solutions, we present the first accurate astronomically calibrated time scale for the early Paleogene (47-65 Ma) uniquely based on astronomical tuning and thus independent of the radioisotopic determination of the Fish Canyon standard. Comparison with geological data confirms the stability of the new La2011 solution back to 54 Ma. Subsequent anchoring of floating chronologies to the La2011 solution using the very long eccentricity nodes provides an absolute age of 55.530 ± 0.05 Ma for the onset of the Paleocene/Eocene Thermal Maximum (PETM), 54.850 ± 0.05 Ma for the early Eocene ash -17, and 65.250 ± 0.06 Ma for the K/Pg boundary. The new astrochronology presented here indicates that the intercalibration and synchronization of U/Pb and 40Ar/39Ar radioisotopic geochronology is much more challenging than previously thought.

  2. Backpropagation and ordered derivatives in the time scales calculus.

    Science.gov (United States)

    Seiffertt, John; Wunsch, Donald C

    2010-08-01

    Backpropagation is the most widely used neural network learning technique. It is based on the mathematical notion of an ordered derivative. In this paper, we present a formulation of ordered derivatives and the backpropagation training algorithm using the important emerging area of mathematics known as the time scales calculus. This calculus, with its potential for application to a wide variety of inter-disciplinary problems, is becoming a key area of mathematics. It is capable of unifying continuous and discrete analysis within one coherent theoretical framework. Using this calculus, we present here a generalization of backpropagation which is appropriate for cases beyond the specifically continuous or discrete. We develop a new multivariate chain rule of this calculus, define ordered derivatives on time scales, prove a key theorem about them, and derive the backpropagation weight update equations for a feedforward multilayer neural network architecture. By drawing together the time scales calculus and the area of neural network learning, we present the first connection of two major fields of research.

  3. A model for AGN variability on multiple time-scales

    Science.gov (United States)

    Sartori, Lia F.; Schawinski, Kevin; Trakhtenbrot, Benny; Caplar, Neven; Treister, Ezequiel; Koss, Michael J.; Urry, C. Megan; Zhang, C. E.

    2018-05-01

    We present a framework to link and describe active galactic nuclei (AGN) variability on a wide range of time-scales, from days to billions of years. In particular, we concentrate on the AGN variability features related to changes in black hole fuelling and accretion rate. In our framework, the variability features observed in different AGN at different time-scales may be explained as realisations of the same underlying statistical properties. In this context, we propose a model to simulate the evolution of AGN light curves with time based on the probability density function (PDF) and power spectral density (PSD) of the Eddington ratio (L/LEdd) distribution. Motivated by general galaxy population properties, we propose that the PDF may be inspired by the L/LEdd distribution function (ERDF), and that a single (or limited number of) ERDF+PSD set may explain all observed variability features. After outlining the framework and the model, we compile a set of variability measurements in terms of structure function (SF) and magnitude difference. We then combine the variability measurements on a SF plot ranging from days to Gyr. The proposed framework enables constraints on the underlying PSD and the ability to link AGN variability on different time-scales, therefore providing new insights into AGN variability and black hole growth phenomena.

  4. Molecular descriptor data explain market prices of a large commercial chemical compound library

    Science.gov (United States)

    Polanski, Jaroslaw; Kucia, Urszula; Duszkiewicz, Roksana; Kurczyk, Agata; Magdziarz, Tomasz; Gasteiger, Johann

    2016-06-01

    The relationship between the structure and a property of a chemical compound is an essential concept in chemistry guiding, for example, drug design. Actually, however, we need economic considerations to fully understand the fate of drugs on the market. We are performing here for the first time the exploration of quantitative structure-economy relationships (QSER) for a large dataset of a commercial building block library of over 2.2 million chemicals. This investigation provided molecular statistics that shows that on average what we are paying for is the quantity of matter. On the other side, the influence of synthetic availability scores is also revealed. Finally, we are buying substances by looking at the molecular graphs or molecular formulas. Thus, those molecules that have a higher number of atoms look more attractive and are, on average, also more expensive. Our study shows how data binning could be used as an informative method when analyzing big data in chemistry.

  5. Molecular dynamics simulations of sputtering of organic overlayers by slow, large clusters

    International Nuclear Information System (INIS)

    Rzeznik, L.; Czerwinski, B.; Garrison, B.J.; Winograd, N.; Postawa, Z.

    2008-01-01

    The ion-stimulated desorption of organic molecules by impact of large and slow clusters is examined using molecular dynamics (MDs) computer simulations. The investigated system, represented by a monolayer of benzene deposited on Ag{1 1 1}, is irradiated with projectiles composed of thousands of noble gas atoms having a kinetic energy of 0.1-20 eV/atom. The sputtering yield of molecular species and the kinetic energy distributions are analyzed and compared to the results obtain for PS4 overlayer. The simulations demonstrate quite clearly that the physics of ejection by large and slow clusters is distinct from the ejection events stimulated by the popular SIMS clusters, like C 60 , Au 3 and SF 5 at tens of keV energies.

  6. Localized diffusive motion on two different time scales in solid alkane nanoparticles

    International Nuclear Information System (INIS)

    Wang, S.-K.; Mamontov, Eugene; Bai, M.; Hansen, F.Y.; Taub, H.; Copley, J.R.D.; Garcia Sakai, V.; Gasparovic, Goran; Jenkins, Timothy; Tyagi, M.; Herwig, Kenneth W.; Neumann, D.A.; Montfrooij, W.; Volkmann, U.G.

    2010-01-01

    High-energy-resolution quasielastic neutron scattering on three complementary spectrometers has been used to investigate molecular diffusive motion in solid nano- to bulk-sized particles of the alkane n-C32H66. The crystalline-to-plastic and plastic-to-fluid phase transition temperatures are observed to decrease as the particle size decreases. In all samples, localized molecular diffusive motion in the plastic phase occurs on two different time scales: a 'fast' motion corresponding to uniaxial rotation about the long molecular axis; and a 'slow' motion attributed to conformational changes of the molecule. Contrary to the conventional interpretation in bulk alkanes, the fast uniaxial rotation begins in the low-temperature crystalline phase.

  7. A hybrid procedure for MSW generation forecasting at multiple time scales in Xiamen City, China

    International Nuclear Information System (INIS)

    Xu, Lilai; Gao, Peiqing; Cui, Shenghui; Liu, Chun

    2013-01-01

    Highlights: ► We propose a hybrid model that combines seasonal SARIMA model and grey system theory. ► The model is robust at multiple time scales with the anticipated accuracy. ► At month-scale, the SARIMA model shows good representation for monthly MSW generation. ► At medium-term time scale, grey relational analysis could yield the MSW generation. ► At long-term time scale, GM (1, 1) provides a basic scenario of MSW generation. - Abstract: Accurate forecasting of municipal solid waste (MSW) generation is crucial and fundamental for the planning, operation and optimization of any MSW management system. Comprehensive information on waste generation for month-scale, medium-term and long-term time scales is especially needed, considering the necessity of MSW management upgrade facing many developing countries. Several existing models are available but of little use in forecasting MSW generation at multiple time scales. The goal of this study is to propose a hybrid model that combines the seasonal autoregressive integrated moving average (SARIMA) model and grey system theory to forecast MSW generation at multiple time scales without needing to consider other variables such as demographics and socioeconomic factors. To demonstrate its applicability, a case study of Xiamen City, China was performed. Results show that the model is robust enough to fit and forecast seasonal and annual dynamics of MSW generation at month-scale, medium- and long-term time scales with the desired accuracy. In the month-scale, MSW generation in Xiamen City will peak at 132.2 thousand tonnes in July 2015 – 1.5 times the volume in July 2010. In the medium term, annual MSW generation will increase to 1518.1 thousand tonnes by 2015 at an average growth rate of 10%. In the long term, a large volume of MSW will be output annually and will increase to 2486.3 thousand tonnes by 2020 – 2.5 times the value for 2010. The hybrid model proposed in this paper can enable decision makers to

  8. A hybrid procedure for MSW generation forecasting at multiple time scales in Xiamen City, China

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Lilai, E-mail: llxu@iue.ac.cn [Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021 (China); Xiamen Key Lab of Urban Metabolism, Xiamen 361021 (China); Gao, Peiqing, E-mail: peiqing15@yahoo.com.cn [Xiamen City Appearance and Environmental Sanitation Management Office, 51 Hexiangxi Road, Xiamen 361004 (China); Cui, Shenghui, E-mail: shcui@iue.ac.cn [Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021 (China); Xiamen Key Lab of Urban Metabolism, Xiamen 361021 (China); Liu, Chun, E-mail: xmhwlc@yahoo.com.cn [Xiamen City Appearance and Environmental Sanitation Management Office, 51 Hexiangxi Road, Xiamen 361004 (China)

    2013-06-15

    Highlights: ► We propose a hybrid model that combines seasonal SARIMA model and grey system theory. ► The model is robust at multiple time scales with the anticipated accuracy. ► At month-scale, the SARIMA model shows good representation for monthly MSW generation. ► At medium-term time scale, grey relational analysis could yield the MSW generation. ► At long-term time scale, GM (1, 1) provides a basic scenario of MSW generation. - Abstract: Accurate forecasting of municipal solid waste (MSW) generation is crucial and fundamental for the planning, operation and optimization of any MSW management system. Comprehensive information on waste generation for month-scale, medium-term and long-term time scales is especially needed, considering the necessity of MSW management upgrade facing many developing countries. Several existing models are available but of little use in forecasting MSW generation at multiple time scales. The goal of this study is to propose a hybrid model that combines the seasonal autoregressive integrated moving average (SARIMA) model and grey system theory to forecast MSW generation at multiple time scales without needing to consider other variables such as demographics and socioeconomic factors. To demonstrate its applicability, a case study of Xiamen City, China was performed. Results show that the model is robust enough to fit and forecast seasonal and annual dynamics of MSW generation at month-scale, medium- and long-term time scales with the desired accuracy. In the month-scale, MSW generation in Xiamen City will peak at 132.2 thousand tonnes in July 2015 – 1.5 times the volume in July 2010. In the medium term, annual MSW generation will increase to 1518.1 thousand tonnes by 2015 at an average growth rate of 10%. In the long term, a large volume of MSW will be output annually and will increase to 2486.3 thousand tonnes by 2020 – 2.5 times the value for 2010. The hybrid model proposed in this paper can enable decision makers to

  9. Transmembrane molecular transport during versus after extremely large, nanosecond electric pulses.

    Science.gov (United States)

    Smith, Kyle C; Weaver, James C

    2011-08-19

    Recently there has been intense and growing interest in the non-thermal biological effects of nanosecond electric pulses, particularly apoptosis induction. These effects have been hypothesized to result from the widespread creation of small, lipidic pores in the plasma and organelle membranes of cells (supra-electroporation) and, more specifically, ionic and molecular transport through these pores. Here we show that transport occurs overwhelmingly after pulsing. First, we show that the electrical drift distance for typical charged solutes during nanosecond pulses (up to 100 ns), even those with very large magnitudes (up to 10 MV/m), ranges from only a fraction of the membrane thickness (5 nm) to several membrane thicknesses. This is much smaller than the diameter of a typical cell (∼16 μm), which implies that molecular drift transport during nanosecond pulses is necessarily minimal. This implication is not dependent on assumptions about pore density or the molecular flux through pores. Second, we show that molecular transport resulting from post-pulse diffusion through minimum-size pores is orders of magnitude larger than electrical drift-driven transport during nanosecond pulses. While field-assisted charge entry and the magnitude of flux favor transport during nanosecond pulses, these effects are too small to overcome the orders of magnitude more time available for post-pulse transport. Therefore, the basic conclusion that essentially all transmembrane molecular transport occurs post-pulse holds across the plausible range of relevant parameters. Our analysis shows that a primary direct consequence of nanosecond electric pulses is the creation (or maintenance) of large populations of small pores in cell membranes that govern post-pulse transmembrane transport of small ions and molecules. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Molecular dynamics based enhanced sampling of collective variables with very large time steps

    Science.gov (United States)

    Chen, Pei-Yang; Tuckerman, Mark E.

    2018-01-01

    Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

  11. Dense molecular clumps associated with the Large Magellanic Cloud supergiant shells LMC 4 and LMC 5

    Energy Technology Data Exchange (ETDEWEB)

    Fujii, Kosuke; Mizuno, Norikazu [Department of Astronomy, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 133-0033 (Japan); Minamidani, Tetsuhiro [Nobeyama Radio Observatory, 462-2 Nobeyama Minamimaki-mura, Minamisaku-gun, Nagano 384-1305 (Japan); Onishi, Toshikazu; Muraoka, Kazuyuki [Department of Physical Science, Osaka Prefecture University, Gakuen 1-1, Sakai, Osaka 599-8531 (Japan); Kawamura, Akiko; Muller, Erik; Tatematsu, Ken' ichi; Hasegawa, Tetsuo; Miura, Rie E.; Ezawa, Hajime [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Dawson, Joanne [Australia Telescope National Facility, CSIRO Astronomy and Space Science, P.O. Box 76, Epping, NSW 1710 (Australia); Tosaki, Tomoka [Joetsu University of Education, Yamayashiki-machi, Joetsu, Niigata 943-8512 (Japan); Sakai, Takeshi [Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585 (Japan); Tsukagoshi, Takashi [College of Science, Ibaraki University, Bunkyo 2-1-1, Mito 310-8512 (Japan); Tanaka, Kunihiko [Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Yokohama, Kanagawa 223-8522 (Japan); Fukui, Yasuo, E-mail: kosuke.fujii@nao.ac.jp [Department of Astrophysics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602 (Japan)

    2014-12-01

    We investigate the effects of supergiant shells (SGSs) and their interaction on dense molecular clumps by observing the Large Magellanic Cloud (LMC) star-forming regions N48 and N49, which are located between two SGSs, LMC 4 and LMC 5. {sup 12}CO (J = 3-2, 1-0) and {sup 13}CO(J = 1-0) observations with the ASTE and Mopra telescopes have been carried out toward these regions. A clumpy distribution of dense molecular clumps is revealed with 7 pc spatial resolution. Large velocity gradient analysis shows that the molecular hydrogen densities (n(H{sub 2})) of the clumps are distributed from low to high density (10{sup 3}-10{sup 5} cm{sup –3}) and their kinetic temperatures (T {sub kin}) are typically high (greater than 50 K). These clumps seem to be in the early stages of star formation, as also indicated from the distribution of Hα, young stellar object candidates, and IR emission. We found that the N48 region is located in the high column density H I envelope at the interface of the two SGSs and the star formation is relatively evolved, whereas the N49 region is associated with LMC 5 alone and the star formation is quiet. The clumps in the N48 region typically show high n(H{sub 2}) and T {sub kin}, which are as dense and warm as the clumps in LMC massive cluster-forming areas (30 Dor, N159). These results suggest that the large-scale structure of the SGSs, especially the interaction of two SGSs, works efficiently on the formation of dense molecular clumps and stars.

  12. CHRONICITY OF DEPRESSION AND MOLECULAR MARKERS IN A LARGE SAMPLE OF HAN CHINESE WOMEN.

    Science.gov (United States)

    Edwards, Alexis C; Aggen, Steven H; Cai, Na; Bigdeli, Tim B; Peterson, Roseann E; Docherty, Anna R; Webb, Bradley T; Bacanu, Silviu-Alin; Flint, Jonathan; Kendler, Kenneth S

    2016-04-25

    Major depressive disorder (MDD) has been associated with changes in mean telomere length and mitochondrial DNA (mtDNA) copy number. This study investigates if clinical features of MDD differentially impact these molecular markers. Data from a large, clinically ascertained sample of Han Chinese women with recurrent MDD were used to examine whether symptom presentation, severity, and comorbidity were related to salivary telomere length and/or mtDNA copy number (maximum N = 5,284 for both molecular and phenotypic data). Structural equation modeling revealed that duration of longest episode was positively associated with mtDNA copy number, while earlier age of onset of most severe episode and a history of dysthymia were associated with shorter telomeres. Other factors, such as symptom presentation, family history of depression, and other comorbid internalizing disorders, were not associated with these molecular markers. Chronicity of depressive symptoms is related to more pronounced telomere shortening and increased mtDNA copy number among individuals with a history of recurrent MDD. As these molecular markers have previously been implicated in physiological aging and morbidity, individuals who experience prolonged depressive symptoms are potentially at greater risk of adverse medical outcomes. © 2016 Wiley Periodicals, Inc.

  13. CARMA LARGE AREA STAR FORMATION SURVEY: OBSERVATIONAL ANALYSIS OF FILAMENTS IN THE SERPENS SOUTH MOLECULAR CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Fernández-López, M.; Looney, L.; Lee, K.; Segura-Cox, D. [Department of Astronomy, University of Illinois at Urbana—Champaign, 1002 West Green Street, Urbana, IL 61801 (United States); Arce, H. G.; Plunkett, A. [Department of Astronomy, Yale University, P.O. Box 208101, New Haven, CT 06520-8101 (United States); Mundy, L. G.; Storm, S.; Teuben, P. J.; Pound, M. [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States); Isella, A.; Kauffmann, J. [Astronomy Department, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Tobin, J. J. [National Radio Astronomy Observatory, Charlottesville, VA 22903 (United States); Rosolowsky, E. [Departments of Physics and Statistics, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, BC V1V 1V7 (Canada); Kwon, W. [SRON Netherlands Institute for Space Research, Landleven 12, 9747-AD Groningen (Netherlands); Ostriker, E. [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States); Tassis, K. [Department of Physics and Institute of Theoretical and Computational Physics, University of Crete, P.O. Box 2208, GR-710 03 Heraklion, Crete (Greece); Shirley, Y. L., E-mail: manferna@gmail.com [Steward Observatory, 933 North Cherry Avenue, Tucson, AZ 85721 (United States)

    2014-08-01

    We present the N{sub 2}H{sup +} (J = 1 → 0) map of the Serpens South molecular cloud obtained as part of the CARMA Large Area Star Formation Survey. The observations cover 250 arcmin{sup 2} and fully sample structures from 3000 AU to 3 pc with a velocity resolution of 0.16 km s{sup –1}, and they can be used to constrain the origin and evolution of molecular cloud filaments. The spatial distribution of the N{sub 2}H{sup +} emission is characterized by long filaments that resemble those observed in the dust continuum emission by Herschel. However, the gas filaments are typically narrower such that, in some cases, two or three quasi-parallel N{sub 2}H{sup +} filaments comprise a single observed dust continuum filament. The difference between the dust and gas filament widths casts doubt on Herschel ability to resolve the Serpens South filaments. Some molecular filaments show velocity gradients along their major axis, and two are characterized by a steep velocity gradient in the direction perpendicular to the filament axis. The observed velocity gradient along one of these filaments was previously postulated as evidence for mass infall toward the central cluster, but these kind of gradients can be interpreted as projection of large-scale turbulence.

  14. Evaluation of Kirkwood-Buff integrals via finite size scaling: a large scale molecular dynamics study

    Science.gov (United States)

    Dednam, W.; Botha, A. E.

    2015-01-01

    Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution

  15. Evaluation of Kirkwood-Buff integrals via finite size scaling: a large scale molecular dynamics study

    International Nuclear Information System (INIS)

    Dednam, W; Botha, A E

    2015-01-01

    Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution

  16. A hierarchy of time-scales and the brain.

    Science.gov (United States)

    Kiebel, Stefan J; Daunizeau, Jean; Friston, Karl J

    2008-11-01

    In this paper, we suggest that cortical anatomy recapitulates the temporal hierarchy that is inherent in the dynamics of environmental states. Many aspects of brain function can be understood in terms of a hierarchy of temporal scales at which representations of the environment evolve. The lowest level of this hierarchy corresponds to fast fluctuations associated with sensory processing, whereas the highest levels encode slow contextual changes in the environment, under which faster representations unfold. First, we describe a mathematical model that exploits the temporal structure of fast sensory input to track the slower trajectories of their underlying causes. This model of sensory encoding or perceptual inference establishes a proof of concept that slowly changing neuronal states can encode the paths or trajectories of faster sensory states. We then review empirical evidence that suggests that a temporal hierarchy is recapitulated in the macroscopic organization of the cortex. This anatomic-temporal hierarchy provides a comprehensive framework for understanding cortical function: the specific time-scale that engages a cortical area can be inferred by its location along a rostro-caudal gradient, which reflects the anatomical distance from primary sensory areas. This is most evident in the prefrontal cortex, where complex functions can be explained as operations on representations of the environment that change slowly. The framework provides predictions about, and principled constraints on, cortical structure-function relationships, which can be tested by manipulating the time-scales of sensory input.

  17. A hierarchy of time-scales and the brain.

    Directory of Open Access Journals (Sweden)

    Stefan J Kiebel

    2008-11-01

    Full Text Available In this paper, we suggest that cortical anatomy recapitulates the temporal hierarchy that is inherent in the dynamics of environmental states. Many aspects of brain function can be understood in terms of a hierarchy of temporal scales at which representations of the environment evolve. The lowest level of this hierarchy corresponds to fast fluctuations associated with sensory processing, whereas the highest levels encode slow contextual changes in the environment, under which faster representations unfold. First, we describe a mathematical model that exploits the temporal structure of fast sensory input to track the slower trajectories of their underlying causes. This model of sensory encoding or perceptual inference establishes a proof of concept that slowly changing neuronal states can encode the paths or trajectories of faster sensory states. We then review empirical evidence that suggests that a temporal hierarchy is recapitulated in the macroscopic organization of the cortex. This anatomic-temporal hierarchy provides a comprehensive framework for understanding cortical function: the specific time-scale that engages a cortical area can be inferred by its location along a rostro-caudal gradient, which reflects the anatomical distance from primary sensory areas. This is most evident in the prefrontal cortex, where complex functions can be explained as operations on representations of the environment that change slowly. The framework provides predictions about, and principled constraints on, cortical structure-function relationships, which can be tested by manipulating the time-scales of sensory input.

  18. Adaptation and learning: characteristic time scales of performance dynamics.

    Science.gov (United States)

    Newell, Karl M; Mayer-Kress, Gottfried; Hong, S Lee; Liu, Yeou-Teh

    2009-12-01

    A multiple time scales landscape model is presented that reveals structures of performance dynamics that were not resolved in the traditional power law analysis of motor learning. It shows the co-existence of separate processes during and between practice sessions that evolve in two independent dimensions characterized by time scales that differ by about an order of magnitude. Performance along the slow persistent dimension of learning improves often as much and sometimes more during rest (memory consolidation and/or insight generation processes) than during a practice session itself. In contrast, the process characterized by the fast, transient dimension of adaptation reverses direction between practice sessions, thereby significantly degrading performance at the beginning of the next practice session (warm-up decrement). The theoretical model fits qualitatively and quantitatively the data from Snoddy's [Snoddy, G. S. (1926). Learning and stability. Journal of Applied Psychology, 10, 1-36] classic learning study of mirror tracing and other averaged and individual data sets, and provides a new account of the processes of change in adaptation and learning. 2009 Elsevier B.V. All rights reserved.

  19. Length and time scales of atmospheric moisture recycling

    Directory of Open Access Journals (Sweden)

    R. J. van der Ent

    2011-03-01

    Full Text Available It is difficult to quantify the degree to which terrestrial evaporation supports the occurrence of precipitation within a certain study region (i.e. regional moisture recycling due to the scale- and shape-dependence of regional moisture recycling ratios. In this paper we present a novel approach to quantify the spatial and temporal scale of moisture recycling, independent of the size and shape of the region under study. In contrast to previous studies, which essentially used curve fitting, the scaling laws presented by us follow directly from the process equation. thus allowing a fair comparison between regions and seasons. The calculation is based on ERA-Interim reanalysis data for the period 1999 to 2008. It is shown that in the tropics or in mountainous terrain the length scale of recycling can be as low as 500 to 2000 km. In temperate climates the length scale is typically between 3000 to 5000 km whereas it amounts to more than 7000 km in desert areas. The time scale of recycling ranges from 3 to 20 days, with the exception of deserts, where it is much longer. The most distinct seasonal differences can be observed over the Northern Hemisphere: in winter, moisture recycling is insignificant, whereas in summer it plays a major role in the climate. The length and time scales of atmospheric moisture recycling can be useful metrics to quantify local climatic effects of land use change.

  20. A Systematic Multi-Time Scale Solution for Regional Power Grid Operation

    Science.gov (United States)

    Zhu, W. J.; Liu, Z. G.; Cheng, T.; Hu, B. Q.; Liu, X. Z.; Zhou, Y. F.

    2017-10-01

    Many aspects need to be taken into consideration in a regional grid while making schedule plans. In this paper, a systematic multi-time scale solution for regional power grid operation considering large scale renewable energy integration and Ultra High Voltage (UHV) power transmission is proposed. In the time scale aspect, we discuss the problem from month, week, day-ahead, within-day to day-behind, and the system also contains multiple generator types including thermal units, hydro-plants, wind turbines and pumped storage stations. The 9 subsystems of the scheduling system are described, and their functions and relationships are elaborated. The proposed system has been constructed in a provincial power grid in Central China, and the operation results further verified the effectiveness of the system.

  1. CAST: a new program package for the accurate characterization of large and flexible molecular systems.

    Science.gov (United States)

    Grebner, Christoph; Becker, Johannes; Weber, Daniel; Bellinger, Daniel; Tafipolski, Maxim; Brückner, Charlotte; Engels, Bernd

    2014-09-15

    The presented program package, Conformational Analysis and Search Tool (CAST) allows the accurate treatment of large and flexible (macro) molecular systems. For the determination of thermally accessible minima CAST offers the newly developed TabuSearch algorithm, but algorithms such as Monte Carlo (MC), MC with minimization, and molecular dynamics are implemented as well. For the determination of reaction paths, CAST provides the PathOpt, the Nudge Elastic band, and the umbrella sampling approach. Access to free energies is possible through the free energy perturbation approach. Along with a number of standard force fields, a newly developed symmetry-adapted perturbation theory-based force field is included. Semiempirical computations are possible through DFTB+ and MOPAC interfaces. For calculations based on density functional theory, a Message Passing Interface (MPI) interface to the Graphics Processing Unit (GPU)-accelerated TeraChem program is available. The program is available on request. Copyright © 2014 Wiley Periodicals, Inc.

  2. Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

    Science.gov (United States)

    Tiwary, Pratyush

    This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well

  3. Symplectic integrators for large scale molecular dynamics simulations: A comparison of several explicit methods

    International Nuclear Information System (INIS)

    Gray, S.K.; Noid, D.W.; Sumpter, B.G.

    1994-01-01

    We test the suitability of a variety of explicit symplectic integrators for molecular dynamics calculations on Hamiltonian systems. These integrators are extremely simple algorithms with low memory requirements, and appear to be well suited for large scale simulations. We first apply all the methods to a simple test case using the ideas of Berendsen and van Gunsteren. We then use the integrators to generate long time trajectories of a 1000 unit polyethylene chain. Calculations are also performed with two popular but nonsymplectic integrators. The most efficient integrators of the set investigated are deduced. We also discuss certain variations on the basic symplectic integration technique

  4. Crystallisation of a Lennard-Jones fluid by large scale molecular dynamics simulation

    International Nuclear Information System (INIS)

    Snook, I.

    1998-01-01

    Full text: The evolution of the structure of a large system of atoms interacting via a Lennard-Jones pair potential was simulated by the use of the Molecular Dynamics computer simulation technique. The system was initially equilibrated in the one phase region of the phase diagram at a temperature above critical then a temperature quench was performed which placed the system in a region were the single fluid phase was unstable. Quenches to below the triple point temperature gave rise to crystallisation The mechanism and final morphology is shown to depend strongly on the starting conditions e.g. the starting density

  5. A Review of Time-Scale Modification of Music Signals

    Directory of Open Access Journals (Sweden)

    Jonathan Driedger

    2016-02-01

    Full Text Available Time-scale modification (TSM is the task of speeding up or slowing down an audio signal’s playback speed without changing its pitch. In digital music production, TSM has become an indispensable tool, which is nowadays integrated in a wide range of music production software. Music signals are diverse—they comprise harmonic, percussive, and transient components, among others. Because of this wide range of acoustic and musical characteristics, there is no single TSM method that can cope with all kinds of audio signals equally well. Our main objective is to foster a better understanding of the capabilities and limitations of TSM procedures. To this end, we review fundamental TSM methods, discuss typical challenges, and indicate potential solutions that combine different strategies. In particular, we discuss a fusion approach that involves recent techniques for harmonic-percussive separation along with time-domain and frequency-domain TSM procedures.

  6. Time scaling internal state predictive control of a solar plant

    Energy Technology Data Exchange (ETDEWEB)

    Silva, R.N. [DEE-FCT/UNL, Caparica (Portugal); Rato, L.M. [INESC-ID/University, Evora (Portugal); Lemos, J.M. [INESC-ID/IST, Lisboa (Portugal)

    2003-12-01

    The control of a distributed collector solar field is addressed in this work, exploiting the plant's transport characteristic. The plant is modeled by a hyperbolic type partial differential equation (PDE) where the transport speed is the manipulated flow, i.e. the controller output. The model has an external distributed source, which is the solar radiation captured along the collector, approximated to depend only of time. From the solution of the PDE, a linear discrete state space model is obtained by using time-scaling and the redefinition of the control input. This method allows overcoming the dependency of the time constants with the operating point. A model-based predictive adaptive controller is derived with the internal temperature distribution estimated with a state observer. Experimental results at the solar power plant are presented, illustrating the advantages of the approach under consideration. (author)

  7. Stability theory for dynamic equations on time scales

    CERN Document Server

    Martynyuk, Anatoly A

    2016-01-01

    This monograph is a first in the world to present three approaches for stability analysis of solutions of dynamic equations. The first approach is based on the application of dynamic integral inequalities and the fundamental matrix of solutions of linear approximation of dynamic equations. The second is based on the generalization of the direct Lyapunovs method for equations on time scales, using scalar, vector and matrix-valued auxiliary functions. The third approach is the application of auxiliary functions (scalar, vector, or matrix-valued ones) in combination with differential dynamic inequalities. This is an alternative comparison method, developed for time continuous and time discrete systems. In recent decades, automatic control theory in the study of air- and spacecraft dynamics and in other areas of modern applied mathematics has encountered problems in the analysis of the behavior of solutions of time continuous-discrete linear and/or nonlinear equations of perturbed motion. In the book “Men of Ma...

  8. BOX-COX REGRESSION METHOD IN TIME SCALING

    Directory of Open Access Journals (Sweden)

    ATİLLA GÖKTAŞ

    2013-06-01

    Full Text Available Box-Cox regression method with λj, for j = 1, 2, ..., k, power transformation can be used when dependent variable and error term of the linear regression model do not satisfy the continuity and normality assumptions. The situation obtaining the smallest mean square error  when optimum power λj, transformation for j = 1, 2, ..., k, of Y has been discussed. Box-Cox regression method is especially appropriate to adjust existence skewness or heteroscedasticity of error terms for a nonlinear functional relationship between dependent and explanatory variables. In this study, the advantage and disadvantage use of Box-Cox regression method have been discussed in differentiation and differantial analysis of time scale concept.

  9. Liquidity spillover in international stock markets through distinct time scales.

    Science.gov (United States)

    Righi, Marcelo Brutti; Vieira, Kelmara Mendes

    2014-01-01

    This paper identifies liquidity spillovers through different time scales based on a wavelet multiscaling method. We decompose daily data from U.S., British, Brazilian and Hong Kong stock markets indices in order to calculate the scale correlation between their illiquidities. The sample is divided in order to consider non-crisis, sub-prime crisis and Eurozone crisis. We find that there are changes in correlations of distinct scales and different periods. Association in finest scales is smaller than in coarse scales. There is a rise on associations in periods of crisis. In frequencies, there is predominance for significant distinctions involving the coarsest scale, while for crises periods there is predominance for distinctions on the finest scale.

  10. Effects of moonlight on the capturability of frugivorous phyllostomid bats (Chiroptera: Phyllostomidae at different time scales

    Directory of Open Access Journals (Sweden)

    Marco A. R. Mello

    2013-08-01

    Full Text Available Some bat species seem to be lunar phobic, i.e., they avoid flying in bright areas or during bright periods of the night; however, the evidence is still controversial. We think that part of this controversy comes from pooling data on bat captures and moonlight intensity according to broad categories, such as moon phases, which conceal the high variability among nights. Therefore, we used detailed, long-term field data on three phyllostomid bat species, in order to test the hypothesis of lunar phobia at two different time scales: 1 among nights, by pooling data of different nights according to moon phases and testing for differences in the distribution of captures; and 2 within a night, by analyzing the relationship between capturability and moonlight intensity (measured as illuminance in one-hour intervals for 29 individual nights. Although most captures of the studied bat species occurred in the first half of the night, their activity pattern varied largely among nights, and was not always unimodal as commonly assumed. At the larger time scale, all studied bat species showed evidence of lunar phobia, as they were more frequently captured on dark moon phases. Nevertheless, at the smaller time scale, only Carollia perspicillata (Linnaeus, 1758 was less frequently captured on brighter periods of the night. We propose that the unimodal activity pattern assumed for frugivorous phyllostomid bats may be an artifact of data organization, and that activity and lunar phobia are much more variable than previously assumed.

  11. A large catalog of accurate distances to molecular clouds from PS1 photometry

    Energy Technology Data Exchange (ETDEWEB)

    Schlafly, E. F.; Rix, H.-W.; Martin, N. F. [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Green, G.; Finkbeiner, D. P. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Bell, E. F. [Department of Astronomy, University of Michigan, 500 Church Street, Ann Arbor, MI 48109 (United States); Burgett, W. S.; Chambers, K. C.; Hodapp, K. W.; Kaiser, N.; Magnier, E. A.; Tonry, J. L. [Institute for Astronomy, University of Hawaii, 2680 Woodlawn Drive, Honolulu, HI 96822 (United States); Draper, P. W.; Metcalfe, N. [Department of Physics, Durham University, South Road, Durham DH1 3LE (United Kingdom); Price, P. A. [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States)

    2014-05-01

    Distance measurements to molecular clouds are important but are often made separately for each cloud of interest, employing very different data and techniques. We present a large, homogeneous catalog of distances to molecular clouds, most of which are of unprecedented accuracy. We determine distances using optical photometry of stars along lines of sight toward these clouds, obtained from PanSTARRS-1. We simultaneously infer the reddenings and distances to these stars, tracking the full probability distribution function using a technique presented in Green et al. We fit these star-by-star measurements using a simple dust screen model to find the distance to each cloud. We thus estimate the distances to almost all of the clouds in the Magnani et al. catalog, as well as many other well-studied clouds, including Orion, Perseus, Taurus, Cepheus, Polaris, California, and Monoceros R2, avoiding only the inner Galaxy. Typical statistical uncertainties in the distances are 5%, though the systematic uncertainty stemming from the quality of our stellar models is about 10%. The resulting catalog is the largest catalog of accurate, directly measured distances to molecular clouds. Our distance estimates are generally consistent with available distance estimates from the literature, though in some cases the literature estimates are off by a factor of more than two.

  12. Prenatal molecular diagnosis of oculocutaneous albinism (OCA) in a large cohort of Israeli families.

    Science.gov (United States)

    Rosenmann, Ada; Bejarano-Achache, Idit; Eli, Dalia; Maftsir, Genia; Mizrahi-Meissonnier, Liliana; Blumenfeld, Anat

    2009-10-01

    To present our accumulated data on prenatal molecular diagnosis of oculocutaneous albinism (OCA) in a large cohort of Israeli albino families. Albinism consists of variable phenotypes, but only families with predicted severely handicapped albino offspring, who declared their wish to terminate a pregnancy of such a fetus, are eligible for prenatal testing. Prenatal testing is not offered otherwise. Following detailed genetic investigation and counseling, molecular prenatal testing was performed using the combination of mutation screening, direct sequencing, and haplotype analysis. A total of 55 prenatal tests were performed in 37 families; in 26 families the propositus was the child, and in 11, a parent or a close relative. In 32 families tyrosinase (TYR) mutations were diagnosed. In 5 families a P gene mutation was detected. Twelve albino fetuses were diagnosed. Following further genetic counseling, all couples elected to terminate the pregnancy. Three additional pregnancies were terminated for other reasons. Families with increased risk for an albino child with severe visual handicap, seek premarital and prenatal genetic counseling and testing, for the prevention of affected offspring. Our combined methods of molecular genetic testing enable a nationwide approach for prevention of albinism. The same paradigm can be applied to other populations affected with albinism.

  13. A hybrid procedure for MSW generation forecasting at multiple time scales in Xiamen City, China.

    Science.gov (United States)

    Xu, Lilai; Gao, Peiqing; Cui, Shenghui; Liu, Chun

    2013-06-01

    Accurate forecasting of municipal solid waste (MSW) generation is crucial and fundamental for the planning, operation and optimization of any MSW management system. Comprehensive information on waste generation for month-scale, medium-term and long-term time scales is especially needed, considering the necessity of MSW management upgrade facing many developing countries. Several existing models are available but of little use in forecasting MSW generation at multiple time scales. The goal of this study is to propose a hybrid model that combines the seasonal autoregressive integrated moving average (SARIMA) model and grey system theory to forecast MSW generation at multiple time scales without needing to consider other variables such as demographics and socioeconomic factors. To demonstrate its applicability, a case study of Xiamen City, China was performed. Results show that the model is robust enough to fit and forecast seasonal and annual dynamics of MSW generation at month-scale, medium- and long-term time scales with the desired accuracy. In the month-scale, MSW generation in Xiamen City will peak at 132.2 thousand tonnes in July 2015 - 1.5 times the volume in July 2010. In the medium term, annual MSW generation will increase to 1518.1 thousand tonnes by 2015 at an average growth rate of 10%. In the long term, a large volume of MSW will be output annually and will increase to 2486.3 thousand tonnes by 2020 - 2.5 times the value for 2010. The hybrid model proposed in this paper can enable decision makers to develop integrated policies and measures for waste management over the long term. Copyright © 2013 Elsevier Ltd. All rights reserved.

  14. Large scale IRAM 30 m CO-observations in the giant molecular cloud complex W43

    Science.gov (United States)

    Carlhoff, P.; Nguyen Luong, Q.; Schilke, P.; Motte, F.; Schneider, N.; Beuther, H.; Bontemps, S.; Heitsch, F.; Hill, T.; Kramer, C.; Ossenkopf, V.; Schuller, F.; Simon, R.; Wyrowski, F.

    2013-12-01

    We aim to fully describe the distribution and location of dense molecular clouds in the giant molecular cloud complex W43. It was previously identified as one of the most massive star-forming regions in our Galaxy. To trace the moderately dense molecular clouds in the W43 region, we initiated W43-HERO, a large program using the IRAM 30 m telescope, which covers a wide dynamic range of scales from 0.3 to 140 pc. We obtained on-the-fly-maps in 13CO (2-1) and C18O (2-1) with a high spectral resolution of 0.1 km s-1 and a spatial resolution of 12''. These maps cover an area of ~1.5 square degrees and include the two main clouds of W43 and the lower density gas surrounding them. A comparison to Galactic models and previous distance calculations confirms the location of W43 near the tangential point of the Scutum arm at approximately 6 kpc from the Sun. The resulting intensity cubes of the observed region are separated into subcubes, which are centered on single clouds and then analyzed in detail. The optical depth, excitation temperature, and H2 column density maps are derived out of the 13CO and C18O data. These results are then compared to those derived from Herschel dust maps. The mass of a typical cloud is several 104 M⊙ while the total mass in the dense molecular gas (>102 cm-3) in W43 is found to be ~1.9 × 106 M⊙. Probability distribution functions obtained from column density maps derived from molecular line data and Herschel imaging show a log-normal distribution for low column densities and a power-law tail for high densities. A flatter slope for the molecular line data probability distribution function may imply that those selectively show the gravitationally collapsing gas. Appendices are available in electronic form at http://www.aanda.orgThe final datacubes (13CO and C18O) for the entire survey are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/560/A24

  15. Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source.

    Science.gov (United States)

    González-Candelas, Fernando; Bracho, María Alma; Wróbel, Borys; Moya, Andrés

    2013-07-19

    Molecular phylogenetic analyses are used increasingly in the epidemiological investigation of outbreaks and transmission cases involving rapidly evolving RNA viruses. Here, we present the results of such an analysis that contributed to the conviction of an anesthetist as being responsible for the infection of 275 of his patients with hepatitis C virus. We obtained sequences of the NS5B and E1-E2 regions in the viral genome for 322 patients suspected to have been infected by the doctor, and for 44 local, unrelated controls. The analysis of 4,184 cloned sequences of the E1-E2 region allowed us to exclude 47 patients from the outbreak. A subset of patients had known dates of infection. We used these data to calibrate a relaxed molecular clock and to determine a rough estimate of the time of infection for each patient. A similar analysis led to an estimate for the time of infection of the source. The date turned out to be 10 years before the detection of the outbreak. The number of patients infected was small at first, but it increased substantially in the months before the detection of the outbreak. We have developed a procedure to integrate molecular phylogenetic reconstructions of rapidly evolving viral populations into a forensic setting adequate for molecular epidemiological analysis of outbreaks and transmission events. We applied this procedure to a large outbreak of hepatitis C virus caused by a single source and the results obtained played a key role in the trial that led to the conviction of the suspected source.

  16. SPECTRAL LINE SURVEY TOWARD MOLECULAR CLOUDS IN THE LARGE MAGELLANIC CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Nishimura, Yuri; Watanabe, Yoshimasa; Yamamoto, Satoshi [Department of Physics, the University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033 (Japan); Shimonishi, Takashi [Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Aramakiazaaoba 6-3, Aoba-ku, Sendai, Miyagi, 980-8578 (Japan); Sakai, Nami [RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Aikawa, Yuri [Center for Computational Sciences, The University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8577 (Japan); Kawamura, Akiko [National Astronomical Observatory of Japan, Osawa, Mitaka, Tokyo, 181-8588 (Japan)

    2016-02-20

    Spectral line survey observations of seven molecular clouds in the Large Magellanic Cloud (LMC) have been conducted in the 3 mm band with the Mopra 22 m telescope to reveal chemical compositions in low metallicity conditions. Spectral lines of fundamental species such as CS, SO, CCH, HCN, HCO{sup +}, and HNC are detected in addition to those of CO and {sup 13}CO, while CH{sub 3}OH is not detected in any source and N{sub 2}H{sup +} is marginally detected in two sources. The molecular-cloud scale (10 pc scale) chemical composition is found to be similar among the seven sources regardless of different star formation activities, and hence, it represents the chemical composition characteristic of the LMC without influences by star formation activities. In comparison with chemical compositions of Galactic sources, the characteristic features are (1) deficient N-bearing molecules, (2) abundant CCH, and (3) deficient CH{sub 3}OH. Feature (1) is due to a lower elemental abundance of nitrogen in the LMC, whereas features (2) and (3) seem to originate from extended photodissociation regions and warmer temperature in cloud peripheries due to a lower abundance of dust grains in the low metallicity condition. In spite of general resemblance of chemical abundances among the seven sources, the CS/HCO{sup +} and SO/HCO{sup +} ratios are found to be slightly higher in a quiescent molecular cloud. An origin of this trend is discussed in relation to possible depletion of sulfur along the molecular cloud formation.

  17. Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia.

    Science.gov (United States)

    Leavey, Katherine; Bainbridge, Shannon A; Cox, Brian J

    2015-01-01

    Preeclampsia (PE) is a life-threatening hypertensive pathology of pregnancy affecting 3-5% of all pregnancies. To date, PE has no cure, early detection markers, or effective treatments short of the removal of what is thought to be the causative organ, the placenta, which may necessitate a preterm delivery. Additionally, numerous small placental microarray studies attempting to identify "PE-specific" genes have yielded inconsistent results. We therefore hypothesize that preeclampsia is a multifactorial disease encompassing several pathology subclasses, and that large cohort placental gene expression analysis will reveal these groups. To address our hypothesis, we utilized known bioinformatic methods to aggregate 7 microarray data sets across multiple platforms in order to generate a large data set of 173 patient samples, including 77 with preeclampsia. Unsupervised clustering of these patient samples revealed three distinct molecular subclasses of PE. This included a "canonical" PE subclass demonstrating elevated expression of known PE markers and genes associated with poor oxygenation and increased secretion, as well as two other subclasses potentially representing a poor maternal response to pregnancy and an immunological presentation of preeclampsia. Our analysis sheds new light on the heterogeneity of PE patients, and offers up additional avenues for future investigation. Hopefully, our subclassification of preeclampsia based on molecular diversity will finally lead to the development of robust diagnostics and patient-based treatments for this disorder.

  18. Purification of a large molecular weight transglutaminase substrate from liver plasma membranes

    International Nuclear Information System (INIS)

    Slife, C.W.; Morris, G.S.; Tyrrell, D.J.

    1986-01-01

    Transglutaminases are enzymes which catalyze the covalent crosslinking of proteins by forming epsilon(γ-glutamyl)lysine isopeptide linkages. In earlier studies, the authors reported that a large molecular weight protein aggregate in rat liver plasma membranes served as a substrate for a plasma membrane-associated transglutaminase. The enzyme specifically incorporated a lysine analog, [ 3 H]putrescine, into a protein complex which remained at the top of an acrylamide gel upon electrophoresis in SDS and reducing agents. The complex has now been isolated by extracting the plasma membranes with detergent (octylglucoside) resuspending the detergent insoluble residues in 6 M guanidine HCl and chromatographing the residue on a 4% agarose column in 6 M guanidine HCl. Most of the radioactivity is found in the void volume fractions from the column. SDS polyacrylamide gel electrophoresis shows that these fractions contain mostly proteins that do not enter the acrylamide gel. Since this purification procedure is essentially the same as that used to isolate a rat hepatocyte adhesion factor from rat liver plasma membranes it is possible that the large molecular weight transglutaminase substrate and the adhesion factor are contained in the same protein aggregate

  19. Large Magnetoresistance at Room Temperature in Organic Molecular Tunnel Junctions with Nonmagnetic Electrodes.

    Science.gov (United States)

    Xie, Zuoti; Shi, Sha; Liu, Feilong; Smith, Darryl L; Ruden, P Paul; Frisbie, C Daniel

    2016-09-27

    We report room-temperature resistance changes of up to 30% under weak magnetic fields (0.1 T) for molecular tunnel junctions composed of oligophenylene thiol molecules, 1-2 nm in length, sandwiched between gold contacts. The magnetoresistance (MR) is independent of field orientation and the length of the molecule; it appears to be an interface effect. Theoretical analysis suggests that the source of the MR is a two-carrier (two-hole) interaction at the interface, resulting in spin coupling between the tunneling hole and a localized hole at the Au/molecule contact. Such coupling leads to significantly different singlet and triplet transmission barriers at the interface. Even weak magnetic fields impede spin relaxation processes and thus modify the ratio of holes tunneling via the singlet state versus the triplet state, which leads to the large MR. Overall, the experiments and analysis suggest significant opportunities to explore large MR effects in molecular tunnel junctions based on widely available molecules.

  20. Analysis of passive scalar advection in parallel shear flows: Sorting of modes at intermediate time scales

    Science.gov (United States)

    Camassa, Roberto; McLaughlin, Richard M.; Viotti, Claudio

    2010-11-01

    The time evolution of a passive scalar advected by parallel shear flows is studied for a class of rapidly varying initial data. Such situations are of practical importance in a wide range of applications from microfluidics to geophysics. In these contexts, it is well-known that the long-time evolution of the tracer concentration is governed by Taylor's asymptotic theory of dispersion. In contrast, we focus here on the evolution of the tracer at intermediate time scales. We show how intermediate regimes can be identified before Taylor's, and in particular, how the Taylor regime can be delayed indefinitely by properly manufactured initial data. A complete characterization of the sorting of these time scales and their associated spatial structures is presented. These analytical predictions are compared with highly resolved numerical simulations. Specifically, this comparison is carried out for the case of periodic variations in the streamwise direction on the short scale with envelope modulations on the long scales, and show how this structure can lead to "anomalously" diffusive transients in the evolution of the scalar onto the ultimate regime governed by Taylor dispersion. Mathematically, the occurrence of these transients can be viewed as a competition in the asymptotic dominance between large Péclet (Pe) numbers and the long/short scale aspect ratios (LVel/LTracer≡k), two independent nondimensional parameters of the problem. We provide analytical predictions of the associated time scales by a modal analysis of the eigenvalue problem arising in the separation of variables of the governing advection-diffusion equation. The anomalous time scale in the asymptotic limit of large k Pe is derived for the short scale periodic structure of the scalar's initial data, for both exactly solvable cases and in general with WKBJ analysis. In particular, the exactly solvable sawtooth flow is especially important in that it provides a short cut to the exact solution to the

  1. Interplay between multiple length and time scales in complex ...

    Indian Academy of Sciences (India)

    Administrator

    sity is generated by the interaction of well-defined components, electrons and .... est in liquid state dynamics and solvation. Protein folding and aggregation are regarded as among the ..... molecular simulation perspective, free energy land.

  2. Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor

    KAUST Repository

    Bagchi, Samik

    2016-06-20

    Granules enriched with anammox bacteria are essential in enhancing the treatment of ammonia-rich wastewater, but little is known about how anammox bacteria grow and multiply inside granules. Here, we combined metatranscriptomics, quantitative PCR and 16S rRNA gene sequencing to study the changes in community composition, metabolic gene content and gene expression in a granular anammox reactor with the objective of understanding the molecular mechanism of anammox growth and multiplication that led to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass. Metatranscriptomics analysis detected all the essential transcripts for anammox metabolism. During the later stage of reactor operation, higher expression of ammonia and nitrite transport proteins and key metabolic enzymes mainly in the bottom large granules facilitated anammox bacteria activity. The high activity resulted in higher growth and multiplication of anammox bacteria and expanded the size of the granules. This conceptual model for large granule formation proposed here may assist in the future design of anammox processes for mainstream wastewater treatment.

  3. Molecular epidemiology of pathogenic Leptospira spp. among large ruminants in the Philippines.

    Science.gov (United States)

    Villanueva, Marvin A; Mingala, Claro N; Balbin, Michelle M; Nakajima, Chie; Isoda, Norikazu; Suzuki, Yasuhiko; Koizumi, Nobuo

    2016-12-01

    The extent of Leptospira infection in large ruminants resulting to economic problems in livestock industry in a leptospirosis-endemic country like the Philippines has not been extensively explored. Therefore, we determined the prevalence and carrier status of leptospirosis in large ruminants using molecular techniques and assessed the risk factors of acquiring leptospirosis in these animals. Water buffalo and cattle urine samples (n=831) collected from 21 farms during 2013-2015 were subjected to flaB-nested PCR to detect pathogenic Leptospira spp. Leptospiral flaB was detected in both species with a detection rate of 16.1%. Leptospiral DNA was detected only in samples from animals managed in communal farms. Sequence analysis of Leptospira flaB in large ruminants revealed the formation of three major clusters with L. borgpetersenii or L. kirschneri. One farm contained Leptospira flaB sequences from all clusters identified in this study, suggesting this farm was the main source of leptospires for other farms. This study suggested that these large ruminants are infected with various pathogenic Leptospira species causing possible major economic loss in the livestock industry as well as potential Leptospira reservoirs that can transmit infection to humans and other animals in the Philippines.

  4. Review of Tropical-Extratropical Teleconnections on Intraseasonal Time Scales

    Science.gov (United States)

    Stan, Cristiana; Straus, David M.; Frederiksen, Jorgen S.; Lin, Hai; Maloney, Eric D.; Schumacher, Courtney

    2017-12-01

    The interactions and teleconnections between the tropical and midlatitude regions on intraseasonal time scales are an important modulator of tropical and extratropical circulation anomalies and their associated weather patterns. These interactions arise due to the impact of the tropics on the extratropics, the impact of the midlatitudes on the tropics, and two-way interactions between the regions. Observational evidence, as well as theoretical studies with models of complexity ranging from the linear barotropic framework to intricate Earth system models, suggest the involvement of a myriad of processes and mechanisms in generating and maintaining these interconnections. At this stage, our understanding of these teleconnections is primarily a collection of concepts; a comprehensive theoretical framework has yet to be established. These intraseasonal teleconnections are increasingly recognized as an untapped source of potential subseasonal predictability. However, the complexity and diversity of mechanisms associated with these teleconnections, along with the lack of a conceptual framework to relate them, prevent this potential predictability from being translated into realized forecast skill. This review synthesizes our progress in understanding the observed characteristics of intraseasonal tropical-extratropical interactions and their associated mechanisms, identifies the significant gaps in this understanding, and recommends new research endeavors to address the remaining challenges.

  5. The pace of aging: Intrinsic time scales in demography

    Directory of Open Access Journals (Sweden)

    Tomasz Wrycza

    2014-05-01

    Full Text Available Background: The pace of aging is a concept that captures the time-related aspect of aging. It formalizesthe idea of a characteristic life span or intrinsic population time scale. In the rapidly developing field of comparative biodemography, measures that account for inter-speciesdifferences in life span are needed to compare how species age. Objective: We aim to provide a mathematical foundation for the concept of pace. We derive desiredmathematical properties of pace measures and suggest candidates which satisfy these properties. Subsequently, we introduce the concept of pace-standardization, which reveals differences in demographic quantities that are not due to pace. Examples and consequences are discussed. Conclusions: Mean life span (i.e., life expectancy from birth or from maturity is intuitively appealing,theoretically justified, and the most appropriate measure of pace. Pace-standardizationprovides a serviceable method for comparative aging studies to explore differences indemographic patterns of aging across species, and it may considerably alter conclusionsabout the strength of aging.

  6. Properties of liquid clusters in large-scale molecular dynamics nucleation simulations

    International Nuclear Information System (INIS)

    Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K.; Tanaka, Hidekazu

    2014-01-01

    We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with 10 9 atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent statistics for cluster properties over a wide range of cluster sizes. The nucleation rates, cluster growth rates, and size distributions are presented in Diemand et al. [J. Chem. Phys. 139, 74309 (2013)], while this paper analyses the properties of the clusters. We explore the cluster temperatures, density profiles, potential energies, and shapes. A thorough understanding of the properties of the clusters is crucial to the formulation of nucleation models. Significant latent heat is retained by stable clusters, by as much as ΔkT = 0.1ε for clusters with size i = 100. We find that the clusters deviate remarkably from spherical—with ellipsoidal axis ratios for critical cluster sizes typically within b/c = 0.7 ± 0.05 and a/c = 0.5 ± 0.05. We examine cluster spin angular momentum, and find that it plays a negligible role in the cluster dynamics. The interfaces of large, stable clusters are thinner than planar equilibrium interfaces by 10%−30%. At the critical cluster size, the cluster central densities are between 5% and 30% lower than the bulk liquid expectations. These lower densities imply larger-than-expected surface areas, which increase the energy cost to form a surface, which lowers nucleation rates

  7. Gamma-ray observations of the Orion Molecular Clouds with the Fermi Large Area Telescope

    Energy Technology Data Exchange (ETDEWEB)

    Ackermann, M.; Ajello, M.; Allafort, A.; Antolini, E.; Baldini, L.; Ballet, J.; Barbiellini, G.; Bastieri, D.; Bechtol, K.; Bellazzini, R.; Berenji, B.; Blandford, R. D.; Bloom, E. D.; Bonamente, E.; Borgland, A. W.; Bottacini, E.; Brandt, T. J.; Bregeon, J.; Brigida, M.; Bruel, P.; Buehler, R.; Buson, S.; Caliandro, G. A.; Cameron, R. A.; Caraveo, P. A.; Cecchi, C.; Chekhtman, A.; Chiang, J.; Ciprini, S.; Claus, R.; Cohen-Tanugi, J.; Conrad, J.; D' Ammando, F.; de Angelis, A.; de Palma, F.; Dermer, C. D.; do Couto e Silva, E.; Drell, P. S.; Drlica-Wagner, A.; Enoto, T.; Falletti, L.; Favuzzi, C.; Fegan, S. J.; Ferrara, E. C.; Focke, W. B.; Fukazawa, Y.; Fukui, Y.; Fusco, P.; Gargano, F.; Gasparrini, D.; Germani, S.; Giglietto, N.; Giordano, F.; Giroletti, M.; Glanzman, T.; Godfrey, G.; Guiriec, S.; Hadasch, D.; Hanabata, Y.; Harding, A. K.; Hayashida, M.; Hayashi, K.; Horan, D.; Hou, X.; Hughes, R. E.; Jackson, M. S.; Jóhannesson, G.; Johnson, A. S.; Kamae, T.; Katagiri, H.; Kataoka, J.; Kerr, M.; Knödlseder, J.; Kuss, M.; Lande, J.; Larsson, S.; Lee, S. -H.; Longo, F.; Loparco, F.; Lovellette, M. N.; Lubrano, P.; Makishima, K.; Mazziotta, M. N.; Mehault, J.; Mitthumsiri, W.; Moiseev, A. A.; Monte, C.; Monzani, M. E.; Morselli, A.; Moskalenko, I. V.; Murgia, S.; Nakamori, T.; Naumann-Godo, M.; Nishino, S.; Norris, J. P.; Nuss, E.; Ohno, M.; Ohsugi, T.; Okumura, A.; Orienti, M.; Orlando, E.; Ormes, J. F.; Ozaki, M.; Paneque, D.; Panetta, J. H.; Parent, D.; Pelassa, V.; Pesce-Rollins, M.; Pierbattista, M.; Piron, F.; Pivato, G.; Porter, T. A.; Rainò, S.; Razzano, M.; Reimer, A.; Reimer, O.; Roth, M.; Sadrozinski, H. F. -W.; Sgrò, C.; Siskind, E. J.; Spandre, G.; Spinelli, P.; Strong, A. W.; Takahashi, H.; Takahashi, T.; Tanaka, T.; Thayer, J. G.; Thayer, J. B.; Tibolla, O.; Tinivella, M.; Torres, D. F.; Tramacere, A.; Troja, E.; Uchiyama, Y.; Usher, T. L.; Vandenbroucke, J.; Vasileiou, V.; Vianello, G.; Vitale, V.; Waite, A. P.; Wang, P.; Winer, B. L.; Wood, K. S.; Yang, Z.; Zimmer, S.

    2012-08-08

    We report on the gamma-ray observations of giant molecular clouds Orion A and B with the Large Area Telescope (LAT) on board the Fermi Gamma-ray Space Telescope. The gamma-ray emission in the energy band between ~100 MeV and ~100 GeV is predicted to trace the gas mass distribution in the clouds through nuclear interactions between the Galactic cosmic rays (CRs) and interstellar gas. The gamma-ray production cross-section for the nuclear interaction is known to ~10% precision which makes the LAT a powerful tool to measure the gas mass column density distribution of molecular clouds for a known CR intensity. We present here such distributions for Orion A and B, and correlate them with those of the velocity-integrated CO intensity (W CO) at a 1° × 1° pixel level. The correlation is found to be linear over a W CO range of ~10-fold when divided in three regions, suggesting penetration of nuclear CRs to most of the cloud volumes. The W CO-to-mass conversion factor, X CO, is found to be ~2.3 × 1020 cm-2(K km s–1)–1 for the high-longitude part of Orion A (l > 212°), ~1.7 times higher than ~1.3 × 1020 found for the rest of Orion A and B. We interpret the apparent high X CO in the high-longitude region of Orion A in the light of recent works proposing a nonlinear relation between H2 and CO densities in the diffuse molecular gas. W CO decreases faster than the H2 column density in the region making the gas "darker" to W CO.

  8. THE MAGELLANIC MOPRA ASSESSMENT (MAGMA). I. THE MOLECULAR CLOUD POPULATION OF THE LARGE MAGELLANIC CLOUD

    International Nuclear Information System (INIS)

    Wong, Tony; Chu, You-Hua; Gruendl, Robert A.; Looney, Leslie W.; Seale, Jonathan; Welty, Daniel E.; Hughes, Annie; Maddison, Sarah; Ott, Jürgen; Muller, Erik; Fukui, Yasuo; Kawamura, Akiko; Mizuno, Yoji; Pineda, Jorge L.; Bernard, Jean-Philippe; Paradis, Deborah; Henkel, Christian; Klein, Ulrich

    2011-01-01

    We present the properties of an extensive sample of molecular clouds in the Large Magellanic Cloud (LMC) mapped at 11 pc resolution in the CO(1-0) line. Targets were chosen based on a limiting CO flux and peak brightness as measured by the NANTEN survey. The observations were conducted with the ATNF Mopra Telescope as part of the Magellanic Mopra Assessment. We identify clouds as regions of connected CO emission and find that the distributions of cloud sizes, fluxes, and masses are sensitive to the choice of decomposition parameters. In all cases, however, the luminosity function of CO clouds is steeper than dN/dL∝L –2 , suggesting that a substantial fraction of mass is in low-mass clouds. A correlation between size and linewidth, while apparent for the largest emission structures, breaks down when those structures are decomposed into smaller structures. We argue that the correlation between virial mass and CO luminosity is the result of comparing two covariant quantities, with the correlation appearing tighter on larger scales where a size-linewidth relation holds. The virial parameter (the ratio of a cloud's kinetic to self-gravitational energy) shows a wide range of values and exhibits no clear trends with the CO luminosity or the likelihood of hosting young stellar object (YSO) candidates, casting further doubt on the assumption of virialization for molecular clouds in the LMC. Higher CO luminosity increases the likelihood of a cloud harboring a YSO candidate, and more luminous YSOs are more likely to be coincident with detectable CO emission, confirming the close link between giant molecular clouds and massive star formation.

  9. Muscle activation described with a differential equation model for large ensembles of locally coupled molecular motors.

    Science.gov (United States)

    Walcott, Sam

    2014-10-01

    Molecular motors, by turning chemical energy into mechanical work, are responsible for active cellular processes. Often groups of these motors work together to perform their biological role. Motors in an ensemble are coupled and exhibit complex emergent behavior. Although large motor ensembles can be modeled with partial differential equations (PDEs) by assuming that molecules function independently of their neighbors, this assumption is violated when motors are coupled locally. It is therefore unclear how to describe the ensemble behavior of the locally coupled motors responsible for biological processes such as calcium-dependent skeletal muscle activation. Here we develop a theory to describe locally coupled motor ensembles and apply the theory to skeletal muscle activation. The central idea is that a muscle filament can be divided into two phases: an active and an inactive phase. Dynamic changes in the relative size of these phases are described by a set of linear ordinary differential equations (ODEs). As the dynamics of the active phase are described by PDEs, muscle activation is governed by a set of coupled ODEs and PDEs, building on previous PDE models. With comparison to Monte Carlo simulations, we demonstrate that the theory captures the behavior of locally coupled ensembles. The theory also plausibly describes and predicts muscle experiments from molecular to whole muscle scales, suggesting that a micro- to macroscale muscle model is within reach.

  10. Tuning the thickness of electrochemically grafted layers in large area molecular junctions

    Energy Technology Data Exchange (ETDEWEB)

    Fluteau, T.; Bessis, C.; Barraud, C., E-mail: clement.barraud@univ-paris-diderot.fr; Della Rocca, M. L.; Lafarge, P. [Université Paris Diderot, Sorbonne Paris Cité, MPQ, UMR 7162, CNRS, 75205 Paris Cedex 13 (France); Martin, P.; Lacroix, J.-C. [Université Paris Diderot, Sorbonne Paris Cité, ITODYS, UMR 7086, CNRS, 15 rue J.-A. de Baïf, 75205 Paris Cedex 13 (France)

    2014-09-21

    We have investigated the thickness, the surface roughness, and the transport properties of oligo(1-(2-bisthienyl)benzene) (BTB) thin films grafted on evaporated Au electrodes, thanks to a diazonium-based electro-reduction process. The thickness of the organic film is tuned by varying the number of electrochemical cycles during the growth process. Atomic force microscopy measurements reveal the evolution of the thickness in the range of 2–27 nm. Its variation displays a linear dependence with the number of cycles followed by a saturation attributed to the insulating behavior of the organic films. Both ultrathin (2 nm) and thin (12 and 27 nm) large area BTB-based junctions have then been fabricated using standard CMOS processes and finally electrically characterized. The electronic responses are fully consistent with a tunneling barrier in case of ultrathin BTB film whereas a pronounced rectifying behavior is reported for thicker molecular films.

  11. Nuclear magnetic resonance provides a quantitative description of protein conformational flexibility on physiologically important time scales.

    Science.gov (United States)

    Salmon, Loïc; Bouvignies, Guillaume; Markwick, Phineus; Blackledge, Martin

    2011-04-12

    A complete description of biomolecular activity requires an understanding of the nature and the role of protein conformational dynamics. In recent years, novel nuclear magnetic resonance-based techniques that provide hitherto inaccessible detail concerning biomolecular motions occurring on physiologically important time scales have emerged. Residual dipolar couplings (RDCs) provide precise information about time- and ensemble-averaged structural and dynamic processes with correlation times up to the millisecond and thereby encode key information for understanding biological activity. In this review, we present the application of two very different approaches to the quantitative description of protein motion using RDCs. The first is purely analytical, describing backbone dynamics in terms of diffusive motions of each peptide plane, using extensive statistical analysis to validate the proposed dynamic modes. The second is based on restraint-free accelerated molecular dynamics simulation, providing statistically sampled free energy-weighted ensembles that describe conformational fluctuations occurring on time scales from pico- to milliseconds, at atomic resolution. Remarkably, the results from these two approaches converge closely in terms of distribution and absolute amplitude of motions, suggesting that this kind of combination of analytical and numerical models is now capable of providing a unified description of protein conformational dynamics in solution.

  12. Preparation of large-area molecular junctions with metallic conducting Langmuir–Blodgett films

    Energy Technology Data Exchange (ETDEWEB)

    Mochizuki, Kengo [Division of Marine Technology, Tokyo University of Marine Science and Technology, 2-1-6 Etchujima Koto-ku, Tokyo 135-8533 (Japan); Ohnuki, Hitoshi, E-mail: ohnuki@kaiyodai.ac.jp [Division of Marine Technology, Tokyo University of Marine Science and Technology, 2-1-6 Etchujima Koto-ku, Tokyo 135-8533 (Japan); Shimizu, Daisuke [Division of Marine Technology, Tokyo University of Marine Science and Technology, 2-1-6 Etchujima Koto-ku, Tokyo 135-8533 (Japan); Imakubo, Tatsuro [Department of Materials and Technology, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188 (Japan); Tsuya, Daiju [National Institute for Materials Science,1-2-1 Sengen, Tsukuba, Ibaraki 305-0047 (Japan); Izumi, Mitsuru [Division of Marine Technology, Tokyo University of Marine Science and Technology, 2-1-6 Etchujima Koto-ku, Tokyo 135-8533 (Japan)

    2014-03-03

    Metallic conducting Langmuir–Blodgett (LB) films were used as soft electrodes to fabricate molecular junctions with self-assembled monolayers (SAMs) of alkanethiols (CH{sub 3}(CH{sub 2}){sub n−1}SH) on an Au surface. Alkanethiols can form highly ordered, stable dielectric SAMs on metal surfaces over large areas. However, it is difficult to establish electrical contacts on such SAMs, which has limited their application. In this work, we used metallic conducting LB films composed of bis(ethylenedioxy)tetrathiafulvalene and stearic acid as a soft electrode onto alkanethiol SAMs (C{sub n}-SAM, n = 12, 14, 16, 18) to prepare Au/SAM/metal junctions of relatively large size (∼ 15.6 × 10{sup 3} μm{sup 2}). The current density–voltage (J–V) characteristics across the junctions exhibited rectifying behavior with a ratio R of ∼ 5 (R = |J(V)|/|J(− V)| at ± 1 V). The lower transfer rate corresponding to the electron transport from Au to the LB films exhibited nonlinear J–V characteristics, while the higher transfer rate of electrons from the LB film to Au showed linear J–V characteristics. Kelvin probe force microscopy revealed that the work function of the metallic LB films was smaller than that of Au. The observed rectification behavior is probably caused by different electron transport mechanisms between the two current directions. - Highlights: • Metallic Langmuir–Blodgett (LB) films were used as soft electrodes. • Molecular junctions of metal–alkanethiol–LB films were fabricated. • The current–voltage curve across the junctions exhibited rectifying behavior. • This is the first observation for alkanethiol monolayer junctions. • The work function difference between the electrodes induces the rectification.

  13. Ozone time scale decomposition and trend assessment from surface observations

    Science.gov (United States)

    Boleti, Eirini; Hueglin, Christoph; Takahama, Satoshi

    2017-04-01

    Emissions of ozone precursors have been regulated in Europe since around 1990 with control measures primarily targeting to industries and traffic. In order to understand how these measures have affected air quality, it is now important to investigate concentrations of tropospheric ozone in different types of environments, based on their NOx burden, and in different geographic regions. In this study, we analyze high quality data sets for Switzerland (NABEL network) and whole Europe (AirBase) for the last 25 years to calculate long-term trends of ozone concentrations. A sophisticated time scale decomposition method, called the Ensemble Empirical Mode Decomposition (EEMD) (Huang,1998;Wu,2009), is used for decomposition of the different time scales of the variation of ozone, namely the long-term trend, seasonal and short-term variability. This allows subtraction of the seasonal pattern of ozone from the observations and estimation of long-term changes of ozone concentrations with lower uncertainty ranges compared to typical methodologies used. We observe that, despite the implementation of regulations, for most of the measurement sites ozone daily mean values have been increasing until around mid-2000s. Afterwards, we observe a decline or a leveling off in the concentrations; certainly a late effect of limitations in ozone precursor emissions. On the other hand, the peak ozone concentrations have been decreasing for almost all regions. The evolution in the trend exhibits some differences between the different types of measurement. In addition, ozone is known to be strongly affected by meteorology. In the applied approach, some of the meteorological effects are already captured by the seasonal signal and already removed in the de-seasonalized ozone time series. For adjustment of the influence of meteorology on the higher frequency ozone variation, a statistical approach based on Generalized Additive Models (GAM) (Hastie,1990;Wood,2006), which corrects for meteorological

  14. Nonequilibrium Physics at Short Time Scales: Formation of Correlations

    International Nuclear Information System (INIS)

    Peliti, L

    2005-01-01

    It is a happy situation when similar concepts and theoretical techniques can be applied to widely different physical systems because of a deep similarity in the situations being studied. The book illustrates this well; it focuses on the description of correlations in quantum systems out of equilibrium at very short time scales, prompted by experiments with short laser pulses in semiconductors, and in complex reactions in heavy nuclei. In both cases the experiments are characterized by nonlinear dynamics and by strong correlations out of equilibrium. In some systems there are also important finite-size effects. The book comprises several independent contributions of moderate length, and I sometimes felt that a more intensive effort in cross-coordination of the different contributions could have been of help. It is divided almost equally between theory and experiment. In the theoretical part, there is a thorough discussion both of the kinematic aspects (description of correlations) and the dynamical ones (evaluation of correlations). The experimental part is naturally divided according to the nature of the system: the interaction of pulsed lasers with matter on the one hand, and the correlations in finite-size systems (nanoparticles and nuclei) on the other. There is also a discussion on the dynamics of superconductors, a subject currently of great interest. Although an effort has been made to keep each contribution self-contained, I must admit that reading level is uneven. However, there are a number of thorough and stimulating contributions that make this book a useful introduction to the topic at the level of graduate students or researchers acquainted with quantum statistical mechanics. (book review)

  15. The Time Scale of Recombination Rate Evolution in Great Apes

    Science.gov (United States)

    Stevison, Laurie S.; Woerner, August E.; Kidd, Jeffrey M.; Kelley, Joanna L.; Veeramah, Krishna R.; McManus, Kimberly F.; Bustamante, Carlos D.; Hammer, Michael F.; Wall, Jeffrey D.

    2016-01-01

    Abstract We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471–475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10–15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives. PMID:26671457

  16. Homogeneous SPC/E water nucleation in large molecular dynamics simulations.

    Science.gov (United States)

    Angélil, Raymond; Diemand, Jürg; Tanaka, Kyoko K; Tanaka, Hidekazu

    2015-08-14

    We perform direct large molecular dynamics simulations of homogeneous SPC/E water nucleation, using up to ∼ 4 ⋅ 10(6) molecules. Our large system sizes allow us to measure extremely low and accurate nucleation rates, down to ∼ 10(19) cm(-3) s(-1), helping close the gap between experimentally measured rates ∼ 10(17) cm(-3) s(-1). We are also able to precisely measure size distributions, sticking efficiencies, cluster temperatures, and cluster internal densities. We introduce a new functional form to implement the Yasuoka-Matsumoto nucleation rate measurement technique (threshold method). Comparison to nucleation models shows that classical nucleation theory over-estimates nucleation rates by a few orders of magnitude. The semi-phenomenological nucleation model does better, under-predicting rates by at worst a factor of 24. Unlike what has been observed in Lennard-Jones simulations, post-critical clusters have temperatures consistent with the run average temperature. Also, we observe that post-critical clusters have densities very slightly higher, ∼ 5%, than bulk liquid. We re-calibrate a Hale-type J vs. S scaling relation using both experimental and simulation data, finding remarkable consistency in over 30 orders of magnitude in the nucleation rate range and 180 K in the temperature range.

  17. Expectation propagation for large scale Bayesian inference of non-linear molecular networks from perturbation data.

    Science.gov (United States)

    Narimani, Zahra; Beigy, Hamid; Ahmad, Ashar; Masoudi-Nejad, Ali; Fröhlich, Holger

    2017-01-01

    Inferring the structure of molecular networks from time series protein or gene expression data provides valuable information about the complex biological processes of the cell. Causal network structure inference has been approached using different methods in the past. Most causal network inference techniques, such as Dynamic Bayesian Networks and ordinary differential equations, are limited by their computational complexity and thus make large scale inference infeasible. This is specifically true if a Bayesian framework is applied in order to deal with the unavoidable uncertainty about the correct model. We devise a novel Bayesian network reverse engineering approach using ordinary differential equations with the ability to include non-linearity. Besides modeling arbitrary, possibly combinatorial and time dependent perturbations with unknown targets, one of our main contributions is the use of Expectation Propagation, an algorithm for approximate Bayesian inference over large scale network structures in short computation time. We further explore the possibility of integrating prior knowledge into network inference. We evaluate the proposed model on DREAM4 and DREAM8 data and find it competitive against several state-of-the-art existing network inference methods.

  18. Reinforced dynamics for enhanced sampling in large atomic and molecular systems

    Science.gov (United States)

    Zhang, Linfeng; Wang, Han; E, Weinan

    2018-03-01

    A new approach for efficiently exploring the configuration space and computing the free energy of large atomic and molecular systems is proposed, motivated by an analogy with reinforcement learning. There are two major components in this new approach. Like metadynamics, it allows for an efficient exploration of the configuration space by adding an adaptively computed biasing potential to the original dynamics. Like deep reinforcement learning, this biasing potential is trained on the fly using deep neural networks, with data collected judiciously from the exploration and an uncertainty indicator from the neural network model playing the role of the reward function. Parameterization using neural networks makes it feasible to handle cases with a large set of collective variables. This has the potential advantage that selecting precisely the right set of collective variables has now become less critical for capturing the structural transformations of the system. The method is illustrated by studying the full-atom explicit solvent models of alanine dipeptide and tripeptide, as well as the system of a polyalanine-10 molecule with 20 collective variables.

  19. NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

    Science.gov (United States)

    Kuperstein, Inna; Cohen, David P A; Pook, Stuart; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei

    2013-10-07

    Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.

  20. A Group Simulation of the Development of the Geologic Time Scale.

    Science.gov (United States)

    Bennington, J. Bret

    2000-01-01

    Explains how to demonstrate to students that the relative dating of rock layers is redundant. Uses two column diagrams to simulate stratigraphic sequences from two different geological time scales and asks students to complete the time scale. (YDS)

  1. On the time-scales of magmatism at island-arc volcanoes.

    Science.gov (United States)

    Turner, S P

    2002-12-15

    Precise information on time-scales and rates of change is fundamental to an understanding of natural processes and the development of quantitative physical models in the Earth sciences. U-series isotope studies are revolutionizing this field by providing time information in the range 10(2)-10(4) years, which is similar to that of many modern Earth processes. I review how the application of U-series isotopes has been used to constrain the time-scales of magma formation, ascent and storage beneath island-arc volcanoes. Different elements are distilled-off the subducting plate at different times and in different places. Contributions from subducted sediments to island-arc lava sources appear to occur some 350 kyr to 4 Myr prior to eruption. Fluid release from the subducting oceanic crust into the mantle wedge may be a multi-stage process and occurs over a period ranging from a few hundred kyr to less than one kyr prior to eruption. This implies that dehydration commences prior to the initiation of partial melting within the mantle wedge, which is consistent with recent evidence that the onset of melting is controlled by an isotherm and thus the thermal structure within the wedge. U-Pa disequilibria appear to require a component of decompression melting, possibly due to the development of gravitational instabilities. The preservation of large (226)Ra disequilibria permits only a short period of time between fluid addition and eruption. This requires rapid melt segregation, magma ascent by channelled flow and minimal residence time within the lithosphere. The evolution from basalt to basaltic andesite probably occurs rapidly during ascent or in magma reservoirs inferred from some geophysical data to lie within the lithospheric mantle. The flux across the Moho is broadly andesitic, and some magmas subsequently stall in more shallow crustal-level magma chambers, where they evolve to more differentiated compositions on time-scales of a few thousand years or less.

  2. FERMI LARGE AREA TELESCOPE STUDY OF COSMIC RAYS AND THE INTERSTELLAR MEDIUM IN NEARBY MOLECULAR CLOUDS

    Energy Technology Data Exchange (ETDEWEB)

    Ackermann, M. [Deutsches Elektronen Synchrotron DESY, D-15738 Zeuthen (Germany); Ajello, M.; Allafort, A.; Bechtol, K.; Berenji, B.; Blandford, R. D.; Bloom, E. D.; Borgland, A. W.; Bottacini, E.; Buehler, R. [W. W. Hansen Experimental Physics Laboratory, Kavli Institute for Particle Astrophysics and Cosmology, Department of Physics and SLAC National Accelerator Laboratory, Stanford University, Stanford, CA 94305 (United States); Baldini, L.; Bellazzini, R.; Bregeon, J. [Istituto Nazionale di Fisica Nucleare, Sezione di Pisa, I-56127 Pisa (Italy); Ballet, J. [Laboratoire AIM, CEA-IRFU/CNRS/Universite Paris Diderot, Service d' Astrophysique, CEA Saclay, F-91191 Gif sur Yvette (France); Barbiellini, G. [Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, I-34127 Trieste (Italy); Bastieri, D. [Istituto Nazionale di Fisica Nucleare, Sezione di Padova, I-35131 Padova (Italy); Bonamente, E. [Istituto Nazionale di Fisica Nucleare, Sezione di Perugia, I-06123 Perugia (Italy); Brandt, T. J. [CNRS, IRAP, F-31028 Toulouse cedex 4 (France); Brigida, M. [Dipartimento di Fisica ' M. Merlin' dell' Universita e del Politecnico di Bari, I-70126 Bari (Italy); Bruel, P., E-mail: hayashi@hep01.hepl.hiroshima-u.ac.jp, E-mail: mizuno@hep01.hepl.hiroshima-u.ac.jp [Laboratoire Leprince-Ringuet, Ecole polytechnique, CNRS/IN2P3, Palaiseau (France); and others

    2012-08-10

    We report an analysis of the interstellar {gamma}-ray emission from the Chamaeleon, R Coronae Australis (R CrA), and Cepheus and Polaris flare regions with the Fermi Large Area Telescope. They are among the nearest molecular cloud complexes, within {approx}300 pc from the solar system. The {gamma}-ray emission produced by interactions of cosmic rays (CRs) and interstellar gas in those molecular clouds is useful to study the CR densities and distributions of molecular gas close to the solar system. The obtained {gamma}-ray emissivities above 250 MeV are (5.9 {+-} 0.1{sub stat}{sup +0.9}{sub -1.0sys}) Multiplication-Sign 10{sup -27} photons s{sup -1} sr{sup -1} H-atom{sup -1}, (10.2 {+-} 0.4{sub stat}{sup +1.2}{sub -1.7sys}) Multiplication-Sign 10{sup -27} photons s{sup -1} sr{sup -1} H-atom{sup -1}, and (9.1 {+-} 0.3{sub stat}{sup +1.5}{sub -0.6sys}) Multiplication-Sign 10{sup -27} photons s{sup -1} sr{sup -1} H-atom{sup -1} for the Chamaeleon, R CrA, and Cepheus and Polaris flare regions, respectively. Whereas the energy dependences of the emissivities agree well with that predicted from direct CR observations at the Earth, the measured emissivities from 250 MeV to 10 GeV indicate a variation of the CR density by {approx}20% in the neighborhood of the solar system, even if we consider systematic uncertainties. The molecular mass calibrating ratio, X{sub CO} = N(H{sub 2})/W{sub CO}, is found to be (0.96 {+-} 0.06{sub stat}{sup +0.15}{sub -0.12sys}) Multiplication-Sign 10{sup 20} H{sub 2}-molecule cm{sup -2} (K km s{sup -1}){sup -1}, (0.99 {+-} 0.08{sub stat}{sup +0.18}{sub -0.10sys}) Multiplication-Sign 10{sup 20} H{sub 2}-molecule cm{sup -2} (K km s{sup -1}){sup -1}, and (0.63 {+-} 0.02{sub stat}{sup +0.09}{sub -0.07sys}) Multiplication-Sign 10{sup 20} H{sub 2}-molecule cm{sup -2} (K km s{sup -1}){sup -1} for the Chamaeleon, R CrA, and Cepheus and Polaris flare regions, respectively, suggesting a variation of X{sub CO} in the vicinity of the solar system. From the

  3. Excess electron is trapped in a large single molecular cage C60F60.

    Science.gov (United States)

    Wang, Yin-Feng; Li, Zhi-Ru; Wu, Di; Sun, Chia-Chung; Gu, Feng-Long

    2010-01-15

    A new kind of solvated electron systems, sphere-shaped e(-)@C60F60 (I(h)) and capsule-shaped e(-)@C60F60 (D6h), in contrast to the endohedral complex M@C60, is represented at the B3LYP/6-31G(d) + dBF (diffusive basis functions) density functional theory. It is proven, by examining the singly occupied molecular orbital (SOMO) and the spin density map of e(-)@C60F60, that the excess electron is indeed encapsulated inside the C60F60 cage. The shape of the electron cloud in SOMO matches with the shape of C60F60 cage. These cage-like single molecular solvated electrons have considerably large vertical electron detachment energies VDE of 4.95 (I(h)) and 4.67 eV (D6h) at B3LYP/6-31+G(3df) + dBF level compared to the VDE of 3.2 eV for an electron in bulk water (Coe et al., Int Rev Phys Chem 2001, 20, 33) and that of 3.66 eV for e(-)@C20F20 (Irikura, J Phys Chem A 2008, 112, 983), which shows their higher stability. The VDE of the sphere-shaped e(-)@C60F60 (I(h)) is greater than that of the capsule-shaped e(-)@C60F60 (D6h), indicating that the excess electron prefers to reside in the cage with the higher symmetry to form the more stable solvated electron. It is also noticed that the cage size [7.994 (I(h)), 5.714 and 9.978 A (D6h) in diameter] is much larger than that (2.826 A) of (H2O)20- dodecahedral cluster (Khan, Chem Phys Lett 2005, 401, 85). Copyright 2009 Wiley Periodicals, Inc.

  4. Effects of forcing time scale on the simulated turbulent flows and turbulent collision statistics of inertial particles

    International Nuclear Information System (INIS)

    Rosa, B.; Parishani, H.; Ayala, O.; Wang, L.-P.

    2015-01-01

    In this paper, we study systematically the effects of forcing time scale in the large-scale stochastic forcing scheme of Eswaran and Pope [“An examination of forcing in direct numerical simulations of turbulence,” Comput. Fluids 16, 257 (1988)] on the simulated flow structures and statistics of forced turbulence. Using direct numerical simulations, we find that the forcing time scale affects the flow dissipation rate and flow Reynolds number. Other flow statistics can be predicted using the altered flow dissipation rate and flow Reynolds number, except when the forcing time scale is made unrealistically large to yield a Taylor microscale flow Reynolds number of 30 and less. We then study the effects of forcing time scale on the kinematic collision statistics of inertial particles. We show that the radial distribution function and the radial relative velocity may depend on the forcing time scale when it becomes comparable to the eddy turnover time. This dependence, however, can be largely explained in terms of altered flow Reynolds number and the changing range of flow length scales present in the turbulent flow. We argue that removing this dependence is important when studying the Reynolds number dependence of the turbulent collision statistics. The results are also compared to those based on a deterministic forcing scheme to better understand the role of large-scale forcing, relative to that of the small-scale turbulence, on turbulent collision of inertial particles. To further elucidate the correlation between the altered flow structures and dynamics of inertial particles, a conditional analysis has been performed, showing that the regions of higher collision rate of inertial particles are well correlated with the regions of lower vorticity. Regions of higher concentration of pairs at contact are found to be highly correlated with the region of high energy dissipation rate

  5. Epidemic mitigation via awareness propagation in communication networks: the role of time scales

    Science.gov (United States)

    Wang, Huijuan; Chen, Chuyi; Qu, Bo; Li, Daqing; Havlin, Shlomo

    2017-07-01

    The participation of individuals in multi-layer networks allows for feedback between network layers, opening new possibilities to mitigate epidemic spreading. For instance, the spread of a biological disease such as Ebola in a physical contact network may trigger the propagation of the information related to this disease in a communication network, e.g. an online social network. The information propagated in the communication network may increase the awareness of some individuals, resulting in them avoiding contact with their infected neighbors in the physical contact network, which might protect the population from the infection. In this work, we aim to understand how the time scale γ of the information propagation (speed that information is spread and forgotten) in the communication network relative to that of the epidemic spread (speed that an epidemic is spread and cured) in the physical contact network influences such mitigation using awareness information. We begin by proposing a model of the interaction between information propagation and epidemic spread, taking into account the relative time scale γ. We analytically derive the average fraction of infected nodes in the meta-stable state for this model (i) by developing an individual-based mean-field approximation (IBMFA) method and (ii) by extending the microscopic Markov chain approach (MMCA). We show that when the time scale γ of the information spread relative to the epidemic spread is large, our IBMFA approximation is better compared to MMCA near the epidemic threshold, whereas MMCA performs better when the prevalence of the epidemic is high. Furthermore, we find that an optimal mitigation exists that leads to a minimal fraction of infected nodes. The optimal mitigation is achieved at a non-trivial relative time scale γ, which depends on the rate at which an infected individual becomes aware. Contrary to our intuition, information spread too fast in the communication network could reduce the

  6. A large-scale molecular dynamics study of the divacancy defect in graphene

    International Nuclear Information System (INIS)

    Leyssale, Jean-Marc; Vignoles, Gerard L.

    2014-01-01

    We report on the dynamical behavior of single divacancy defects in large graphene sheets as studied by extensive classical molecular dynamics (MD) simulations at high temperatures and static calculations. In the first part of the paper, the ability of the used interatomic potential to properly render the stability and dynamics (energy barriers) of such defects is validated against electronic structure calculations from the literature. Then, results from MD simulations are presented. In agreement with recent TEM studies, some mobility is observed through a series of Stone-Wales-like bond rotations involving the 5-8-5, 555-777, and 5555-6-7777 reconstructions. Although these three structures are by far the most probable structures of the DV defect, not less than 18 other full reconstructions, including the experimentally observed 55-66-77 defect, were occasionally observed in the ∼1.5 μs of MD trajectories analyzed in this work. Most of these additional reconstructions have moderate formation energies and can be formed by a bond rotation mechanism from one of the aforementioned structures, with a lower activation energy than the one required to form a Stone-Wales defect in graphene. Therefore their future experimental observation is highly probable. The results presented here also suggest that the barrier to a conventional Stone-Wales transformation (the formation of two pentagon/heptagon pairs from four hexagons) can be significantly reduced in the vicinity of an existing defect, strengthening a recently proposed melting mechanism for graphene based on the aggregation of Stone-Wales defects. From a structural point of view, in addition to pentagons, heptagons, and octagons, these new DV reconstructions can also contain four- and nine-member rings and show a particularly large spatial extent of up to 13 rings (42 atoms) against three (14 atoms) for the original 5-8-5 defect. (authors)

  7. Transport on intermediate time scales in flows with cat's eye patterns

    Science.gov (United States)

    Pöschke, Patrick; Sokolov, Igor M.; Zaks, Michael A.; Nepomnyashchy, Alexander A.

    2017-12-01

    We consider the advection-diffusion transport of tracers in a one-parameter family of plane periodic flows where the patterns of streamlines feature regions of confined circulation in the shape of "cat's eyes," separated by meandering jets with ballistic motion inside them. By varying the parameter, we proceed from the regular two-dimensional lattice of eddies without jets to the sinusoidally modulated shear flow without eddies. When a weak thermal noise is added, i.e., at large Péclet numbers, several intermediate time scales arise, with qualitatively and quantitatively different transport properties: depending on the parameter of the flow, the initial position of a tracer, and the aging time, motion of the tracers ranges from subdiffusive to superballistic. We report on results of extensive numerical simulations of the mean-squared displacement for different initial conditions in ordinary and aged situations. These results are compared with a theory based on a Lévy walk that describes the intermediate-time ballistic regime and gives a reasonable description of the behavior for a certain class of initial conditions. The interplay of the walk process with internal circulation dynamics in the trapped state results at intermediate time scales in nonmonotonic characteristics of aging not captured by the Lévy walk model.

  8. Dancing to CHANGA: a self-consistent prediction for close SMBH pair formation time-scales following galaxy mergers

    Science.gov (United States)

    Tremmel, M.; Governato, F.; Volonteri, M.; Quinn, T. R.; Pontzen, A.

    2018-04-01

    We present the first self-consistent prediction for the distribution of formation time-scales for close supermassive black hole (SMBH) pairs following galaxy mergers. Using ROMULUS25, the first large-scale cosmological simulation to accurately track the orbital evolution of SMBHs within their host galaxies down to sub-kpc scales, we predict an average formation rate density of close SMBH pairs of 0.013 cMpc-3 Gyr-1. We find that it is relatively rare for galaxy mergers to result in the formation of close SMBH pairs with sub-kpc separation and those that do form are often the result of Gyr of orbital evolution following the galaxy merger. The likelihood and time-scale to form a close SMBH pair depends strongly on the mass ratio of the merging galaxies, as well as the presence of dense stellar cores. Low stellar mass ratio mergers with galaxies that lack a dense stellar core are more likely to become tidally disrupted and deposit their SMBH at large radii without any stellar core to aid in their orbital decay, resulting in a population of long-lived `wandering' SMBHs. Conversely, SMBHs in galaxies that remain embedded within a stellar core form close pairs in much shorter time-scales on average. This time-scale is a crucial, though often ignored or very simplified, ingredient to models predicting SMBH mergers rates and the connection between SMBH and star formation activity.

  9. Synthesis and properties of large crystal of aluminum-deficient ultrasil molecular sieve materials

    International Nuclear Information System (INIS)

    Durrani, J.; Akhtar, J.; Chughtai, N.A.; Arif, M.; Saeed, K.; Ahmed, M.; Siddique, M.

    2003-01-01

    Large crystals of aluminum-deficient and silica rich molecular sieve materials such as Silicalite-I, Silicalite-II ZSM11-B and ZSM11-Fe have been synthesized hydro thermally from the aqueous silicate gel of (R/sub 2/O -SiO/sub 2/- B/sub 2/O/sub 3/ -Fe/sub 2/O/ sub 3/ -H/sub 2/O) using PTFE-lined stainless digestion bomb. The term R is a alkyl group. The synthesized materials were identified for crystallinity, thermal stability, phase, crystal structure, morphology and unit cell dimensions using thermogravimetry (TG/DTA), differential scanning calorimetric(DSC), X-ray diffraction (XRD), scanning electron microscopy (SEM) and other analytical techniques. All product materials were found to be white crystalline and crysto-graphically pure. Surface area and particle size distribution of materials were also ascertained. /sup 57/Fe Mossbauer spectroscopic studies on as-synthesized and calcined samples have confirmed the uniform dispersion of Fe/sup 3+/ ions in the tetrahedral framework of ZSM11-Fe material. (author)

  10. Trees of unusual size: biased inference of early bursts from large molecular phylogenies.

    Directory of Open Access Journals (Sweden)

    Matthew W Pennell

    Full Text Available An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive radiations. One often-overlooked source of bias in these studies is that of sampling at the level of whole clades, as researchers tend to choose large, speciose clades to study. In this paper, we investigate the performance of common methods across the distribution of clade sizes that can be generated by a constant-rate birth-death process. Clades which are larger than expected for a given constant-rate branching process tend to show a pattern of an early burst even when both speciation and extinction rates are constant through time. All methods evaluated were susceptible to detecting this false signature when extinction was low. Under moderate extinction, both the [Formula: see text]-statistic and diversity-dependent models did not detect such a slowdown but only because the signature of a slowdown was masked by subsequent extinction. Some models which estimate time-varying speciation rates are able to detect early bursts under higher extinction rates, but are extremely prone to sampling bias. We suggest that examining clades in isolation may result in spurious inferences that rates of diversification have changed through time.

  11. Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes.

    Science.gov (United States)

    Risthaus, Tobias; Grimme, Stefan

    2013-03-12

    A new test set (S12L) containing 12 supramolecular noncovalently bound complexes is presented and used to evaluate seven different methods to account for dispersion in DFT (DFT-D3, DFT-D2, DFT-NL, XDM, dDsC, TS-vdW, M06-L) at different basis set levels against experimental, back-corrected reference energies. This allows conclusions about the performance of each method in an explorative research setting on "real-life" problems. Most DFT methods show satisfactory performance but, due to the largeness of the complexes, almost always require an explicit correction for the nonadditive Axilrod-Teller-Muto three-body dispersion interaction to get accurate results. The necessity of using a method capable of accounting for dispersion is clearly demonstrated in that the two-body dispersion contributions are on the order of 20-150% of the total interaction energy. MP2 and some variants thereof are shown to be insufficient for this while a few tested D3-corrected semiempirical MO methods perform reasonably well. Overall, we suggest the use of this benchmark set as a "sanity check" against overfitting to too small molecular cases.

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

    International Nuclear Information System (INIS)

    Schwerdtfeger, Christine A.; Soudackov, Alexander V.; Hammes-Schiffer, Sharon

    2014-01-01

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

  13. Molecular and Clinical Characterization of Albinism in a Large Cohort of Italian Patients

    Science.gov (United States)

    Gargiulo, Annagiusi; Testa, Francesco; Rossi, Settimio; Di Iorio, Valentina; Fecarotta, Simona; de Berardinis, Teresa; Iovine, Antonello; Magli, Adriano; Signorini, Sabrina; Fazzi, Elisa; Galantuomo, Maria Silvana; Fossarello, Maurizio; Montefusco, Sandro; Ciccodicola, Alfredo; Neri, Alberto; Macaluso, Claudio; Simonelli, Francesca; Surace, Enrico Maria

    2011-01-01

    Purpose. The purpose of this study was to identify the molecular basis of albinism in a large cohort of Italian patients showing typical ocular landmarks of the disease and to provide a full characterization of the clinical ophthalmic manifestations. Methods. DNA samples from 45 patients with ocular manifestations of albinism were analyzed by direct sequencing analysis of five genes responsible for albinism: TYR, P, TYRP1, SLC45A2 (MATP), and OA1. All patients studied showed a variable degree of skin and hair hypopigmentation. Eighteen patients with distinct mutations in each gene associated with OCA were evaluated by detailed ophthalmic analysis, optical coherence tomography (OCT), and fundus autofluorescence. Results. Disease-causing mutations were identified in more than 95% of analyzed patients with OCA (28/45 [62.2%] cases with two or more mutations; 15/45 [33.3%] cases with one mutation). Thirty-five different mutant alleles were identified of which 15 were novel. Mutations in TYR were the most frequent (73.3%), whereas mutations in P occurred more rarely (13.3%) than previously reported. Novel mutations were also identified in rare loci such as TYRP1 and MATP. Mutations in the OA1 gene were not detected. Clinical assessment revealed that patients with iris and macular pigmentation had significantly higher visual acuity than did severe hypopigmented phenotypes. Conclusions. TYR gene mutations represent a relevant cause of oculocutaneous albinism in Italy, whereas mutations in P present a lower frequency than that found in other populations. Clinical analysis revealed that the severity of the ocular manifestations depends on the degree of retinal pigmentation. PMID:20861488

  14. Large turbulent reservoirs of cold molecular gas around high-redshift starburst galaxies.

    Science.gov (United States)

    Falgarone, E; Zwaan, M A; Godard, B; Bergin, E; Ivison, R J; Andreani, P M; Bournaud, F; Bussmann, R S; Elbaz, D; Omont, A; Oteo, I; Walter, F

    2017-08-24

    Starburst galaxies at the peak of cosmic star formation are among the most extreme star-forming engines in the Universe, producing stars over about 100 million years (ref. 2). The star-formation rates of these galaxies, which exceed 100 solar masses per year, require large reservoirs of cold molecular gas to be delivered to their cores, despite strong feedback from stars or active galactic nuclei. Consequently, starburst galaxies are ideal for studying the interplay between this feedback and the growth of a galaxy. The methylidyne cation, CH + , is a most useful molecule for such studies because it cannot form in cold gas without suprathermal energy input, so its presence indicates dissipation of mechanical energy or strong ultraviolet irradiation. Here we report the detection of CH + (J = 1-0) emission and absorption lines in the spectra of six lensed starburst galaxies at redshifts near 2.5. This line has such a high critical density for excitation that it is emitted only in very dense gas, and is absorbed in low-density gas. We find that the CH + emission lines, which are broader than 1,000 kilometres per second, originate in dense shock waves powered by hot galactic winds. The CH + absorption lines reveal highly turbulent reservoirs of cool (about 100 kelvin), low-density gas, extending far (more than 10 kiloparsecs) outside the starburst galaxies (which have radii of less than 1 kiloparsec). We show that the galactic winds sustain turbulence in the 10-kiloparsec-scale environments of the galaxies, processing these environments into multiphase, gravitationally bound reservoirs. However, the mass outflow rates are found to be insufficient to balance the star-formation rates. Another mass input is therefore required for these reservoirs, which could be provided by ongoing mergers or cold-stream accretion. Our results suggest that galactic feedback, coupled jointly to turbulence and gravity, extends the starburst phase of a galaxy instead of quenching it.

  15. Past and future changes in streamflow in the U.S. Midwest: Bridging across time scales

    Science.gov (United States)

    Villarini, G.; Slater, L. J.; Salvi, K. A.

    2017-12-01

    Streamflows have increased notably across the U.S. Midwest over the past century, principally due to changes in precipitation and land use / land cover. Improving our understanding of the physical drivers that are responsible for the observed changes in discharge may enhance our capability of predicting and projecting these changes, and may have large implications for water resources management over this area. This study will highlight our efforts towards the statistical attribution of changes in discharge across the U.S. Midwest, with analyses performed at the seasonal scale from low to high flows. The main drivers of changing streamflows that we focus on are: urbanization, agricultural land cover, basin-averaged temperature, basin-averaged precipitation, and antecedent soil moisture. Building on the insights from this attribution, we will examine the potential predictability of streamflow across different time scales, with lead times ranging from seasonal to decadal, and discuss a potential path forward for engineering design for future conditions.

  16. Theoretical Modeling of Molecular Mechanisms, Time Scales and Strains in Prion Diseases

    Science.gov (United States)

    2008-01-01

    106 46 (Lou Gehrig’s (20% of cases) stress all ALS) disease)53 Type II diabetes54 IAPP ? High ( obesity 14 106 per year (U.S.) 40 trigger...and in enhancing conversion kinetics for inherited forms of the disease and explain resistance (for canines ) involving hypothesized coupling to...bovine spongiform encephalopathy (BSE) prions in England through contaminated protein supplements, canines , cervids, and pigs appear to have escaped

  17. Long-Time Data Storage: Relevant Time Scales

    Directory of Open Access Journals (Sweden)

    Miko C. Elwenspoek

    2011-02-01

    Full Text Available Dynamic processes relevant for long-time storage of information about human kind are discussed, ranging from biological and geological processes to the lifecycle of stars and the expansion of the universe. Major results are that life will end ultimately and the remaining time that the earth is habitable for complex life is about half a billion years. A system retrieved within the next million years will be read by beings very closely related to Homo sapiens. During this time the surface of the earth will change making it risky to place a small number of large memory systems on earth; the option to place it on the moon might be more favorable. For much longer timescales both options do not seem feasible because of geological processes on the earth and the flux of small meteorites to the moon.

  18. Time scales for dissolution of calcite fracture fillings and implications for saturated zone radionuclide transport at Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Winterle, J.R.; Murphy, W.M.

    1999-01-01

    An analysis was performed to estimate time scales for dissolution of calcite fracture fillings in the fractured tuff aquifer that underlies Yucca Mountain (YM), Nevada, where groundwater is chemically undersaturated with respect to calcite. The impetus for this analysis originates from speculation that undissolved calcite in the saturated zone is evidence for limited diffusive exchange between fracture and matrix waters. Assuming that matrix diffusion is the rate-limiting process, the time scale for dissolution of calcite fracture fillings depends on the amount of calcite initially deposited, the distance between flowing fractures, the degree of chemical disequilibrium, and the rate of diffusion. Assuming geochemistry of J-13 well water in free-flowing fractures, estimated time scales for complete dissolution of matrix-entrapped calcite range from about 10 4 yr for a 2 mm-thick deposit located 1 m from a flowing fracture, to over 10 7 yr for a 2 cm-thick deposit located 100 m from a flowing fracture. The authors conclude that, given the geochemical and hydrologic characteristics observed at YM, the persistence of calcite minerals over geologic time scales in aquifers where flowing water is under-saturated with calcite does not necessarily preclude matrix diffusion as a dilution mechanism. However, the model suggests that the effective spacing between flowing fractures may be large enough to diminish the overall benefit of matrix diffusion to proposed high-level waste repository performance

  19. Neural Computations in a Dynamical System with Multiple Time Scales

    Directory of Open Access Journals (Sweden)

    Yuanyuan Mi

    2016-09-01

    Full Text Available Neural systems display rich short-term dynamics at various levels, e.g., spike-frequencyadaptation (SFA at single neurons, and short-term facilitation (STF and depression (STDat neuronal synapses. These dynamical features typically covers a broad range of time scalesand exhibit large diversity in different brain regions. It remains unclear what the computationalbenefit for the brain to have such variability in short-term dynamics is. In this study, we proposethat the brain can exploit such dynamical features to implement multiple seemingly contradictorycomputations in a single neural circuit. To demonstrate this idea, we use continuous attractorneural network (CANN as a working model and include STF, SFA and STD with increasing timeconstants in their dynamics. Three computational tasks are considered, which are persistent activity,adaptation, and anticipative tracking. These tasks require conflicting neural mechanisms, andhence cannot be implemented by a single dynamical feature or any combination with similar timeconstants. However, with properly coordinated STF, SFA and STD, we show that the network isable to implement the three computational tasks concurrently. We hope this study will shed lighton the understanding of how the brain orchestrates its rich dynamics at various levels to realizediverse cognitive functions.

  20. Time scales of transient enhanced diffusion: Free and clustered interstitials

    Science.gov (United States)

    Cowern, N. E. B.; Huizing, H. G. A.; Stolk, P. A.; Visser, C. C. G.; de Kruif, R. C. M.; Kyllesbech Larsen, K.; Privitera, V.; Nanver, L. K.; Crans, W.

    1996-12-01

    Transient enhanced diffusion (TED) and electrical activation after nonamorphizing Si implantations into lightly B-doped Si multilayers shows two distinct timescales, each related to a different class of interstitial defect. At 700°C, ultrafast TED occurs within the first 15 s with a B diffusivity enhancement of > 2 × 10 5. Immobile clustered B is present at low concentration levels after the ultrafast transient and persists for an extended period (˜ 10 2-10 3 s). The later phase of TED exhibits a near-constant diffusivity enhancement of ≈ 1 × 10 4, consistent with interstitial injection controlled by dissolving {113} interstitial clusters. The relative contributions of the ultrafast and regular TED regimes to the final diffusive broadening of the B profile depends on the proportion of interstitials that escape capture by {113} clusters growing within the implant damage region upon annealing. Our results explain the ultrafast TED recently observed after medium-dose B implantation. In that case there are enough B atoms to trap a large proportion of interstitials in SiB clusters, and the remaining interstitials contribute to TED without passing through an intermediate {113} defect stage. The data on the ultrafast TED pulse allows us to extract lower limits for the diffusivities of the Si interstitial ( DI > 2 × 10 -10 cm 2s -1) and the B interstitial(cy) defect ( DBi > 2 × 10 -13 cm 2s -1) at 700°C.

  1. Structure and dating errors in the geologic time scale and periodicity in mass extinctions

    Science.gov (United States)

    Stothers, Richard B.

    1989-01-01

    Structure in the geologic time scale reflects a partly paleontological origin. As a result, ages of Cenozoic and Mesozoic stage boundaries exhibit a weak 28-Myr periodicity that is similar to the strong 26-Myr periodicity detected in mass extinctions of marine life by Raup and Sepkoski. Radiometric dating errors in the geologic time scale, to which the mass extinctions are stratigraphically tied, do not necessarily lessen the likelihood of a significant periodicity in mass extinctions, but do spread the acceptable values of the period over the range 25-27 Myr for the Harland et al. time scale or 25-30 Myr for the DNAG time scale. If the Odin time scale is adopted, acceptable periods fall between 24 and 33 Myr, but are not robust against dating errors. Some indirect evidence from independently-dated flood-basalt volcanic horizons tends to favor the Odin time scale.

  2. Large resistance change on magnetic tunnel junction based molecular spintronics devices

    Science.gov (United States)

    Tyagi, Pawan; Friebe, Edward

    2018-05-01

    Molecular bridges covalently bonded to two ferromagnetic electrodes can transform ferromagnetic materials and produce intriguing spin transport characteristics. This paper discusses the impact of molecule induced strong coupling on the spin transport. To study molecular coupling effect the octametallic molecular cluster (OMC) was bridged between two ferromagnetic electrodes of a magnetic tunnel junction (Ta/Co/NiFe/AlOx/NiFe/Ta) along the exposed side edges. OMCs induced strong inter-ferromagnetic electrode coupling to yield drastic changes in transport properties of the magnetic tunnel junction testbed at the room temperature. These OMCs also transformed the magnetic properties of magnetic tunnel junctions. SQUID and ferromagnetic resonance studies provided insightful data to explain transport studies on the magnetic tunnel junction based molecular spintronics devices.

  3. A Study on Time-Scales Ratio and Turbulent Prandtl Number in Ducts of Industrial Applications

    DEFF Research Database (Denmark)

    Rokni, Masoud

    2006-01-01

    is solved using a two-equation heat flux model. The computed results compare satisfactory with the available experimental data. The time-scale ratio R is defined as the ratio between the dynamic time-scale (k/ε) and the scalar time-scale(0.5θθ/εθ). Based on existing DNS data and calculations in this work...... of heat exchangers for various applications area....

  4. Time scales of solar microwave bursts and scenarios of flare enregy release

    International Nuclear Information System (INIS)

    Krueger, A.; Kliem, B.; Hildebrandt, J.

    1989-01-01

    Based on earlier observational evidence that characteristic time scales of different solar microwave burst types are distributed over a wide range (10 -3 -10 4 sec), different mechanisms of energy release have been considered to account for the impulsive flux increase (time scale 3 sec). Among different competing processes the coalescence instability is found to be a promising candidate to combine sufficiently short time scales with substantial energy release. (author). 20 refs.; 1 fig

  5. Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations

    Science.gov (United States)

    Salvalaglio, Matteo; Tiwary, Pratyush; Maggioni, Giovanni Maria; Mazzotti, Marco; Parrinello, Michele

    2016-12-01

    Condensation of a liquid droplet from a supersaturated vapour phase is initiated by a prototypical nucleation event. As such it is challenging to compute its rate from atomistic molecular dynamics simulations. In fact at realistic supersaturation conditions condensation occurs on time scales that far exceed what can be reached with conventional molecular dynamics methods. Another known problem in this context is the distortion of the free energy profile associated to nucleation due to the small, finite size of typical simulation boxes. In this work the problem of time scale is addressed with a recently developed enhanced sampling method while contextually correcting for finite size effects. We demonstrate our approach by studying the condensation of argon, and showing that characteristic nucleation times of the order of magnitude of hours can be reliably calculated. Nucleation rates spanning a range of 10 orders of magnitude are computed at moderate supersaturation levels, thus bridging the gap between what standard molecular dynamics simulations can do and real physical systems.

  6. Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor

    KAUST Repository

    Bagchi, Samik; Lamendella, Regina; Strutt, Steven; Van Loosdrecht, Mark C. M.; Saikaly, Pascal

    2016-01-01

    to formation of large granules. Size distribution analysis revealed the spatial distribution of granules in which large granules having higher abundance of anammox bacteria (genus Brocadia) dominated the bottom biomass. Metatranscriptomics analysis detected all

  7. Integrating experimental and simulation length and time scales in mechanistic studies of friction

    International Nuclear Information System (INIS)

    Sawyer, W G; Perry, S S; Phillpot, S R; Sinnott, S B

    2008-01-01

    Friction is ubiquitous in all aspects of everyday life and has consequently been under study for centuries. Classical theories of friction have been developed and used to successfully solve numerous tribological problems. However, modern applications that involve advanced materials operating under extreme environments can lead to situations where classical theories of friction are insufficient to describe the physical responses of sliding interfaces. Here, we review integrated experimental and computational studies of atomic-scale friction and wear at solid-solid interfaces across length and time scales. The influence of structural orientation in the case of carbon nanotube bundles, and molecular orientation in the case of polymer films of polytetrafluoroethylene and polyethylene, on friction and wear are discussed. In addition, while friction in solids is generally considered to be athermal, under certain conditions thermally activated friction is observed for polymers, carbon nanotubes and graphite. The conditions under which these transitions occur, and their proposed origins, are discussed. Lastly, a discussion of future directions is presented

  8. A study of photothermal laser ablation of various polymers on microsecond time scales.

    Science.gov (United States)

    Kappes, Ralf S; Schönfeld, Friedhelm; Li, Chen; Golriz, Ali A; Nagel, Matthias; Lippert, Thomas; Butt, Hans-Jürgen; Gutmann, Jochen S

    2014-01-01

    To analyze the photothermal ablation of polymers, we designed a temperature measurement setup based on spectral pyrometry. The setup allows to acquire 2D temperature distributions with 1 μm size and 1 μs time resolution and therefore the determination of the center temperature of a laser heating process. Finite element simulations were used to verify and understand the heat conversion and heat flow in the process. With this setup, the photothermal ablation of polystyrene, poly(α-methylstyrene), a polyimide and a triazene polymer was investigated. The thermal stability, the glass transition temperature Tg and the viscosity above Tg were governing the ablation process. Thermal decomposition for the applied laser pulse of about 10 μs started at temperatures similar to the start of decomposition in thermogravimetry. Furthermore, for polystyrene and poly(α-methylstyrene), both with a Tg in the range between room and decomposition temperature, ablation already occurred at temperatures well below the decomposition temperature, only at 30-40 K above Tg. The mechanism was photomechanical, i.e. a stress due to the thermal expansion of the polymer was responsible for ablation. Low molecular weight polymers showed differences in photomechanical ablation, corresponding to their lower Tg and lower viscosity above the glass transition. However, the difference in ablated volume was only significant at higher temperatures in the temperature regime for thermal decomposition at quasi-equilibrium time scales.

  9. EFFECTS OF LARGE-SCALE POULTRY FARMS ON AQUATIC MICROBIAL COMMUNITIES: A MOLECULAR INVESTIGATION.

    Science.gov (United States)

    The effects of large-scale poultry production operations on water quality and human health are largely unknown. Poultry litter is frequently applied as fertilizer to agricultural lands adjacent to large poultry farms. Run-off from the land introduces a variety of stressors into t...

  10. Variations in VLT/UVES-based OH rotational temperatures for time scales from hours to 15 years

    Science.gov (United States)

    Noll, Stefan; Kimeswenger, Stefan; Proxauf, Bastian; Kausch, Wolfgang; Unterguggenberger, Stefanie; Jones, Amy M.

    2017-04-01

    Hydroxyl (OH) emission is an important tracer of the climate, chemistry, and dynamics of the Earth's mesopause region. However, the relation of intensity variations in different OH lines is not well understood yet. This is critical for the most popular use of OH lines: the estimate of ambient temperatures based on transitions at low rotational levels of the same band. It is possible that the measured variability of the derived rotational temperature does not coincide with changes in the ambient temperature. Such differences can be caused by varying deviations from the local thermodynamic equilibrium (LTE) for the population distribution over the considered rotational levels. The non-LTE effects depend on the ratio of the thermalising collisions (mostly related to molecular oxygen) and competing radiative transitions or collisions without thermalisation of the rotational level distribution. Therefore, significant changes in the vertical structure of excited OH and its main quenchers can affect the temperature measurements. We have investigated the variability of OH rotational temperatures and the corresponding contributions of non-LTE effects for different OH bands and time scales up to 15 years based on data of the high-resolution echelle spectrograph UVES at the Very Large Telescope at Cerro Paranal in Chile. In order to link the measured rotational temperatures with the structure of the OH emission layer, we have also studied OH emission and kinetic temperature profiles from the multi-channel radiometer SABER on the TIMED satellite taken between 2002 and 2015. The results show that non-LTE contributions can significantly affect the OH rotational temperatures. Their variations can be especially strong during the night and for high upper vibrational levels of the transitions, where amplitudes of several Kelvins can be measured. They appear to be weak if long-term variations such as those caused by the solar cycle are investigated. These differences in the response

  11. Measures of spike train synchrony for data with multiple time scales

    NARCIS (Netherlands)

    Satuvuori, Eero; Mulansky, Mario; Bozanic, Nebojsa; Malvestio, Irene; Zeldenrust, Fleur; Lenk, Kerstin; Kreuz, Thomas

    2017-01-01

    Background Measures of spike train synchrony are widely used in both experimental and computational neuroscience. Time-scale independent and parameter-free measures, such as the ISI-distance, the SPIKE-distance and SPIKE-synchronization, are preferable to time scale parametric measures, since by

  12. Qualitative aspects of Volterra integro-dynamic system on time scales

    Directory of Open Access Journals (Sweden)

    Vasile Lupulescu

    2013-01-01

    Full Text Available This paper deals with the resolvent, asymptotic stability and boundedness of the solution of time-varying Volterra integro-dynamic system on time scales in which the coefficient matrix is not necessarily stable. We generalize at time scale some known properties about asymptotic behavior and boundedness from the continuous case. Some new results for discrete case are obtained.

  13. Large-scale molecular dynamics simulations of self-assembling systems.

    Science.gov (United States)

    Klein, Michael L; Shinoda, Wataru

    2008-08-08

    Relentless increases in the size and performance of multiprocessor computers, coupled with new algorithms and methods, have led to novel applications of simulations across chemistry. This Perspective focuses on the use of classical molecular dynamics and so-called coarse-grain models to explore phenomena involving self-assembly in complex fluids and biological systems.

  14. The consistency of large concerted motions in proteins in molecular dynamics simulations

    NARCIS (Netherlands)

    de Groot, B.L.; van Aalten, D.M.F.; Amadei, A; Berendsen, H.J.C.

    1996-01-01

    A detailed investigation is presented into the effect of limited sampling time and small changes in the force field on molecular dynamics simulations of a protein. Thirteen independent simulations of the B1 IgG-binding domain of streptococcal protein G were performed, with small changes in the

  15. Large Scale Molecular Simulation of Nanoparticle-Biomolecule Interactions and their Implications in Nanomedicine

    Science.gov (United States)

    Zhou, Ruhong

    Nanoscale particles have become promising materials in various biomedical applications, however, in order to stimulate and facilitate these applications, there is an urgent need for a better understanding of their biological effects and related molecular mechanism/physics as well. In this talk, I will discuss some of our recent works, mostly molecular modelling, on nanotoxicity and their implications in de novo design of nanomedicine. We show that carbon-based nanoparticles (carbon nanotubes, graphene nanosheets, and fullerenes) can interact and disrupt the structures and functions of many important proteins. The hydrophobic interactions between the carbon nanotubes and hydrophobic residues, particularly aromatic residues through the so-called π- π stacking interactions, are found to play key roles. Meanwhile, metallofullerenol Gd@C82(OH)22 is found to inhibit tumour growth and metastases with both experimental and theoretical approaches. Graphene and graphene oxide (GO) nanosheets show strong destructive interactions to E. coli cell membranes (antibacterial activity) and A β amyloid fibrils (anti-AD, Alzheimer's disease, capability) with unique molecular mechanisms, while on the other hand, they also show a strong supportive role in enzyme immobilisation such as lipases through lid opening. In particular, the lid opening is assisted by lipase's sophisticated interaction with GO, which allows the adsorbed lipase to enhance its enzyme activity. The lipase enzymatic activity can be further optimized through fine tuning of the GO surface hydrophobicity. These findings might provide a better understanding of ``nanotoxicity'' at the molecular level with implications in de novo nanomedicine design.

  16. Exploiting large-pore metal-organic frameworks for separations through entropic molecular mechanisms

    NARCIS (Netherlands)

    Torres-Knoop, A.; Dubbeldam, D.

    2015-01-01

    We review the molecular mechanisms behind adsorption and the separations of mixtures in metal-organic frameworks and zeolites. Separation mechanisms can be based on differences in the affinity of the adsorbate with the framework and on entropic effects. To develop next-generation adsorbents, the

  17. A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.

    Science.gov (United States)

    Hirano, Toshiyuki; Sato, Fumitoshi

    2014-07-28

    We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.

  18. Electronic sputtering of large organic molecules and its application in bio molecular mass spectrometry

    International Nuclear Information System (INIS)

    Sundqvist, B.U.R.

    1992-01-01

    This is a review of research which has its origin in the discovery of Plasma Desorption Mass Spectrometry (PDMS). Two main fields of research have developed, namely fundamental studies of the ejection process at fast ion impact and studies of applications of the new mass spectrometric technique. In this review the emphasis will be on the process of electronic sputtering of organic solids but also applications of this process in bio molecular mass spectrometry will be discussed. (author)

  19. MicroRNA Expression Profiling Identifies Molecular Diagnostic Signatures for Anaplastic Large Cell Lymphoma

    DEFF Research Database (Denmark)

    Liu, Cuiling; Iqbal, Javeed; Teruya-Feldstein, Julie

    2013-01-01

    distinct clustering of ALCL, PTCL-NOS, and the AITL subtype of PTCL. Cases of ALK(+) ALCL and ALK(-) ALCL were interspersed in unsupervised analysis, suggesting a close relationship at the molecular level. We identified an miRNA signature of 7 miRNAs (5 upregulated: miR-512-3p, miR-886-5p, miR-886-3p, mi...

  20. LARGE-SCALE CO MAPS OF THE LUPUS MOLECULAR CLOUD COMPLEX

    International Nuclear Information System (INIS)

    Tothill, N. F. H.; Loehr, A.; Stark, A. A.; Lane, A. P.; Harnett, J. I.; Bourke, T. L.; Myers, P. C.; Parshley, S. C.; Wright, G. A.; Walker, C. K.

    2009-01-01

    Fully sampled degree-scale maps of the 13 CO 2-1 and CO 4-3 transitions toward three members of the Lupus Molecular Cloud Complex-Lupus I, III, and IV-trace the column density and temperature of the molecular gas. Comparison with IR extinction maps from the c2d project requires most of the gas to have a temperature of 8-10 K. Estimates of the cloud mass from 13 CO emission are roughly consistent with most previous estimates, while the line widths are higher, around 2 km s -1 . CO 4-3 emission is found throughout Lupus I, indicating widespread dense gas, and toward Lupus III and IV. Enhanced line widths at the NW end and along the edge of the B 228 ridge in Lupus I, and a coherent velocity gradient across the ridge, are consistent with interaction between the molecular cloud and an expanding H I shell from the Upper-Scorpius subgroup of the Sco-Cen OB Association. Lupus III is dominated by the effects of two HAe/Be stars, and shows no sign of external influence. Slightly warmer gas around the core of Lupus IV and a low line width suggest heating by the Upper-Centaurus-Lupus subgroup of Sco-Cen, without the effects of an H I shell.

  1. THE SECOND SURVEY OF THE MOLECULAR CLOUDS IN THE LARGE MAGELLANIC CLOUD BY NANTEN. II. STAR FORMATION

    International Nuclear Information System (INIS)

    Kawamura, Akiko; Mizuno, Yoji; Minamidani, Tetsuhiro; Mizuno, Norikazu; Onishi, Toshikazu; Fukui, Yasuo; Fillipovic, Miroslav D.; Staveley-Smith, Lister; Kim, Sungeun; Mizuno, Akira

    2009-01-01

    We studied star formation activities in the molecular clouds in the Large Magellanic Cloud. We have utilized the second catalog of 272 molecular clouds obtained by NANTEN to compare the cloud distribution with signatures of massive star formation including stellar clusters, and optical and radio H II regions. We find that the molecular clouds are classified into three types according to the activities of massive star formation: Type I shows no signature of massive star formation; Type II is associated with relatively small H II region(s); and Type III with both H II region(s) and young stellar cluster(s). The radio continuum sources were used to confirm that Type I giant molecular clouds (GMCs) do not host optically hidden H II regions. These signatures of massive star formation show a good spatial correlation with the molecular clouds in the sense that they are located within ∼100 pc of the molecular clouds. Among possible ideas to explain the GMC types, we favor that the types indicate an evolutionary sequence; i.e., the youngest phase is Type I, followed by Type II, and the last phase is Type III, where the most active star formation takes place leading to cloud dispersal. The number of the three types of GMCs should be proportional to the timescale of each evolutionary stage if a steady state of massive star and cluster formation is a good approximation. By adopting the timescale of the youngest stellar clusters, 10 Myr, we roughly estimate the timescales of Types I, II, and III to be 6 Myr, 13 Myr, and 7 Myr, respectively, corresponding to a lifetime of 20-30 Myr for the GMCs with a mass above the completeness limit, 5 x 10 4 M sun .

  2. The sensitivity of the atmospheric branch of the global water cycle to temperature fluctuations at synoptic to decadal time-scales in different satellite- and model-based products

    Science.gov (United States)

    Nogueira, Miguel

    2018-02-01

    Spectral analysis of global-mean precipitation, P, evaporation, E, precipitable water, W, and surface temperature, Ts, revealed significant variability from sub-daily to multi-decadal time-scales, superposed on high-amplitude diurnal and yearly peaks. Two distinct regimes emerged from a transition in the spectral exponents, β. The weather regime covering time-scales 1-2 years, while at time-scales global-ocean and full-globe averages, ρDCCA showed large spread of the C-C importance for P and E variability amongst different datasets at multi-year time-scales, ranging from negligible (governing mechanisms.

  3. Calibration of the Ångström-Prescott coefficients (a, b) under different time scales and their impacts in estimating global solar radiation in the Yellow River basin

    DEFF Research Database (Denmark)

    Liu, Xiaoyling; Mei, Xurong; Li, Yuzhong

    2009-01-01

    is the calibration of the locally specific coefficients. Although the coefficients have been extensively studied and calibrated in many places over the world, their relations with time scale are much less investigated. This paper addressed the variation in these coefficients caused by time scale and how...... location. However, the large effect of time scales on a and b produced no significant impact on the estimation accuracy of Rs because of the conservative response of the sum a + b to time scale. In this sense, the coefficients calibrated at daily scale are interchangeable with those calibrated at monthly...

  4. Reduced linear noise approximation for biochemical reaction networks with time-scale separation: The stochastic tQSSA+

    Science.gov (United States)

    Herath, Narmada; Del Vecchio, Domitilla

    2018-03-01

    Biochemical reaction networks often involve reactions that take place on different time scales, giving rise to "slow" and "fast" system variables. This property is widely used in the analysis of systems to obtain dynamical models with reduced dimensions. In this paper, we consider stochastic dynamics of biochemical reaction networks modeled using the Linear Noise Approximation (LNA). Under time-scale separation conditions, we obtain a reduced-order LNA that approximates both the slow and fast variables in the system. We mathematically prove that the first and second moments of this reduced-order model converge to those of the full system as the time-scale separation becomes large. These mathematical results, in particular, provide a rigorous justification to the accuracy of LNA models derived using the stochastic total quasi-steady state approximation (tQSSA). Since, in contrast to the stochastic tQSSA, our reduced-order model also provides approximations for the fast variable stochastic properties, we term our method the "stochastic tQSSA+". Finally, we demonstrate the application of our approach on two biochemical network motifs found in gene-regulatory and signal transduction networks.

  5. Sensory information in local field potentials and spikes from visual and auditory cortices: time scales and frequency bands.

    Science.gov (United States)

    Belitski, Andrei; Panzeri, Stefano; Magri, Cesare; Logothetis, Nikos K; Kayser, Christoph

    2010-12-01

    Studies analyzing sensory cortical processing or trying to decode brain activity often rely on a combination of different electrophysiological signals, such as local field potentials (LFPs) and spiking activity. Understanding the relation between these signals and sensory stimuli and between different components of these signals is hence of great interest. We here provide an analysis of LFPs and spiking activity recorded from visual and auditory cortex during stimulation with natural stimuli. In particular, we focus on the time scales on which different components of these signals are informative about the stimulus, and on the dependencies between different components of these signals. Addressing the first question, we find that stimulus information in low frequency bands (50 Hz), in contrast, is scale dependent, and is larger when the energy is averaged over several hundreds of milliseconds. Indeed, combined analysis of signal reliability and information revealed that the energy of slow LFP fluctuations is well related to the stimulus even when considering individual or few cycles, while the energy of fast LFP oscillations carries information only when averaged over many cycles. Addressing the second question, we find that stimulus information in different LFP bands, and in different LFP bands and spiking activity, is largely independent regardless of time scale or sensory system. Taken together, these findings suggest that different LFP bands represent dynamic natural stimuli on distinct time scales and together provide a potentially rich source of information for sensory processing or decoding brain activity.

  6. Global Exponential Stability of Delayed Cohen-Grossberg BAM Neural Networks with Impulses on Time Scales

    Directory of Open Access Journals (Sweden)

    Yongkun Li

    2009-01-01

    Full Text Available Based on the theory of calculus on time scales, the homeomorphism theory, Lyapunov functional method, and some analysis techniques, sufficient conditions are obtained for the existence, uniqueness, and global exponential stability of the equilibrium point of Cohen-Grossberg bidirectional associative memory (BAM neural networks with distributed delays and impulses on time scales. This is the first time applying the time-scale calculus theory to unify the discrete-time and continuous-time Cohen-Grossberg BAM neural network with impulses under the same framework.

  7. Magnetically enhanced triode etching of large area silicon membranes in a molecular bromine plasma

    International Nuclear Information System (INIS)

    Wolfe, J.C.; Sen, S.; Pendharkar, S.V.; Mauger, P.; Shimkunas, A.R.

    1992-01-01

    The optimization of a process for etching 125 mm silicon membranes formed on 150 mm wafers and bonded to Pyrex rings is discussed. A magnetically enhanced triode etching system was designed to provide an intense, remote plasma surrounding the membrane while, at the same time, suppressing the discharge over the membrane itself. For the optimized molecular bromine process, the silicon etch rate is 40 nm/min and the selectivity relative to SiO 2 is 160:1. 14 refs., 6 figs

  8. Ozone time scale decomposition and trend assessment from surface observations in National Parks of the United States

    Science.gov (United States)

    Mao, H.; McGlynn, D. F.; Wu, Z.; Sive, B. C.

    2017-12-01

    A time scale decomposition technique, the Ensemble Empirical Mode Decomposition (EEMD), has been employed to decompose the time scales in long-term ozone measurement data at 24 US National Park Service sites. Time scales of interest include the annual cycle, variability by large scale climate oscillations, and the long-term trend. The implementation of policy regulations was found to have had a greater effect on sites nearest to urban regions. Ozone daily mean values increased until around the late 1990s followed by decreasing trends during the ensuing decades for sites in the East, southern California, and northwestern Washington. Sites in the Midwest did not experience a reversal of trends from positive to negative until the mid- to late 2000s. The magnitude of the annual amplitude decreased for nine sites and increased for three sites. Stronger decreases in the annual amplitude occurred in the East, with more sites in the East experiencing decreases in annual amplitude than in the West. The date of annual ozone peaks and minimums has changed for 12 sites in total, but those with a shift in peak date did not necessarily have a shift in the trough date. There appeared to be a link between peak dates occurring earlier and a decrease in the annual amplitude. This is likely related to a decrease in ozone titration due to NOx emission reductions. Furthermore, it was found that the shift in the Pacific Decadal Oscillation (PDO) regime from positive to negative in 1998-1999 resulting in an increase in occurrences of La Niña-like conditions had the effect of directing more polluted air masses from East Asia to higher latitudes over North America. This change in PDO regime was likely one main factor causing the increase in ozone concentrations on all time scales at an Alaskan site DENA-HQ.

  9. Saharan Dust Deposition May Affect Phytoplankton Growth in the Mediterranean Sea at Ecological Time Scales

    Science.gov (United States)

    Gallisai, Rachele; Peters, Francesc; Volpe, Gianluca; Basart, Sara; Baldasano, José Maria

    2014-01-01

    The surface waters of the Mediterranean Sea are extremely poor in the nutrients necessary for plankton growth. At the same time, the Mediterranean Sea borders with the largest and most active desert areas in the world and the atmosphere over the basin is subject to frequent injections of mineral dust particles. We describe statistical correlations between dust deposition over the Mediterranean Sea and surface chlorophyll concentrations at ecological time scales. Aerosol deposition of Saharan origin may explain 1 to 10% (average 5%) of seasonally detrended chlorophyll variability in the low nutrient-low chlorophyll Mediterranean. Most of the statistically significant correlations are positive with main effects in spring over the Eastern and Central Mediterranean, conforming to a view of dust events fueling needed nutrients to the planktonic community. Some areas show negative effects of dust deposition on chlorophyll, coinciding with regions under a large influence of aerosols from European origin. The influence of dust deposition on chlorophyll dynamics may become larger in future scenarios of increased aridity and shallowing of the mixed layer. PMID:25333783

  10. Extending the length and time scales of Gram–Schmidt Lyapunov vector computations

    Energy Technology Data Exchange (ETDEWEB)

    Costa, Anthony B., E-mail: acosta@northwestern.edu [Department of Chemistry, Northwestern University, Evanston, IL 60208 (United States); Green, Jason R., E-mail: jason.green@umb.edu [Department of Chemistry, Northwestern University, Evanston, IL 60208 (United States); Department of Chemistry, University of Massachusetts Boston, Boston, MA 02125 (United States)

    2013-08-01

    Lyapunov vectors have found growing interest recently due to their ability to characterize systems out of thermodynamic equilibrium. The computation of orthogonal Gram–Schmidt vectors requires multiplication and QR decomposition of large matrices, which grow as N{sup 2} (with the particle count). This expense has limited such calculations to relatively small systems and short time scales. Here, we detail two implementations of an algorithm for computing Gram–Schmidt vectors. The first is a distributed-memory message-passing method using Scalapack. The second uses the newly-released MAGMA library for GPUs. We compare the performance of both codes for Lennard–Jones fluids from N=100 to 1300 between Intel Nahalem/Infiniband DDR and NVIDIA C2050 architectures. To our best knowledge, these are the largest systems for which the Gram–Schmidt Lyapunov vectors have been computed, and the first time their calculation has been GPU-accelerated. We conclude that Lyapunov vector calculations can be significantly extended in length and time by leveraging the power of GPU-accelerated linear algebra.

  11. Extending the length and time scales of Gram–Schmidt Lyapunov vector computations

    International Nuclear Information System (INIS)

    Costa, Anthony B.; Green, Jason R.

    2013-01-01

    Lyapunov vectors have found growing interest recently due to their ability to characterize systems out of thermodynamic equilibrium. The computation of orthogonal Gram–Schmidt vectors requires multiplication and QR decomposition of large matrices, which grow as N 2 (with the particle count). This expense has limited such calculations to relatively small systems and short time scales. Here, we detail two implementations of an algorithm for computing Gram–Schmidt vectors. The first is a distributed-memory message-passing method using Scalapack. The second uses the newly-released MAGMA library for GPUs. We compare the performance of both codes for Lennard–Jones fluids from N=100 to 1300 between Intel Nahalem/Infiniband DDR and NVIDIA C2050 architectures. To our best knowledge, these are the largest systems for which the Gram–Schmidt Lyapunov vectors have been computed, and the first time their calculation has been GPU-accelerated. We conclude that Lyapunov vector calculations can be significantly extended in length and time by leveraging the power of GPU-accelerated linear algebra

  12. Physical processes affecting turbidity in a tidal marsh across a range of time scales

    Science.gov (United States)

    Arnold, W.; Poindexter, C.

    2016-12-01

    -occurrence with semiannual tides having tidal excursions large enough to bring resuspended sediment to First Mallard. This finding underpins the importance of analyzing tidal marsh sediment fluxes over longer time scales and the crucial role that climatic and subembayment interactions can play in these sediment fluxes.

  13. Advances in the molecular diagnosis of diffuse large B-cell lymphoma in the era of precision medicine.

    Science.gov (United States)

    Araf, Shamzah; Korfi, Koorosh; Rahim, Tahrima; Davies, Andrew; Fitzgibbon, Jude

    2016-10-01

    The adoption of high-throughput technologies has led to a transformation in our ability to classify diffuse large B-cell lymphoma (DLBCL) into unique molecular subtypes. In parallel, the expansion of agents targeting key genetic and gene expression signatures has led to an unprecedented opportunity to personalize cancer therapies, paving the way for precision medicine. Areas covered: This review summarizes the key molecular subtypes of DLBCL and outlines the novel technology platforms in development to discriminate clinically relevant subtypes. Expert commentary: The application of emerging diagnostic tests into routine clinical practise is gaining momentum following the demonstration of subtype specific activity by novel agents. Co-ordinated efforts are required to ensure that these state of the art technologies provide reliable and clinically meaningful results accessible to the wider haematology community.

  14. Multiple time scale analysis of pressure oscillations in solid rocket motors

    Science.gov (United States)

    Ahmed, Waqas; Maqsood, Adnan; Riaz, Rizwan

    2018-03-01

    In this study, acoustic pressure oscillations for single and coupled longitudinal acoustic modes in Solid Rocket Motor (SRM) are investigated using Multiple Time Scales (MTS) method. Two independent time scales are introduced. The oscillations occur on fast time scale whereas the amplitude and phase changes on slow time scale. Hopf bifurcation is employed to investigate the properties of the solution. The supercritical bifurcation phenomenon is observed for linearly unstable system. The amplitude of the oscillations result from equal energy gain and loss rates of longitudinal acoustic modes. The effect of linear instability and frequency of longitudinal modes on amplitude and phase of oscillations are determined for both single and coupled modes. For both cases, the maximum amplitude of oscillations decreases with the frequency of acoustic mode and linear instability of SRM. The comparison of analytical MTS results and numerical simulations demonstrate an excellent agreement.

  15. OSCILLATION CRITERIA FOR A FOURTH ORDER SUBLINEAR DYNAMIC EQUATION ON TIME SCALE

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Some new criteria for the oscillation of a fourth order sublinear and/or linear dynamic equation on time scale are established. Our results are new for the corresponding fourth order differential equations as well as difference equations.

  16. Multiple Positive Symmetric Solutions to p-Laplacian Dynamic Equations on Time Scales

    Directory of Open Access Journals (Sweden)

    You-Hui Su

    2009-01-01

    two examples are given to illustrate the main results and their differences. These results are even new for the special cases of continuous and discrete equations, as well as in the general time-scale setting.

  17. Time scale algorithm: Definition of ensemble time and possible uses of the Kalman filter

    Science.gov (United States)

    Tavella, Patrizia; Thomas, Claudine

    1990-01-01

    The comparative study of two time scale algorithms, devised to satisfy different but related requirements, is presented. They are ALGOS(BIPM), producing the international reference TAI at the Bureau International des Poids et Mesures, and AT1(NIST), generating the real-time time scale AT1 at the National Institute of Standards and Technology. In each case, the time scale is a weighted average of clock readings, but the weight determination and the frequency prediction are different because they are adapted to different purposes. The possibility of using a mathematical tool, such as the Kalman filter, together with the definition of the time scale as a weighted average, is also analyzed. Results obtained by simulation are presented.

  18. The multiple time scales of sleep dynamics as a challenge for modelling the sleeping brain.

    Science.gov (United States)

    Olbrich, Eckehard; Claussen, Jens Christian; Achermann, Peter

    2011-10-13

    A particular property of the sleeping brain is that it exhibits dynamics on very different time scales ranging from the typical sleep oscillations such as sleep spindles and slow waves that can be observed in electroencephalogram (EEG) segments of several seconds duration over the transitions between the different sleep stages on a time scale of minutes to the dynamical processes involved in sleep regulation with typical time constants in the range of hours. There is an increasing body of work on mathematical and computational models addressing these different dynamics, however, usually considering only processes on a single time scale. In this paper, we review and present a new analysis of the dynamics of human sleep EEG at the different time scales and relate the findings to recent modelling efforts pointing out both the achievements and remaining challenges.

  19. A Dynamical System Approach Explaining the Process of Development by Introducing Different Time-scales.

    Science.gov (United States)

    Hashemi Kamangar, Somayeh Sadat; Moradimanesh, Zahra; Mokhtari, Setareh; Bakouie, Fatemeh

    2018-06-11

    A developmental process can be described as changes through time within a complex dynamic system. The self-organized changes and emergent behaviour during development can be described and modeled as a dynamical system. We propose a dynamical system approach to answer the main question in human cognitive development i.e. the changes during development happens continuously or in discontinuous stages. Within this approach there is a concept; the size of time scales, which can be used to address the aforementioned question. We introduce a framework, by considering the concept of time-scale, in which "fast" and "slow" is defined by the size of time-scales. According to our suggested model, the overall pattern of development can be seen as one continuous function, with different time-scales in different time intervals.

  20. Off-Policy Reinforcement Learning: Optimal Operational Control for Two-Time-Scale Industrial Processes.

    Science.gov (United States)

    Li, Jinna; Kiumarsi, Bahare; Chai, Tianyou; Lewis, Frank L; Fan, Jialu

    2017-12-01

    Industrial flow lines are composed of unit processes operating on a fast time scale and performance measurements known as operational indices measured at a slower time scale. This paper presents a model-free optimal solution to a class of two time-scale industrial processes using off-policy reinforcement learning (RL). First, the lower-layer unit process control loop with a fast sampling period and the upper-layer operational index dynamics at a slow time scale are modeled. Second, a general optimal operational control problem is formulated to optimally prescribe the set-points for the unit industrial process. Then, a zero-sum game off-policy RL algorithm is developed to find the optimal set-points by using data measured in real-time. Finally, a simulation experiment is employed for an industrial flotation process to show the effectiveness of the proposed method.

  1. Fission time-scale from the measurement of pre-scission light ...

    Indian Academy of Sciences (India)

    and hence can only probe a part of the fission time distribution. .... with the conclusion of recent fission time-scale measurements using the fission probability ... using the statistical model code JOANNE2 suitably modified to include the GDR ...

  2. Diffusion of hydrogen, hydrogen sulfide and large molecular weight anions in bentonite

    International Nuclear Information System (INIS)

    Eriksen, T.E.; Jacobsson, A.

    1982-01-01

    The diffusivities of HS - and H 2 have been determined from profile analysis and steady state transport experiments. The diffusivity of HS - was found to be 9x10 - 12 and 4x10xsec 1 in MX-80 and Erbsloeh bentonite respectively. The results are in fair agreement with the results earlier obtained for Cl - and I - . The H 2 diffusivity calculated from steady state transport was found to be surprisingly low (3.6x10 - 12 m 2 xsec - 1 ). Various heavy anions with molecular weights 290-30x10 3 were found to migrate through MX-80 bentonite with diffusivities in the range (2,1-0,75)x10 - 15 m 2 xsec - 1 . (Author)

  3. Parallel continuous simulated tempering and its applications in large-scale molecular simulations

    Energy Technology Data Exchange (ETDEWEB)

    Zang, Tianwu; Yu, Linglin; Zhang, Chong [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Ma, Jianpeng, E-mail: jpma@bcm.tmc.edu [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, Texas 77030 (United States)

    2014-07-28

    In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); C. Zhang and J. Ma, J. Chem. Phys. 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2–3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard-Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.

  4. Energy Decomposition Analysis Based on Absolutely Localized Molecular Orbitals for Large-Scale Density Functional Theory Calculations in Drug Design.

    Science.gov (United States)

    Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

    2016-07-12

    We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design.

  5. Time Scale Inequalities of the Ostrowski Type for Functions Differentiable on the Coordinates

    Directory of Open Access Journals (Sweden)

    Eze R. Nwaeze

    2018-01-01

    Full Text Available In 2016, some inequalities of the Ostrowski type for functions (of two variables differentiable on the coordinates were established. In this paper, we extend these results to an arbitrary time scale by means of a parameter λ∈0,1. The aforementioned results are regained for the case when the time scale T=R. Besides extension, our results are employed to the continuous and discrete calculus to get some new inequalities in this direction.

  6. Physical time scale in kinetic Monte Carlo simulations of continuous-time Markov chains.

    Science.gov (United States)

    Serebrinsky, Santiago A

    2011-03-01

    We rigorously establish a physical time scale for a general class of kinetic Monte Carlo algorithms for the simulation of continuous-time Markov chains. This class of algorithms encompasses rejection-free (or BKL) and rejection (or "standard") algorithms. For rejection algorithms, it was formerly considered that the availability of a physical time scale (instead of Monte Carlo steps) was empirical, at best. Use of Monte Carlo steps as a time unit now becomes completely unnecessary.

  7. Bounds of Double Integral Dynamic Inequalities in Two Independent Variables on Time Scales

    Directory of Open Access Journals (Sweden)

    S. H. Saker

    2011-01-01

    Full Text Available Our aim in this paper is to establish some explicit bounds of the unknown function in a certain class of nonlinear dynamic inequalities in two independent variables on time scales which are unbounded above. These on the one hand generalize and on the other hand furnish a handy tool for the study of qualitative as well as quantitative properties of solutions of partial dynamic equations on time scales. Some examples are considered to demonstrate the applications of the results.

  8. Time-scale invariance as an emergent property in a perceptron with realistic, noisy neurons.

    Science.gov (United States)

    Buhusi, Catalin V; Oprisan, Sorinel A

    2013-05-01

    In most species, interval timing is time-scale invariant: errors in time estimation scale up linearly with the estimated duration. In mammals, time-scale invariance is ubiquitous over behavioral, lesion, and pharmacological manipulations. For example, dopaminergic drugs induce an immediate, whereas cholinergic drugs induce a gradual, scalar change in timing. Behavioral theories posit that time-scale invariance derives from particular computations, rules, or coding schemes. In contrast, we discuss a simple neural circuit, the perceptron, whose output neurons fire in a clockwise fashion based on the pattern of coincidental activation of its input neurons. We show numerically that time-scale invariance emerges spontaneously in a perceptron with realistic neurons, in the presence of noise. Under the assumption that dopaminergic drugs modulate the firing of input neurons, and that cholinergic drugs modulate the memory representation of the criterion time, we show that a perceptron with realistic neurons reproduces the pharmacological clock and memory patterns, and their time-scale invariance, in the presence of noise. These results suggest that rather than being a signature of higher order cognitive processes or specific computations related to timing, time-scale invariance may spontaneously emerge in a massively connected brain from the intrinsic noise of neurons and circuits, thus providing the simplest explanation for the ubiquity of scale invariance of interval timing. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Fractional Sobolev’s Spaces on Time Scales via Conformable Fractional Calculus and Their Application to a Fractional Differential Equation on Time Scales

    Directory of Open Access Journals (Sweden)

    Yanning Wang

    2016-01-01

    Full Text Available Using conformable fractional calculus on time scales, we first introduce fractional Sobolev spaces on time scales, characterize them, and define weak conformable fractional derivatives. Second, we prove the equivalence of some norms in the introduced spaces and derive their completeness, reflexivity, uniform convexity, and compactness of some imbeddings, which can be regarded as a novelty item. Then, as an application, we present a recent approach via variational methods and critical point theory to obtain the existence of solutions for a p-Laplacian conformable fractional differential equation boundary value problem on time scale T:  Tα(Tαup-2Tα(u(t=∇F(σ(t,u(σ(t, Δ-a.e.  t∈a,bTκ2, u(a-u(b=0, Tα(u(a-Tα(u(b=0, where Tα(u(t denotes the conformable fractional derivative of u of order α at t, σ is the forward jump operator, a,b∈T,  01, and F:[0,T]T×RN→R. By establishing a proper variational setting, we obtain three existence results. Finally, we present two examples to illustrate the feasibility and effectiveness of the existence results.

  10. Comparison of prestellar core elongations and large-scale molecular cloud structures in the Lupus I region

    Energy Technology Data Exchange (ETDEWEB)

    Poidevin, Frédérick [UCL, KLB, Department of Physics and Astronomy, Gower Place, London WC1E 6BT (United Kingdom); Ade, Peter A. R.; Hargrave, Peter C.; Nutter, David [School of Physics and Astronomy, Cardiff University, Queens Buildings, The Parade, Cardiff CF24 3AA (United Kingdom); Angile, Francesco E.; Devlin, Mark J.; Klein, Jeffrey [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104 (United States); Benton, Steven J.; Netterfield, Calvin B. [Department of Physics, University of Toronto, 60 St. George Street, Toronto, ON M5S 1A7 (Canada); Chapin, Edward L. [XMM SOC, ESAC, Apartado 78, E-28691 Villanueva de la Canãda, Madrid (Spain); Fissel, Laura M.; Gandilo, Natalie N. [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George Street, Toronto, ON M5S 3H4 (Canada); Fukui, Yasuo [Department of Physics, Nagoya University, Chikusa-ku, Nagoya, Aichi 464-8601 (Japan); Gundersen, Joshua O. [Department of Physics, University of Miami, 1320 Campo Sano Drive, Coral Gables, FL 33146 (United States); Korotkov, Andrei L. [Department of Physics, Brown University, 182 Hope Street, Providence, RI 02912 (United States); Matthews, Tristan G.; Novak, Giles [Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 (United States); Moncelsi, Lorenzo; Mroczkowski, Tony K. [California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 (United States); Olmi, Luca, E-mail: fpoidevin@iac.es [Physics Department, University of Puerto Rico, Rio Piedras Campus, Box 23343, UPR station, San Juan, PR 00931 (United States); and others

    2014-08-10

    Turbulence and magnetic fields are expected to be important for regulating molecular cloud formation and evolution. However, their effects on sub-parsec to 100 parsec scales, leading to the formation of starless cores, are not well understood. We investigate the prestellar core structure morphologies obtained from analysis of the Herschel-SPIRE 350 μm maps of the Lupus I cloud. This distribution is first compared on a statistical basis to the large-scale shape of the main filament. We find the distribution of the elongation position angle of the cores to be consistent with a random distribution, which means no specific orientation of the morphology of the cores is observed with respect to the mean orientation of the large-scale filament in Lupus I, nor relative to a large-scale bent filament model. This distribution is also compared to the mean orientation of the large-scale magnetic fields probed at 350 μm with the Balloon-borne Large Aperture Telescope for Polarimetry during its 2010 campaign. Here again we do not find any correlation between the core morphology distribution and the average orientation of the magnetic fields on parsec scales. Our main conclusion is that the local filament dynamics—including secondary filaments that often run orthogonally to the primary filament—and possibly small-scale variations in the local magnetic field direction, could be the dominant factors for explaining the final orientation of each core.

  11. Rapid molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus L., based on large Y-chromosomal insertions.

    Science.gov (United States)

    Bakker, Theo C M; Giger, Thomas; Frommen, Joachim G; Largiadèr, Carlo R

    2017-08-01

    There is a need for rapid and reliable molecular sexing of three-spined sticklebacks, Gasterosteus aculeatus, the supermodel species for evolutionary biology. A DNA region at the 5' end of the sex-linked microsatellite Gac4202 was sequenced for the X chromosome of six females and the Y chromosome of five males from three populations. The Y chromosome contained two large insertions, which did not recombine with the phenotype of sex in a cross of 322 individuals. Genetic variation (SNPs and indels) within the insertions was smaller than on flanking DNA sequences. Three molecular PCR-based sex tests were developed, in which the first, the second or both insertions were covered. In five European populations (from DE, CH, NL, GB) of three-spined sticklebacks, tests with both insertions combined showed two clearly separated bands on agarose minigels in males and one band in females. The tests with the separate insertions gave similar results. Thus, the new molecular sexing method gave rapid and reliable results for sexing three-spined sticklebacks and is an improvement and/or alternative to existing methods.

  12. Large modulation of carrier transport by grain-boundary molecular packing and microstructure in organic thin films

    KAUST Repository

    Rivnay, Jonathan

    2009-11-08

    Solution-processable organic semiconductors are central to developing viable printed electronics, and performance comparable to that of amorphous silicon has been reported for films grown from soluble semiconductors. However, the seemingly desirable formation of large crystalline domains introduces grain boundaries, resulting in substantial device-to-device performance variations. Indeed, for films where the grain-boundary structure is random, a few unfavourable grain boundaries may dominate device performance. Here we isolate the effects of molecular-level structure at grain boundaries by engineering the microstructure of the high-performance n-type perylenediimide semiconductor PDI8-CN 2 and analyse their consequences for charge transport. A combination of advanced X-ray scattering, first-principles computation and transistor characterization applied to PDI8-CN 2 films reveals that grain-boundary orientation modulates carrier mobility by approximately two orders of magnitude. For PDI8-CN 2 we show that the molecular packing motif (that is, herringbone versus slip-stacked) plays a decisive part in grain-boundary-induced transport anisotropy. The results of this study provide important guidelines for designing device-optimized molecular semiconductors. © 2009 Macmillan Publishers Limited. All rights reserved.

  13. Prenatal Diagnosis and Molecular Analysis of a Large Novel Deletion (- -JS) Causing α0-Thalassemia.

    Science.gov (United States)

    Cao, Jinru; He, Shuzhen; Pu, Yudong; Liu, Jingjing; Liu, Fuping; Feng, Jun

    α-Thalassemia (α-thal) is a very common single gene hereditary disease caused by large deletions or point mutations of the α-globin gene cluster in tropical and subtropical regions of the world. Here, we report for the first time, a novel large α-thal deletion in a Chinese family from Jiangsu Province, People's Republic of China (PRC), which removes almost the entire α2 and α1 genes from the α-globin gene cluster. Thus, it was named the Jiangsu deletion (- - JS ) on the α-globin gene cluster causing α 0 -thal. Heterozygotes for this deletion showed an α-thal trait phenotype with reduced mean corpuscular volume (MCV) and mean corpuscular hemoglobin (Hb) (MCH) levels. The sequencing results showed that a 2538 bp deletion (NG_000006.1: g.35801_38338) existed in this novel genotype on the basis of -α 4.2 (leftward), indicating a deletion of about 6.8 kb from the α-globin cluster. In addition, a 29 bp sequence was inserted into the deletion during the recombination events that led to this deletion. Through pedigree analysis, we knew that the proband inherited the novel allele from his mother.

  14. Benzothienobenzothiophene-Based Molecular Conductors: High Conductivity, Large Thermoelectric Power Factor, and One-Dimensional Instability.

    Science.gov (United States)

    Kiyota, Yasuhiro; Kadoya, Tomofumi; Yamamoto, Kaoru; Iijima, Kodai; Higashino, Toshiki; Kawamoto, Tadashi; Takimiya, Kazuo; Mori, Takehiko

    2016-03-23

    On the basis of an excellent transistor material, [1]benzothieno[3,2-b][1]benzothiophene (BTBT), a series of highly conductive organic metals with the composition of (BTBT)2XF6 (X = P, As, Sb, and Ta) are prepared and the structural and physical properties are investigated. The room-temperature conductivity amounts to 4100 S cm(-1) in the AsF6 salt, corresponding to the drift mobility of 16 cm(2) V(-1) s(-1). Owing to the high conductivity, this salt shows a thermoelectric power factor of 55-88 μW K(-2) m(-1), which is a large value when this compound is regarded as an organic thermoelectric material. The thermoelectric power and the reflectance spectrum indicate a large bandwidth of 1.4 eV. These salts exhibit an abrupt resistivity jump under 200 K, which turns to an insulating state below 60 K. The paramagnetic spin susceptibility, and the Raman and the IR spectra suggest 4kF charge-density waves as an origin of the low-temperature insulating state.

  15. Molecular beam epitaxy of large-area SnSe2 with monolayer thickness fluctuation

    Science.gov (United States)

    Park, Young Woon; Jerng, Sahng-Kyoon; Jeon, Jae Ho; Roy, Sanjib Baran; Akbar, Kamran; Kim, Jeong; Sim, Yumin; Seong, Maeng-Je; Kim, Jung Hwa; Lee, Zonghoon; Kim, Minju; Yi, Yeonjin; Kim, Jinwoo; Noh, Do Young; Chun, Seung-Hyun

    2017-03-01

    The interest in layered materials is largely based on the expectation that they will be beneficial for a variety of applications, from low-power-consuming, wearable electronics to energy harvesting. However, the properties of layered materials are highly dependent on thickness, and the difficulty of controlling thickness over a large area has been a bottleneck for commercial applications. Here, we report layer-by-layer growth of SnSe2, a layered semiconducting material, via van der Waals epitaxy. The films were fabricated on insulating mica substrates with substrate temperatures in the range of 210 °C-370 °C. The surface consists of a mixture of N and (N ± 1) layers, showing that the thickness of the film can be defined with monolayer accuracy (±0.6 nm). High-resolution transmission electron microscopy reveals a polycrystalline film with a grain size of ˜100 nm and clear Moiré patterns from overlapped grains with similar thickness. We also report field effect mobility values of 3.7 cm2 V-1 s-1 and 6.7 cm2 V-1 s-1 for 11 and 22 nm thick SnSe2, respectively. SnSe2 films with customizable thickness can provide valuable platforms for industry and academic researchers to fully exploit the potential of layered materials.

  16. Comprehensive molecular diagnosis of a large cohort of Japanese retinitis pigmentosa and Usher syndrome patients by next-generation sequencing.

    Science.gov (United States)

    Oishi, Maho; Oishi, Akio; Gotoh, Norimoto; Ogino, Ken; Higasa, Koichiro; Iida, Kei; Makiyama, Yukiko; Morooka, Satoshi; Matsuda, Fumihiko; Yoshimura, Nagahisa

    2014-10-16

    Retinitis pigmentosa (RP), a major cause of blindness in developed countries, has multiple causative genes; its prevalence differs by ethnicity. Usher syndrome is the most common form of syndromic RP and is accompanied by hearing impairment. Although molecular diagnosis is challenging, recent technological advances such as targeted high-throughput resequencing are efficient screening tools. We performed comprehensive molecular testing in 329 Japanese RP and Usher syndrome patients by using a custom capture panel that covered the coding exons and exon/intron boundaries of all 193 known inherited eye disease genes combined with Illumina HiSequation 2500. Candidate variants were screened using systematic data analyses, and their potential pathogenicity was assessed according to the frequency of the variants in normal populations, in silico prediction tools, and compatibility with known phenotypes or inheritance patterns. Molecular diagnoses were made in 115/317 RP patients (36.3%) and 6/12 Usher syndrome patients (50%). We identified 104 distinct mutations, including 66 novel mutations. EYS, USH2A, and RHO were common causative genes. In particular, mutations in EYS accounted for 15.0% of the autosomal recessive/simplex RP patients or 10.7% of the entire RP cohort. Among the 189 previously reported mutations detected in the current study, 55 (29.1%) were found commonly in Japanese or other public databases and were excluded from molecular diagnoses. By screening a large cohort of patients, this study catalogued the genetic variations involved in RP and Usher syndrome in a Japanese population and highlighted the different distribution of causative genes among populations. Copyright 2014 The Association for Research in Vision and Ophthalmology, Inc.

  17. ALMA Reveals Molecular Cloud N55 in the Large Magellanic Cloud as a Site of Massive Star Formation

    Science.gov (United States)

    Naslim, N.; Tokuda, K.; Onishi, T.; Kemper, F.; Wong, T.; Morata, O.; Takada, S.; Harada, R.; Kawamura, A.; Saigo, K.; Indebetouw, R.; Madden, S. C.; Hony, S.; Meixner, M.

    2018-02-01

    We present the molecular cloud properties of N55 in the Large Magellanic Cloud using 12CO(1–0) and 13CO(1–0) observations obtained with Atacama Large Millimeter Array. We have done a detailed study of molecular gas properties, to understand how the cloud properties of N55 differ from Galactic clouds. Most CO emission appears clumpy in N55, and molecular cores that have young stellar objects (YSOs) show larger linewidths and masses. The massive clumps are associated with high and intermediate mass YSOs. The clump masses are determined by local thermodynamic equilibrium and virial analysis of the 12CO and 13CO emissions. These mass estimates lead to the conclusion that (a) the clumps are in self-gravitational virial equilibrium, and (b) the 12CO(1–0)-to-H2 conversion factor, {X}{CO}, is 6.5 × 1020 cm‑2 (K km s‑1)‑1. This CO-to-H2 conversion factor for N55 clumps is measured at a spatial scale of ∼0.67 pc, which is about two times higher than the {X}{CO} value of the Orion cloud at a similar spatial scale. The core mass function of N55 clearly show a turnover below 200 {M}ȯ , separating the low-mass end from the high-mass end. The low-mass end of the 12CO mass spectrum is fitted with a power law of index 0.5 ± 0.1, while for 13CO it is fitted with a power law index 0.6 ± 0.2. In the high-mass end, the core mass spectrum is fitted with a power index of 2.0 ± 0.3 for 12CO, and with 2.5 ± 0.4 for 13CO. This power law behavior of the core mass function in N55 is consistent with many Galactic clouds.

  18. Molecular understanding of atmospheric particle formation from sulfuric acid and large oxidized organic molecules

    CERN Document Server

    Schobesberger, Siegfried; Bianchi, Federico; Lönn, Gustaf; Ehn, Mikael; Lehtipalo, Katrianne; Dommen, Josef; Ehrhart, Sebastian; Ortega, Ismael K; Franchin, Alessandro; Nieminen, Tuomo; Riccobono, Francesco; Hutterli, Manuel; Duplissy, Jonathan; Almeida, João; Amorim, Antonio; Breitenlechner, Martin; Downard, Andrew J; Dunne, Eimear M; Flagan, Richard C; Kajos, Maija; Keskinen, Helmi; Kirkby, Jasper; Kupc, Agnieszka; Kürten, Andreas; Kurtén, Theo; Laaksonen, Ari; Mathot, Serge; Onnela, Antti; Praplan, Arnaud P; Rondo, Linda; Santos, Filipe D; Schallhart, Simon; Schnitzhofer, Ralf; Sipilä, Mikko; Tomé, António; Tsagkogeorgas, Georgios; Vehkamäki, Hanna; Wimmer, Daniela; Baltensperger, Urs; Carslaw, Kenneth S; Curtius, Joachim; Hansel, Armin; Petäjä, Tuukka; Kulmala, Markku; Donahue, Neil M; Worsnop, Douglas R

    2013-01-01

    Atmospheric aerosols formed by nucleation of vapors affect radiative forcing and therefore climate. However, the underlying mechanisms of nucleation remain unclear, particularly the involvement of organic compounds. Here, we present high-resolution mass spectra of ion clusters observed during new particle formation experiments performed at the Cosmics Leaving Outdoor Droplets chamber at the European Organization for Nuclear Research. The experiments involved sulfuric acid vapor and different stabilizing species, including ammonia and dimethylamine, as well as oxidation products of pinanediol, a surrogate for organic vapors formed from monoterpenes. A striking resemblance is revealed between the mass spectra from the chamber experiments with oxidized organics and ambient data obtained during new particle formation events at the Hyytiälä boreal forest research station. We observe that large oxidized organic compounds, arising from the oxidation of monoterpenes, cluster directly with single sulfuric acid molec...

  19. Characteristic time scales for diffusion processes through layers and across interfaces

    Science.gov (United States)

    Carr, Elliot J.

    2018-04-01

    This paper presents a simple tool for characterizing the time scale for continuum diffusion processes through layered heterogeneous media. This mathematical problem is motivated by several practical applications such as heat transport in composite materials, flow in layered aquifers, and drug diffusion through the layers of the skin. In such processes, the physical properties of the medium vary across layers and internal boundary conditions apply at the interfaces between adjacent layers. To characterize the time scale, we use the concept of mean action time, which provides the mean time scale at each position in the medium by utilizing the fact that the transition of the transient solution of the underlying partial differential equation model, from initial state to steady state, can be represented as a cumulative distribution function of time. Using this concept, we define the characteristic time scale for a multilayer diffusion process as the maximum value of the mean action time across the layered medium. For given initial conditions and internal and external boundary conditions, this approach leads to simple algebraic expressions for characterizing the time scale that depend on the physical and geometrical properties of the medium, such as the diffusivities and lengths of the layers. Numerical examples demonstrate that these expressions provide useful insight into explaining how the parameters in the model affect the time it takes for a multilayer diffusion process to reach steady state.

  20. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes.

    Science.gov (United States)

    Chapuy, Bjoern; Stewart, Chip; Dunford, Andrew J; Kim, Jaegil; Kamburov, Atanas; Redd, Robert A; Lawrence, Mike S; Roemer, Margaretha G M; Li, Amy J; Ziepert, Marita; Staiger, Annette M; Wala, Jeremiah A; Ducar, Matthew D; Leshchiner, Ignaty; Rheinbay, Ester; Taylor-Weiner, Amaro; Coughlin, Caroline A; Hess, Julian M; Pedamallu, Chandra S; Livitz, Dimitri; Rosebrock, Daniel; Rosenberg, Mara; Tracy, Adam A; Horn, Heike; van Hummelen, Paul; Feldman, Andrew L; Link, Brian K; Novak, Anne J; Cerhan, James R; Habermann, Thomas M; Siebert, Reiner; Rosenwald, Andreas; Thorner, Aaron R; Meyerson, Matthew L; Golub, Todd R; Beroukhim, Rameen; Wulf, Gerald G; Ott, German; Rodig, Scott J; Monti, Stefano; Neuberg, Donna S; Loeffler, Markus; Pfreundschuh, Michael; Trümper, Lorenz; Getz, Gad; Shipp, Margaret A

    2018-04-30

    Diffuse large B cell lymphoma (DLBCL), the most common lymphoid malignancy in adults, is a clinically and genetically heterogeneous disease that is further classified into transcriptionally defined activated B cell (ABC) and germinal center B cell (GCB) subtypes. We carried out a comprehensive genetic analysis of 304 primary DLBCLs and identified low-frequency alterations, captured recurrent mutations, somatic copy number alterations, and structural variants, and defined coordinate signatures in patients with available outcome data. We integrated these genetic drivers using consensus clustering and identified five robust DLBCL subsets, including a previously unrecognized group of low-risk ABC-DLBCLs of extrafollicular/marginal zone origin; two distinct subsets of GCB-DLBCLs with different outcomes and targetable alterations; and an ABC/GCB-independent group with biallelic inactivation of TP53, CDKN2A loss, and associated genomic instability. The genetic features of the newly characterized subsets, their mutational signatures, and the temporal ordering of identified alterations provide new insights into DLBCL pathogenesis. The coordinate genetic signatures also predict outcome independent of the clinical International Prognostic Index and suggest new combination treatment strategies. More broadly, our results provide a roadmap for an actionable DLBCL classification.

  1. Molecular evidence for the induction of large interstitial deletions on mouse chromosome 8 by ionizing radiation

    International Nuclear Information System (INIS)

    Turker, Mitchell S.; Pieretti, Maura; Kumar, Sudha

    1997-01-01

    The P19H22 mouse embryonal carcinoma cell line is characterized by a hemizygous deficiency for the chromosome 8 encoded aprt (adenine phosphoribosyltransferase) gene and heterozygosity for many chromosome 8 loci. We have previously demonstrated that this cell line is suitable for mutational studies because it is permissive of events ranging in size from base-pair substitutions at the aprt locus to apparent loss of chromosome 8. Large mutational events, defined by loss of the remaining aprt allele, were found to predominate in spontaneous mutants and those induced by ionizing radiation. In this study we have used a PCR based assay to screen for loss of heterozygosity at microsatellite loci both proximal and distal to aprt in 137 Cs-induced and spontaneous aprt mutants. This approach allowed us to distinguish apparent interstitial deletional events from apparent recombinational events. Significantly, 32.5% (26 of 80) of the mutational events induced by 137 Cs appeared to be interstitial deletions as compared with 7.7% (6 of 78) in the spontaneous group. This difference was statistically significant (p 137 Cs caused a significant number of deletion mutations. Most 137 Cs-induced interstitial deletions were larger than 6 cM, whereas none of the spontaneous deletions were larger than 6 cM. These results provide further support for the notion that ionizing radiation induces deletion mutations and validate the use of the P19H22 cell line for the study of events induced by ionizing radiation

  2. Multiple time step integrators in ab initio molecular dynamics

    International Nuclear Information System (INIS)

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-01-01

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy

  3. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

    Science.gov (United States)

    Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

    2013-02-19

    Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

  4. Immunohistochemical and molecular characteristics with prognostic significance in diffuse large B-cell lymphoma.

    Directory of Open Access Journals (Sweden)

    Carmen Bellas

    Full Text Available Diffuse large B-cell lymphoma (DLBCL is an aggressive non-Hodgkin lymphoma with marked biologic heterogeneity. We analyzed 100 cases of DLBCL to evaluate the prognostic value of immunohistochemical markers derived from the gene expression profiling-defined cell origin signature, including MYC, BCL2, BCL6, and FOXP1 protein expression. We also investigated genetic alterations in BCL2, BCL6, MYC and FOXP1 using fluorescence in situ hybridization and assessed their prognostic significance. BCL6 rearrangements were detected in 29% of cases, and BCL6 gene alteration (rearrangement and/or amplification was associated with the non-germinal center B subtype (non-GCB. BCL2 translocation was associated with the GCB phenotype, and BCL2 protein expression was associated with the translocation and/or amplification of 18q21. MYC rearrangements were detected in 15% of cases, and MYC protein expression was observed in 29% of cases. FOXP1 expression, mainly of the non-GCB subtype, was demonstrated in 37% of cases. Co-expression of the MYC and BCL2 proteins, with non-GCB subtype predominance, was observed in 21% of cases. We detected an association between high FOXP1 expression and a high proliferation rate as well as a significant positive correlation between MYC overexpression and FOXP1 overexpression. MYC, BCL2 and FOXP1 expression were significant predictors of overall survival. The co-expression of MYC and BCL2 confers a poorer clinical outcome than MYC or BCL2 expression alone, whereas cases negative for both markers had the best outcomes. Our study confirms that DLBCL, characterized by the co-expression of MYC and BCL2 proteins, has a poor prognosis and establishes a significant positive correlation with MYC and FOXP1 over-expression in this entity.

  5. Focused ultrasound-facilitated brain drug delivery using optimized nanodroplets: vaporization efficiency dictates large molecular delivery

    Science.gov (United States)

    Wu, Shih-Ying; Fix, Samantha M.; Arena, Christopher B.; Chen, Cherry C.; Zheng, Wenlan; Olumolade, Oluyemi O.; Papadopoulou, Virginie; Novell, Anthony; Dayton, Paul A.; Konofagou, Elisa E.

    2018-02-01

    Focused ultrasound with nanodroplets could facilitate localized drug delivery after vaporization with potentially improved in vivo stability, drug payload, and minimal interference outside of the focal zone compared with microbubbles. While the feasibility of blood-brain barrier (BBB) opening using nanodroplets has been previously reported, characterization of the associated delivery has not been achieved. It was hypothesized that the outcome of drug delivery was associated with the droplet’s sensitivity to acoustic energy, and can be modulated with the boiling point of the liquid core. Therefore, in this study, octafluoropropane (OFP) and decafluorobutane (DFB) nanodroplets were used both in vitro for assessing their relative vaporization efficiency with high-speed microscopy, and in vivo for delivering molecules with a size relevant to proteins (40 kDa dextran) to the murine brain. It was found that at low pressures (300-450 kPa), OFP droplets vaporized into a greater number of microbubbles compared to DFB droplets at higher pressures (750-900 kPa) in the in vitro study. In the in vivo study, successful delivery was achieved with OFP droplets at 300 kPa and 450 kPa without evidence of cavitation damage using ¼ dosage, compared to DFB droplets at 900 kPa where histology indicated tissue damage due to inertial cavitation. In conclusion, the vaporization efficiency of nanodroplets positively impacted the amount of molecules delivered to the brain. The OFP droplets due to the higher vaporization efficiency served as better acoustic agents to deliver large molecules efficiently to the brain compared with the DFB droplets.

  6. A Novel Multiple-Time Scale Integrator for the Hybrid Monte Carlo Algorithm

    International Nuclear Information System (INIS)

    Kamleh, Waseem

    2011-01-01

    Hybrid Monte Carlo simulations that implement the fermion action using multiple terms are commonly used. By the nature of their formulation they involve multiple integration time scales in the evolution of the system through simulation time. These different scales are usually dealt with by the Sexton-Weingarten nested leapfrog integrator. In this scheme the choice of time scales is somewhat restricted as each time step must be an exact multiple of the next smallest scale in the sequence. A novel generalisation of the nested leapfrog integrator is introduced which allows for far greater flexibility in the choice of time scales, as each scale now must only be an exact multiple of the smallest step size.

  7. Crowdsourcing the General Public for Large Scale Molecular Pathology Studies in Cancer.

    Science.gov (United States)

    Candido Dos Reis, Francisco J; Lynn, Stuart; Ali, H Raza; Eccles, Diana; Hanby, Andrew; Provenzano, Elena; Caldas, Carlos; Howat, William J; McDuffus, Leigh-Anne; Liu, Bin; Daley, Frances; Coulson, Penny; Vyas, Rupesh J; Harris, Leslie M; Owens, Joanna M; Carton, Amy F M; McQuillan, Janette P; Paterson, Andy M; Hirji, Zohra; Christie, Sarah K; Holmes, Amber R; Schmidt, Marjanka K; Garcia-Closas, Montserrat; Easton, Douglas F; Bolla, Manjeet K; Wang, Qin; Benitez, Javier; Milne, Roger L; Mannermaa, Arto; Couch, Fergus; Devilee, Peter; Tollenaar, Robert A E M; Seynaeve, Caroline; Cox, Angela; Cross, Simon S; Blows, Fiona M; Sanders, Joyce; de Groot, Renate; Figueroa, Jonine; Sherman, Mark; Hooning, Maartje; Brenner, Hermann; Holleczek, Bernd; Stegmaier, Christa; Lintott, Chris; Pharoah, Paul D P

    2015-07-01

    Citizen science, scientific research conducted by non-specialists, has the potential to facilitate biomedical research using available large-scale data, however validating the results is challenging. The Cell Slider is a citizen science project that intends to share images from tumors with the general public, enabling them to score tumor markers independently through an internet-based interface. From October 2012 to June 2014, 98,293 Citizen Scientists accessed the Cell Slider web page and scored 180,172 sub-images derived from images of 12,326 tissue microarray cores labeled for estrogen receptor (ER). We evaluated the accuracy of Citizen Scientist's ER classification, and the association between ER status and prognosis by comparing their test performance against trained pathologists. The area under ROC curve was 0.95 (95% CI 0.94 to 0.96) for cancer cell identification and 0.97 (95% CI 0.96 to 0.97) for ER status. ER positive tumors scored by Citizen Scientists were associated with survival in a similar way to that scored by trained pathologists. Survival probability at 15 years were 0.78 (95% CI 0.76 to 0.80) for ER-positive and 0.72 (95% CI 0.68 to 0.77) for ER-negative tumors based on Citizen Scientists classification. Based on pathologist classification, survival probability was 0.79 (95% CI 0.77 to 0.81) for ER-positive and 0.71 (95% CI 0.67 to 0.74) for ER-negative tumors. The hazard ratio for death was 0.26 (95% CI 0.18 to 0.37) at diagnosis and became greater than one after 6.5 years of follow-up for ER scored by Citizen Scientists, and 0.24 (95% CI 0.18 to 0.33) at diagnosis increasing thereafter to one after 6.7 (95% CI 4.1 to 10.9) years of follow-up for ER scored by pathologists. Crowdsourcing of the general public to classify cancer pathology data for research is viable, engages the public and provides accurate ER data. Crowdsourced classification of research data may offer a valid solution to problems of throughput requiring human input.

  8. Time scales of magma transport and mixing at Kīlauea Volcano, Hawai’i

    OpenAIRE

    Rae, Auriol S.P.; Edmonds, Marie; Maclennan, John; Morgan, Daniel; Houghton, Bruce; Hartley, Margaret E.; Sides, Isobel

    2016-01-01

    Modeling of volcanic processes is limited by a lack of knowledge of the time scales of storage, mixing, and final ascent of magmas into the shallowest portions of volcanic plumbing systems immediately prior to eruption. It is impossible to measure these time scales directly; however, micro-analytical techniques provide indirect estimates based on the extent of diffusion of species through melts and crystals. We use diffusion in olivine phenocrysts from the A.D. 1959 Kīlauea Iki (Hawai‘i, USA)...

  9. Doubly stochastic Poisson process models for precipitation at fine time-scales

    Science.gov (United States)

    Ramesh, Nadarajah I.; Onof, Christian; Xie, Dichao

    2012-09-01

    This paper considers a class of stochastic point process models, based on doubly stochastic Poisson processes, in the modelling of rainfall. We examine the application of this class of models, a neglected alternative to the widely-known Poisson cluster models, in the analysis of fine time-scale rainfall intensity. These models are mainly used to analyse tipping-bucket raingauge data from a single site but an extension to multiple sites is illustrated which reveals the potential of this class of models to study the temporal and spatial variability of precipitation at fine time-scales.

  10. Time scale of scour around a pile in combined waves and current

    DEFF Research Database (Denmark)

    Petersen, Thor Ugelvig; Sumer, B. Mutlu; Fredsøe, Jørgen

    The time scale of the scour process around a circular vertical pile is studied in combined waves and current. A series of tests were carried out in a flume with pile diameters 40 mm and 75 mm, in both steady current, waves and combined waves and current. In the combined wave and current flow regime...... the waves and the current were co-directional. All the tests were conducted in the live bed regime. The time scale of scour in combined waves and current is governed by three parameters, namely the current-velocity-to-wave-velocity ratio (Ucw), the Keulegan–Carpenter number (KC) and Shields parameter (Θw...

  11. Rapid-mixing studies on the time-scale of radiation damage in cells

    International Nuclear Information System (INIS)

    Adams, G.E.; Michael, B.D.; Asquith, J.C.; Shenoy, M.A.; Watts, M.E.; Whillans, D.W.

    1975-01-01

    Rapid mixing studies were performed to determine the time scale of radiation damage in cells. There is evidence that the sensitizing effects of oxygen and other chemical dose-modifying agents on the response of cells to ionizing radiation involve fast free-radical processes. Fast response technique studies in bacterial systems have shown that extremely fast processes occur when the bacteria are exposed to oxygen or other dose-modifying agents during irradiation. The time scales observed were consistent with the involvement of fast free-radical reactions in the expression of these effects

  12. New Bounds of Ostrowski–Gruss Type Inequality for (k + 1 Points on Time Scales

    Directory of Open Access Journals (Sweden)

    Eze R. Nwaeze

    2017-11-01

    Full Text Available The aim of this paper is to present three new bounds of the Ostrowski--Gr\\"uss type inequality for points $x_0,x_1,x_2,\\cdots,x_k$ on time scales. Our results generalize result of Ng\\^o and Liu, and extend results of Ujevi\\'c to time scales with $(k+1$ points. We apply our results to the continuous, discrete, and quantum calculus to obtain many new interesting inequalities. An example is also considered. The estimates obtained in this paper will be very useful in numerical integration especially for the continuous case.

  13. Multiple time scales in modeling the incidence of infections acquired in intensive care units

    Directory of Open Access Journals (Sweden)

    Martin Wolkewitz

    2016-09-01

    Full Text Available Abstract Background When patients are admitted to an intensive care unit (ICU their risk of getting an infection will be highly depend on the length of stay at-risk in the ICU. In addition, risk of infection is likely to vary over calendar time as a result of fluctuations in the prevalence of the pathogen on the ward. Hence risk of infection is expected to depend on two time scales (time in ICU and calendar time as well as competing events (discharge or death and their spatial location. The purpose of this paper is to develop and apply appropriate statistical models for the risk of ICU-acquired infection accounting for multiple time scales, competing risks and the spatial clustering of the data. Methods A multi-center data base from a Spanish surveillance network was used to study the occurrence of an infection due to Methicillin-resistant Staphylococcus aureus (MRSA. The analysis included 84,843 patient admissions between January 2006 and December 2011 from 81 ICUs. Stratified Cox models were used to study multiple time scales while accounting for spatial clustering of the data (patients within ICUs and for death or discharge as competing events for MRSA infection. Results Both time scales, time in ICU and calendar time, are highly associated with the MRSA hazard rate and cumulative risk. When using only one basic time scale, the interpretation and magnitude of several patient-individual risk factors differed. Risk factors concerning the severity of illness were more pronounced when using only calendar time. These differences disappeared when using both time scales simultaneously. Conclusions The time-dependent dynamics of infections is complex and should be studied with models allowing for multiple time scales. For patient individual risk-factors we recommend stratified Cox regression models for competing events with ICU time as the basic time scale and calendar time as a covariate. The inclusion of calendar time and stratification by ICU

  14. Time scales of the stick–slip dynamics of the peeling of an adhesive tape

    Science.gov (United States)

    Mishra, Nachiketa; Parida, Nigam Chandra; Raha, Soumyendu

    2015-01-01

    The stick–slip dynamics of the peeling of an adhesive tape is characterized by bifurcations that have been experimentally well studied. In this work, we investigate the time scale in which the the stick–slips happen leading to the bifurcations. This is fundamental to understanding the triboluminescence and acoustic emissions associated with the bifurcations. We establish a relationship between the time scale of the bifurcations and the inherent mathematical structure of the peeling dynamics by studying a characteristic time quantity associated with the dynamics. PMID:25663802

  15. Molecular characterisation of methicillin-resistant Staphylococcus aureus (MRSA) isolated at a large referral hospital in Zambia.

    Science.gov (United States)

    Samutela, Mulemba Tillika; Kalonda, Annie; Mwansa, James; Lukwesa-Musyani, Chileshe; Mwaba, John; Mumbula, Enoch Mulowa; Mwenya, Darlington; Simulundu, Edgar; Kwenda, Geoffrey

    2017-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is globally recognized as an important public health problem. Whereas comprehensive molecular typing data of MRSA strains is available, particularly in Europe, North America and Australia, similar information is very limited in sub-Saharan Africa including Zambia. In this study, thirty two clinical isolates of Staphylococcus aureus , collected at a large referral hospital in Lusaka, Zambia between June 2009 and December 2012 were analysed by Staphylococcal cassette chromosome mec (SCCmec), Staphylococcus protein A gene typing (spa) and detection of the Panton-Valentine Leukocidin genes (pvl) . Three SCC mec types were identified namely SCC mec type IV (65.6%), SCCmec type III (21.9%), SCC mec type I (3.1%). Nine point four percent (9.4%) of the isolates were untypable. Five spa types, which included a novel type, were detected and the most prevalent spa type was t064 (40.6%). Other spa types included spa types t2104 (31.3%), t355 (3.1%) and t1257 (21.9%). The pvl genes were detected in 3 out of 32 isolates. These molecular typing data indicated that the MRSA strains collected in Lusaka were diverse. Although the source of these MRSA was not established, these results stress the need for assessing infection prevention and control procedures at this health-care facility in order to curtail possible nosocomial infections. Furthermore, country-wide surveillance of MRSA in both the community and health-care facilities is recommended for infection prevention and control. To our knowledge, this represents the first study to characterise MRSA using molecular tools in Zambia.

  16. Clinical, Endocrine, and Molecular Genetic Analysis of a Large Cohort of Saudi Arabian Patients with Laron Syndrome.

    Science.gov (United States)

    Al-Ashwal, Abdullah A; Al-Sagheir, Afaf; Ramzan, Khushnooda; Al-Owain, Mohammed; Allam, Rabab; Qari, Alya; Al-Numair, Nouf S; Imtiaz, Faiqa

    2017-01-01

    Laron syndrome (LS) is an autosomal recessive disease characterized by marked short stature and very low serum IGF-1 and IGFBP-3 levels. This study assessed the clinical and endocrine features alongside determining the growth hormone receptor gene (GHR) mutation in Saudi Arabian patients with LS in order to establish whether or not a genotype/phenotype correlation is evident in this large cohort. A total of 40 Saudi Arabian patients with a suspected diagnosis of LS were recruited and subjected to a full clinical and endocrine investigation together with direct sequencing of the coding regions of the GHR gene. GHR mutations were identified in 34 patients from 22 separate nuclear families. All 34 molecularly confirmed patients had the typical clinical and endocrinological manifestations of LS. Eleven different mutations (9 previously unreported) were detected in this cohort of patients, all inherited in an autosomal recessive homozygous form. No genotype/phenotype correlation was apparent. The identification of pathogenic mutations causing LS will be of tremendous use for the molecular diagnosis of patients in Saudi Arabia and the region in general, with respect to prevention of this disease in the forms of future carrier testing, prenatal testing, premarital screening and preimplantation genetic diagnosis. © 2017 S. Karger AG, Basel.

  17. Large-scale structure of the Taurus molecular complex. II. Analysis of velocity fluctuations and turbulence. III. Methods for turbulence

    International Nuclear Information System (INIS)

    Kleiner, S.C.; Dickman, R.L.

    1985-01-01

    The velocity autocorrelation function (ACF) of observed spectral line centroid fluctuations is noted to effectively reproduce the actual ACF of turbulent gas motions within an interstellar cloud, thereby furnishing a framework for the study of the large scale velocity structure of the Taurus dark cloud complex traced by the present C-13O J = 1-0 observations of this region. The results obtained are discussed in the context of recent suggestions that widely observed correlations between molecular cloud widths and cloud sizes indicate the presence of a continuum of turbulent motions within the dense interstellar medium. Attention is then given to a method for the quantitative study of these turbulent motions, involving the mapping of a source in an optically thin spectral line and studying the spatial correlation properties of the resulting velocity centroid map. 61 references

  18. Large Area, High Resolution N2H+ studies of dense gas in the Perseus and Serpens Molecular Clouds

    Science.gov (United States)

    Storm, Shaye; Mundy, Lee

    2014-07-01

    Star formation in molecular clouds occurs over a wide range of spatial scales and physical densities. Understanding the origin of dense cores thus requires linking the structure and kinematics of gas and dust from cloud to core scales. The CARMA Large Area Star Formation Survey (CLASSy) is a CARMA Key Project that spectrally imaged five diverse regions of the Perseus and Serpens Molecular Clouds in N2H+ (J=1-0), totaling over 800 square arcminutes. The observations have 7’’ angular resolution (~0.01 pc spatial resolution) to probe dense gas down to core scales, and use combined interferometric and single-dish data to fully recover line emission up to parsec scales. CLASSy observations are complete, and this talk will focus on three science results. First, the dense gas in regions with existing star formation has complex hierarchical structure. We present a non-binary dendrogram analysis for all regions and show that dense gas hierarchy correlates with star formation activity. Second, well-resolved velocity information for each dendrogram-identified structure allows a new way of looking at linewidth-size relations in clouds. Specifically, we find that non-thermal line-of-sight velocity dispersion varies weakly with structure size, while rms variation in the centroid velocity increases strongly with structure size. We argue that the typical line-of-sight depth of a cloud can be estimated from these relations, and that our regions have depths that are several times less than their extent on the plane of the sky. This finding is consistent with numerical simulations of molecular cloud turbulence that show that high-density sheets are a generic result. Third, N2H+ is a good tracer of cold, dense gas in filaments; we resolve multiple beams across many filaments, some of which are narrower than 0.1 pc. The centroid velocity fields of several filaments show gradients perpendicular to their major axis, which is a common feature in filaments formed from numerical

  19. Hardy inequality on time scales and its application to half-linear dynamic equations

    Directory of Open Access Journals (Sweden)

    Řehák Pavel

    2005-01-01

    Full Text Available A time-scale version of the Hardy inequality is presented, which unifies and extends well-known Hardy inequalities in the continuous and in the discrete setting. An application in the oscillation theory of half-linear dynamic equations is given.

  20. Modeling heat dominated electric breakdown in air, with adaptivity to electron or ion time scales

    NARCIS (Netherlands)

    Agnihotri, A.; Hundsdorfer, W.; Ebert, U.

    2017-01-01

    We model heat dominated electrical breakdown in air in a short planar gap. We couple the discharge dynamics in fluid approximation with the hydrodynamic motion of the air heated by the discharge. To be computationally efficient, we derive a reduced model on the ion time scale, and we switch between

  1. A multiple-time-scale approach to the control of ITBs on JET

    Energy Technology Data Exchange (ETDEWEB)

    Laborde, L.; Mazon, D.; Moreau, D. [EURATOM-CEA Association (DSM-DRFC), CEA Cadarache, 13 - Saint Paul lez Durance (France); Moreau, D. [Culham Science Centre, EFDA-JET, Abingdon, OX (United Kingdom); Ariola, M. [EURATOM/ENEA/CREATE Association, Univ. Napoli Federico II, Napoli (Italy); Cordoliani, V. [Ecole Polytechnique, 91 - Palaiseau (France); Tala, T. [EURATOM-Tekes Association, VTT Processes (Finland)

    2005-07-01

    The simultaneous real-time control of the current and temperature gradient profiles could lead to the steady state sustainment of an internal transport barrier (ITB) and so to a stationary optimized plasma regime. Recent experiments in JET have demonstrated significant progress in achieving such a control: different current and temperature gradient target profiles have been reached and sustained for several seconds using a controller based on a static linear model. It's worth noting that the inverse safety factor profile evolves on a slow time scale (resistive time) while the normalized electron temperature gradient reacts on a faster one (confinement time). Moreover these experiments have shown that the controller was sensitive to rapid plasma events such as transient ITBs during the safety factor profile evolution or MHD instabilities which modify the pressure profiles on the confinement time scale. In order to take into account the different dynamics of the controlled profiles and to better react to rapid plasma events the control technique is being improved by using a multiple-time-scale approximation. The paper describes the theoretical analysis and closed-loop simulations using a control algorithm based on two-time-scale state-space model. These closed-loop simulations using the full dynamic but linear model used for the controller design to simulate the plasma response have demonstrated that this new controller allows the normalized electron temperature gradient target profile to be reached faster than the one used in previous experiments. (A.C.)

  2. A limit set trichotomy for order-preserving systems on time scales

    Directory of Open Access Journals (Sweden)

    Christian Poetzsche

    2004-04-01

    Full Text Available In this paper we derive a limit set trichotomy for abstract order-preserving 2-parameter semiflows in normal cones of strongly ordered Banach spaces. Additionally, to provide an example, Muller's theorem is generalized to dynamic equations on arbitrary time scales and applied to a model from population dynamics.

  3. A multiple-time-scale approach to the control of ITBs on JET

    International Nuclear Information System (INIS)

    Laborde, L.; Mazon, D.; Moreau, D.; Moreau, D.; Ariola, M.; Cordoliani, V.; Tala, T.

    2005-01-01

    The simultaneous real-time control of the current and temperature gradient profiles could lead to the steady state sustainment of an internal transport barrier (ITB) and so to a stationary optimized plasma regime. Recent experiments in JET have demonstrated significant progress in achieving such a control: different current and temperature gradient target profiles have been reached and sustained for several seconds using a controller based on a static linear model. It's worth noting that the inverse safety factor profile evolves on a slow time scale (resistive time) while the normalized electron temperature gradient reacts on a faster one (confinement time). Moreover these experiments have shown that the controller was sensitive to rapid plasma events such as transient ITBs during the safety factor profile evolution or MHD instabilities which modify the pressure profiles on the confinement time scale. In order to take into account the different dynamics of the controlled profiles and to better react to rapid plasma events the control technique is being improved by using a multiple-time-scale approximation. The paper describes the theoretical analysis and closed-loop simulations using a control algorithm based on two-time-scale state-space model. These closed-loop simulations using the full dynamic but linear model used for the controller design to simulate the plasma response have demonstrated that this new controller allows the normalized electron temperature gradient target profile to be reached faster than the one used in previous experiments. (A.C.)

  4. Extension of the astronomically calibrated (polarity) time scale to the Miocene/Pliocene boundary

    NARCIS (Netherlands)

    Hilgen, F.J.

    1991-01-01

    The early Pleistocene to late Pliocene astronormcally calibrated time scale of Shackleton et al. [1] and Hllgen [2] is extended to the Mlocene/Pllocene boundary This is done by correlating the detailed record of CaCO 3 cycles in the Trubl and the lower part of the overlying Narbone Formation

  5. Fixation of competing strategies when interacting agents differ in the time scale of strategy updating

    NARCIS (Netherlands)

    Zhang, Jianlei; Weissing, Franz J.; Cao, Ming

    2016-01-01

    A commonly used assumption in evolutionary game theory is that natural selection acts on individuals in the same time scale; e.g., players use the same frequency to update their strategies. Variation in learning rates within populations suggests that evolutionary game theory may not necessarily be

  6. Natural variability of atmospheric temperatures and geomagnetic intensity over a wide range of time scales.

    Science.gov (United States)

    Pelletier, Jon D

    2002-02-19

    The majority of numerical models in climatology and geomagnetism rely on deterministic finite-difference techniques and attempt to include as many empirical constraints on the many processes and boundary conditions applicable to their very complex systems. Despite their sophistication, many of these models are unable to reproduce basic aspects of climatic or geomagnetic dynamics. We show that a simple stochastic model, which treats the flux of heat energy in the atmosphere by convective instabilities with random advection and diffusive mixing, does a remarkable job at matching the observed power spectrum of historical and proxy records for atmospheric temperatures from time scales of one day to one million years (Myr). With this approach distinct changes in the power-spectral form can be associated with characteristic time scales of ocean mixing and radiative damping. Similarly, a simple model of the diffusion of magnetic intensity in Earth's core coupled with amplification and destruction of the local intensity can reproduce the observed 1/f noise behavior of Earth's geomagnetic intensity from time scales of 1 (Myr) to 100 yr. In addition, the statistics of the fluctuations in the polarity reversal rate from time scales of 1 Myr to 100 Myr are consistent with the hypothesis that reversals are the result of variations in 1/f noise geomagnetic intensity above a certain threshold, suggesting that reversals may be associated with internal fluctuations rather than changes in mantle thermal or magnetic boundary conditions.

  7. Time scales: from Nabla calculus to Delta calculus and vice versa via duality

    OpenAIRE

    Caputo, M. Cristina

    2009-01-01

    In this note we show how one can obtain results from the nabla calculus from results on the delta calculus and vice versa via a duality argument. We provide applications of the main results to the calculus of variations on time scales.

  8. A Visual Method of Time Scale Determination using a PC for Radio ...

    Indian Academy of Sciences (India)

    Abstract. Variability is one of the extremely observational properties. In the radio bands, variability is caused by the shock in the jet. In this case, emissions increase rapidly following an exponential curve, and then decrease rapidly also in an exponential curve. The variability time scale is important with regard to the physics ...

  9. Anti-control of chaos of single time-scale brushless DC motor.

    Science.gov (United States)

    Ge, Zheng-Ming; Chang, Ching-Ming; Chen, Yen-Sheng

    2006-09-15

    Anti-control of chaos of single time-scale brushless DC motors is studied in this paper. In order to analyse a variety of periodic and chaotic phenomena, we employ several numerical techniques such as phase portraits, bifurcation diagrams and Lyapunov exponents. Anti-control of chaos can be achieved by adding an external constant term or an external periodic term.

  10. Principal and nonprincipal solutions of symplectic dynamic systems on time scales

    Directory of Open Access Journals (Sweden)

    Ondrej Dosly

    2000-01-01

    Full Text Available We establish the concept of the principal and nonprincipal solution for the so-called symplectic dynamic systems on time scales. We also present a brief survey of the history of these concept for differential and difference equations.

  11. Towards a Unified Formulation of Dynamics and Thermodynamics I. From Microscopic to Macroscopic Time Scales

    Czech Academy of Sciences Publication Activity Database

    Durand, P.; Paidarová, Ivana

    2011-01-01

    Roč. 111, č. 2 (2011), s. 225-236 ISSN 0020-7608 R&D Projects: GA AV ČR IAA100400501; GA AV ČR IAA401870702 Institutional research plan: CEZ:AV0Z40400503 Keywords : Liouville equation * time scales * chemical kinetics and dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.357, year: 2011

  12. Assessment of the methods for determining net radiation at different time-scales of meteorological variables

    Directory of Open Access Journals (Sweden)

    Ni An

    2017-04-01

    Full Text Available When modeling the soil/atmosphere interaction, it is of paramount importance to determine the net radiation flux. There are two common calculation methods for this purpose. Method 1 relies on use of air temperature, while Method 2 relies on use of both air and soil temperatures. Nowadays, there has been no consensus on the application of these two methods. In this study, the half-hourly data of solar radiation recorded at an experimental embankment are used to calculate the net radiation and long-wave radiation at different time-scales (half-hourly, hourly, and daily using the two methods. The results show that, compared with Method 2 which has been widely adopted in agronomical, geotechnical and geo-environmental applications, Method 1 is more feasible for its simplicity and accuracy at shorter time-scale. Moreover, in case of longer time-scale, daily for instance, less variations of net radiation and long-wave radiation are obtained, suggesting that no detailed soil temperature variations can be obtained. In other words, shorter time-scales are preferred in determining net radiation flux.

  13. Global Stability of Complex-Valued Genetic Regulatory Networks with Delays on Time Scales

    Directory of Open Access Journals (Sweden)

    Wang Yajing

    2016-01-01

    Full Text Available In this paper, the global exponential stability of complex-valued genetic regulatory networks with delays is investigated. Besides presenting conditions guaranteeing the existence of a unique equilibrium pattern, its global exponential stability is discussed. Some numerical examples for different time scales.

  14. Influence of the time scale on the construction of financial networks.

    Science.gov (United States)

    Emmert-Streib, Frank; Dehmer, Matthias

    2010-09-30

    In this paper we investigate the definition and formation of financial networks. Specifically, we study the influence of the time scale on their construction. For our analysis we use correlation-based networks obtained from the daily closing prices of stock market data. More precisely, we use the stocks that currently comprise the Dow Jones Industrial Average (DJIA) and estimate financial networks where nodes correspond to stocks and edges correspond to none vanishing correlation coefficients. That means only if a correlation coefficient is statistically significant different from zero, we include an edge in the network. This construction procedure results in unweighted, undirected networks. By separating the time series of stock prices in non-overlapping intervals, we obtain one network per interval. The length of these intervals corresponds to the time scale of the data, whose influence on the construction of the networks will be studied in this paper. Numerical analysis of four different measures in dependence on the time scale for the construction of networks allows us to gain insights about the intrinsic time scale of the stock market with respect to a meaningful graph-theoretical analysis.

  15. New time scale based k-epsilon model for near-wall turbulence

    Science.gov (United States)

    Yang, Z.; Shih, T. H.

    1993-01-01

    A k-epsilon model is proposed for wall bonded turbulent flows. In this model, the eddy viscosity is characterized by a turbulent velocity scale and a turbulent time scale. The time scale is bounded from below by the Kolmogorov time scale. The dissipation equation is reformulated using this time scale and no singularity exists at the wall. The damping function used in the eddy viscosity is chosen to be a function of R(sub y) = (k(sup 1/2)y)/v instead of y(+). Hence, the model could be used for flows with separation. The model constants used are the same as in the high Reynolds number standard k-epsilon model. Thus, the proposed model will be also suitable for flows far from the wall. Turbulent channel flows at different Reynolds numbers and turbulent boundary layer flows with and without pressure gradient are calculated. Results show that the model predictions are in good agreement with direct numerical simulation and experimental data.

  16. How the constants in Hille-Nehari theorems depend on time scales

    Czech Academy of Sciences Publication Activity Database

    Řehák, Pavel

    2006-01-01

    Roč. 2006, - (2006), s. 1-15 ISSN 1687-1839 R&D Pro jects: GA ČR(CZ) GA201/01/0079; GA ČR(CZ) GP201/01/P041 Institutional research plan: CEZ:AV0Z10190503 Keywords : dynamic equation * time scales * oscillation criteria Subject RIV: BA - General Mathematics

  17. Theoretical and Numerical Properties of a Gyrokinetic Plasma: Issues Related to Transport Time Scale Simulation

    International Nuclear Information System (INIS)

    Lee, W.W.

    2003-01-01

    Particle simulation has played an important role for the recent investigations on turbulence in magnetically confined plasmas. In this paper, theoretical and numerical properties of a gyrokinetic plasma as well as its relationship with magnetohydrodynamics (MHD) are discussed with the ultimate aim of simulating microturbulence in transport time scale using massively parallel computers

  18. Non-Abelian Kubo formula and the multiple time-scale method

    International Nuclear Information System (INIS)

    Zhang, X.; Li, J.

    1996-01-01

    The non-Abelian Kubo formula is derived from the kinetic theory. That expression is compared with the one obtained using the eikonal for a Chern endash Simons theory. The multiple time-scale method is used to study the non-Abelian Kubo formula, and the damping rate for longitudinal color waves is computed. copyright 1996 Academic Press, Inc

  19. Multi-Time Scale Coordinated Scheduling Strategy with Distributed Power Flow Controllers for Minimizing Wind Power Spillage

    Directory of Open Access Journals (Sweden)

    Yi Tang

    2017-11-01

    Full Text Available The inherent variability and randomness of large-scale wind power integration have brought great challenges to power flow control and dispatch. The distributed power flow controller (DPFC has the higher flexibility and capacity in power flow control in the system with wind generation. This paper proposes a multi-time scale coordinated scheduling model with DPFC to minimize wind power spillage. Configuration of DPFCs is initially determined by stochastic method. Afterward, two sequential procedures containing day-head and real-time scales are applied for determining maximum schedulable wind sources, optimal outputs of generating units and operation setting of DPFCs. The generating plan is obtained initially in day-ahead scheduling stage and modified in real-time scheduling model, while considering the uncertainty of wind power and fast operation of DPFC. Numerical simulation results in IEEE-RTS79 system illustrate that wind power is maximum scheduled with the optimal deployment and operation of DPFC, which confirms the applicability and effectiveness of the proposed method.

  20. Synchronization and Causality Across Time-scales: Complex Dynamics and Extremes in El Niño/Southern Oscillation

    Science.gov (United States)

    Jajcay, N.; Kravtsov, S.; Tsonis, A.; Palus, M.

    2017-12-01

    A better understanding of dynamics in complex systems, such as the Earth's climate is one of the key challenges for contemporary science and society. A large amount of experimental data requires new mathematical and computational approaches. Natural complex systems vary on many temporal and spatial scales, often exhibiting recurring patterns and quasi-oscillatory phenomena. The statistical inference of causal interactions and synchronization between dynamical phenomena evolving on different temporal scales is of vital importance for better understanding of underlying mechanisms and a key for modeling and prediction of such systems. This study introduces and applies information theory diagnostics to phase and amplitude time series of different wavelet components of the observed data that characterizes El Niño. A suite of significant interactions between processes operating on different time scales was detected, and intermittent synchronization among different time scales has been associated with the extreme El Niño events. The mechanisms of these nonlinear interactions were further studied in conceptual low-order and state-of-the-art dynamical, as well as statistical climate models. Observed and simulated interactions exhibit substantial discrepancies, whose understanding may be the key to an improved prediction. Moreover, the statistical framework which we apply here is suitable for direct usage of inferring cross-scale interactions in nonlinear time series from complex systems such as the terrestrial magnetosphere, solar-terrestrial interactions, seismic activity or even human brain dynamics.

  1. The swan song in context: long-time-scale X-ray variability of NGC 4051

    Science.gov (United States)

    Uttley, P.; McHardy, I. M.; Papadakis, I. E.; Guainazzi, M.; Fruscione, A.

    1999-07-01

    On 1998 May 9-11, the highly variable, low-luminosity Seyfert 1 galaxy NGC 4051 was observed in an unusual low-flux state by BeppoSAX, RXTE and EUVE. We present fits of the 4-15keV RXTE spectrum and BeppoSAX MECS spectrum obtained during this observation, which are consistent with the interpretation that the source had switched off, leaving only the spectrum of pure reflection from distant cold matter. We place this result in context by showing the X-ray light curve of NGC 4051 obtained by our RXTE monitoring campaign over the past two and a half years, which shows that the low state lasted for ~150d before the May observations (implying that the reflecting material is >10^17cm from the continuum source) and forms part of a light curve showing distinct variations in long-term average flux over time-scales > months. We show that the long-time-scale component to X-ray variability is intrinsic to the primary continuum and is probably distinct from the variability at shorter time-scales. The long-time-scale component to variability maybe associated with variations in the accretion flow of matter on to the central black hole. As the source approaches the low state, the variability process becomes non-linear. NGC 4051 may represent a microcosm of all X-ray variability in radio-quiet active galactic nuclei (AGNs), displaying in a few years a variety of flux states and variability properties which more luminous AGNs may pass through on time-scales of decades to thousands of years.

  2. Evaluation of scalar mixing and time scale models in PDF simulations of a turbulent premixed flame

    Energy Technology Data Exchange (ETDEWEB)

    Stoellinger, Michael; Heinz, Stefan [Department of Mathematics, University of Wyoming, Laramie, WY (United States)

    2010-09-15

    Numerical simulation results obtained with a transported scalar probability density function (PDF) method are presented for a piloted turbulent premixed flame. The accuracy of the PDF method depends on the scalar mixing model and the scalar time scale model. Three widely used scalar mixing models are evaluated: the interaction by exchange with the mean (IEM) model, the modified Curl's coalescence/dispersion (CD) model and the Euclidean minimum spanning tree (EMST) model. The three scalar mixing models are combined with a simple model for the scalar time scale which assumes a constant C{sub {phi}}=12 value. A comparison of the simulation results with available measurements shows that only the EMST model calculates accurately the mean and variance of the reaction progress variable. An evaluation of the structure of the PDF's of the reaction progress variable predicted by the three scalar mixing models confirms this conclusion: the IEM and CD models predict an unrealistic shape of the PDF. Simulations using various C{sub {phi}} values ranging from 2 to 50 combined with the three scalar mixing models have been performed. The observed deficiencies of the IEM and CD models persisted for all C{sub {phi}} values considered. The value C{sub {phi}}=12 combined with the EMST model was found to be an optimal choice. To avoid the ad hoc choice for C{sub {phi}}, more sophisticated models for the scalar time scale have been used in simulations using the EMST model. A new model for the scalar time scale which is based on a linear blending between a model for flamelet combustion and a model for distributed combustion is developed. The new model has proven to be very promising as a scalar time scale model which can be applied from flamelet to distributed combustion. (author)

  3. Spatiotemporal patterns of drought at various time scales in Shandong Province of Eastern China

    Science.gov (United States)

    Zuo, Depeng; Cai, Siyang; Xu, Zongxue; Li, Fulin; Sun, Wenchao; Yang, Xiaojing; Kan, Guangyuan; Liu, Pin

    2018-01-01

    The temporal variations and spatial patterns of drought in Shandong Province of Eastern China were investigated by calculating the standardized precipitation evapotranspiration index (SPEI) at 1-, 3-, 6-, 12-, and 24-month time scales. Monthly precipitation and air temperature time series during the period 1960-2012 were collected at 23 meteorological stations uniformly distributed over the region. The non-parametric Mann-Kendall test was used to explore the temporal trends of precipitation, air temperature, and the SPEI drought index. S-mode principal component analysis (PCA) was applied to identify the spatial patterns of drought. The results showed that an insignificant decreasing trend in annual total precipitation was detected at most stations, a significant increase of annual average air temperature occurred at all the 23 stations, and a significant decreasing trend in the SPEI was mainly detected at the coastal stations for all the time scales. The frequency of occurrence of extreme and severe drought at different time scales generally increased with decades; higher frequency and larger affected area of extreme and severe droughts occurred as the time scale increased, especially for the northwest of Shandong Province and Jiaodong peninsular. The spatial pattern of drought for SPEI-1 contains three regions: eastern Jiaodong Peninsular and northwestern and southern Shandong. As the time scale increased to 3, 6, and 12 months, the order of the three regions was transformed into another as northwestern Shandong, eastern Jiaodong Peninsular, and southern Shandong. For SPEI-24, the location identified by REOF1 was slightly shifted from northwestern Shandong to western Shandong, and REOF2 and REOF3 identified another two weak patterns in the south edge and north edge of Jiaodong Peninsular, respectively. The potential causes of drought and the impact of drought on agriculture in the study area have also been discussed. The temporal variations and spatial patterns

  4. Existence and global exponential stability of periodic solutions for n-dimensional neutral dynamic equations on time scales.

    Science.gov (United States)

    Li, Bing; Li, Yongkun; Zhang, Xuemei

    2016-01-01

    In this paper, by using the existence of the exponential dichotomy of linear dynamic equations on time scales and the theory of calculus on time scales, we study the existence and global exponential stability of periodic solutions for a class of n-dimensional neutral dynamic equations on time scales. We also present an example to illustrate the feasibility of our results. The results of this paper are completely new and complementary to the previously known results even in both the case of differential equations (time scale [Formula: see text]) and the case of difference equations (time scale [Formula: see text]).

  5. Large-scale Patterns of 14C Age of Bulk Organic Carbon and Various Molecular Components in Grassland Soils

    Science.gov (United States)

    Jia, J.; Liu, Z.; Cao, Z.; Chen, L.; He, J. S.; Haghipour, N.; Wacker, L.; Eglinton, T. I.; Feng, X.

    2017-12-01

    Unraveling the fate of organic carbon (OC) in soils is essential to understanding the impact of global changes on the global carbon cycle. Previous studies have shown that while various soil OC components have different decomposability, chemically labile OC can have old 14C ages. However, few studies have compared the 14C age of various soil OC components on a large scale, which may provide important information on the link between the age or turnover of soil OC components to their sources, molecular structures as well as environmental variables. In this project, a suite of soil profiles were sampled along a large-scale transect of temperate and alpine grasslands across the Tibetan and Mongolian Plateaus in China with contrasting climatic, vegetation and soil properties. Bulk OC and source-specific compounds (including fatty acids (FAs), diacids (DAs) and lignin phenols) were radiocarbon-dated to investigate the age and turnover dynamics of different OC pools and the mechanisms controlling their stability. Our results show that lignin phenols displayed a large 14C variability. Short-chain (C16, 18) FAs sourced from vascular plants as well as microorganisms were younger than plant-derived long-chain FAs and DAs, indicating that short-chain FAs were easier to be decomposed or newly synthesized. In the temperate grasslands, long-chain DAs were younger than FAs, while the opposite trend was observed in the alpine grasslands. Preliminary correlation analysis suggests that the age of short-chain FAs were mainly influenced by clay contents and climate, while reactive minerals, clay or silt particles were important factors in the stabilization of long-chain FAs, DAs and lignin phenols. Overall, our study provided a unique 14 C dataset of soil OC components in grasslands, which will provide important constraints on soil carbon turnover in future investigations.

  6. Filament and core formation in nearby molecular clouds: results from the CARMA Large Area Star Formation Survey

    Science.gov (United States)

    Storm, Shaye; Mundy, Lee G.; Fernández-López, Manuel; Lee, Katherine I.; Ostriker, Eve C.; Looney, Leslie; Chen, Che-Yu; Classy Collaboration

    2015-01-01

    Stars rarely form in isolation, so it is critical to understand how the parsec-scale molecular cloud environment shapes the formation of individual dense cores at the sub-0.1 pc scale. To address the pathway to core formation in a clustered environment, I co-developed the CARMA Large Area Star Formation Survey, which spectrally imaged dense gas tracer lines across 800 square arcminutes of the Perseus and Serpens Molecular clouds with 7'' angular resolution. There are four key results from initial papers. First, I created a new non-binary dendrogram code that shows correlation between the hierarchical complexity of dense, N2H+ (J=1-0) structures and the amount of star formation activity in a cluster. This may imply that feedback from young protostars changes the structure of dense gas within a cluster and increases the amount of high column density material. Second, we discovered strong radial velocity gradients within filaments that are an order of magnitude larger than detected axial gradients. We see similar radial gradients in filaments formed in numerical simulations of converging, turbulent flows; this suggests that the observed filaments are accreting material from an environment that is flattened at larger scales, and that they are more likely to fragment locally into cores than to support the flow of gas along the filament length. Third, we constructed two size-linewidth relations using the dendrogram-identified gas structures and our high resolution maps of the gas centroid velocity and line-of-sight velocity dispersion. The two relations show distinct behavior, and we developed a theoretical framework based on isotropic turbulence to show that they support the clustered regions being flattened (sheet-like) at parsec scales, with depths on the order 0.1-0.2 pc into the sky. Finally, we found that many filaments seen with Herschel show substructure in our high resolution maps, which implies that measuring the widths of filaments may be more complex than

  7. Time scale defined by the fractal structure of the price fluctuations in foreign exchange markets

    Science.gov (United States)

    Kumagai, Yoshiaki

    2010-04-01

    In this contribution, a new time scale named C-fluctuation time is defined by price fluctuations observed at a given resolution. The intraday fractal structures and the relations of the three time scales: real time (physical time), tick time and C-fluctuation time, in foreign exchange markets are analyzed. The data set used is trading prices of foreign exchange rates; US dollar (USD)/Japanese yen (JPY), USD/Euro (EUR), and EUR/JPY. The accuracy of the data is one minute and data within a minute are recorded in order of transaction. The series of instantaneous velocity of C-fluctuation time flowing are exponentially distributed for small C when they are measured by real time and for tiny C when they are measured by tick time. When the market is volatile, for larger C, the series of instantaneous velocity are exponentially distributed.

  8. Fission time-scale in experiments and in multiple initiation model

    Energy Technology Data Exchange (ETDEWEB)

    Karamian, S. A., E-mail: karamian@nrmail.jinr.ru [Joint Institute for Nuclear Research (Russian Federation)

    2011-12-15

    Rate of fission for highly-excited nuclei is affected by the viscose character of the systemmotion in deformation coordinates as was reported for very heavy nuclei with Z{sub C} > 90. The long time-scale of fission can be described in a model of 'fission by diffusion' that includes an assumption of the overdamped diabatic motion. The fission-to-spallation ratio at intermediate proton energy could be influenced by the viscosity, as well. Within a novel approach of the present work, the cross examination of the fission probability, time-scales, and pre-fission neutron multiplicities is resulted in the consistent interpretation of a whole set of the observables. Earlier, different aspects could be reproduced in partial simulations without careful coordination.

  9. Continent-scale global change attribution in European birds - combining annual and decadal time scales

    DEFF Research Database (Denmark)

    Jørgensen, Peter Søgaard; Böhning-Gaese, Katrin; Thorup, Kasper

    2016-01-01

    foundation for attributing species responses to global change may be achieved by complementing an attributes-based approach by one estimating the relationship between repeated measures of organismal and environmental changes over short time scales. To assess the benefit of this multiscale perspective, we...... on or in the peak of the breeding season with the largest effect sizes observed in cooler parts of species' climatic ranges. Our results document the potential of combining time scales and integrating both species attributes and environmental variables for global change attribution. We suggest such an approach......Species attributes are commonly used to infer impacts of environmental change on multiyear species trends, e.g. decadal changes in population size. However, by themselves attributes are of limited value in global change attribution since they do not measure the changing environment. A broader...

  10. Chaos anticontrol and synchronization of three time scales brushless DC motor system

    International Nuclear Information System (INIS)

    Ge Zhengming; Cheng Juiwen; Chen Yensheng

    2004-01-01

    Chaos anticontrol of three time scale brushless dc motors and chaos synchronization of different order systems are studied. Nondimensional dynamic equations of three time scale brushless DC motor system are presented. Using numerical results, such as phase diagram, bifurcation diagram, and Lyapunov exponent, periodic and chaotic motions can be observed. By adding constant term, periodic square wave, the periodic triangle wave, the periodic sawtooth wave, and kx vertical bar x vertical bar term, to achieve anticontrol of chaotic or periodic systems, it is found that more chaotic phenomena of the system can be observed. Then, by coupled terms and linearization of error dynamics, we obtain the partial synchronization of two different order systems, i.e. brushless DC motor system and rate gyroscope system

  11. Full-scale and time-scale heating experiments at Stripa: preliminary results

    International Nuclear Information System (INIS)

    Cook, N.G.W.; Hood, Michael; California Univ., Berkeley

    1978-01-01

    Two full-scale heating experiments and a time-scale heating experiment have recently been started in granite 340 meters below surface. The purpose of the full-scale heating experiments is to assess the near-field effects of thermal loading for the design of an underground repository of nuclear wastes. That of the time-scale heating experiments is to obtain field data of the interaction between heaters and its effect on the rock mass during a period of about two years, which corresponds to about twenty years of full-scale operation. Geological features of the rock around each experiment have been mapped carefully, and temperatures, stresses and displacements induced in the rock by heating have been calculated in advance of the experiments. Some 800 different measurements are recorded at frequent intervals by a computer system situated underground. These data can be compared at any time with predictions made earlier on video display units underground

  12. Periodic Solution of Second-Order Hamiltonian Systems with a Change Sign Potential on Time Scales

    Directory of Open Access Journals (Sweden)

    You-Hui Su

    2009-01-01

    Full Text Available This paper is concerned with the second-order Hamiltonian system on time scales 𝕋 of the form uΔΔ(ρ(t+μb(t|u(t|μ−2u(t+∇¯H(t,u(t=0, Δ-a.e. t∈[0,T]𝕋 , u(0−u(T=uΔ(ρ(0−uΔ(ρ(T=0, where 0,T∈𝕋. By using the minimax methods in critical theory, an existence theorem of periodic solution for the above system is established. As an application, an example is given to illustrate the result. This is probably the first time the existence of periodic solutions for second-order Hamiltonian system on time scales has been studied by critical theory.

  13. Time-scale effects on the gain-loss asymmetry in stock indices

    Science.gov (United States)

    Sándor, Bulcsú; Simonsen, Ingve; Nagy, Bálint Zsolt; Néda, Zoltán

    2016-08-01

    The gain-loss asymmetry, observed in the inverse statistics of stock indices is present for logarithmic return levels that are over 2 % , and it is the result of the non-Pearson-type autocorrelations in the index. These non-Pearson-type correlations can be viewed also as functionally dependent daily volatilities, extending for a finite time interval. A generalized time-window shuffling method is used to show the existence of such autocorrelations. Their characteristic time scale proves to be smaller (less than 25 trading days) than what was previously believed. It is also found that this characteristic time scale has decreased with the appearance of program trading in the stock market transactions. Connections with the leverage effect are also established.

  14. Modes of correlated angular motion in live cells across three distinct time scales

    International Nuclear Information System (INIS)

    Harrison, Andrew W; Kenwright, David A; Woodman, Philip G; Allan, Victoria J; Waigh, Thomas A

    2013-01-01

    Particle tracking experiments with high speed digital microscopy yield the positions and trajectories of lipid droplets inside living cells. Angular correlation analysis shows that the lipid droplets have uncorrelated motion at short time scales (τ 10 ms, becomes persistent, indicating directed movement. The motion at all time scales is associated with the lipid droplets being tethered to and driven along the microtubule network. The point at which the angular correlation changes from anti-persistent to persistent motion corresponds to the cross over between sub-diffusive and super diffusive motion, as observed by mean square displacement analysis. Correct analysis of the angular correlations of the detector noise is found to be crucial in modelling the observed phenomena. (paper)

  15. Virtual water trade and time scales for loss of water sustainability: a comparative regional analysis.

    Science.gov (United States)

    Goswami, Prashant; Nishad, Shiv Narayan

    2015-03-20

    Assessment and policy design for sustainability in primary resources like arable land and water need to adopt long-term perspective; even small but persistent effects like net export of water may influence sustainability through irreversible losses. With growing consumption, this virtual water trade has become an important element in the water sustainability of a nation. We estimate and contrast the virtual (embedded) water trades of two populous nations, India and China, to present certain quantitative measures and time scales. Estimates show that export of embedded water alone can lead to loss of water sustainability. With the current rate of net export of water (embedded) in the end products, India is poised to lose its entire available water in less than 1000 years; much shorter time scales are implied in terms of water for production. The two cases contrast and exemplify sustainable and non-sustainable virtual water trade in long term perspective.

  16. Antipersistent dynamics in short time scale variability of self-potential signals

    OpenAIRE

    Cuomo, V.; Lanfredi, M.; Lapenna, V.; Macchiato, M.; Ragosta, M.; Telesca, L.

    2000-01-01

    Time scale properties of self-potential signals are investigated through the analysis of the second order structure function (variogram), a powerful tool to investigate the spatial and temporal variability of observational data. In this work we analyse two sequences of self-potential values measured by means of a geophysical monitoring array located in a seismically active area of Southern Italy. The range of scales investigated goes from a few minutes to several days. It is shown that signal...

  17. Influence of the Time Scale on the Construction of Financial Networks

    OpenAIRE

    Emmert-Streib, Frank; Dehmer, Matthias

    2010-01-01

    BACKGROUND: In this paper we investigate the definition and formation of financial networks. Specifically, we study the influence of the time scale on their construction. METHODOLOGY/PRINCIPAL FINDINGS: For our analysis we use correlation-based networks obtained from the daily closing prices of stock market data. More precisely, we use the stocks that currently comprise the Dow Jones Industrial Average (DJIA) and estimate financial networks where nodes correspond to stocks and edges correspon...

  18. A typology of time-scale mismatches and behavioral interventions to diagnose and solve conservation problems

    Science.gov (United States)

    Wilson, Robyn S.; Hardisty, David J.; Epanchin-Niell, Rebecca S.; Runge, Michael C.; Cottingham, Kathryn L.; Urban, Dean L.; Maguire, Lynn A.; Hastings, Alan; Mumby, Peter J.; Peters, Debra P.C.

    2016-01-01

    Ecological systems often operate on time scales significantly longer or shorter than the time scales typical of human decision making, which causes substantial difficulty for conservation and management in socioecological systems. For example, invasive species may move faster than humans can diagnose problems and initiate solutions, and climate systems may exhibit long-term inertia and short-term fluctuations that obscure learning about the efficacy of management efforts in many ecological systems. We adopted a management-decision framework that distinguishes decision makers within public institutions from individual actors within the social system, calls attention to the ways socioecological systems respond to decision makers’ actions, and notes institutional learning that accrues from observing these responses. We used this framework, along with insights from bedeviling conservation problems, to create a typology that identifies problematic time-scale mismatches occurring between individual decision makers in public institutions and between individual actors in the social or ecological system. We also considered solutions that involve modifying human perception and behavior at the individual level as a means of resolving these problematic mismatches. The potential solutions are derived from the behavioral economics and psychology literature on temporal challenges in decision making, such as the human tendency to discount future outcomes at irrationally high rates. These solutions range from framing environmental decisions to enhance the salience of long-term consequences, to using structured decision processes that make time scales of actions and consequences more explicit, to structural solutions aimed at altering the consequences of short-sighted behavior to make it less appealing. Additional application of these tools and long-term evaluation measures that assess not just behavioral changes but also associated changes in ecological systems are needed.

  19. A typology of time-scale mismatches and behavioral interventions to diagnose and solve conservation problems.

    Science.gov (United States)

    Wilson, Robyn S; Hardisty, David J; Epanchin-Niell, Rebecca S; Runge, Michael C; Cottingham, Kathryn L; Urban, Dean L; Maguire, Lynn A; Hastings, Alan; Mumby, Peter J; Peters, Debra P C

    2016-02-01

    Ecological systems often operate on time scales significantly longer or shorter than the time scales typical of human decision making, which causes substantial difficulty for conservation and management in socioecological systems. For example, invasive species may move faster than humans can diagnose problems and initiate solutions, and climate systems may exhibit long-term inertia and short-term fluctuations that obscure learning about the efficacy of management efforts in many ecological systems. We adopted a management-decision framework that distinguishes decision makers within public institutions from individual actors within the social system, calls attention to the ways socioecological systems respond to decision makers' actions, and notes institutional learning that accrues from observing these responses. We used this framework, along with insights from bedeviling conservation problems, to create a typology that identifies problematic time-scale mismatches occurring between individual decision makers in public institutions and between individual actors in the social or ecological system. We also considered solutions that involve modifying human perception and behavior at the individual level as a means of resolving these problematic mismatches. The potential solutions are derived from the behavioral economics and psychology literature on temporal challenges in decision making, such as the human tendency to discount future outcomes at irrationally high rates. These solutions range from framing environmental decisions to enhance the salience of long-term consequences, to using structured decision processes that make time scales of actions and consequences more explicit, to structural solutions aimed at altering the consequences of short-sighted behavior to make it less appealing. Additional application of these tools and long-term evaluation measures that assess not just behavioral changes but also associated changes in ecological systems are needed. © 2015

  20. Nonlinearities in Drug Release Process from Polymeric Microparticles: Long-Time-Scale Behaviour

    Directory of Open Access Journals (Sweden)

    Elena Simona Bacaita

    2012-01-01

    Full Text Available A theoretical model of the drug release process from polymeric microparticles (a particular type of polymer matrix, through dispersive fractal approximation of motion, is built. As a result, the drug release process takes place through cnoidal oscillations modes of a normalized concentration field. This indicates that, in the case of long-time-scale evolutions, the drug particles assemble in a lattice of nonlinear oscillators occur macroscopically, through variations of drug concentration. The model is validated by experimental results.

  1. Chaos synchronization and parameter identification of three time scales brushless DC motor system

    International Nuclear Information System (INIS)

    Ge, Z.-M.; Cheng, J.-W.

    2005-01-01

    Chaotic anticontrol and chaos synchronization of brushless DC motor system are studied in this paper. Nondimensional dynamic equations of three time scale brushless DC motor system are presented. Using numerical results, such as phase diagram, bifurcation diagram, and Lyapunov exponent, periodic and chaotic motions can be observed. Then, chaos synchronization of two identical systems via additional inputs and Lyapunov stability theory are studied. And further, the parameter of the system is traced via adaptive control and random optimization method

  2. Fine Scale Baleen Whale Behavior Observed Via Tagging Over Daily Time Scales

    Science.gov (United States)

    2014-09-30

    system to do a comparison between the two. While at Wildlife Computers, I also asked for and they kindly provided a small change in how their MK10...cetacean behavior at intermediate daily time scales. Recent efforts to assess the impacts of sound on marine mammals and to estimate foraging ...efficiency have called for the need to measure daily activity budgets to quantify how much of each day an individual devotes to foraging , resting

  3. Measurement of 14C time scale of the rings of a tree by accelerator mass spectrometry

    International Nuclear Information System (INIS)

    Oda, Hirotaka; Furukawa, Michiaki; Yonenobu, Hitoshi; Ikeda, Akiko; Nakamura, Toshio.

    1996-01-01

    14 C time scale is different from a histrical data in order that it is calculated by assuming that the concentration of 14 C in the sample has not been changed by age. The object of this work is to make clear the errors in measurement of 14 C time scale of the ring of a tree known the tree age. The every year ring of a Hinoki in Kiso, 950 years old, was used as a sample. The most external ring is determined as 1923 years old on the basis of the dendrochronology. The rings after 1120 years were used as the samples. α-cellulose, the most stable component in the structural components of cell of tree, was prepared from each ring. About 8 mg of α-cellulose was reduced to graphite to be measured by the tandem thoron analytic meter. The results obtained showed that 14 C time scale was older than that of the histrical data in the twelfth and thirteenth century, but it was more new than that of the histrical data from the late seventeenth to the middle of eighteenth century. The results were agreement with that of Stuiver and Pearson (1933). (S.Y.)

  4. Antipersistent dynamics in short time scale variability of self-potential signals

    Directory of Open Access Journals (Sweden)

    M. Ragosta

    2000-06-01

    Full Text Available Time scale properties of self-potential signals are investigated through the analysis of the second order structure function (variogram, a powerful tool to investigate the spatial and temporal variability of observational data. In this work we analyse two sequences of self-potential values measured by means of a geophysical monitoring array located in a seismically active area of Southern Italy. The range of scales investigated goes from a few minutes to several days. It is shown that signal fluctuations are characterised by two time scale ranges in which self-potential variability appears to follow slightly different dynamical behaviours. Results point to the presence of fractal, non stationary features expressing a long term correlation with scaling coefficients which are the clue of stabilising mechanisms. In the scale ranges in which the series show scale invariant behaviour, self-potentials evolve like fractional Brownian motions with anticorrelated increments typical of processes regulated by negative feedback mechanisms (antipersistence. On scales below about 6 h the strength of such an antipersistence appears to be slightly greater than that observed on larger time scales where the fluctuations are less efficiently stabilised.

  5. Multiple time scale analysis of sediment and runoff changes in the Lower Yellow River

    Directory of Open Access Journals (Sweden)

    K. Chi

    2018-06-01

    Full Text Available Sediment and runoff changes of seven hydrological stations along the Lower Yellow River (LYR (Huayuankou Station, Jiahetan Station, Gaocun Station, Sunkou Station, Ai Shan Station, Qikou Station and Lijin Station from 1980 to 2003 were alanyzed at multiple time scale. The maximum value of monthly, daily and hourly sediment load and runoff conservations were also analyzed with the annually mean value. Mann–Kendall non-parametric mathematics correlation test and Hurst coefficient method were adopted in the study. Research results indicate that (1 the runoff of seven hydrological stations was significantly reduced in the study period at different time scales. However, the trends of sediment load in these stations were not obvious. The sediment load of Huayuankou, Jiahetan and Aishan stations even slightly increased with the runoff decrease. (2 The trends of the sediment load with different time scale showed differences at Luokou and Lijin stations. Although the annually and monthly sediment load were broadly flat, the maximum hourly sediment load showed decrease trend. (3 According to the Hurst coefficients, the trend of sediment and runoff will be continue without taking measures, which proved the necessary of runoff-sediment regulation scheme.

  6. Modeling Climate Responses to Spectral Solar Forcing on Centennial and Decadal Time Scales

    Science.gov (United States)

    Wen, G.; Cahalan, R.; Rind, D.; Jonas, J.; Pilewskie, P.; Harder, J.

    2012-01-01

    We report a series of experiments to explore clima responses to two types of solar spectral forcing on decadal and centennial time scales - one based on prior reconstructions, and another implied by recent observations from the SORCE (Solar Radiation and Climate Experiment) SIM (Spectral 1rradiance Monitor). We apply these forcings to the Goddard Institute for Space Studies (GISS) Global/Middle Atmosphere Model (GCMAM). that couples atmosphere with ocean, and has a model top near the mesopause, allowing us to examine the full response to the two solar forcing scenarios. We show different climate responses to the two solar forCing scenarios on decadal time scales and also trends on centennial time scales. Differences between solar maximum and solar minimum conditions are highlighted, including impacts of the time lagged reSponse of the lower atmosphere and ocean. This contrasts with studies that assume separate equilibrium conditions at solar maximum and minimum. We discuss model feedback mechanisms involved in the solar forced climate variations.

  7. Molecular dynamics simulations with electronic stopping can reproduce experimental sputtering yields of metals impacted by large cluster ions

    Science.gov (United States)

    Tian, Jiting; Zhou, Wei; Feng, Qijie; Zheng, Jian

    2018-03-01

    An unsolved problem in research of sputtering from metals induced by energetic large cluster ions is that molecular dynamics (MD) simulations often produce sputtering yields much higher than experimental results. Different from the previous simulations considering only elastic atomic interactions (nuclear stopping), here we incorporate inelastic electrons-atoms interactions (electronic stopping, ES) into MD simulations using a friction model. In this way we have simulated continuous 45° impacts of 10-20 keV C60 on a Ag(111) surface, and found that the calculated sputtering yields can be very close to the experimental results when the model parameter is appropriately assigned. Conversely, when we ignore the effect of ES, the yields are much higher, just like the previous studies. We further expand our research to the sputtering of Au induced by continuous keV C60 or Ar100 bombardments, and obtain quite similar results. Our study indicates that the gap between the experimental and the simulated sputtering yields is probably induced by the ignorance of ES in the simulations, and that a careful treatment of this issue is important for simulations of cluster-ion-induced sputtering, especially for those aiming to compare with experiments.

  8. Fullerene/layered antiferromagnetic reconstructed spinterface: Subsurface layer dominates molecular orbitals' spin-split and large induced magnetic moment

    Science.gov (United States)

    Shao, Yangfan; Pang, Rui; Pan, Hui; Shi, Xingqiang

    2018-03-01

    The interfaces between organic molecules and magnetic metals have gained increasing interest for both fundamental reasons and applications. Among them, the C60/layered antiferromagnetic (AFM) interfaces have been studied only for C60 bonded to the outermost ferromagnetic layer [S. L. Kawahara et al., Nano Lett. 12, 4558 (2012) and D. Li et al., Phys. Rev. B 93, 085425 (2016)]. Here, via density functional theory calculations combined with evidence from the literature, we demonstrate that C60 adsorption can reconstruct the layered-AFM Cr(001) surface at elevated annealing temperatures so that C60 bonds to both the outermost and the subsurface Cr layers in opposite spin directions. Surface reconstruction drastically changes the adsorbed molecule spintronic properties: (1) the spin-split p-d hybridization involves multi-orbitals of C60 and top two layers of Cr with opposite spin-polarization, (2) the subsurface Cr atom dominates the C60 electronic properties, and (3) the reconstruction induces a large magnetic moment of 0.58 μB in C60 as a synergistic effect of the top two Cr layers. The induced magnetic moment in C60 can be explained by the magnetic direct-exchange mechanism, which can be generalized to other C60/magnetic metal systems. Understanding these complex hybridization behaviors is a crucial step for molecular spintronic applications.

  9. Earth History databases and visualization - the TimeScale Creator system

    Science.gov (United States)

    Ogg, James; Lugowski, Adam; Gradstein, Felix

    2010-05-01

    The "TimeScale Creator" team (www.tscreator.org) and the Subcommission on Stratigraphic Information (stratigraphy.science.purdue.edu) of the International Commission on Stratigraphy (www.stratigraphy.org) has worked with numerous geoscientists and geological surveys to prepare reference datasets for global and regional stratigraphy. All events are currently calibrated to Geologic Time Scale 2004 (Gradstein et al., 2004, Cambridge Univ. Press) and Concise Geologic Time Scale (Ogg et al., 2008, Cambridge Univ. Press); but the array of intercalibrations enable dynamic adjustment to future numerical age scales and interpolation methods. The main "global" database contains over 25,000 events/zones from paleontology, geomagnetics, sea-level and sequence stratigraphy, igneous provinces, bolide impacts, plus several stable isotope curves and image sets. Several regional datasets are provided in conjunction with geological surveys, with numerical ages interpolated using a similar flexible inter-calibration procedure. For example, a joint program with Geoscience Australia has compiled an extensive Australian regional biostratigraphy and a full array of basin lithologic columns with each formation linked to public lexicons of all Proterozoic through Phanerozoic basins - nearly 500 columns of over 9,000 data lines plus hot-curser links to oil-gas reference wells. Other datapacks include New Zealand biostratigraphy and basin transects (ca. 200 columns), Russian biostratigraphy, British Isles regional stratigraphy, Gulf of Mexico biostratigraphy and lithostratigraphy, high-resolution Neogene stable isotope curves and ice-core data, human cultural episodes, and Circum-Arctic stratigraphy sets. The growing library of datasets is designed for viewing and chart-making in the free "TimeScale Creator" JAVA package. This visualization system produces a screen display of the user-selected time-span and the selected columns of geologic time scale information. The user can change the

  10. Towards a High-resolution Time Scale for the Early Devonian

    Science.gov (United States)

    Dekkers, M. J.; da Silva, A. C.

    2017-12-01

    High-resolution time scales are crucial to understand Earth's history in detail. The construction of a robust geological time scale, however, inevitably becomes increasingly harder further back in time. Uncertainties associated with anchor radiometric ages increase in size, not speaking of the mere presence of suitable datable strata. However, durations of stages can be tightly constrained by making use of cyclic expressions in sediments, an approach that revolutionized the Cenozoic time scale. When precisely determined durations are stitched together, ultimately, a very precise time scale is the result. For the Mesozoic and Paleozoic an astronomical solution as a tuning target is not available but the dominant periods of eccentricity, obliquity and precession are reasonably well constrained for the entire Phanerozoic which enables their detection by means of spectral analysis. Eccentricity is time-invariant and is used as the prime building block. Here we focus on the Early Devonian, on its lowermost three stages: the Lochkovian, Pragian and Emsian. The uncertainties on the Devonian stage boundaries are currently in the order of several millions of years. The preservation of climatic cycles in diagenetically or even anchimetamorphically affected successions, however, is essential. The fit of spectral peak ratios with those calculated for orbital cycles, is classically used as a strong argument for a preserved climatic signal. Here we use primarily the low field magnetic susceptibility (MS) as proxy parameter, supported by gamma-ray spectrometry to test for consistency. Continuous Wavelet Transform, Evolutive Harmonic Analysis, Multitaper Method, and Average Spectral Misfit are used to reach an optimal astronomical interpretation. We report on classic Early Devonian sections from the Czech Republic: the Pozar-CS (Lochkovian and Pragian), Pod Barrandovem (Pragian and Lower Emsian), and Zlichov (Middle-Upper Emsian). Also a Middle-Upper Emsian section from the US

  11. Analytical Solutions for Multi-Time Scale Fractional Stochastic Differential Equations Driven by Fractional Brownian Motion and Their Applications

    OpenAIRE

    Xiao-Li Ding; Juan J. Nieto

    2018-01-01

    In this paper, we investigate analytical solutions of multi-time scale fractional stochastic differential equations driven by fractional Brownian motions. We firstly decompose homogeneous multi-time scale fractional stochastic differential equations driven by fractional Brownian motions into independent differential subequations, and give their analytical solutions. Then, we use the variation of constant parameters to obtain the solutions of nonhomogeneous multi-time scale fractional stochast...

  12. Resurgent Toba – field, chronologic, and model constraints on time scales and mechanisms of resurgence at large calderas

    Directory of Open Access Journals (Sweden)

    Shanaka L De Silva

    2015-06-01

    Full Text Available New data reveal details of the post-caldera history at the Earth’s youngest resurgent supervolcano, Toba caldera in Sumatra. Resurgence after the caldera-forming ~74 ka Youngest Toba Tuff eruption uplifted the caldera floor as a resurgent dome, Samosir Island, capped with 100m of lake sediments. 14C age data from the uppermost datable sediments reveal that Samosir Island was submerged beneath lake level (~900m a.s.l ~33.7 ky. Since then, Samosir experienced 700m of uplift as a tilted block dipping to the west. Using 14C ages and elevations of sediment along a transect of Samosir reveal that minimum uplift rates were ~4.9 cm/yr from ~33.7 to 22.5 ka, but diminished to ~0.7 cm/yr after 22.5ka. Thermo-mechanical models informed by these rates reveal that detumescence does not produce the uplift nor the uplift rates estimated for Samosir. However, models calculating the effect of volume change of the magma reservoir within a temperature-dependent viscoelastic host rock reveal that a single pulse of ~475 km3 of magma produces a better fit to the uplift data than a constant flux. Reproducing the uplift rates require more sophisticated models. Motivation for resurgent uplift of the caldera floor is rebound of remnant magma as the system re-established magmastatic and isostatic equilibrium after the caldera collapse. Previous assertions that the caldera floor was apparently at 400m a.s.l or lower requires that uplift must have initiated between sometime between 33.7 ka and 74 ka at a minimum average uplift rate of ~1.1 cm/ year. The change in uplift rate from pre-33.7 ka to immediately post-33.7 ka suggests a role for deep recharge augmenting rebound. Average minimum rates of resurgent uplift at Toba are at least an order of magnitude slower than net rates of restlessness at currently active calderas. This connotes a distinction between resurgence and restlessness controlled by different processes, scales of process, and controlling variables.

  13. THE INFLUENCE OF FAR-ULTRAVIOLET RADIATION ON THE PROPERTIES OF MOLECULAR CLOUDS IN THE 30 DOR REGION OF THE LARGE MAGELLANIC CLOUD

    International Nuclear Information System (INIS)

    Pineda, Jorge L.; Klein, Ulrich; Ott, Juergen; Wong, Tony; Muller, Erik; Hughes, Annie

    2009-01-01

    We present a complete 12 CO J = 1 → 0 map of the prominent molecular ridge in the Large Magellanic Cloud (LMC) obtained with the 22 m ATNF Mopra Telescope. The region stretches southward by ∼2 deg. (or 1.7 kpc) from 30 Doradus, the most vigorous star-forming region in the Local Group. The location of this molecular ridge is unique insofar as it allows us to study the properties of molecular gas as a function of the ambient radiation field in a low-metallicity environment. We find that the physical properties of CO-emitting clumps within the molecular ridge do not vary with the strength of the far-ultraviolet radiation field. Since the peak CO brightness of the clumps shows no correlation with the radiation field strength, the observed constant value for CO-to-H 2 conversion factor along the ridge seems to require an increase in the kinetic temperature of the molecular gas that is offset by a decrease in the angular filling factor of the CO emission. We find that the difference between the CO-to-H 2 conversion factor in the molecular ridge and the outer Milky Way is smaller than has been reported by previous studies of the CO emission: applying the same cloud identification and analysis methods to our CO observations of the LMC molecular ridge and CO data from the outer Galaxy survey by Dame et al., we find that the average CO-to-H 2 conversion factor in the molecular ridge is X CO ≅ (3.9 ± 2.5) x 10 20 cm -2 (K km s -1 ) -1 , approximately twice the value that we determine for the outer Galaxy clouds. The mass spectrum and the scaling relations between the properties of the CO clumps in the molecular ridge are similar, but not identical, to those that have been established for Galactic molecular clouds.

  14. A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies.

    Directory of Open Access Journals (Sweden)

    Jerome C Regier

    Full Text Available Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies.483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity.Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also shows that some nodes get strong support only when

  15. Comparison of pathogen DNA isolation methods from large volumes of whole blood to improve molecular diagnosis of bloodstream infections.

    Directory of Open Access Journals (Sweden)

    Anne J M Loonen

    Full Text Available For patients suffering from bloodstream infections (BSI molecular diagnostics from whole blood holds promise to provide fast and adequate treatment. However, this approach is hampered by the need of large blood volumes. Three methods for pathogen DNA isolation from whole blood were compared, i.e. an enzymatic method (MolYsis, 1-5 ml, the novel non-enzymatic procedure (Polaris, 1-5 ml, and a method that does not entail removal of human DNA (Triton-Tris-EDTA EasyMAG, 200 µl. These methods were evaluated by processing blood spiked with 0-1000 CFU/ml of Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans. Downstream detection was performed with real-time PCR assays. Polaris and MolYsis processing followed by real-time PCRs enabled pathogen detection at clinically relevant concentrations of 1-10 CFU/ml blood. By increasing sample volumes, concurrent lower cycle threshold (Ct values were obtained at clinically relevant pathogen concentrations, demonstrating the benefit of using larger blood volumes. A 100% detection rate at a concentration of 10 CFU/ml for all tested pathogens was obtained with the Polaris enrichment, whereas comparatively lower detection rates were measured for MolYsis (50-67% and EasyMAG (58-79%. For the samples with a concentration of 1 CFU/ml Polaris resulted in most optimal detection rates of 70-75% (MolYsis 17-50% and TTE-EasyMAG 20-36%. The Polaris method was more reproducible, less labour intensive, and faster (45 minutes (including Qiagen DNA extraction vs. 2 hours (MolYsis. In conclusion, Polaris and MolYsis enrichment followed by DNA isolation and real-time PCR enables reliable and sensitive detection of bacteria and fungi from 5 ml blood. With Polaris results are available within 3 hours, showing potential for improved BSI diagnostics.

  16. Synthesis of Mesoporous Carbons from Date Pits for the Adsorption of Large Molecular Weight Micropollutants in Wastewater

    KAUST Repository

    Al Jeffrey, Ahmed

    2013-07-01

    Efficient reuse of waste water requires removal of micro-pollutants from waste water streams by affordable and sustainable methods. Activated carbon is considered a powerful adsorbent due to its high surface area and low cost of treatment, compared to other expensive methods such as membrane filtration. Producing activated carbon with larger mesoporosity (>2nm) is of particular interest in industry in the removal of larger molecular sized pollutants. This study reports the synthesis of mesoporous activated carbons from a nonsoluble biomass precursor (date-pits) along with chemical activation using ZnCl2. Thus, produced activated carbon showed high surface area and large mesopore volume up to 1571 m2/g and 2.00 cm3/g respectively. In addition, the pore size of the product was as high as 9.30 nm. As a method of verification, HRTEM (Highresolution transmission electron microscopy) was used to directly authenticate the pore size of the synthesized activated carbons. Tannic acid and atrazine were used as model waste water pollutants and the adsorption capability of the produced activated carbon for these pollutants were evaluated and compared to a commercial mesoporous carbon: G60 from Norit. The results showed that the sorption capacity of produced activated carbon for tannic acid was 2 times that of G60 while the sorption capacity of produced activated carbon for atrazine was lower than that of G60. The activated carbon was also evaluated for adsorption of real secondary effluent municipal wastewater and the results suggest that the produced activated carbon was able to sorb a greater amount of biopolymers than G60. These results demonstrate that the thus-produced activated carbon may be a promising sorbent for waste water treatment.

  17. A Molecular Dynamics Study of Lunasin | Singh | South African ...

    African Journals Online (AJOL)

    A Molecular Dynamics Study of Lunasin. ... profile of lunasin,using classical molecular dynamics (MD) simulations at the time scale of 300 ns. ... Keywords: Lunasin, molecular dynamics, amber, CLASICO, α-helix, β-turn, PTRAJ, RGD, RMSD ...

  18. Influence of molecular weight and pH on adsorption of chitosan at the surface of large and giant vesicles.

    Science.gov (United States)

    Quemeneur, Francois; Rinaudo, Marguerite; Pépin-Donat, Brigitte

    2008-01-01

    This paper describes the mechanisms of adsorption of chitosan, a positively charged polyelectrolyte, on the DOPC lipid membrane of large and giant unilamellar vesicles (respectively, LUVs and GUVs). We observe that the variation of the zeta potential of LUVs as a function of chitosan concentration is independent on the chitosan molecular weight (Mw). This result is interpreted in terms of electrostatic interactions, which induce a flat adsorption of the chitosan on the surface of the membrane. The role of electrostatic interactions is further studied by observing the variation of the zeta potential as a function of the chitosan concentration for two different charge densities tuned by the pH. Results show a stronger chitosan-membrane affinity at pH 6 (lipids are negatively charged, and 40% chitosan amino groups are protonated) than at pH 3.4 (100% of protonated amino groups but zwitterionic lipids are positively charged) which confirms that adsorption is of electrostatic origin. Then, we investigate the stability of decorated LUVs and GUVs in a large range of pH (6.0 pH variation of the zeta potential as a function of the pH (2.0 pH pH pH > 10.0, in the absence of chitosan, the vesicles present complex shapes, contrary to the chitosan-decorated vesicles which remain spherical, confirming thus that chitosan remains adsorbed on vesicles in basic conditions up to pH = 12.0. These results, in addition with our previous data, show that the chitosan-decorated vesicles are stable over a very broad range of pH (2.0 pH < 12.0), which holds promise for their in vivo applications. Finally, the quantification of the chitosan adsorption on a LUV membrane is performed by zeta potential and fluorescence measurements. The fraction of membrane surface covered by chitosan is estimated to be lower than 40 %, which corresponds to the formation of a flat layer of chitosan on the membrane surface on an electrostatic basis.

  19. Insights into the Molecular Pathogenesis of Activated B-Cell-like Diffuse Large B-Cell Lymphoma and Its Therapeutic Implications

    Directory of Open Access Journals (Sweden)

    Georg Lenz

    2015-05-01

    Full Text Available Within the last couple of years, the understanding of the molecular mechanisms that drive the pathogenesis of diffuse large B-cell lymphoma (DLBCL has significantly improved. Large-scale gene expression profiling studies have led to the discovery of several molecularly defined subtypes that are characterized by specific oncogene addictions and significant differences in their outcome. Next generation sequencing efforts combined with RNA interference screens frequently identify crucial oncogenes that lead to constitutive activation of various signaling pathways that drive lymphomagenesis. This review summarizes our current understanding of the molecular pathogenesis of the activated B-cell-like (ABC DLBCL subtype that is characterized by poor prognosis. A special emphasis is put on findings that might impact therapeutic strategies of affected patients.

  20. Insights into the Molecular Pathogenesis of Activated B-Cell-like Diffuse Large B-Cell Lymphoma and Its Therapeutic Implications

    Energy Technology Data Exchange (ETDEWEB)

    Lenz, Georg [Translational Oncology, Department of Medicine A, Albert-Schweitzer Campus 1, University Hospital Münster, 48149 Münster (Germany); Cluster of Excellence EXC 1003, Cells in Motion, 48149 Münster (Germany)

    2015-05-22

    Within the last couple of years, the understanding of the molecular mechanisms that drive the pathogenesis of diffuse large B-cell lymphoma (DLBCL) has significantly improved. Large-scale gene expression profiling studies have led to the discovery of several molecularly defined subtypes that are characterized by specific oncogene addictions and significant differences in their outcome. Next generation sequencing efforts combined with RNA interference screens frequently identify crucial oncogenes that lead to constitutive activation of various signaling pathways that drive lymphomagenesis. This review summarizes our current understanding of the molecular pathogenesis of the activated B-cell-like (ABC) DLBCL subtype that is characterized by poor prognosis. A special emphasis is put on findings that might impact therapeutic strategies of affected patients.

  1. The Steppengrille (Gryllus spec./assimilis: selective filters and signal mismatch on two time scales.

    Directory of Open Access Journals (Sweden)

    Matti Michael Rothbart

    Full Text Available In Europe, several species of crickets are available commercially as pet food. Here we investigated the calling song and phonotactic selectivity for sound patterns on the short and long time scales for one such a cricket, Gryllus spec., available as "Gryllus assimilis", the Steppengrille, originally from Ecuador. The calling song consisted of short chirps (2-3 pulses, carrier frequency: 5.0 kHz emitted with a pulse period of 30.2 ms and chirp rate of 0.43 per second. Females exhibited high selectivity on both time scales. The preference for pulse period peaked at 33 ms which was higher then the pulse period produced by males. Two consecutive pulses per chirp at the correct pulse period were already sufficient for positive phonotaxis. The preference for the chirp pattern was limited by selectivity for small chirp duty cycles and for chirp periods between 200 ms and 500 ms. The long chirp period of the songs of males was unattractive to females. On both time scales a mismatch between the song signal of the males and the preference of females was observed. The variability of song parameters as quantified by the coefficient of variation was below 50% for all temporal measures. Hence, there was not a strong indication for directional selection on song parameters by females which could account for the observed mismatch. The divergence of the chirp period and female preference may originate from a founder effect, when the Steppengrille was cultured. Alternatively the mismatch was a result of selection pressures exerted by commercial breeders on low singing activity, to satisfy customers with softly singing crickets. In the latter case the prominent divergence between male song and female preference was the result of domestication and may serve as an example of rapid evolution of song traits in acoustic communication systems.

  2. Time scales of foam stability in shallow conduits: Insights from analogue experiments

    Science.gov (United States)

    Spina, L.; Scheu, B.; Cimarelli, C.; Arciniega-Ceballos, A.; Dingwell, D. B.

    2016-10-01

    Volcanic systems can exhibit periodical trends in degassing activity, characterized by a wide range of time scales. Understanding the dynamics that control such periodic behavior can provide a picture of the processes occurring in the feeding system. Toward this end, we analyzed the periodicity of outgassing in a series of decompression experiments performed on analogue material (argon-saturated silicone oil plus glass beads/fibers) scaled to serve as models of basaltic magma. To define the effects of liquid viscosity and crystal content on the time scale of outgassing, we investigated both: (1) pure liquid systems, at differing viscosities (100 and 1000 Pa s), and (2) particle-bearing suspensions (diluted and semidiluted). The results indicate that under dynamic conditions (e.g., decompressive bubble growth and fluid ascent within the conduit), the periodicity of foam disruption may be up to several orders of magnitude less than estimates based on the analysis of static conditions. This difference in foam disruption time scale is inferred to result from the contribution of bubble shear and bubble growth to inter-bubble film thinning. The presence of particles in the semidiluted regime is further linked to shorter bubble bursting times, likely resulting from contributions of the presence of a solid network and coalescence processes to the relative increase in bubble breakup rates. Finally, it is argued that these experiments represent a good analogue of gas-piston activity (i.e., the periodical rise-and-fall of a basaltic lava lake surface), implying a dominant role for shallow foam accumulation as a source process for these phenomena.

  3. Stability and periodicity of solutions for delay dynamic systems on time scales

    Directory of Open Access Journals (Sweden)

    Zhi-Qiang Zhu

    2014-04-01

    Full Text Available This article concerns the stability and periodicity of solutions to the delay dynamic system $$ x^{\\triangle}(t=A(t x(t + F(t, x(t, x(g(t+C(t $$ on a time scale. By the inequality technique for vectors, we obtain some stability criteria for the above system. Then, by using the Horn fixed point theorem, we present some conditions under which our system is asymptotically periodic and its periodic solution is unique. In particular, the periodic solution is positive under proper assumptions.

  4. A critical oscillation constant as a variable of time scales for half-linear dynamic equations

    Czech Academy of Sciences Publication Activity Database

    Řehák, Pavel

    2010-01-01

    Roč. 60, č. 2 (2010), s. 237-256 ISSN 0139-9918 R&D Projects: GA AV ČR KJB100190701 Institutional research plan: CEZ:AV0Z10190503 Keywords : dynamic equation * time scale * half-linear equation * (non)oscillation criteria * Hille-Nehari criteria * Kneser criteria * critical constant * oscillation constant * Hardy inequality Subject RIV: BA - General Mathematics Impact factor: 0.316, year: 2010 http://link.springer.com/article/10.2478%2Fs12175-010-0009-7

  5. Hybrid approximations via second order combined dynamic derivatives on time scales

    Directory of Open Access Journals (Sweden)

    Qin Sheng

    2007-09-01

    Full Text Available This article focuses on the approximation of conventional second order derivative via the combined (diamond-$\\alpha$ dynamic derivative on time scales with necessary smoothness conditions embedded. We will show the constraints under which the second order dynamic derivative provides a consistent approximation to the conventional second derivative; the cases where the dynamic derivative approximates the derivative only via a proper modification of the existing formula; and the situations in which the dynamic derivative can never approximate consistently even with the help of available structure correction methods. Constructive error analysis will be given via asymptotic expansions for practical hybrid modeling and computational applications.

  6. Transport equation for the time scale of a turbulent scalar field

    International Nuclear Information System (INIS)

    Kurbatskij, A.F.

    1999-01-01

    The two-parametric turbulence models cause serious difficulties by modeling the near-wall flows due to absence of the natural boundary condition on the wall for dissipation of the ε turbulence energy and the ε θ scalar field destruction. This difficulty may be overcome, if instead of the ε and ε θ , as the second parameter of the model, to apply the time scales of the turbulent dynamic and scalar fields. The equation of the scalar field is derived and numerical coefficients included therein, are determined from the simplest problems on the turbulent heat transfer [ru

  7. Long time scale hard X-ray variability in Seyfert 1 galaxies

    Science.gov (United States)

    Markowitz, Alex Gary

    This dissertation examines the relationship between long-term X-ray variability characteristics, black hole mass, and luminosity of Seyfert 1 Active Galactic Nuclei. High dynamic range power spectral density functions (PSDs) have been constructed for six Seyfert 1 galaxies. These PSDs show "breaks" or characteristic time scales, typically on the order of a few days. There is resemblance to PSDs of lower-mass Galactic X-ray binaries (XRBs), with the ratios of putative black hole masses and variability time scales approximately the same (106--7) between the two classes of objects. The data are consistent with a linear correlation between Seyfert PSD break time scale and black hole mass estimate; the relation extrapolates reasonably well over 6--7 orders of magnitude to XRBs. All of this strengthens the case for a physical similarity between Seyfert galaxies and XRBs. The first six years of RXTE monitoring of Seyfert 1s have been systematically analyzed to probe hard X-ray variability on multiple time scales in a total of 19 Seyfert is in an expansion of the survey of Markowitz & Edelson (2001). Correlations between variability amplitude, luminosity, and black hole mass are explored, the data support the model of PSD movement with black hole mass suggested by the PSD survey. All of the continuum variability results are consistent with relatively more massive black holes hosting larger X-ray emission regions, resulting in 'slower' observed variability. Nearly all sources in the sample exhibit stronger variability towards softer energies, consistent with softening as they brighten. Direct time-resolved spectral fitting has been performed on continuous RXTE monitoring of seven Seyfert is to study long-term spectral variability and Fe Kalpha variability characteristics. The Fe Kalpha line displays a wide range of behavior but varies less strongly than the broadband continuum. Overall, however, there is no strong evidence for correlated variability between the line and

  8. The predictability of a lake phytoplankton community, over time-scales of hours to years

    DEFF Research Database (Denmark)

    Thomas, Mridul K.; Fontana, Simone; Reyes, Marta

    2018-01-01

    monitoring data (biological, physical and chemical) to assess the predictability of phytoplankton cell density in one lake across an unprecedented range of time-scales. Communities were highly predictable over hours to months: model R2 decreased from 0.89 at 4 hours to 0.74 at 1 month, and in a long......Forecasting changes to ecological communities is one of the central challenges in ecology. However, nonlinear dependencies, biotic interactions and data limitations have limited our ability to assess how predictable communities are. Here, we used a machine learning approach and environmental...

  9. Pre- versus post-mass extinction divergence of Mesozoic marine reptiles dictated by time-scale dependence of evolutionary rates.

    Science.gov (United States)

    Motani, Ryosuke; Jiang, Da-Yong; Tintori, Andrea; Ji, Cheng; Huang, Jian-Dong

    2017-05-17

    The fossil record of a major clade often starts after a mass extinction even though evolutionary rates, molecular or morphological, suggest its pre-extinction emergence (e.g. squamates, placentals and teleosts). The discrepancy is larger for older clades, and the presence of a time-scale-dependent methodological bias has been suggested, yet it has been difficult to avoid the bias using Bayesian phylogenetic methods. This paradox raises the question of whether ecological vacancies, such as those after mass extinctions, prompt the radiations. We addressed this problem by using a unique temporal characteristic of the morphological data and a high-resolution stratigraphic record, for the oldest clade of Mesozoic marine reptiles, Ichthyosauromorpha. The evolutionary rate was fastest during the first few million years of ichthyosauromorph evolution and became progressively slower over time, eventually becoming six times slower. Using the later slower rates, estimates of divergence time become excessively older. The fast, initial rate suggests the emergence of ichthyosauromorphs after the end-Permian mass extinction, matching an independent result from high-resolution stratigraphic confidence intervals. These reptiles probably invaded the sea as a new ecosystem was formed after the end-Permian mass extinction. Lack of information on early evolution biased Bayesian clock rates. © 2017 The Author(s).

  10. A new approach to motion control of torque-constrained manipulators by using time-scaling of reference trajectories

    Energy Technology Data Exchange (ETDEWEB)

    Moreno-Valenzuela, Javier; Orozco-Manriquez, Ernesto [Digital del IPN, CITEDI-IPN, Tijuana, (Mexico)

    2009-12-15

    We introduce a control scheme based on using a trajectory tracking controller and an algorithm for on-line time scaling of the reference trajectories. The reference trajectories are time-scaled according to the measured tracking errors and the detected torque/acceleration saturation. Experiments are presented to illustrate the advantages of the proposed approach

  11. A new approach to motion control of torque-constrained manipulators by using time-scaling of reference trajectories

    International Nuclear Information System (INIS)

    Moreno-Valenzuela, Javier; Orozco-Manriquez, Ernesto

    2009-01-01

    We introduce a control scheme based on using a trajectory tracking controller and an algorithm for on-line time scaling of the reference trajectories. The reference trajectories are time-scaled according to the measured tracking errors and the detected torque/acceleration saturation. Experiments are presented to illustrate the advantages of the proposed approach

  12. Explicit Bounds to Some New Gronwall-Bellman-Type Delay Integral Inequalities in Two Independent Variables on Time Scales

    Directory of Open Access Journals (Sweden)

    Fanwei Meng

    2011-01-01

    Full Text Available Some new Gronwall-Bellman-type delay integral inequalities in two independent variables on time scales are established, which provide a handy tool in the research of qualitative and quantitative properties of solutions of delay dynamic equations on time scales. The established inequalities generalize some of the results in the work of Zhang and Meng 2008, Pachpatte 2002, and Ma 2010.

  13. Similar star formation rate and metallicity variability time-scales drive the fundamental metallicity relation

    Science.gov (United States)

    Torrey, Paul; Vogelsberger, Mark; Hernquist, Lars; McKinnon, Ryan; Marinacci, Federico; Simcoe, Robert A.; Springel, Volker; Pillepich, Annalisa; Naiman, Jill; Pakmor, Rüdiger; Weinberger, Rainer; Nelson, Dylan; Genel, Shy

    2018-06-01

    The fundamental metallicity relation (FMR) is a postulated correlation between galaxy stellar mass, star formation rate (SFR), and gas-phase metallicity. At its core, this relation posits that offsets from the mass-metallicity relation (MZR) at a fixed stellar mass are correlated with galactic SFR. In this Letter, we use hydrodynamical simulations to quantify the time-scales over which populations of galaxies oscillate about the average SFR and metallicity values at fixed stellar mass. We find that Illustris and IllustrisTNG predict that galaxy offsets from the star formation main sequence and MZR oscillate over similar time-scales, are often anticorrelated in their evolution, evolve with the halo dynamical time, and produce a pronounced FMR. Our models indicate that galaxies oscillate about equilibrium SFR and metallicity values - set by the galaxy's stellar mass - and that SFR and metallicity offsets evolve in an anticorrelated fashion. This anticorrelated variability of the metallicity and SFR offsets drives the existence of the FMR in our models. In contrast to Illustris and IllustrisTNG, we speculate that the SFR and metallicity evolution tracks may become decoupled in galaxy formation models dominated by feedback-driven globally bursty SFR histories, which could weaken the FMR residual correlation strength. This opens the possibility of discriminating between bursty and non-bursty feedback models based on the strength and persistence of the FMR - especially at high redshift.

  14. Prewhitening of hydroclimatic time series? Implications for inferred change and variability across time scales

    Science.gov (United States)

    Razavi, Saman; Vogel, Richard

    2018-02-01

    Prewhitening, the process of eliminating or reducing short-term stochastic persistence to enable detection of deterministic change, has been extensively applied to time series analysis of a range of geophysical variables. Despite the controversy around its utility, methodologies for prewhitening time series continue to be a critical feature of a variety of analyses including: trend detection of hydroclimatic variables and reconstruction of climate and/or hydrology through proxy records such as tree rings. With a focus on the latter, this paper presents a generalized approach to exploring the impact of a wide range of stochastic structures of short- and long-term persistence on the variability of hydroclimatic time series. Through this approach, we examine the impact of prewhitening on the inferred variability of time series across time scales. We document how a focus on prewhitened, residual time series can be misleading, as it can drastically distort (or remove) the structure of variability across time scales. Through examples with actual data, we show how such loss of information in prewhitened time series of tree rings (so-called "residual chronologies") can lead to the underestimation of extreme conditions in climate and hydrology, particularly droughts, reconstructed for centuries preceding the historical period.

  15. Characterization of Microbial Fuel Cells at Microbially and Electrochemically Meaningful Time scales

    KAUST Repository

    Ren, Zhiyong

    2011-03-15

    The variable biocatalyst density in a microbial fuel cell (MFC) anode biofilm is a unique feature of MFCs relative to other electrochemical systems, yet performance characterizations of MFCs typically involve analyses at electrochemically relevant time scales that are insufficient to account for these variable biocatalyst effects. This study investigated the electrochemical performance and the development of anode biofilm architecture under different external loadings, with duplicate acetate-fed singlechamber MFCs stabilized at each resistance for microbially relevant time scales. Power density curves from these steady-state reactors generally showed comparable profiles despite the fact that anode biofilm architectures and communities varied considerably, showing that steady-state biofilm differences had little influence on electrochemical performance until the steady-state external loading was much larger than the reactor internal resistance. Filamentous bacteria were dominant on the anodes under high external resistances (1000 and 5000 Ω), while more diverse rod-shaped cells formed dense biofilms under lower resistances (10, 50, and 265 Ω). Anode charge transfer resistance decreased with decreasing fixed external resistances, but was consistently 2 orders of magnitude higher than the resistance at the cathode. Cell counting showed an inverse exponential correlation between cell numbers and external resistances. This direct link ofMFCanode biofilm evolution with external resistance and electricity production offers several operational strategies for system optimization. © 2011 American Chemical Society.

  16. Multi-time-scale heat transfer modeling of turbid tissues exposed to short-pulsed irradiations.

    Science.gov (United States)

    Kim, Kyunghan; Guo, Zhixiong

    2007-05-01

    A combined hyperbolic radiation and conduction heat transfer model is developed to simulate multi-time-scale heat transfer in turbid tissues exposed to short-pulsed irradiations. An initial temperature response of a tissue to an ultrashort pulse irradiation is analyzed by the volume-average method in combination with the transient discrete ordinates method for modeling the ultrafast radiation heat transfer. This response is found to reach pseudo steady state within 1 ns for the considered tissues. The single pulse result is then utilized to obtain the temperature response to pulse train irradiation at the microsecond/millisecond time scales. After that, the temperature field is predicted by the hyperbolic heat conduction model which is solved by the MacCormack's scheme with error terms correction. Finally, the hyperbolic conduction is compared with the traditional parabolic heat diffusion model. It is found that the maximum local temperatures are larger in the hyperbolic prediction than the parabolic prediction. In the modeled dermis tissue, a 7% non-dimensional temperature increase is found. After about 10 thermal relaxation times, thermal waves fade away and the predictions between the hyperbolic and parabolic models are consistent.

  17. Selective visual scaling of time-scale processes facilitates broadband learning of isometric force frequency tracking.

    Science.gov (United States)

    King, Adam C; Newell, Karl M

    2015-10-01

    The experiment investigated the effect of selectively augmenting faster time scales of visual feedback information on the learning and transfer of continuous isometric force tracking tasks to test the generality of the self-organization of 1/f properties of force output. Three experimental groups tracked an irregular target pattern either under a standard fixed gain condition or with selectively enhancement in the visual feedback display of intermediate (4-8 Hz) or high (8-12 Hz) frequency components of the force output. All groups reduced tracking error over practice, with the error lowest in the intermediate scaling condition followed by the high scaling and fixed gain conditions, respectively. Selective visual scaling induced persistent changes across the frequency spectrum, with the strongest effect in the intermediate scaling condition and positive transfer to novel feedback displays. The findings reveal an interdependence of the timescales in the learning and transfer of isometric force output frequency structures consistent with 1/f process models of the time scales of motor output variability.

  18. Model based analysis of the time scales associated to pump start-ups

    Energy Technology Data Exchange (ETDEWEB)

    Dazin, Antoine, E-mail: antoine.dazin@lille.ensam.fr [Arts et métiers ParisTech/LML Laboratory UMR CNRS 8107, 8 bld Louis XIV, 59046 Lille cedex (France); Caignaert, Guy [Arts et métiers ParisTech/LML Laboratory UMR CNRS 8107, 8 bld Louis XIV, 59046 Lille cedex (France); Dauphin-Tanguy, Geneviève, E-mail: genevieve.dauphin-tanguy@ec-lille.fr [Univ Lille Nord de France, Ecole Centrale de Lille/CRISTAL UMR CNRS 9189, BP 48, 59651, Villeneuve d’Ascq cedex F 59000 (France)

    2015-11-15

    Highlights: • A dynamic model of a hydraulic system has been built. • Three periods in a pump start-up have been identified. • The time scales of each period have been estimated. • The parameters affecting the rapidity of a pump start-up have been explored. - Abstract: The paper refers to a non dimensional analysis of the behaviour of a hydraulic system during pump fast start-ups. The system is composed of a radial flow pump and its suction and delivery pipes. It is modelled using the bond graph methodology. The prediction of the model is validated by comparison to experimental results. An analysis of the time evolution of the terms acting on the total pump pressure is proposed. It allows for a decomposition of the start-up into three consecutive periods. The time scales associated with these periods are estimated. The effects of parameters (angular acceleration, final rotation speed, pipe length and resistance) affecting the start-up rapidity are then explored.

  19. Two-time scale subordination in physical processes with long-term memory

    International Nuclear Information System (INIS)

    Stanislavsky, Aleksander; Weron, Karina

    2008-01-01

    We describe dynamical processes in continuous media with a long-term memory. Our consideration is based on a stochastic subordination idea and concerns two physical examples in detail. First we study a temporal evolution of the species concentration in a trapping reaction in which a diffusing reactant is surrounded by a sea of randomly moving traps. The analysis uses the random-variable formalism of anomalous diffusive processes. We find that the empirical trapping-reaction law, according to which the reactant concentration decreases in time as a product of an exponential and a stretched exponential function, can be explained by a two-time scale subordination of random processes. Another example is connected with a state equation for continuous media with memory. If the pressure and the density of a medium are subordinated in two different random processes, then the ordinary state equation becomes fractional with two-time scales. This allows one to arrive at the Bagley-Torvik type of state equation

  20. Entangled time in flocking: Multi-time-scale interaction reveals emergence of inherent noise.

    Science.gov (United States)

    Niizato, Takayuki; Murakami, Hisashi

    2018-01-01

    Collective behaviors that seem highly ordered and result in collective alignment, such as schooling by fish and flocking by birds, arise from seamless shuffling (such as super-diffusion) and bustling inside groups (such as Lévy walks). However, such noisy behavior inside groups appears to preclude the collective behavior: intuitively, we expect that noisy behavior would lead to the group being destabilized and broken into small sub groups, and high alignment seems to preclude shuffling of neighbors. Although statistical modeling approaches with extrinsic noise, such as the maximum entropy approach, have provided some reasonable descriptions, they ignore the cognitive perspective of the individuals. In this paper, we try to explain how the group tendency, that is, high alignment, and highly noisy individual behavior can coexist in a single framework. The key aspect of our approach is multi-time-scale interaction emerging from the existence of an interaction radius that reflects short-term and long-term predictions. This multi-time-scale interaction is a natural extension of the attraction and alignment concept in many flocking models. When we apply this method in a two-dimensional model, various flocking behaviors, such as swarming, milling, and schooling, emerge. The approach also explains the appearance of super-diffusion, the Lévy walk in groups, and local equilibria. At the end of this paper, we discuss future developments, including extending our model to three dimensions.

  1. Time Scale Analysis of Interest Rate Spreads and Output Using Wavelets

    Directory of Open Access Journals (Sweden)

    Marco Gallegati

    2013-04-01

    Full Text Available This paper adds to the literature on the information content of different spreads for real activity by explicitly taking into account the time scale relationship between a variety of monetary and financial indicators (real interest rate, term and credit spreads and output growth. By means of wavelet-based exploratory data analysis we obtain richer results relative to the aggregate analysis by identifying the dominant scales of variation in the data and the scales and location at which structural breaks have occurred. Moreover, using the “double residuals” regression analysis on a scale-by-scale basis, we find that changes in the spread in several markets have different information content for output at different time frames. This is consistent with the idea that allowing for different time scales of variation in the data can provide a fruitful understanding of the complex dynamics of economic relationships between variables with non-stationary or transient components, certainly richer than those obtained using standard time domain methods.

  2. Modified multiple time scale method for solving strongly nonlinear damped forced vibration systems

    Science.gov (United States)

    Razzak, M. A.; Alam, M. Z.; Sharif, M. N.

    2018-03-01

    In this paper, modified multiple time scale (MTS) method is employed to solve strongly nonlinear forced vibration systems. The first-order approximation is only considered in order to avoid complexicity. The formulations and the determination of the solution procedure are very easy and straightforward. The classical multiple time scale (MS) and multiple scales Lindstedt-Poincare method (MSLP) do not give desire result for the strongly damped forced vibration systems with strong damping effects. The main aim of this paper is to remove these limitations. Two examples are considered to illustrate the effectiveness and convenience of the present procedure. The approximate external frequencies and the corresponding approximate solutions are determined by the present method. The results give good coincidence with corresponding numerical solution (considered to be exact) and also provide better result than other existing results. For weak nonlinearities with weak damping effect, the absolute relative error measures (first-order approximate external frequency) in this paper is only 0.07% when amplitude A = 1.5 , while the relative error gives MSLP method is surprisingly 28.81%. Furthermore, for strong nonlinearities with strong damping effect, the absolute relative error found in this article is only 0.02%, whereas the relative error obtained by MSLP method is 24.18%. Therefore, the present method is not only valid for weakly nonlinear damped forced systems, but also gives better result for strongly nonlinear systems with both small and strong damping effect.

  3. Dynamics analysis of the fast-slow hydro-turbine governing system with different time-scale coupling

    Science.gov (United States)

    Zhang, Hao; Chen, Diyi; Wu, Changzhi; Wang, Xiangyu

    2018-01-01

    Multi-time scales modeling of hydro-turbine governing system is crucial in precise modeling of hydropower plant and provides support for the stability analysis of the system. Considering the inertia and response time of the hydraulic servo system, the hydro-turbine governing system is transformed into the fast-slow hydro-turbine governing system. The effects of the time-scale on the dynamical behavior of the system are analyzed and the fast-slow dynamical behaviors of the system are investigated with different time-scale. Furthermore, the theoretical analysis of the stable regions is presented. The influences of the time-scale on the stable region are analyzed by simulation. The simulation results prove the correctness of the theoretical analysis. More importantly, the methods and results of this paper provide a perspective to multi-time scales modeling of hydro-turbine governing system and contribute to the optimization analysis and control of the system.

  4. Evolutionary and Biogeographic Insights on the Macaronesian Beta-Patellifolia Species (Amaranthaceae from a Time-Scaled Molecular Phylogeny.

    Directory of Open Access Journals (Sweden)

    Maria M Romeiras

    Full Text Available The Western Mediterranean Region and Macaronesian Islands are one of the top biodiversity hotspots of Europe, containing a significant native genetic diversity of global value among the Crop Wild Relatives (CWR. Sugar beet is the primary crop of the genus Beta (subfamily Betoideae, Amaranthaceae and despite the great economic importance of this genus, and of the close relative Patellifolia species, a reconstruction of their evolutionary history is still lacking. We analyzed nrDNA (ITS and cpDNA gene (matK, trnH-psbA, trnL intron, rbcL sequences to: (i investigate the phylogenetic relationships within the Betoideae subfamily, and (ii elucidate the historical biogeography of wild beet species in the Western Mediterranean Region, including the Macaronesian Islands. The results support the Betoideae as a monophyletic group (excluding the Acroglochin genus and provide a detailed inference of relationships within this subfamily, revealing: (i a deep genetic differentiation between Beta and Patellifolia species, which may have occurred in Late Oligocene; and (ii the occurrence of a West-East genetic divergence within Beta, indicating that the Mediterranean species probably differentiated by the end of the Miocene. This was interpreted as a signature of species radiation induced by dramatic habitat changes during the Messinian Salinity Crisis (MSC, 5.96-5.33 Mya. Moreover, colonization events during the Pleistocene also played a role in shaping the current diversity patterns among and within the Macaronesian Islands. The origin and number of these events could not be revealed due to insufficient phylogenetic resolution, suggesting that the diversification was quite recent in these archipelagos, and unravelling potential complex biogeographic patterns with hybridization and gene flow playing an important role. Finally, three evolutionary lineages were identified corresponding to major gene pools of sugar beet wild relatives, which provide useful information for establishing in situ and ex situ conservation priorities in the hotspot area of the Macaronesian Islands.

  5. Spintronics: The molecular way

    Science.gov (United States)

    Cornia, Andrea; Seneor, Pierre

    2017-05-01

    Molecular spintronics is an interdisciplinary field at the interface between organic spintronics, molecular magnetism, molecular electronics and quantum computing, which is advancing fast and promises large technological payoffs.

  6. The geological processes time scale of the Ingozersky block TTG complex (Kola Peninsula)

    Science.gov (United States)

    Nitkina, Elena

    2013-04-01

    Ingozersky block located in the Tersky Terrane of the Kola Peninsula is composed of Archean gneisses and granitoids [1; 5; 8]. The Archaean basement complexes on the regional geological maps have called tonalite-trondemit-gneisses (TTG) complexes [6]. In the previous studies [1; 3; 4; 5; 7] within Ingozersky block the following types of rocks were established: biotite, biotite-amphibole, amphibole-biotite gneisses, granites, granodiorites and pegmatites [2]. In the rocks of the complex following corresponding sequence of endogenous processes observed (based on [5]): stage 1 - the biotitic gneisses formation; 2 - the introduction of dikes of basic rocks; 3 phase - deformation and foliation; 4 stage - implementation bodies of granite and migmatization; 5 stage - implementation of large pegmatite bodies; stage 6 - the formation of differently pegmatite and granite veins of low power, with and without garnet; stage 7 - quartz veins. Previous U-Pb isotopic dating of the samples was done for biotite gneisses, amphibole-biotite gneisses and biotite-amphibole gneisses. Thus, some Sm-Nd TDM ages are 3613 Ma - biotite gnesses, 2596 Ma - amphibole-biotite gnesses and 3493 Ma biotite-amphibole gneisses.. U-Pb ages of the metamorphism processes in the TTG complex are obtained: 2697±9 Ma - for the biotite gneiss, 2725±2 and 2667±7 Ma - for the amphibole-biotite gneisses, and 2727±5 Ma for the biotite-amphibole gneisses. The age defined for the biotite gneisses by using single zircon dating to be about 3149±46 Ma corresponds to the time of the gneisses protolith formation. The purpose of these studies is the age establishing of granite and pegmatite bodies emplacement and finding a geological processes time scale of the Ingozerskom block. Preliminary U-Pb isotopic dating of zircon and other accessory minerals were held for granites - 2615±8 Ma, migmatites - 2549±30 Ma and veined granites - 1644±7 Ma. As a result of the isotope U-Pb dating of the different Ingozerskogo TTG

  7. Geometry and time scales of self-consistent orbits in a modified SU(2) model

    International Nuclear Information System (INIS)

    Jezek, D.M.; Hernandez, E.S.; Solari, H.G.

    1986-01-01

    We investigate the time-dependent Hartree-Fock flow pattern of a two-level many fermion system interacting via a two-body interaction which does not preserve the parity symmetry of standard SU(2) models. The geometrical features of the time-dependent Hartree-Fock energy surface are analyzed and a phase instability is clearly recognized. The time evolution of one-body observables along self-consistent and exact trajectories are examined together with the overlaps between both orbits. Typical time scales for the determinantal motion can be set and the validity of the time-dependent Hartree-Fock approach in the various regions of quasispin phase space is discussed

  8. Impact of speculator's expectations of returns and time scales of investment on crude oil price behaviors

    International Nuclear Information System (INIS)

    He, Ling-Yun; Fan, Ying; Wei, Yi-Ming

    2009-01-01

    Based on time series of crude oil prices (daily spot), this paper analyses price fluctuation with two significant parameters τ (speculators' time scales of investment) and ε (speculators' expectations of return) by using Zipf analysis technique, specifically, by mapping τ-returns of prices into 3-alphabeted sequences (absolute frequencies) and 2-alphabeted sequences (relative frequencies), containing the fundamental information of price fluctuations. This paper empirically explores parameters and identifies various types of speculators' cognition patterns of price behavior. In order to quantify the degree of distortion, a feasible reference is proposed: an ideal speculator. Finally, this paper discusses the similarities and differences between those cognition patterns of speculators' and those of an ideal speculator. The resultant analyses identify the possible distortion of price behaviors by their patterns. (author)

  9. On the nonlinear dynamics of trolling-mode AFM: Analytical solution using multiple time scales method

    Science.gov (United States)

    Sajjadi, Mohammadreza; Pishkenari, Hossein Nejat; Vossoughi, Gholamreza

    2018-06-01

    Trolling mode atomic force microscopy (TR-AFM) has resolved many imaging problems by a considerable reduction of the liquid-resonator interaction forces in liquid environments. The present study develops a nonlinear model of the meniscus force exerted to the nanoneedle of TR-AFM and presents an analytical solution to the distributed-parameter model of TR-AFM resonator utilizing multiple time scales (MTS) method. Based on the developed analytical solution, the frequency-response curves of the resonator operation in air and liquid (for different penetration length of the nanoneedle) are obtained. The closed-form analytical solution and the frequency-response curves are validated by the comparison with both the finite element solution of the main partial differential equations and the experimental observations. The effect of excitation angle of the resonator on horizontal oscillation of the probe tip and the effect of different parameters on the frequency-response of the system are investigated.

  10. Accessible methods for the dynamic time-scale decomposition of biochemical systems.

    Science.gov (United States)

    Surovtsova, Irina; Simus, Natalia; Lorenz, Thomas; König, Artjom; Sahle, Sven; Kummer, Ursula

    2009-11-01

    The growing complexity of biochemical models asks for means to rationally dissect the networks into meaningful and rather independent subnetworks. Such foregoing should ensure an understanding of the system without any heuristics employed. Important for the success of such an approach is its accessibility and the clarity of the presentation of the results. In order to achieve this goal, we developed a method which is a modification of the classical approach of time-scale separation. This modified method as well as the more classical approach have been implemented for time-dependent application within the widely used software COPASI. The implementation includes different possibilities for the representation of the results including 3D-visualization. The methods are included in COPASI which is free for academic use and available at www.copasi.org. irina.surovtsova@bioquant.uni-heidelberg.de Supplementary data are available at Bioinformatics online.

  11. Multi-time scale energy management of wind farms based on comprehensive evaluation technology

    Science.gov (United States)

    Xu, Y. P.; Huang, Y. H.; Liu, Z. J.; Wang, Y. F.; Li, Z. Y.; Guo, L.

    2017-11-01

    A novel energy management of wind farms is proposed in this paper. Firstly, a novel comprehensive evaluation system is proposed to quantify economic properties of each wind farm to make the energy management more economical and reasonable. Then, a combination of multi time-scale schedule method is proposed to develop a novel energy management. The day-ahead schedule optimizes unit commitment of thermal power generators. The intraday schedule is established to optimize power generation plan for all thermal power generating units, hydroelectric generating sets and wind power plants. At last, the power generation plan can be timely revised in the process of on-line schedule. The paper concludes with simulations conducted on a real provincial integrated energy system in northeast China. Simulation results have validated the proposed model and corresponding solving algorithms.

  12. Long time scale plasma dynamics driven by the double tearing mode in reversed shear plasmas

    International Nuclear Information System (INIS)

    Ishii, Y.; Azumi, M.; Kishimoto, Y.; Leboeuf, J.N.

    2003-01-01

    The new nonlinear destabilization process is found in the nonlinear phase of the double tearing mode (DTM) by using the reduced MHD equations in a helical symmetry. The nonlinear destabilization causes the abrupt growth of DTM and subsequent collapse after long time scale evolution in the Rutherford-type regime. The nonlinear growth of the DTM is suddenly triggered, when the triangular deformation of magnetic islands with sharp current point at the x-point around the outer rational surface exceeds a certain value. Such structure deformation is accelerated during the nonlinear growth phase. Decreasing the resistivity increases the sharpness of the triangularity and the spontaneous growth rate in the abrupt growth phase is almost independent on the resistivity. Current point formation is also confirmed in the multi-helicity simulation, where the magnetic fields become stochastic between two rational surfaces. (author)

  13. Long time scale plasma dynamics driven by the double tearing mode in reversed shear plasmas

    International Nuclear Information System (INIS)

    Ishii, Yasutomo; Azumi, M.; Kishimoto, Y.

    2003-01-01

    The new nonlinear destabilization process is found in the nonlinear phase of the double tearing mode(DTM) by using the reduced MHD equations in a helical symmetry. The nonlinear destabilization causes the abrupt growth of DTM and subsequent collapse after long time scale evolution in the Rutherford-type regime. The nonlinear growth of the DTM is suddenly triggered, when the triangular deformation of magnetic islands with sharp current point at the x-point around the outer rational surface exceeds a certain value. Such structure deformation is accelerated during the nonlinear growth phase. Decreasing the resistivity increases the sharpness of the triangularity and the spontaneous growth rate in the abrupt growth phase is almost independent on the resistivity. Current point formation is also confirmed in the multi-helicity simulation, where the magnetic fields become stochastic between two rational surfaces. (author)

  14. Multiple-Time-Scales Hierarchical Frequency Stability Control Strategy of Medium-Voltage Isolated Microgrid

    DEFF Research Database (Denmark)

    Zhao, Zhuoli; Yang, Ping; Guerrero, Josep M.

    2016-01-01

    In this paper, an islanded medium-voltage (MV) microgrid placed in Dongao Island is presented, which integrates renewable-energy-based distributed generations (DGs), energy storage system (ESS), and local loads. In an isolated microgrid without connection to the main grid to support the frequency......, it is more complex to control and manage. Thus in order to maintain the frequency stability in multiple-time-scales, a hierarchical control strategy is proposed. The proposed control architecture divides the system frequency in three zones: (A) stable zone, (B) precautionary zone and (C) emergency zone...... of Zone B. Theoretical analysis, time-domain simulation and field test results under various conditions and scenarios in the Dongao Island microgrid are presented to prove the validity of the introduced control strategy....

  15. The effect of polymer type on electric breakdown strength on a nanosecond time scale

    Institute of Scientific and Technical Information of China (English)

    Zhao Liang; Su Jian-Cang; Pan Ya-Feng; Zhang Xi-Bo

    2012-01-01

    Based on the concepts of fast polarization,effective electric field and electron impact ionization criterion,the effect of polymer type on electric breakdown strength (EBD) on a nanosecond time scale is investigated,and a formula that qualitatively characterizes the relation between the electric breakdown strength and the polymer type is derived.According to this formula,it is found that the electric breakdown strength decreases with an increase in the effective relative dielectric constants of the polymers.By calculating the effective relative dielectric constants for different types of polymers,the theoretical relation for the electric breakdown strengths of common polymers is predicted.To verify the prediction,the polymers of PE (polyethylene),PTFE (polytetrafluoroethelene),PMMA (organic glass) and Nylon are tested with a nanosecond-pulse generator.The experimental result shows EBD (PTFE) > EBD (PMMA) > EBD (Nylon) > EBD (PE).This result is consistent with the theoretical prediction.

  16. Modelling accelerated degradation data using Wiener diffusion with a time scale transformation.

    Science.gov (United States)

    Whitmore, G A; Schenkelberg, F

    1997-01-01

    Engineering degradation tests allow industry to assess the potential life span of long-life products that do not fail readily under accelerated conditions in life tests. A general statistical model is presented here for performance degradation of an item of equipment. The degradation process in the model is taken to be a Wiener diffusion process with a time scale transformation. The model incorporates Arrhenius extrapolation for high stress testing. The lifetime of an item is defined as the time until performance deteriorates to a specified failure threshold. The model can be used to predict the lifetime of an item or the extent of degradation of an item at a specified future time. Inference methods for the model parameters, based on accelerated degradation test data, are presented. The model and inference methods are illustrated with a case application involving self-regulating heating cables. The paper also discusses a number of practical issues encountered in applications.

  17. Measurements of Electron Transport in Foils Irradiated with a Picosecond Time Scale Laser Pulse

    International Nuclear Information System (INIS)

    Brown, C. R. D.; Hoarty, D. J.; James, S. F.; Swatton, D.; Hughes, S. J.; Morton, J. W.; Guymer, T. M.; Hill, M. P.; Chapman, D. A.; Andrew, J. E.; Comley, A. J.; Shepherd, R.; Dunn, J.; Chen, H.; Schneider, M.; Brown, G.; Beiersdorfer, P.; Emig, J.

    2011-01-01

    The heating of solid foils by a picosecond time scale laser pulse has been studied by using x-ray emission spectroscopy. The target material was plastic foil with a buried layer of a spectroscopic tracer material. The laser pulse length was either 0.5 or 2 ps, which resulted in a laser irradiance that varied over the range 10 16 -10 19 W/cm 2 . Time-resolved measurements of the buried layer emission spectra using an ultrafast x-ray streak camera were used to infer the density and temperature conditions as a function of laser parameters and depth of the buried layer. Comparison of the data to different models of electron transport showed that they are consistent with a model of electron transport that predicts the bulk of the target heating is due to return currents.

  18. Time-Scale and Time-Frequency Analyses of Irregularly Sampled Astronomical Time Series

    Directory of Open Access Journals (Sweden)

    S. Roques

    2005-09-01

    Full Text Available We evaluate the quality of spectral restoration in the case of irregular sampled signals in astronomy. We study in details a time-scale method leading to a global wavelet spectrum comparable to the Fourier period, and a time-frequency matching pursuit allowing us to identify the frequencies and to control the error propagation. In both cases, the signals are first resampled with a linear interpolation. Both results are compared with those obtained using Lomb's periodogram and using the weighted waveletZ-transform developed in astronomy for unevenly sampled variable stars observations. These approaches are applied to simulations and to light variations of four variable stars. This leads to the conclusion that the matching pursuit is more efficient for recovering the spectral contents of a pulsating star, even with a preliminary resampling. In particular, the results are almost independent of the quality of the initial irregular sampling.

  19. Time scales of critical events around the Cretaceous-Paleogene boundary.

    Science.gov (United States)

    Renne, Paul R; Deino, Alan L; Hilgen, Frederik J; Kuiper, Klaudia F; Mark, Darren F; Mitchell, William S; Morgan, Leah E; Mundil, Roland; Smit, Jan

    2013-02-08

    Mass extinctions manifest in Earth's geologic record were turning points in biotic evolution. We present (40)Ar/(39)Ar data that establish synchrony between the Cretaceous-Paleogene boundary and associated mass extinctions with the Chicxulub bolide impact to within 32,000 years. Perturbation of the atmospheric carbon cycle at the boundary likely lasted less than 5000 years, exhibiting a recovery time scale two to three orders of magnitude shorter than that of the major ocean basins. Low-diversity mammalian fauna in the western Williston Basin persisted for as little as 20,000 years after the impact. The Chicxulub impact likely triggered a state shift of ecosystems already under near-critical stress.

  20. Multi-Time Scale Control of Demand Flexibility in Smart Distribution Networks

    DEFF Research Database (Denmark)

    Bhattarai, Bishnu P.; Myers, Kurt S.; Bak-Jensen, Birgitte

    2017-01-01

    , and distribution system operator’s perspectives. A hierarchical control architecture (HCA) comprising scheduling, coordinative, and adaptive layers is then designed to realize their coordinative goal. This is realized by integrating multi-time scale controls that work from a day-ahead scheduling up to real-time...... adaptive control. The performance of the developed method is investigated with high EV penetration in a typical residential distribution grid. The simulation results demonstrate that HCA efficiently utilizes demand flexibility stemming from EVs to solve grid unbalancing and congestions with simultaneous...... maximization of economic benefits to the participating actors. This is ensured by enabling EV participation in day-ahead, balancing, and regulation markets. For the given network configuration and pricing structure, HCA ensures the EV owners to get paid up to five times the cost they were paying without...

  1. Effects of demographic stochasticity on biological community assembly on evolutionary time scales

    KAUST Repository

    Murase, Yohsuke

    2010-04-13

    We study the effects of demographic stochasticity on the long-term dynamics of biological coevolution models of community assembly. The noise is induced in order to check the validity of deterministic population dynamics. While mutualistic communities show little dependence on the stochastic population fluctuations, predator-prey models show strong dependence on the stochasticity, indicating the relevance of the finiteness of the populations. For a predator-prey model, the noise causes drastic decreases in diversity and total population size. The communities that emerge under influence of the noise consist of species strongly coupled with each other and have stronger linear stability around the fixed-point populations than the corresponding noiseless model. The dynamics on evolutionary time scales for the predator-prey model are also altered by the noise. Approximate 1/f fluctuations are observed with noise, while 1/ f2 fluctuations are found for the model without demographic noise. © 2010 The American Physical Society.

  2. Effects of demographic stochasticity on biological community assembly on evolutionary time scales

    KAUST Repository

    Murase, Yohsuke; Shimada, Takashi; Ito, Nobuyasu; Rikvold, Per Arne

    2010-01-01

    We study the effects of demographic stochasticity on the long-term dynamics of biological coevolution models of community assembly. The noise is induced in order to check the validity of deterministic population dynamics. While mutualistic communities show little dependence on the stochastic population fluctuations, predator-prey models show strong dependence on the stochasticity, indicating the relevance of the finiteness of the populations. For a predator-prey model, the noise causes drastic decreases in diversity and total population size. The communities that emerge under influence of the noise consist of species strongly coupled with each other and have stronger linear stability around the fixed-point populations than the corresponding noiseless model. The dynamics on evolutionary time scales for the predator-prey model are also altered by the noise. Approximate 1/f fluctuations are observed with noise, while 1/ f2 fluctuations are found for the model without demographic noise. © 2010 The American Physical Society.

  3. Non-monotonicity and divergent time scale in Axelrod model dynamics

    Science.gov (United States)

    Vazquez, F.; Redner, S.

    2007-04-01

    We study the evolution of the Axelrod model for cultural diversity, a prototypical non-equilibrium process that exhibits rich dynamics and a dynamic phase transition between diversity and an inactive state. We consider a simple version of the model in which each individual possesses two features that can assume q possibilities. Within a mean-field description in which each individual has just a few interaction partners, we find a phase transition at a critical value qc between an active, diverse state for q < qc and a frozen state. For q lesssim qc, the density of active links is non-monotonic in time and the asymptotic approach to the steady state is controlled by a time scale that diverges as (q-qc)-1/2.

  4. Control of modular multilevel converters based on time-scale analysis and orthogonal functions

    DEFF Research Database (Denmark)

    Zarri, L.; Tani, A.; Mengoni, M.

    2014-01-01

    current is still a complex task and cannot be fully tackled with traditional linear control techniques. In this paper a multiple time-scale analysis is proposed to determine an approximated model of the MMC that can be used to solve the control problem of the capacitor voltages. In addition, it is shown...... that the reference signal of the circulating current can be built by combining orthogonal functions of the measured voltages and currents. Numerical simulations are used to test the feasibility of the developed approach.......Modular multilevel converter (MMC) is a promising multilevel topology for high-voltage applications that has been developed in recent years. The control of MMCs has been analyzed in detail in many papers, showing that the converter capacitors can be kept charged and balanced by controlling...

  5. Existence of positive solutions for semipositone dynamic system on time scales

    Directory of Open Access Journals (Sweden)

    You-Wei Zhang

    2008-08-01

    Full Text Available In this paper, we study the following semipositone dynamic system on time scales $$displaylines{ -x^{DeltaDelta}(t=f(t,y+p(t, quad tin(0,T_{mathbb{T}},cr -y^{DeltaDelta}(t=g(t,x, quad tin(0,T_{mathbb{T}},cr x(0=x(sigma^{2}(T=0, cr alpha{y(0}-eta{y^{Delta}{(0}}= gamma{y(sigma(T}+delta{y^{Delta}(sigma(T}=0. }$$ Using fixed point index theory, we show the existence of at least one positive solution. The interesting point is the that nonlinear term is allowed to change sign and may tend to negative infinity.

  6. Attractors of relaxation discrete-time systems with chaotic dynamics on a fast time scale

    International Nuclear Information System (INIS)

    Maslennikov, Oleg V.; Nekorkin, Vladimir I.

    2016-01-01

    In this work, a new type of relaxation systems is considered. Their prominent feature is that they comprise two distinct epochs, one is slow regular motion and another is fast chaotic motion. Unlike traditionally studied slow-fast systems that have smooth manifolds of slow motions in the phase space and fast trajectories between them, in this new type one observes, apart the same geometric objects, areas of transient chaos. Alternating periods of slow regular motions and fast chaotic ones as well as transitions between them result in a specific chaotic attractor with chaos on a fast time scale. We formulate basic properties of such attractors in the framework of discrete-time systems and consider several examples. Finally, we provide an important application of such systems, the neuronal electrical activity in the form of chaotic spike-burst oscillations.

  7. Multi-time-scale X-ray reverberation mapping of accreting black holes

    Science.gov (United States)

    Mastroserio, Guglielmo; Ingram, Adam; van der Klis, Michiel

    2018-04-01

    Accreting black holes show characteristic reflection features in their X-ray spectrum, including an iron Kα line, resulting from hard X-ray continuum photons illuminating the accretion disc. The reverberation lag resulting from the path-length difference between direct and reflected emission provides a powerful tool to probe the innermost regions around both stellar-mass and supermassive black holes. Here, we present for the first time a reverberation mapping formalism that enables modelling of energy-dependent time lags and variability amplitude for a wide range of variability time-scales, taking the complete information of the cross-spectrum into account. We use a pivoting power-law model to account for the spectral variability of the continuum that dominates over the reverberation lags for longer time-scale variability. We use an analytic approximation to self-consistently account for the non-linear effects caused by this continuum spectral variability, which have been ignored by all previous reverberation studies. We find that ignoring these non-linear effects can bias measurements of the reverberation lags, particularly at low frequencies. Since our model is analytic, we are able to fit simultaneously for a wide range of Fourier frequencies without prohibitive computational expense. We also introduce a formalism of fitting to real and imaginary parts of our cross-spectrum statistic, which naturally avoids some mistakes/inaccuracies previously common in the literature. We perform proof-of-principle fits to Rossi X-ray Timing Explorer data of Cygnus X-1.

  8. Dynamic response of materials on subnanosecond time scales, and beryllium properties for inertial confinement fusion

    International Nuclear Information System (INIS)

    Swift, Damian C.; Tierney, Thomas E.; Luo Shengnian; Paisley, Dennis L.; Kyrala, George A.; Hauer, Allan; Greenfield, Scott R.; Koskelo, Aaron C.; McClellan, Kenneth J.; Lorenzana, Hector E.; Kalantar, Daniel; Remington, Bruce A.; Peralta, Pedro; Loomis, Eric

    2005-01-01

    During the past few years, substantial progress has been made in developing experimental techniques capable of investigating the response of materials to dynamic loading on nanosecond time scales and shorter, with multiple diagnostics probing different aspects of the behavior. These relatively short time scales are scientifically interesting because plastic flow and phase changes in common materials with simple crystal structures--such as iron--may be suppressed, allowing unusual states to be induced and the dynamics of plasticity and polymorphism to be explored. Loading by laser-induced ablation can be particularly convenient: this technique has been used to impart shocks and isentropic compression waves from ∼1 to 200 GPa in a range of elements and alloys, with diagnostics including line imaging surface velocimetry, surface displacement (framed area imaging), x-ray diffraction (single crystal and polycrystal), ellipsometry, and Raman spectroscopy. A major motivation has been the study of the properties of beryllium under conditions relevant to the fuel capsule in inertial confinement fusion: magnetically driven shock and isentropic compression shots at Z were used to investigate the equation of state and shock melting characteristics, complemented by laser ablation experiments to investigate plasticity and heterogeneous response from the polycrystalline microstructure. These results will help to constrain acceptable tolerances on manufacturing, and possible loading paths, for inertial fusion ignition experiments at the National Ignition Facility. Laser-based techniques are being developed further for future material dynamics experiments, where it should be possible to obtain high quality data on strength and phase changes up to at least 1 TPa

  9. Climate scenarios for Olkiluoto on a time-scale of 120,000 years

    International Nuclear Information System (INIS)

    Pimenoff, N.; Venaelaeinen, A.; Jaervinen, H.

    2011-12-01

    Posiva Oy is planning to dispose of spent nuclear fuel in a repository, to be constructed at a depth of 400 m in the crystalline bedrock at Olkiluoto, Finland. Planning the storage requires careful consideration of many aspects, including an assessment of long-term repository safety. For estimating possible climate states at Olkiluoto on a time-scale of 120,000 years, we analyze climate simulations of an Earth System Model of Intermediate Complexity (CLIMBER-2) coupled with an ice sheet model (SICOPOLIS). The simulations into the future clearly show that the onset of the next glaciation is strongly dependent on the Earth's orbital variations and the atmospheric CO 2 concentration. It is evident that due to global warming, the climate of the next centuries will be warmer and wetter than at present. Most likely, due to global warming and low variations in the Earth's orbit around the sun, the present interglacial will last for at least the next 30,000 years. Further, the future simulations showed that the insolation minima on the Northern Hemisphere 50,000-60,000 and 90,000-100,000 years after the present hold a potential for the onset of the next glaciation. Hence, on a time-scale of 120,000 years, one must take into account climate periods lasting several thousand years having the following features: an interglacial climate, a periglacial climate, a climate with an ice sheet margin near Olkiluoto, a glacial climate with an ice sheet covering Olkiluoto, and a climate with Olkiluoto being depressed below sea level after glaciation due to isostatic depression. Due to the uncertainties related to the evolution of the future climate, it is recommended the simulations into the far future to be used only qualitatively. Quantitative information about glacial climate is achieved from the reconstructions and simulations of the past climate. (orig.)

  10. Climate scenarios for Olkiluoto on a time-scale of 100,000 years

    International Nuclear Information System (INIS)

    Pimenoff, N.; Venaelaeinen, A.; Jaervinen, H.

    2011-01-01

    Posiva Oy is planning to dispose of spent nuclear fuel in a repository, to be constructed at a depth of 400 m in the crystalline bedrock at Olkiluoto, Finland. Planning the storage requires careful consideration of many aspects, including an assessment of long-term repository safety. For estimating possible climate states at Olkiluoto on a time-scale of 100,000 years, we analyze climate simulations of an Earth System Model of Intermediate Complexity (CLIMBER-2) coupled with an ice sheet model (SICOPOLIS). The simulations into the future clearly show that the onset of the next glaciation is strongly dependent on the Earth's orbital variations and the atmospheric CO 2 concentration. It is evident that due to global warming, the climate of the next centuries will be warmer and wetter than at present. Most likely, due to global warming and low variations in the Earth's orbit around the sun, the present interglacial will last for at least the next 30,000 years. Further, the future simulations showed that the insolation minima on the Northern Hemisphere 50,000-60,000 and 90,000-100,000 years after the present hold a potential for the onset of the next glaciation. Hence, on a time-scale of 100,000 years, one must take into account climate periods lasting several thousand years having the following features: an interglacial climate, a periglacial climate, a climate with an ice sheet margin near Olkiluoto, a glacial climate with an ice sheet covering Olkiluoto, and a climate with Olkiluoto being depressed below sea level after glaciation due to isostatic depression. Due to the uncertainties related to the evolution of the future climate, it is recommended the simulations into the far future to be used only qualitatively. Quantitative information about glacial climate is achieved from the reconstructions and simulations of the past climate. (orig.)

  11. Climate scenarios for Olkiluoto on a time-scale of 120,000 years

    Energy Technology Data Exchange (ETDEWEB)

    Pimenoff, N.; Venaelaeinen, A.; Jaervinen, H. [Finnish Meteorological Institute, Helsinki (Finland)

    2011-12-15

    Posiva Oy is planning to dispose of spent nuclear fuel in a repository, to be constructed at a depth of 400 m in the crystalline bedrock at Olkiluoto, Finland. Planning the storage requires careful consideration of many aspects, including an assessment of long-term repository safety. For estimating possible climate states at Olkiluoto on a time-scale of 120,000 years, we analyze climate simulations of an Earth System Model of Intermediate Complexity (CLIMBER-2) coupled with an ice sheet model (SICOPOLIS). The simulations into the future clearly show that the onset of the next glaciation is strongly dependent on the Earth's orbital variations and the atmospheric CO{sub 2} concentration. It is evident that due to global warming, the climate of the next centuries will be warmer and wetter than at present. Most likely, due to global warming and low variations in the Earth's orbit around the sun, the present interglacial will last for at least the next 30,000 years. Further, the future simulations showed that the insolation minima on the Northern Hemisphere 50,000-60,000 and 90,000-100,000 years after the present hold a potential for the onset of the next glaciation. Hence, on a time-scale of 120,000 years, one must take into account climate periods lasting several thousand years having the following features: an interglacial climate, a periglacial climate, a climate with an ice sheet margin near Olkiluoto, a glacial climate with an ice sheet covering Olkiluoto, and a climate with Olkiluoto being depressed below sea level after glaciation due to isostatic depression. Due to the uncertainties related to the evolution of the future climate, it is recommended the simulations into the far future to be used only qualitatively. Quantitative information about glacial climate is achieved from the reconstructions and simulations of the past climate. (orig.)

  12. Analytical Solutions for Multi-Time Scale Fractional Stochastic Differential Equations Driven by Fractional Brownian Motion and Their Applications

    Directory of Open Access Journals (Sweden)

    Xiao-Li Ding

    2018-01-01

    Full Text Available In this paper, we investigate analytical solutions of multi-time scale fractional stochastic differential equations driven by fractional Brownian motions. We firstly decompose homogeneous multi-time scale fractional stochastic differential equations driven by fractional Brownian motions into independent differential subequations, and give their analytical solutions. Then, we use the variation of constant parameters to obtain the solutions of nonhomogeneous multi-time scale fractional stochastic differential equations driven by fractional Brownian motions. Finally, we give three examples to demonstrate the applicability of our obtained results.

  13. Assembled microneedle arrays enhance the transport of compounds varying over a large range of molecular weight across human dermatomed skin

    NARCIS (Netherlands)

    Verbaan, F.J.; Bal, S.M.; van den Berg, D.J.; Groenink, W.H.H.; Verpoorten, H.; Lüttge, Regina; Bouwstra, J.A.

    2007-01-01

    In this study, we demonstrate the feasibility to use microneedle arrays manufactured from commercially available 30G hypodermal needles to enhance the transport of compounds up to a molecular weight of 72 kDa. Piercing of human dermatomed skin with microneedle arrays was studied by Trypan Blue

  14. Links between ocean properties, ice cover, and plankton dynamics on interannual time scales in the Canadian Arctic Archipelago

    Science.gov (United States)

    Hamilton, James M.; Collins, Kate; Prinsenberg, Simon J.

    2013-10-01

    A decade of instrumented mooring data from Barrow Strait in the eastern Canadian Arctic Archipelago reveals connections between sea ice, water characteristics, and zooplankton dynamics on interannual time scales. On the North side of the Strait, the timing of breakup is positively related to the timing of freezeup in the previous year and negatively related to spring water temperature. This suggests that an early freezeup insulates the ocean from a cold autumn atmosphere, allowing heat to be retained until spring when it contributes to early sea ice erosion. There is also a very strong negative association between the timing of freezeup and late summer salinity, suggesting that monitoring of salinity in real time could be used to predict freezeup. A zooplankton biomass index derived from acoustic Doppler current profiler echo intensity data is used to demonstrate that on the North side there are also strong connections between early summer water temperature and the start, length, and productivity of the zooplankton growth season. On the South side of the Strait where currents are stronger, the relationships seen on the North side were not observed. But here integrated zooplankton biomass index and measured currents are used to identify interannual variability in the zooplankton biomass being delivered downstream into Lancaster Sound. Also on the South side, two yearlong records of daily fluorescence profiles reveal a large difference in the phytoplankton biomass being delivered downstream between years and demonstrate a strong relationship between the timing of the spring phytoplankton bloom and that of breakup.

  15. Reduced α-stable dynamics for multiple time scale systems forced with correlated additive and multiplicative Gaussian white noise

    Science.gov (United States)

    Thompson, William F.; Kuske, Rachel A.; Monahan, Adam H.

    2017-11-01

    Stochastic averaging problems with Gaussian forcing have been the subject of numerous studies, but far less attention has been paid to problems with infinite-variance stochastic forcing, such as an α-stable noise process. It has been shown that simple linear systems driven by correlated additive and multiplicative (CAM) Gaussian noise, which emerge in the context of reduced atmosphere and ocean dynamics, have infinite variance in certain parameter regimes. In this study, we consider the stochastic averaging of systems where a linear CAM noise process in the infinite variance parameter regime drives a comparatively slow process. We use (semi)-analytical approximations combined with numerical illustrations to compare the averaged process to one that is forced by a white α-stable process, demonstrating consistent properties in the case of large time-scale separation. We identify the conditions required for the fast linear CAM process to have such an influence in driving a slower process and then derive an (effectively) equivalent fast, infinite-variance process for which an existing stochastic averaging approximation is readily applied. The results are illustrated using numerical simulations of a set of example systems.

  16. Hour time-scale QPOs in the X-ray and radio emission of LS I +61°303

    Science.gov (United States)

    Nösel, S.; Sharma, R.; Massi, M.; Cimò, G.; Chernyakova, M.

    2018-05-01

    LS I +61°303 is an X-ray binary with a radio outburst every ˜27 d. Previous studies of the stellar system revealed radio microflares superimposed on the large radio outburst. We present here new radio observations of LS I +61°303 at 2.2 GHz with the Westerbork Synthesis Radio Telescope (WSRT). Using various timing analysis methods, we find significant quasi-periodic oscillations (QPOs) of 55 min stable over the duration of 4 d. We also use archival data obtained from the Suzaku satellite at X-ray wavelengths. We report here for the first time significant X-ray QPOs of about 2 h present over the time span of 21 h. We compare our results with the previously reported QPO observations and we conclude that the QPOs seem to be associated with the radio outburst, independent of the amplitude of the outburst. Finally, the different QPO time-scales are discussed in the context of magnetic reconnection.

  17. Reducing uncertainty in Climate Response Time Scale by Bayesian Analysis of the 8.2 ka event

    Science.gov (United States)

    Lorenz, A.; Held, H.; Bauer, E.; Schneider von Deimling, T.

    2009-04-01

    We analyze the possibility of uncertainty reduction in Climate Response Time Scale by utilizing Greenland ice-core data that contain the 8.2 ka event within a Bayesian model-data intercomparison with the Earth system model of intermediate complexity, CLIMBER-2.3. Within a stochastic version of the model it has been possible to mimic the 8.2 ka event within a plausible experimental setting and with relatively good accuracy considering the timing of the event in comparison to other modeling exercises [1]. The simulation of the centennial cold event is effectively determined by the oceanic cooling rate which depends largely on the ocean diffusivity described by diffusion coefficients of relatively wide uncertainty ranges. The idea now is to discriminate between the different values of diffusivities according to their likelihood to rightly represent the duration of the 8.2 ka event and thus to exploit the paleo data to constrain uncertainty in model parameters in analogue to [2]. Implementing this inverse Bayesian Analysis with this model the technical difficulty arises to establish the related likelihood numerically in addition to the uncertain model parameters: While mainstream uncertainty analyses can assume a quasi-Gaussian shape of likelihood, with weather fluctuating around a long term mean, the 8.2 ka event as a highly nonlinear effect precludes such an a priori assumption. As a result of this study [3] the Bayesian Analysis showed a reduction of uncertainty in vertical ocean diffusivity parameters of factor 2 compared to prior knowledge. This learning effect on the model parameters is propagated to other model outputs of interest; e.g. the inverse ocean heat capacity, which is important for the dominant time scale of climate response to anthropogenic forcing which, in combination with climate sensitivity, strongly influences the climate systems reaction for the near- and medium-term future. 1 References [1] E. Bauer, A. Ganopolski, M. Montoya: Simulation of the

  18. Time-scale calibration by U-Pb geochronology: Examples from the Triassic Period

    Science.gov (United States)

    Mundil, R.

    2009-05-01

    U-Pb zircon geochronology, pioneered by Tom Krogh, is a cornerstone for the calibration of the time scale. Before Krogh's innovations, U-Pb geochronology was essentially limited by laboratory blank Pb (typically hundreds of nanograms) inherent in the then existing zircon dissolution and purification methods. The introduction of high pressure HF dissolution combined with miniature ion exchange columns (1) reduced the blank by orders of magnitude and allowed mass-spectrometric analyses of minute amounts of material (picograms of Pb and U). Krogh also recognized the need for minimizing the effects of Pb loss, and the introduction of the air-abrasion technique was the method of choice for two decades (2), until the development of the combined annealing and chemical abrasion technique resulted in essentially closed system zircons (3). These are the prerequisite for obtaining precise (permil-level) and accurate radio-isotopic ages of individual zircons contained in primary volcanic ash deposits, which are primary targets for the calibration of the time scale if they occur within fossil bearing sediments. A prime example is the calibration of the Triassic time scale which improved significantly using these techniques. The ages for the base and the top of the Triassic are constrained by U-Pb ages to 252.3 (4) and 201.5 Ma (5), respectively. These dates also constrain the ages of major extinction events at the Permian-Triassic and Triassic-Jurassic boundaries, and are statistically indistinguishable from ages obtained for the Siberian Traps and volcanic products from the Central Atlantic Magmatic Province, respectively, suggesting a causal link. Ages for these continental volcanics, however, are mostly from the K-Ar (40Ar/39Ar) system which requires accounting and correcting for a systematic bias of ca 1 % between U-Pb and 40Ar/39Ar isotopic ages (the 40Ar/39Ar ages being younger) (6). Robust U-Pb age constraints also exist for the Induan- Olenekian boundary (251.2 Ma, (7

  19. High-Resolution Liquid Chromatography Tandem Mass Spectrometry Enables Large Scale Molecular Characterization of Dissolved Organic Matter

    Directory of Open Access Journals (Sweden)

    Daniel Petras

    2017-12-01

    Full Text Available Dissolved organic matter (DOM is arguably one of the most complex exometabolomes on earth, and is comprised of thousands of compounds, that together contribute more than 600 × 1015 g carbon. This reservoir is primarily the product of interactions between the upper ocean's microbial food web, yet abiotic processes that occur over millennia have also modified many of its molecules. The compounds within this reservoir play important roles in determining the rate and extent of element exchange between inorganic reservoirs and the marine biosphere, while also mediating microbe-microbe interactions. As such, there has been a widespread effort to characterize DOM using high-resolution analytical methods including nuclear magnetic resonance spectroscopy (NMR and mass spectrometry (MS. To date, molecular information in DOM has been primarily obtained through calculated molecular formulas from exact mass. This approach has the advantage of being non-targeted, accessing the inherent complexity of DOM. Molecular structures are however still elusive and the most commonly used instruments are costly. More recently, tandem mass spectrometry has been employed to more precisely identify DOM components through comparison to library mass spectra. Here we describe a data acquisition and analysis workflow that expands the repertoire of high-resolution analytical approaches available to access the complexity of DOM molecules that are amenable to electrospray ionization (ESI MS. We couple liquid chromatographic separation with tandem MS (LC-MS/MS and a data analysis pipeline, that integrates peak extraction from extracted ion chromatograms (XIC, molecular formula calculation and molecular networking. This provides more precise structural characterization. Although only around 1% of detectable DOM compounds can be annotated through publicly available spectral libraries, community-wide participation in populating and annotating DOM datasets could rapidly increase the

  20. Influence of time scale wind speed data on sustainability analysis for irrigating greenhouse crops

    Science.gov (United States)

    Díaz Méndez, Rodrigo; García Llaneza, Joaquín; Peillón, Manuel; Perdigones, Alicia; Sanchez, Raul; Tarquis, Ana M.; Garcia, Jose Luis

    2014-05-01

    Appropriate water supply at crop/farm level, with suitable costs, is becoming more and more important. Energy management is closely related to water supply in this context, being wind energy one of the options to be considered, using wind pumps for irrigation water supply. Therefore, it is important to characterize the wind speed frequency distribution to study the technical feasibility to use its energy for irrigation management purpose. The general objective of this present research is to analyze the impact of time scale recorded wind speed data in the sustainability for tomato (Solanum lycopersicum L.) grown under greenhouse at Cuban conditions using drip irrigation system. For this porpoise, a daily estimation balance between water needs and water availability was used to evaluate the feasibility of the most economic windmill irrigation system. Several factors were included: wind velocity (W, m/s) in function of the time scale averaged, flow supplied by the wind pump as a function of the elevation height (H, m) and daily greenhouse evapotranspiration. Monthly volumes of water required for irrigation (Dr, m3/ha) and in the water tank (Vd, m3), as well as the monthly irrigable area (Ar, ha), were estimated by cumulative deficit water budgeting taking in account these factors. Three-hourly wind velocity (W3h, m/s) data from 1992 till 2008 was available for this study. The original data was grouped in six and twelve hourly data (W6h and W12h respectively) as well as daily data (W24h). For each time scale the daily estimation balance was applied. A comparison of the results points out a need for at least three-hourly data to be used mainly in the months in which mean wind speed are close or below the pumps threshold speed to start-up functioning. References Manuel Esteban Peillon Mesa, Ana Maria Tarquis Alfonso, José Luis García Fernández, and Raúl Sánchez Calvo. The use of wind pumps for irrigating greenhouse tomato crops: a case study in Cuba. Geophysical

  1. Necessary and Sufficient Conditions for the Existence of Positive Solution for Singular Boundary Value Problems on Time Scales

    Directory of Open Access Journals (Sweden)

    Zhang Xuemei

    2009-01-01

    Full Text Available By constructing available upper and lower solutions and combining the Schauder's fixed point theorem with maximum principle, this paper establishes sufficient and necessary conditions to guarantee the existence of as well as positive solutions for a class of singular boundary value problems on time scales. The results significantly extend and improve many known results for both the continuous case and more general time scales. We illustrate our results by one example.

  2. Modeling of GIC Impacts in Different Time Scales, and Validation with Measurement Data

    Science.gov (United States)

    Shetye, K.; Birchfield, A.; Overbye, T. J.; Gannon, J. L.

    2016-12-01

    Geomagnetically induced currents (GICs) have mostly been associated with geomagnetic disturbances (GMDs) originating from natural events such as solar coronal mass ejections. There is another, man-made, phenomenon that can induce GICs in the bulk power grid. Detonation of nuclear devices at high altitudes can give rise to electromagnetic pulses (EMPs) that induce electric fields at the earth's surface. EMPs cause three types of waves on different time scales, the slowest of which, E3, can induce GICs similar to the way GMDs do. The key difference between GMDs and EMPs is the rise time of the associated electric field. E3 electric fields are in the msec. to sec. range, whereas GMD electric fields are slower (sec. to min.). Similarly, the power grid and its components also operate and respond to disturbances in various time frames, right from electromagnetic transients (eg. lightning propagation) in the micro second range to steady state power flow ( hours). Hence, different power system component models need to be used to analyze the impacts of GICs caused by GMDs, and EMPs. For instance, for the slower GMD based GICs, a steady-state (static) analysis of the system is sufficient. That is, one does not need to model the dynamic components of a power system, such as the rotating machine of a generator, or generator controls such as exciters, etc. The latter become important in the case of an E3 EMP wave, which falls in the power system transient stability time frame of msec. to sec. This talk will first give an overview of the different time scales and models associated with power system operations, and where GMD and EMPs fit in. This is helpful to develop appropriate system models and test systems for analyzing impacts of GICs from various sources, and developing mitigation measures. Example test systems developed for GMD and EMP analysis, and their key modeling and analysis differences will be presented. After the modeling is discussed, results of validating

  3. Farmer response to climatic and agricultural market drivers: characteristic time scales and sensitivities

    Science.gov (United States)

    Wurster, P. M.; Maneta, M. P.; Vicente-Serrano, S. M.; Beguería, S.; Silverman, N. L.; Holden, Z.

    2017-12-01

    Agriculture in the intermountain western United States is dominated by extensive farming and ranching, mostly reliant on rainfed crops and therefore very exposed to precipitation shortfalls. It is also poorly diversified, dominated by five or six major grain crops, which makes it vulnerable to changes in agricultural markets. The economy of the region is very reliant on this type of agriculture, making the entire economy vulnerable to climatic and market fluctuations. Western agriculture is also of significant importance for national food security. Resource managers in the region are increasingly concerned with the impacts that more frequent and severe droughts, or the collapse of crop prices, may have on producers and food production. Effective resource management requires an understanding not only of the regional impact of adverse climatic and market events, but also of which geographic areas are most vulnerable, and why. Unfortunately, few studies exist that look into how farmers in different geographic areas respond to climate and market drivers. In this study we analyze the influence of precipitation and crop price anomalies on crop production, and map the characteristic time scale of these anomalies that correlate best with production anomalies for the 56 counties of Montana, U.S.A. We conduct this analysis using the standardized precipitation index (SPI), and defining a standardized crop value index (SCVI) and a standardized crop production index (SCPI). We use 38 years of data to calculate precipitation anomalies at monthly time scales and annual data to calculate crop price and production anomalies. The standardization of the indices allows for straightforward comparison of the relative influence of climatic and market fluctuations on production anomalies. We apply our methodology to winter wheat, spring durum wheat, barley, alfalfa, and beets which are the most valuable crops produced in the state. Results from this study show that precipitation anomalies

  4. Variability of interconnected wind plants: correlation length and its dependence on variability time scale

    Science.gov (United States)

    St. Martin, Clara M.; Lundquist, Julie K.; Handschy, Mark A.

    2015-04-01

    The variability in wind-generated electricity complicates the integration of this electricity into the electrical grid. This challenge steepens as the percentage of renewably-generated electricity on the grid grows, but variability can be reduced by exploiting geographic diversity: correlations between wind farms decrease as the separation between wind farms increases. But how far is far enough to reduce variability? Grid management requires balancing production on various timescales, and so consideration of correlations reflective of those timescales can guide the appropriate spatial scales of geographic diversity grid integration. To answer ‘how far is far enough,’ we investigate the universal behavior of geographic diversity by exploring wind-speed correlations using three extensive datasets spanning continents, durations and time resolution. First, one year of five-minute wind power generation data from 29 wind farms span 1270 km across Southeastern Australia (Australian Energy Market Operator). Second, 45 years of hourly 10 m wind-speeds from 117 stations span 5000 km across Canada (National Climate Data Archive of Environment Canada). Finally, four years of five-minute wind-speeds from 14 meteorological towers span 350 km of the Northwestern US (Bonneville Power Administration). After removing diurnal cycles and seasonal trends from all datasets, we investigate dependence of correlation length on time scale by digitally high-pass filtering the data on 0.25-2000 h timescales and calculating correlations between sites for each high-pass filter cut-off. Correlations fall to zero with increasing station separation distance, but the characteristic correlation length varies with the high-pass filter applied: the higher the cut-off frequency, the smaller the station separation required to achieve de-correlation. Remarkable similarities between these three datasets reveal behavior that, if universal, could be particularly useful for grid management. For high

  5. Theta-frequency resonance at the cerebellum input stage improves spike-timing on the millisecond time-scale

    Directory of Open Access Journals (Sweden)

    Daniela eGandolfi

    2013-04-01

    Full Text Available The neuronal circuits of the brain are thought to use resonance and oscillations to improve communication over specific frequency bands (Llinas, 1988; Buzsaki, 2006. However, the properties and mechanism of these phenomena in brain circuits remain largely unknown. Here we show that, at the cerebellum input stage, the granular layer generates its maximum response at 5-7 Hz both in vivo following tactile sensory stimulation of the whisker pad and in acute slices following mossy fiber-bundle stimulation. The spatial analysis of granular layer activity performed using voltage-sensitive dye (VSD imaging revealed 5-7 Hz resonance covering large granular layer areas. In single granule cells, resonance appeared as a reorganization of output spike bursts on the millisecond time-scale, such that the first spike occurred earlier and with higher temporal precision and the probability of spike generation increased. Resonance was independent from circuit inhibition, as it persisted with little variation in the presence of the GABAA receptor blocker, gabazine. However, circuit inhibition reduced the resonance area more markedly at 7 Hz. Simulations with detailed computational models suggested that resonance depended on intrinsic granule cells ionic mechanisms: specifically, Kslow (M-like and KA currents acted as resonators and the persistent Na current and NMDA current acted as amplifiers. This form of resonance may play an important role for enhancing coherent spike emission from the granular layer when theta-frequency bursts are transmitted by the cerebral cortex and peripheral sensory structures during sensory-motor processing, cognition and learning.

  6. Long-lived and largely red-shifted photoluminescence of solid-state rhodamine dyes: Molecular exciton coupling and structural effect

    International Nuclear Information System (INIS)

    Zhang, Xian-Fu; Zhang, Ya-Kui

    2015-01-01

    The optical absorption and fluorescence properties of five rhodamine dyes in solid-state are measured and show large difference from that in their gas phase or liquid solvents. All solid-state rhodamine dyes strongly absorb all light in UV and visible region, but emit only red and NIR fluorescence (680–800 nm, >100 nm red-shifted from that in solution). Further more, the absorption maxima of a solid-state rhodamine show a large red-shifted band (~100 nm) and blue-shifted peak (~125 nm) compared to that in solutions, indicating a strong molecular exciton coupling between molecules. All solid-state rhodamines still show reasonably good fluorescence quantum yield (Φ f ). In particular, solid-state Rhodamine B butyl ester and sulfonyl Rhodamine B showed a much longer emission lifetime (τ f ) than that of the corresponding molecular rhodamine, i.e. 4.12 and 4.14 ns in solid state compared to 1.61 and 2.47 ns in solution. The chemical structure of a rhodamine molecule showed dramatic effect on Φ f and τ f values for solid state rhodamine. The larger substituent in the benzene moiety favors higher Φ f and τ f values of rhodamine solids. These effects can be elucidated by the relation between structure-molecular distance and molecular exciton couplings. - Highlights: • Optical properties of solid rhodamines show large difference from that in solutions. • Solid-state rhodamine dyes emit red and NIR fluorescence (680–800 nm). • Solid-state rhodamines still show reasonably good fluorescence quantum yield. • Solid-state rhodamines have much longer fluorescence lifetimes than that in solutions

  7. Long-lived and largely red-shifted photoluminescence of solid-state rhodamine dyes: Molecular exciton coupling and structural effect

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xian-Fu, E-mail: zhangxianfu@tsinghua.org.cn [Institute of Applied Photochemistry & Center of Analysis and Measurements, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei Province (China); MPC Technologies, Hamilton, ON, Canada L8S 3H4 (Canada); Zhang, Ya-Kui [Institute of Applied Photochemistry & Center of Analysis and Measurements, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei Province (China)

    2015-10-15

    The optical absorption and fluorescence properties of five rhodamine dyes in solid-state are measured and show large difference from that in their gas phase or liquid solvents. All solid-state rhodamine dyes strongly absorb all light in UV and visible region, but emit only red and NIR fluorescence (680–800 nm, >100 nm red-shifted from that in solution). Further more, the absorption maxima of a solid-state rhodamine show a large red-shifted band (~100 nm) and blue-shifted peak (~125 nm) compared to that in solutions, indicating a strong molecular exciton coupling between molecules. All solid-state rhodamines still show reasonably good fluorescence quantum yield (Φ{sub f}). In particular, solid-state Rhodamine B butyl ester and sulfonyl Rhodamine B showed a much longer emission lifetime (τ{sub f}) than that of the corresponding molecular rhodamine, i.e. 4.12 and 4.14 ns in solid state compared to 1.61 and 2.47 ns in solution. The chemical structure of a rhodamine molecule showed dramatic effect on Φ{sub f} and τ{sub f} values for solid state rhodamine. The larger substituent in the benzene moiety favors higher Φ{sub f} and τ{sub f} values of rhodamine solids. These effects can be elucidated by the relation between structure-molecular distance and molecular exciton couplings. - Highlights: • Optical properties of solid rhodamines show large difference from that in solutions. • Solid-state rhodamine dyes emit red and NIR fluorescence (680–800 nm). • Solid-state rhodamines still show reasonably good fluorescence quantum yield. • Solid-state rhodamines have much longer fluorescence lifetimes than that in solutions.

  8. 234Th/238U disequilibrium in near-shore sediment: particle reworking and diagenetic time scales

    International Nuclear Information System (INIS)

    Aller, R.C.; Cochran, J.K.

    1976-01-01

    The distribution of 234 Th (tsub(1.2)=24.1 days) in excess of its parent 238 U in the upper layers of near-shore sediment makes possible the evaluation of short-term sediment reworking and diagenetic rates. 234 Th has a maximum residence time in Long Island Sound water of 1.4 days. Seasonal measurement of 234 Th/ 238 U disequilibrium in sediment at a single station in central Long Island Sound demonstrates rapid particle reworking and high 234 Thsub(XS)(>1 dpm/g) in the upper 4 cm of sediment with slower, irregular reworking and low 234 Thsub(XS) to at least 12 cm. The rate of rapid particle reworking varies seasonally and is highest in the fall. The rapidly mixed zone is characterized by steep gradients in sediment chemistry implying fast reactions spanned by 234 Th decay time scales. 238 U is depleted in the upper mixed zone and shows addition in reducing sediment at depth. (Auth.)

  9. The time scales of the climate-economy feedback and the climatic cost of growth

    International Nuclear Information System (INIS)

    Hallegatte, Stephane

    2005-04-01

    This paper is based on the perception that the inertia of climate and socio-economic systems are key parameters in the climate change issue. In a first part, it develops and implements a new approach based on a simple integrated model with a particular focus on an innovative transient impact and adaptation modelling. In a second part, a climate-economy feedback is defined and characterized. It is found that: (i) it has a 70-year characteristic time, which is long when compared to the system's other time-scales, and it cannot act as a natural damping process of climate change; (ii) mitigation has to be anticipated since the feedback of an emission reduction on the economy is significant only after a 20-year delay and really efficient after a one-century delay; (iii) the IPCC methodology, that neglects the feedback from impacts to emissions, is acceptable up to 2100, whatever is the level of impacts. This analysis allows also to define a climatic cost of growth as the additional climate change damages due to the additional emissions linked to economic growth. Usefully, this metric for climate change damages is particularly independent of the baseline scenario. (orig.)

  10. Extracting surface waves, hum and normal modes: time-scale phase-weighted stack and beyond

    Science.gov (United States)

    Ventosa, Sergi; Schimmel, Martin; Stutzmann, Eleonore

    2017-10-01

    Stacks of ambient noise correlations are routinely used to extract empirical Green's functions (EGFs) between station pairs. The time-frequency phase-weighted stack (tf-PWS) is a physically intuitive nonlinear denoising method that uses the phase coherence to improve EGF convergence when the performance of conventional linear averaging methods is not sufficient. The high computational cost of a continuous approach to the time-frequency transformation is currently a main limitation in ambient noise studies. We introduce the time-scale phase-weighted stack (ts-PWS) as an alternative extension of the phase-weighted stack that uses complex frames of wavelets to build a time-frequency representation that is much more efficient and fast to compute and that preserve the performance and flexibility of the tf-PWS. In addition, we propose two strategies: the unbiased phase coherence and the two-stage ts-PWS methods to further improve noise attenuation, quality of the extracted signals and convergence speed. We demonstrate that these approaches enable to extract minor- and major-arc Rayleigh waves (up to the sixth Rayleigh wave train) from many years of data from the GEOSCOPE global network. Finally we also show that fundamental spheroidal modes can be extracted from these EGF.

  11. Toward a continuous 405-kyr-calibrated Astronomical Time Scale for the Mesozoic Era

    Science.gov (United States)

    Hinnov, Linda; Ogg, James; Huang, Chunju

    2010-05-01

    Mesozoic cyclostratigraphy is being assembled into a continuous Astronomical Time Scale (ATS) tied to the Earth's cyclic orbital parameters. Recognition of a nearly ubiquitous, dominant ~400-kyr cycling in formations throughout the era has been particularly striking. Composite formations spanning contiguous intervals up to 50 myr clearly express these long-eccentricity cycles, and in some cases, this cycling is defined by third- or fourth-order sea-level sequences. This frequency is associated with the 405-kyr orbital eccentricity cycle, which provides a basic metronome and enables the extension of the well-defined Cenozoic ATS to scale the majority of the Mesozoic Era. This astronomical calibration has a resolution comparable to the 1% to 0.1% precision for radioisotope dating of Mesozoic ash beds, but with the added benefit of providing continuous stratigraphic coverage between dated beds. Extended portions of the Mesozoic ATS provide solutions to long-standing geologic problems of tectonics, eustasy, paleoclimate change, and rates of seafloor spreading.

  12. Mesozoic cyclostratigraphy, the 405-kyr orbital eccentricity metronome, and the Astronomical Time Scale (Invited)

    Science.gov (United States)

    Hinnov, L.; Ogg, J. G.

    2009-12-01

    Mesozoic cyclostratigraphy from around the world is being assessed to construct a continuous Astronomical Time Scale (ATS) based on Earth’s cyclic orbital parameters. The recognition of a prevalent sedimentary cycling with a ~400-kyr period associated with forcing by the stable 405-kyr orbital eccentricity variation is an important development. Numerous formations spanning 10 to 20 myr (and longer) intervals in the Cretaceous, Jurassic and Triassic clearly express this dominant cycle and provide a robust basis for 405-kyr-scale calibration of the ATS. This 405-kyr metronome will enable extension of the well-defined Cenozoic ATS for scaling of the past quarter-billion years of Earth history. This astronomical calibration has a resolution comparable to the 1% to 0.1% precision for radioisotope dating of Mesozoic ash beds, with the added benefit of providing continuous stratigraphic coverage between dated beds. Extended portions of the Mesozoic ATS have already provided new insights into long-standing geologic problems of seafloor spreading, tectonics, eustasy, and paleoclimate change. Ongoing work is focused on closing gaps in coverage and on collecting duplicate cyclostratigraphic records for the entire Mesozoic Era.

  13. Size-selective sorting in bubble streaming flows: Particle migration on fast time scales

    Science.gov (United States)

    Thameem, Raqeeb; Rallabandi, Bhargav; Hilgenfeldt, Sascha

    2015-11-01

    Steady streaming from ultrasonically driven microbubbles is an increasingly popular technique in microfluidics because such devices are easily manufactured and generate powerful and highly controllable flows. Combining streaming and Poiseuille transport flows allows for passive size-sensitive sorting at particle sizes and selectivities much smaller than the bubble radius. The crucial particle deflection and separation takes place over very small times (milliseconds) and length scales (20-30 microns) and can be rationalized using a simplified geometric mechanism. A quantitative theoretical description is achieved through the application of recent results on three-dimensional streaming flow field contributions. To develop a more fundamental understanding of the particle dynamics, we use high-speed photography of trajectories in polydisperse particle suspensions, recording the particle motion on the time scale of the bubble oscillation. Our data reveal the dependence of particle displacement on driving phase, particle size, oscillatory flow speed, and streaming speed. With this information, the effective repulsive force exerted by the bubble on the particle can be quantified, showing for the first time how fast, selective particle migration is effected in a streaming flow. We acknowledge support by the National Science Foundation under grant number CBET-1236141.

  14. Gradient plasticity for thermo-mechanical processes in metals with length and time scales

    Science.gov (United States)

    Voyiadjis, George Z.; Faghihi, Danial

    2013-03-01

    A thermodynamically consistent framework is developed in order to characterize the mechanical and thermal behavior of metals in small volume and on the fast transient time. In this regard, an enhanced gradient plasticity theory is coupled with the application of a micromorphic approach to the temperature variable. A physically based yield function based on the concept of thermal activation energy and the dislocation interaction mechanisms including nonlinear hardening is taken into consideration in the derivation. The effect of the material microstructural interface between two materials is also incorporated in the formulation with both temperature and rate effects. In order to accurately address the strengthening and hardening mechanisms, the theory is developed based on the decomposition of the mechanical state variables into energetic and dissipative counterparts which endowed the constitutive equations to have both energetic and dissipative gradient length scales for the bulk material and the interface. Moreover, the microstructural interaction effect in the fast transient process is addressed by incorporating two time scales into the microscopic heat equation. The numerical example of thin film on elastic substrate or a single phase bicrystal under uniform tension is addressed here. The effects of individual counterparts of the framework on the thermal and mechanical responses are investigated. The model is also compared with experimental results.

  15. Field Experience with and Potential for Multi-time Scale Grid Transactions from Responsive Commercial Buildings

    Energy Technology Data Exchange (ETDEWEB)

    Piette, Mary Ann; Kiliccote, Sila; Ghatikar, Girish

    2014-08-01

    The need for and concepts behind demand response are evolving. As the electric system changes with more intermittent renewable electric supply systems, there is a need to allow buildings to provide more flexible demand. This paper presents results from field studies and pilots, as well as engineering estimates of the potential capabilities of fast load responsiveness in commercial buildings. We present a sector wide analysis of flexible loads in commercial buildings, which was conducted to improve resource planning and determine which loads to evaluate in future demonstrations. These systems provide important capabilities for future transactional systems. The field analysis is based on results from California, plus projects in the northwest and east coast. End-uses considered include heating, ventilation, air conditioning and lighting. The timescales of control include day-ahead, as well as day-of, 10-minute ahead and even faster response. This technology can provide DR signals on different times scales to interact with responsive building loads. We describe the latency of the control systems in the building and the round trip communications with the wholesale grid operators.

  16. Modeling and simulation of nuclear fuel in scenarios with long time scales

    Energy Technology Data Exchange (ETDEWEB)

    Espinosa, Carlos E.; Bodmann, Bardo E.J., E-mail: eduardo.espinosa@ufrgs.br, E-mail: bardo.bodmann@ufrgs.br [Universidade Federal do Rio Grande do Sul (DENUC/PROMEC/UFRGS), Porto Alegre, RS (Brazil). Departamento de Engenharia Nuclear. Programa de Pos Graduacao em Engenharia Mecanica

    2015-07-01

    Nuclear reactors play a key role in defining the energy matrix. A study by the Fraunhofer Society shows in different time scales for long periods of time the distribution of energy sources. Regardless of scale, the use of nuclear energy is practically constant. In these scenarios, the nuclear fuel behavior over time is of interest. For kinetics of long-term scales, changing the chemical composition of fuel is significant. Thus, it is appropriate to consider fission products called neutron poisons. Such products are of interest in the nuclear reactor, since they become parasitic neutron absorbers and result in long thermal heat sources. The objective of this work is to solve the kinetics system coupled to neutron poison products. To solve this system, we use similar ideas to the method of Adomian decomposition. Initially, one separates the system of equations as the sum of a linear part and a non-linear part in order to solve a recursive system. The nonlinearity is treated as Adomian polynomial. We present numerical results of the effects of changing the power of a reactor, scenarios such as start-up and shut-down. For these results we consider time dependent reactivity, such as linear reactivity, quadratic polynomial and oscillatory. With these results one can simulate the chemical composition of the fuel due to the reuse of the spent fuel in subsequent cycles. (author)

  17. The time scales of the climate-economy feedback and the climatic cost of growth

    Energy Technology Data Exchange (ETDEWEB)

    Hallegatte, Stephane [CIRED - CNRM, Nogent-sur-Marne (France)

    2005-04-01

    This paper is based on the perception that the inertia of climate and socio-economic systems are key parameters in the climate change issue. In a first part, it develops and implements a new approach based on a simple integrated model with a particular focus on an innovative transient impact and adaptation modelling. In a second part, a climate-economy feedback is defined and characterized. It is found that: (i) it has a 70-year characteristic time, which is long when compared to the system's other time-scales, and it cannot act as a natural damping process of climate change; (ii) mitigation has to be anticipated since the feedback of an emission reduction on the economy is significant only after a 20-year delay and really efficient after a one-century delay; (iii) the IPCC methodology, that neglects the feedback from impacts to emissions, is acceptable up to 2100, whatever is the level of impacts. This analysis allows also to define a climatic cost of growth as the additional climate change damages due to the additional emissions linked to economic growth. Usefully, this metric for climate change damages is particularly independent of the baseline scenario. (orig.)

  18. Climate change-driven cliff and beach evolution at decadal to centennial time scales

    Science.gov (United States)

    Erikson, Li; O'Neill, Andrea; Barnard, Patrick; Vitousek, Sean; Limber, Patrick

    2017-01-01

    Here we develop a computationally efficient method that evolves cross-shore profiles of sand beaches with or without cliffs along natural and urban coastal environments and across expansive geographic areas at decadal to centennial time-scales driven by 21st century climate change projections. The model requires projected sea level rise rates, extrema of nearshore wave conditions, bluff recession and shoreline change rates, and cross-shore profiles representing present-day conditions. The model is applied to the ~470-km long coast of the Southern California Bight, USA, using recently available projected nearshore waves and bluff recession and shoreline change rates. The results indicate that eroded cliff material, from unarmored cliffs, contribute 11% to 26% to the total sediment budget. Historical beach nourishment rates will need to increase by more than 30% for a 0.25 m sea level rise (~2044) and by at least 75% by the year 2100 for a 1 m sea level rise, if evolution of the shoreline is to keep pace with rising sea levels.

  19. Time scales of DNAPL migration in sandy aquifers examined via numerical simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gerhard, J.I.; Pang, T.; Kueper, B.H. [University of Edinburgh, Edinburgh (United Kingdom). Inst. of Infrastructure & Environmental

    2007-03-15

    The time required for dense nonaqueous phase liquid (DNAPL) to cease migrating following release to the subsurface is a valuable component of a site conceptual model. This study uses numerical simulation to investigate the migration of six different DNAPLs in sandy aquifers. The most influential parameters governing migration cessation time are the density and viscosity of the DNAPL and the mean hydraulic conductivity of the aquifer. Releases of between 1 and 40 drums of chlorinated solvent DNAPLs, characterized by relatively high density and low viscosity, require on the order of months to a few years to cease migrating in a heterogeneous medium sand aquifer having an average hydraulic conductivity of 7.4 x 10{sup -3} cm/s. In contrast to this, the release of 20 drums of coal tar {rho}{sub D} = 1061 kg/m{sup 3}, {mu}{sub D} = 0.161 Pa(.)s) requires more than 100 years to cease migrating in the same aquifer. Altering the mean hydraulic conductivity of the aquifer results in a proportional change in cessation times. Parameters that exhibit relatively little influence on migration time scales are the DNAPL-water interfacial tension, release volume, source capillary pressure, mean aquifer porosity, and ambient ground water hydraulic gradient. This study also demonstrates that low-density DNAPLs (e.g., coal tar) give rise to greater amounts of lateral spreading and greater amounts of pooling on capillary barriers than high-density DNAPLs such as trichloroethylene or tetrachloroethylene.

  20. US stock market efficiency over weekly, monthly, quarterly and yearly time scales

    Science.gov (United States)

    Rodriguez, E.; Aguilar-Cornejo, M.; Femat, R.; Alvarez-Ramirez, J.

    2014-11-01

    In financial markets, the weak form of the efficient market hypothesis implies that price returns are serially uncorrelated sequences. In other words, prices should follow a random walk behavior. Recent developments in evolutionary economic theory (Lo, 2004) have tailored the concept of adaptive market hypothesis (AMH) by proposing that market efficiency is not an all-or-none concept, but rather market efficiency is a characteristic that varies continuously over time and across markets. Within the AMH framework, this work considers the Dow Jones Index Average (DJIA) for studying the deviations from the random walk behavior over time. It is found that the market efficiency also varies over different time scales, from weeks to years. The well-known detrended fluctuation analysis was used for the characterization of the serial correlations of the return sequences. The results from the empirical showed that interday and intraday returns are more serially correlated than overnight returns. Also, some insights in the presence of business cycles (e.g., Juglar and Kuznets) are provided in terms of time variations of the scaling exponent.

  1. Myosin-II sets the optimal response time scale of chemotactic amoeba

    Science.gov (United States)

    Hsu, Hsin-Fang; Westendorf, Christian; Tarantola, Marco; Bodenschatz, Eberhard; Beta, Carsten

    2014-03-01

    The response dynamics of the actin cytoskeleton to external chemical stimuli plays a fundamental role in numerous cellular functions. One of the key players that governs the dynamics of the actin network is the motor protein myosin-II. Here we investigate the role of myosin-II in the response of the actin system to external stimuli. We used a microfluidic device in combination with a photoactivatable chemoattractant to apply stimuli to individual cells with high temporal resolution. We directly compare the actin dynamics in Dictyostelium discodelium wild type (WT) cells to a knockout mutant that is deficient in myosin-II (MNL). Similar to the WT a small population of MNL cells showed self-sustained oscillations even in absence of external stimuli. The actin response of MNL cells to a short pulse of chemoattractant resembles WT during the first 15 sec but is significantly delayed afterward. The amplitude of the dominant peak in the power spectrum from the response time series of MNL cells to periodic stimuli with varying period showed a clear resonance peak at a forcing period of 36 sec, which is significantly delayed as compared to the resonance at 20 sec found for the WT. This shift indicates an important role of myosin-II in setting the response time scale of motile amoeba. Institute of Physics und Astronomy, University of Potsdam, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.

  2. Multi-Time Scale Control of Demand Flexibility in Smart Distribution Networks

    Directory of Open Access Journals (Sweden)

    Bishnu P. Bhattarai

    2017-01-01

    Full Text Available This paper presents a multi-timescale control strategy to deploy electric vehicle (EV demand flexibility for simultaneously providing power balancing, grid congestion management, and economic benefits to participating actors. First, an EV charging problem is investigated from consumer, aggregator, and distribution system operator’s perspectives. A hierarchical control architecture (HCA comprising scheduling, coordinative, and adaptive layers is then designed to realize their coordinative goal. This is realized by integrating multi-time scale controls that work from a day-ahead scheduling up to real-time adaptive control. The performance of the developed method is investigated with high EV penetration in a typical residential distribution grid. The simulation results demonstrate that HCA efficiently utilizes demand flexibility stemming from EVs to solve grid unbalancing and congestions with simultaneous maximization of economic benefits to the participating actors. This is ensured by enabling EV participation in day-ahead, balancing, and regulation markets. For the given network configuration and pricing structure, HCA ensures the EV owners to get paid up to five times the cost they were paying without control.

  3. EEG correlates of cognitive time scales in the Necker-Zeno model for bistable perception.

    Science.gov (United States)

    Kornmeier, J; Friedel, E; Wittmann, M; Atmanspacher, H

    2017-08-01

    The Necker-Zeno model of bistable perception provides a formal relation between the average duration of meta-stable percepts (dwell times T) of ambiguous figures and two other basic time scales (t 0 , ΔT) underlying cognitive processing. The model predicts that dwell times T covary with t 0 , ΔT or both. We tested this prediction by exploiting that observers, in particular experienced meditators, can volitionally control dwell times T. Meditators and non-meditators observed bistable Necker cubes either passively or tried to hold their current percept. The latencies of a centro-parietal event-related potential (CPP) were recorded as a physiological correlate of t 0 . Dwell times T and the CPP latencies, correlated with t 0 , differed between conditions and observer groups, while ΔT remained constant in the range predicted by the model. The covariation of CPP latencies and dwell times, as well as their quadratic functional dependence extends previous psychophysical confirmation of the Necker-Zeno model to psychophysiological measures. Copyright © 2017. Published by Elsevier Inc.

  4. Thermospheric mass density model error variance as a function of time scale

    Science.gov (United States)

    Emmert, J. T.; Sutton, E. K.

    2017-12-01

    In the increasingly crowded low-Earth orbit environment, accurate estimation of orbit prediction uncertainties is essential for collision avoidance. Poor characterization of such uncertainty can result in unnecessary and costly avoidance maneuvers (false positives) or disregard of a collision risk (false negatives). Atmospheric drag is a major source of orbit prediction uncertainty, and is particularly challenging to account for because it exerts a cumulative influence on orbital trajectories and is therefore not amenable to representation by a single uncertainty parameter. To address this challenge, we examine the variance of measured accelerometer-derived and orbit-derived mass densities with respect to predictions by thermospheric empirical models, using the data-minus-model variance as a proxy for model uncertainty. Our analysis focuses mainly on the power spectrum of the residuals, and we construct an empirical model of the variance as a function of time scale (from 1 hour to 10 years), altitude, and solar activity. We find that the power spectral density approximately follows a power-law process but with an enhancement near the 27-day solar rotation period. The residual variance increases monotonically with altitude between 250 and 550 km. There are two components to the variance dependence on solar activity: one component is 180 degrees out of phase (largest variance at solar minimum), and the other component lags 2 years behind solar maximum (largest variance in the descending phase of the solar cycle).

  5. Strain in shock-loaded skeletal muscle and the time scale of muscular wobbling mass dynamics.

    Science.gov (United States)

    Christensen, Kasper B; Günther, Michael; Schmitt, Syn; Siebert, Tobias

    2017-10-16

    In terrestrial locomotion, muscles undergo damped oscillations in response to limb impacts with the ground. Muscles are also actuators that generate mechanical power to allow locomotion. The corresponding elementary contractile process is the work stroke of an actin-myosin cross-bridge, which may be forcibly detached by superposed oscillations. By experimentally emulating rat leg impacts, we found that full activity and non-fatigue must meet to possibly prevent forcible cross-bridge detachment. Because submaximal muscle force represents the ordinary locomotor condition, our results show that forcible, eccentric cross-bridge detachment is a common, physiological process even during isometric muscle contractions. We also calculated the stiffnesses of the whole muscle-tendon complex and the fibre material separately, as well as Young's modulus of the latter: 1.8 MPa and 0.75 MPa for fresh, fully active and passive fibres, respectively. Our inferred Young's modulus of the tendon-aponeurosis complex suggests that stiffness in series to the fibre material is determined by the elastic properties of the aponeurosis region, rather than the tendon material. Knowing these stiffnesses and the muscle mass, the complex' eigenfrequency for responses to impacts can be quantified, as well as the size-dependency of this time scale of muscular wobbling mass dynamics.

  6. Modeling and simulation of nuclear fuel in scenarios with long time scales

    International Nuclear Information System (INIS)

    Espinosa, Carlos E.; Bodmann, Bardo E.J.

    2015-01-01

    Nuclear reactors play a key role in defining the energy matrix. A study by the Fraunhofer Society shows in different time scales for long periods of time the distribution of energy sources. Regardless of scale, the use of nuclear energy is practically constant. In these scenarios, the nuclear fuel behavior over time is of interest. For kinetics of long-term scales, changing the chemical composition of fuel is significant. Thus, it is appropriate to consider fission products called neutron poisons. Such products are of interest in the nuclear reactor, since they become parasitic neutron absorbers and result in long thermal heat sources. The objective of this work is to solve the kinetics system coupled to neutron poison products. To solve this system, we use similar ideas to the method of Adomian decomposition. Initially, one separates the system of equations as the sum of a linear part and a non-linear part in order to solve a recursive system. The nonlinearity is treated as Adomian polynomial. We present numerical results of the effects of changing the power of a reactor, scenarios such as start-up and shut-down. For these results we consider time dependent reactivity, such as linear reactivity, quadratic polynomial and oscillatory. With these results one can simulate the chemical composition of the fuel due to the reuse of the spent fuel in subsequent cycles. (author)

  7. Insights into the photochemical disproportionation of transition metal dimers on the picosecond time scale.

    Science.gov (United States)

    Lomont, Justin P; Nguyen, Son C; Harris, Charles B

    2013-05-09

    The reactivity of five transition metal dimers toward photochemical, in-solvent-cage disproportionation has been investigated using picosecond time-resolved infrared spectroscopy. Previous ultrafast studies on [CpW(CO)3]2 established the role of an in-cage disproportionation mechanism involving electron transfer between 17- and 19-electron radicals prior to diffusion out of the solvent cage. New results from time-resolved infrared studies reveal that the identity of the transition metal complex dictates whether the in-cage disproportionation mechanism can take place, as well as the more fundamental issue of whether 19-electron intermediates are able to form on the picosecond time scale. Significantly, the in-cage disproportionation mechanism observed previously for the tungsten dimer does not characterize the reactivity of four out of the five transition metal dimers in this study. The differences in the ability to form 19-electron intermediates are interpreted either in terms of differences in the 17/19-electron equilibrium or of differences in an energetic barrier to associative coordination of a Lewis base, whereas the case for the in-cage vs diffusive disproportionation mechanisms depends on whether the 19-electron reducing agent is genuinely characterized by 19-electron configuration at the metal center or if it is better described as an 18 + δ complex. These results help to better understand the factors that dictate mechanisms of radical disproportionation and carry implications for radical chain mechanisms.

  8. HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens.

    Science.gov (United States)

    Kosakovsky Pond, Sergei L; Weaver, Steven; Leigh Brown, Andrew J; Wertheim, Joel O

    2018-01-31

    In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoeleather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, i.e., on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from github.com/veg/hivtrace, along with the accompanying result visualization module from github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  9. Application of a gradient diffusion and dissipation time scale ratio model for prediction of mean and fluctuating temperature fields in liquid sodium downstream of a multi-bore jet block

    International Nuclear Information System (INIS)

    Bremhorst, K.; Listijono, J.B.H.; Krebs, L.; Mueller, U.

    1989-01-01

    A previously developed diffusivity based based model, for the prediction of mean and fluctuating temperatures in water flow downstream of a multi-bore jet block in which one jet is heated, is applied to a flow of sodium in apparatus of similar geometry. Some measurements not readily possible in sodium or water flows for this geometry are made using air in order to verify assumptions used in the model. The earlier derived mathematical model is modified to remove assumptions relating to turbulence. Reynolds number and turbulence Peclet number in the relationship between velocity and temperature microscales. Spalding's model, relating fluctuating velocity and temperature dissipation rates, is tested. A significant effect on this relationship due to the low Prandtl number of liquid sodium is identified. Measurements performed behind a multi-bore jet block with air as the working fluid have verified the non-isotropic nature of the large-scale flow. Results clearly show that measurements performed in water can be transferred to liquid sodium provided that molecular diffusion is included in the mean temperature equation, allowance is made for the Prandtl number effect on the dissipation time scale ratio and the coefficient of gradient diffusion of mean square temperature fluctuations is assumed equal to the eddy diffusivity of heat. (author)

  10. A short-time scale colloidal system reveals early bacterial adhesion dynamics.

    Directory of Open Access Journals (Sweden)

    Christophe Beloin

    2008-07-01

    Full Text Available The development of bacteria on abiotic surfaces has important public health and sanitary consequences. However, despite several decades of study of bacterial adhesion to inert surfaces, the biophysical mechanisms governing this process remain poorly understood, due, in particular, to the lack of methodologies covering the appropriate time scale. Using micrometric colloidal surface particles and flow cytometry analysis, we developed a rapid multiparametric approach to studying early events in adhesion of the bacterium Escherichia coli. This approach simultaneously describes the kinetics and amplitude of early steps in adhesion, changes in physicochemical surface properties within the first few seconds of adhesion, and the self-association state of attached and free-floating cells. Examination of the role of three well-characterized E. coli surface adhesion factors upon attachment to colloidal surfaces--curli fimbriae, F-conjugative pilus, and Ag43 adhesin--showed clear-cut differences in the very initial phases of surface colonization for cell-bearing surface structures, all known to promote biofilm development. Our multiparametric analysis revealed a correlation in the adhesion phase with cell-to-cell aggregation properties and demonstrated that this phenomenon amplified surface colonization once initial cell-surface attachment was achieved. Monitoring of real-time physico-chemical particle surface properties showed that surface-active molecules of bacterial origin quickly modified surface properties, providing new insight into the intricate relations connecting abiotic surface physicochemical properties and bacterial adhesion. Hence, the biophysical analytical method described here provides a new and relevant approach to quantitatively and kinetically investigating bacterial adhesion and biofilm development.

  11. Relationship between the Arctic oscillation and surface air temperature in multi-decadal time-scale

    Science.gov (United States)

    Tanaka, Hiroshi L.; Tamura, Mina

    2016-09-01

    In this study, a simple energy balance model (EBM) was integrated in time, considering a hypothetical long-term variability in ice-albedo feedback mimicking the observed multi-decadal temperature variability. A natural variability was superimposed on a linear warming trend due to the increasing radiative forcing of CO2. The result demonstrates that the superposition of the natural variability and the background linear trend can offset with each other to show the warming hiatus for some period. It is also stressed that the rapid warming during 1970-2000 can be explained by the superposition of the natural variability and the background linear trend at least within the simple model. The key process of the fluctuating planetary albedo in multi-decadal time scale is investigated using the JRA-55 reanalysis data. It is found that the planetary albedo increased for 1958-1970, decreased for 1970-2000, and increased for 2000-2012, as expected by the simple EBM experiments. The multi-decadal variability in the planetary albedo is compared with the time series of the AO mode and Barents Sea mode of surface air temperature. It is shown that the recent AO negative pattern showing warm Arctic and cold mid-latitudes is in good agreement with planetary albedo change indicating negative anomaly in high latitudes and positive anomaly in mid-latitudes. Moreover, the Barents Sea mode with the warm Barents Sea and cold mid-latitudes shows long-term variability similar to planetary albedo change. Although further studies are needed, the natural variabilities of both the AO mode and Barents Sea mode indicate some possible link to the planetary albedo as suggested by the simple EBM to cause the warming hiatus in recent years.

  12. Arctic energy budget in relation to sea-ice variability on monthly to annual time scales

    Science.gov (United States)

    Krikken, Folmer; Hazeleger, Wilco

    2015-04-01

    The strong decrease in Arctic sea-ice in recent years has triggered a strong interest in Arctic sea-ice predictions on seasonal to decadal time scales. Hence, it is key to understand physical processes that provide enhanced predictability beyond persistence of sea ice anomalies. The authors report on an analysis of natural variability of Arctic sea-ice from an energy budget perspective, using 15 CMIP5 climate models, and comparing these results to atmospheric and oceanic reanalyses data. We quantify the persistence of sea ice anomalies and the cross-correlation with the surface and top energy budget components. The Arctic energy balance components primarily indicate the important role of the seasonal sea-ice albedo feedback, in which sea-ice anomalies in the melt season reemerge in the growth season. This is a robust anomaly reemergence mechanism among all 15 climate models. The role of ocean lies mainly in storing heat content anomalies in spring, and releasing them in autumn. Ocean heat flux variations only play a minor role. The role of clouds is further investigated. We demonstrate that there is no direct atmospheric response of clouds to spring sea-ice anomalies, but a delayed response is evident in autumn. Hence, there is no cloud-ice feedback in late spring and summer, but there is a cloud-ice feedback in autumn, which strengthens the ice-albedo feedback. Anomalies in insolation are positively correlated with sea-ice variability. This is primarily a result of reduced multiple-reflection of insolation due to an albedo decrease. This effect counteracts the sea-ice albedo effect up to 50%. ERA-Interim and ORAS4 confirm the main findings from the climate models.

  13. Global Precipitation Analyses at Time Scales of Monthly to 3-Hourly

    Science.gov (United States)

    Adler, Robert F.; Huffman, George; Curtis, Scott; Bolvin, David; Nelkin, Eric; Einaudi, Franco (Technical Monitor)

    2002-01-01

    Global precipitation analysis covering the last few decades and the impact of the new TRMM precipitation observations are discussed. The 20+ year, monthly, globally complete precipitation analysis of the World Climate Research Program's (WCRP/GEWEX) Global Precipitation Climatology Project (GPCP) is used to explore global and regional variations and trends and is compared to the much shorter TRMM (Tropical Rainfall Measuring Mission) tropical data set. The GPCP data set shows no significant trend in precipitation over the twenty years, unlike the positive trend in global surface temperatures over the past century. Regional trends are also analyzed. A trend pattern that is a combination of both El Nino and La Nina precipitation features is evident in the Goodyear data set. This pattern is related to an increase with time in the number of combined months of El Nino and La Nina during the Goodyear period. Monthly anomalies of precipitation are related to ENRON variations with clear signals extending into middle and high latitudes of both hemispheres. The GPCP daily, 1 degree latitude-longitude analysis, which is available from January 1997 to the present is described and the evolution of precipitation patterns on this time scale related to El Nino and La Nina is described. Finally, a TRMM-based Based analysis is described that uses TRMM to calibrate polar-orbit microwave observations from SSM/I and geosynchronous OR observations and merges the various calibrated observations into a final, Baehr resolution map. This TRMM standard product will be available for the entire TRMM period (January Represent). A real-time version of this merged product is being produced and is available at 0.25 degree latitude-longitude resolution over the latitude range from 50 deg. N -50 deg. S. Examples will be shown, including its use in monitoring flood conditions.

  14. Mean-cluster approach indicates cell sorting time scales are determined by collective dynamics

    Science.gov (United States)

    Beatrici, Carine P.; de Almeida, Rita M. C.; Brunnet, Leonardo G.

    2017-03-01

    Cell migration is essential to cell segregation, playing a central role in tissue formation, wound healing, and tumor evolution. Considering random mixtures of two cell types, it is still not clear which cell characteristics define clustering time scales. The mass of diffusing clusters merging with one another is expected to grow as td /d +2 when the diffusion constant scales with the inverse of the cluster mass. Cell segregation experiments deviate from that behavior. Explanations for that could arise from specific microscopic mechanisms or from collective effects, typical of active matter. Here we consider a power law connecting diffusion constant and cluster mass to propose an analytic approach to model cell segregation where we explicitly take into account finite-size corrections. The results are compared with active matter model simulations and experiments available in the literature. To investigate the role played by different mechanisms we considered different hypotheses describing cell-cell interaction: differential adhesion hypothesis and different velocities hypothesis. We find that the simulations yield normal diffusion for long time intervals. Analytic and simulation results show that (i) cluster evolution clearly tends to a scaling regime, disrupted only at finite-size limits; (ii) cluster diffusion is greatly enhanced by cell collective behavior, such that for high enough tendency to follow the neighbors, cluster diffusion may become independent of cluster size; (iii) the scaling exponent for cluster growth depends only on the mass-diffusion relation, not on the detailed local segregation mechanism. These results apply for active matter systems in general and, in particular, the mechanisms found underlying the increase in cell sorting speed certainly have deep implications in biological evolution as a selection mechanism.

  15. What is the Time Scale for Orbital Forcing of the Martian Water Cycle?

    Science.gov (United States)

    Hecht, M. H.

    2003-01-01

    Calculation of the periodic variations in the martian orbital parameters by Ward and subsequent refinements to the theory have inspired numerous models of variation of the martian water cycle. Most of these models have focused on variations in planetary obliquity on a both a short-term (110 kyr) time scale as well as larger oscillations occuring over millions of years. To a lesser extent, variations in planetary eccentricity have also been considered. The third and fastest mode of variation, the precession of the longitude of perihelion, has generally been deemphasized because, among the three parameters, it is the only one that does not change the integrated annual insolation. But as a result of this precession, the asymmetry in peak summer insolation between the poles exceeds 50%, with the maximum cycling between poles every 25.5 kyrs. The relative contribution of these different elements to orbital forcing of climate takes on particular importance in the context of apparently recent waterrelated features such as gullies or polar layered deposits (PLD). Christensen, for example, recently indentified mantling of heavily gullied crater walls as residual dust-covered snow deposits that were responsible for the formation of the gullies in a previous epoch. Christensen assumed that the snow was originally deposited at a period of high obliquity which was stabilized against sublimation by a lag deposit of dust. It is suggested here that not obliquity, but the shortterm oscillations associated with precession of the perihelion may play the dominant role in the formation of gullies, major strata in the polar layered deposits (PLD), and other water-related features.

  16. Design and implementation of the Molecular Imaging Unit for large animais at the National Center for Cardiovascular Research

    International Nuclear Information System (INIS)

    Lopez, G.; Delgado Alberquilla, R.; Moreno Lopez, J.; Escudero Toro, R.

    2011-01-01

    in this paper describes the most iraportant imaging techniques to be used with the latest equipment as well as the future of PET-MRI combination, its application in research on large animals and the implications for the design of the units, shielding calculation management, sources of radiation and waste. This has reguired value and integrate the specific requirements of a research center in terms of bio security, care of large animals (pigs), health status of animals in an environment of highly demanding conditions PR.

  17. KINEMATIC STRUCTURE OF MOLECULAR GAS AROUND HIGH-MASS YSO, PAPILLON NEBULA, IN N159 EAST IN THE LARGE MAGELLANIC CLOUD: A NEW PERSPECTIVE WITH ALMA

    Energy Technology Data Exchange (ETDEWEB)

    Saigo, Kazuya; Harada, Ryohei; Kawamura, Akiko [Chile Observatory, National Astronomical Observatory of Japan, National Institutes of Natural Science, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Onishi, Toshikazu; Tokuda, Kazuki; Morioka, Yuuki [Department of Physical Science, Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531 (Japan); Nayak, Omnarayani; Meixner, Margaret [The Johns Hopkins University, Department of Physics and Astronomy, 366 Bloomberg Center, 3400 N. Charles Street, Baltimore, MD 21218 (United States); Sewiło, Marta [NASA Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, MD 20771 (United States); Indebetouw, Remy [Department of Astronomy, University of Virginia, P.O. Box 400325, Charlottesville, VA 22904 (United States); Torii, Kazufumi; Ohama, Akio; Hattori, Yusuke; Yamamoto, Hiroaki; Tachihara, Kengo [Department of Physics, Nagoya University, Chikusa-ku, Nagoya 464-8602 (Japan); Minamidani, Tetsuhiro [Nobeyama Radio Observatory, 462-2 Nobeyama Minamimaki-mura, Minamisaku-gun, Nagano 384-1305 (Japan); Inoue, Tsuyoshi [Division of Theoretical Astronomy, National Astronomical Observatory (Japan); Madden, Suzanne; Lebouteiller, Vianney [Laboratoire AIM, CEA, Universite Paris VII, IRFU/Service d’Astrophysique, Bat. 709, F-91191 Gif-sur-Yvette (France); Galametz, Maud [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); and others

    2017-01-20

    We present the ALMA Band 3 and Band 6 results of {sup 12}CO(2-1), {sup 13}CO(2-1), H30 α recombination line, free–free emission around 98 GHz, and the dust thermal emission around 230 GHz toward the N159 East Giant Molecular Cloud (N159E) in the Large Magellanic Cloud (LMC). LMC is the nearest active high-mass star-forming face-on galaxy at a distance of 50 kpc and is the best target for studing high-mass star formation. ALMA observations show that N159E is the complex of filamentary clouds with the width and length of ∼1 pc and several parsecs. The total molecular mass is 0.92 × 10{sup 5} M {sub ⊙} from the {sup 13}CO(2-1) intensity. N159E harbors the well-known Papillon Nebula, a compact high-excitation H ii region. We found that a YSO associated with the Papillon Nebula has the mass of 35 M {sub ⊙} and is located at the intersection of three filamentary clouds. It indicates that the formation of the high-mass YSO was induced by the collision of filamentary clouds. Fukui et al. reported a similar kinematic structure toward two YSOs in the N159 West region, which are the other YSOs that have the mass of ≳35 M {sub ⊙}. This suggests that the collision of filamentary clouds is a primary mechanism of high-mass star formation. We found a small molecular hole around the YSO in Papillon Nebula with a sub-parsec scale. It is filled by free–free and H30 α emission. The temperature of the molecular gas around the hole reaches ∼80 K. It indicates that this YSO has just started the distruction of parental molecular cloud.

  18. KINEMATIC STRUCTURE OF MOLECULAR GAS AROUND HIGH-MASS YSO, PAPILLON NEBULA, IN N159 EAST IN THE LARGE MAGELLANIC CLOUD: A NEW PERSPECTIVE WITH ALMA

    International Nuclear Information System (INIS)

    Saigo, Kazuya; Harada, Ryohei; Kawamura, Akiko; Onishi, Toshikazu; Tokuda, Kazuki; Morioka, Yuuki; Nayak, Omnarayani; Meixner, Margaret; Sewiło, Marta; Indebetouw, Remy; Torii, Kazufumi; Ohama, Akio; Hattori, Yusuke; Yamamoto, Hiroaki; Tachihara, Kengo; Minamidani, Tetsuhiro; Inoue, Tsuyoshi; Madden, Suzanne; Lebouteiller, Vianney; Galametz, Maud

    2017-01-01

    We present the ALMA Band 3 and Band 6 results of 12 CO(2-1), 13 CO(2-1), H30 α recombination line, free–free emission around 98 GHz, and the dust thermal emission around 230 GHz toward the N159 East Giant Molecular Cloud (N159E) in the Large Magellanic Cloud (LMC). LMC is the nearest active high-mass star-forming face-on galaxy at a distance of 50 kpc and is the best target for studing high-mass star formation. ALMA observations show that N159E is the complex of filamentary clouds with the width and length of ∼1 pc and several parsecs. The total molecular mass is 0.92 × 10 5 M ⊙ from the 13 CO(2-1) intensity. N159E harbors the well-known Papillon Nebula, a compact high-excitation H ii region. We found that a YSO associated with the Papillon Nebula has the mass of 35 M ⊙ and is located at the intersection of three filamentary clouds. It indicates that the formation of the high-mass YSO was induced by the collision of filamentary clouds. Fukui et al. reported a similar kinematic structure toward two YSOs in the N159 West region, which are the other YSOs that have the mass of ≳35 M ⊙ . This suggests that the collision of filamentary clouds is a primary mechanism of high-mass star formation. We found a small molecular hole around the YSO in Papillon Nebula with a sub-parsec scale. It is filled by free–free and H30 α emission. The temperature of the molecular gas around the hole reaches ∼80 K. It indicates that this YSO has just started the distruction of parental molecular cloud.

  19. Hepatitis C virus positive diffuse large B-cell lymphomas have distinct molecular features and lack BCL2 translocations

    DEFF Research Database (Denmark)

    Visco, Carlo; Wang, Jinfen; Tisi, Maria Chiara

    2017-01-01

    apoptotic pathways, have higher proliferative index, and lack BCL2 translocations. CONCLUSIONS: HCV-positive DLBCL have distinct molecular and pathological features compared to the HCV-negative counterparts.British Journal of Cancer advance online publication, 26 September 2017; doi:10.1038/bjc.2017.345 www.bjcancer.com....... in lymphomagenesis, as witnessed by the curative potential of antiviral therapy in HCV-related low-grade B-cell lymphomas. METHODS: We performed a case-control study including 44 HCV-positive cases of de novo DLBCL, comparing them with 132 HCV-negative patients as controls (ratio 3 to 1). Cases and controls were...... for MYC, BCL2 and BCL6, TP53 mutations, and diagnostic specimens reviewed to exclude transformation from low-grade lymphoma. RESULTS: Compared to the HCV-negative controls, patients with HCV-positive de novo DLBCL had differential expression of genes that regulate innate immune response and modulate...

  20. Laminar and dorsoventral molecular organization of the medial entorhinal cortex revealed by large-scale anatomical analysis of gene expression.

    Directory of Open Access Journals (Sweden)

    Helen L Ramsden

    2015-01-01

    Full Text Available Neural circuits in the medial entorhinal cortex (MEC encode an animal's position and orientation in space. Within the MEC spatial representations, including grid and directional firing fields, have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellular properties. Yet, in part due to the challenges of integrating anatomical data at the resolution of cortical layers and borders, we know little about the molecular components underlying this organization. To address this we develop a new computational pipeline for high-throughput analysis and comparison of in situ hybridization (ISH images at laminar resolution. We apply this pipeline to ISH data for over 16,000 genes in the Allen Brain Atlas and validate our analysis with RNA sequencing of MEC tissue from adult mice. We find that differential gene expression delineates the borders of the MEC with neighboring brain structures and reveals its laminar and dorsoventral organization. We propose a new molecular basis for distinguishing the deep layers of the MEC and show that their similarity to corresponding layers of neocortex is greater than that of superficial layers. Our analysis identifies ion channel-, cell adhesion- and synapse-related genes as candidates for functional differentiation of MEC layers and for encoding of spatial information at different scales along the dorsoventral axis of the MEC. We also reveal laminar organization of genes related to disease pathology and suggest that a high metabolic demand predisposes layer II to neurodegenerative pathology. In principle, our computational pipeline can be applied to high-throughput analysis of many forms of neuroanatomical data. Our results support the hypothesis that differences in gene expression contribute to functional specialization of superficial layers of the MEC and dorsoventral organization of the scale of spatial representations.

  1. Cellular and molecular deviations in bovine in vitro-produced embryos are related to the large offspring syndrome

    NARCIS (Netherlands)

    Lazzari, G.; Wrenzycki, C.; Herrmann, D.; Duchi, R.; Kruip, T.; Niemann, H.; Galli, C.

    2002-01-01

    The large offspring syndrome (LOS) is observed in bovine and ovine offspring following transfer of in vitro-produced (IVP) or cloned embryos and is characterized by a multitude of pathologic changes, of which extended gestation length and increased birthweight are predominant features. In the

  2. Climatic changes on orbital and sub-orbital time scale recorded by the Guliya ice core in Tibetan Plateau

    Institute of Scientific and Technical Information of China (English)

    姚檀栋; 徐柏青; 蒲健辰

    2001-01-01

    Based on ice core records in the Tibetan Plateau and Greenland, the features and possible causes of climatic changes on orbital and sub-orbital time scale were discussed. Orbital time scale climatic change recorded in ice core from the Tibetan Plateau is typically ahead of that from polar regions, which indicates that climatic change in the Tibetan Plateau might be earlier than polar regions. The solar radiation change is a major factor that dominates the climatic change on orbital time scale. However, climatic events on sub-orbital time scale occurred later in the Tibetan Plateau than in the Arctic Region, indicating a different mechanism. For example, the Younger Dryas and Heinrich events took place earlier in Greenland ice core record than in Guliya ice core record. It is reasonable to propose the hypothesis that these climatic events were affected possibly by the Laurentide Ice Sheet. Therefore, ice sheet is critically important to climatic change on sub-orbital time scale in some ice ages.

  3. The plasma transport equations derived by multiple time-scale expansions and turbulent transport. I. General theory

    International Nuclear Information System (INIS)

    Edenstrasser, J.W.

    1995-01-01

    A multiple time-scale derivative expansion scheme is applied to the dimensionless Fokker--Planck equation and to Maxwell's equations, where the parameter range of a typical fusion plasma was assumed. Within kinetic theory, the four time scales considered are those of Larmor gyration, particle transit, collisions, and classical transport. The corresponding magnetohydrodynamic (MHD) time scales are those of ion Larmor gyration, Alfven, MHD collision, and resistive diffusion. The solution of the zeroth-order equations results in the force-free equilibria and ideal Ohm's law. The solution of the first-order equations leads under the assumption of a weak collisional plasma to the ideal MHD equations. On the MHD-collision time scale, not only the full set of the MHD transport equations is obtained, but also turbulent terms, where the related transport quantities are one order in the expansion parameter larger than those of classical transport. Finally, at the resistive diffusion time scale the known transport equations are arrived at including, however, also turbulent contributions. copyright 1995 American Institute of Physics

  4. Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model.

    Directory of Open Access Journals (Sweden)

    Guido Gigante

    2015-11-01

    Full Text Available Cortical networks, in-vitro as well as in-vivo, can spontaneously generate a variety of collective dynamical events such as network spikes, UP and DOWN states, global oscillations, and avalanches. Though each of them has been variously recognized in previous works as expression of the excitability of the cortical tissue and the associated nonlinear dynamics, a unified picture of the determinant factors (dynamical and architectural is desirable and not yet available. Progress has also been partially hindered by the use of a variety of statistical measures to define the network events of interest. We propose here a common probabilistic definition of network events that, applied to the firing activity of cultured neural networks, highlights the co-occurrence of network spikes, power-law distributed avalanches, and exponentially distributed 'quasi-orbits', which offer a third type of collective behavior. A rate model, including synaptic excitation and inhibition with no imposed topology, synaptic short-term depression, and finite-size noise, accounts for all these different, coexisting phenomena. We find that their emergence is largely regulated by the proximity to an oscillatory instability of the dynamics, where the non-linear excitable behavior leads to a self-amplification of activity fluctuations over a wide range of scales in space and time. In this sense, the cultured network dynamics is compatible with an excitation-inhibition balance corresponding to a slightly sub-critical regime. Finally, we propose and test a method to infer the characteristic time of the fatigue process, from the observed time course of the network's firing rate. Unlike the model, possessing a single fatigue mechanism, the cultured network appears to show multiple time scales, signalling the possible coexistence of different fatigue mechanisms.

  5. Short time-scale optical variability properties of the largest AGN sample observed with Kepler/K2

    Science.gov (United States)

    Aranzana, E.; Körding, E.; Uttley, P.; Scaringi, S.; Bloemen, S.

    2018-05-01

    We present the first short time-scale (˜hours to days) optical variability study of a large sample of active galactic nuclei (AGNs) observed with the Kepler/K2 mission. The sample contains 252 AGN observed over four campaigns with ˜30 min cadence selected from the Million Quasar Catalogue with R magnitude <19. We performed time series analysis to determine their variability properties by means of the power spectral densities (PSDs) and applied Monte Carlo techniques to find the best model parameters that fit the observed power spectra. A power-law model is sufficient to describe all the PSDs of our sample. A variety of power-law slopes were found indicating that there is not a universal slope for all AGNs. We find that the rest-frame amplitude variability in the frequency range of 6 × 10-6-10-4 Hz varies from 1to10 per cent with an average of 1.7 per cent. We explore correlations between the variability amplitude and key parameters of the AGN, finding a significant correlation of rest-frame short-term variability amplitude with redshift. We attribute this effect to the known `bluer when brighter' variability of quasars combined with the fixed bandpass of Kepler data. This study also enables us to distinguish between Seyferts and blazars and confirm AGN candidates. For our study, we have compared results obtained from light curves extracted using different aperture sizes and with and without detrending. We find that limited detrending of the optimal photometric precision light curve is the best approach, although some systematic effects still remain present.

  6. Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management.

    Science.gov (United States)

    Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

    2015-01-01

    HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.

  7. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

    Science.gov (United States)

    Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

    2012-01-01

    We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

  8. Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale

    Czech Academy of Sciences Publication Activity Database

    Islam, B.; Sgobba, M.; Laughton, C.; Orozco, M.; Šponer, Jiří; Neidle, S.; Haider, S.

    2013-01-01

    Roč. 41, č. 4 (2013), s. 2723-2735 ISSN 0305-1048 R&D Projects: GA ČR(CZ) GAP208/11/1822 Grant - others:GA ČR(CZ) ED1.1.00/02.0068 Program:ED Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS * CRYSTAL-STRUCTURE * B-DNA Subject RIV: BO - Biophysics Impact factor: 8.808, year: 2013

  9. Study of fission time scale from measurement of pre-scission light particle and γ-ray multiplicities

    International Nuclear Information System (INIS)

    Ramachandran, K.; Chatterjee, A.; Navin, A.

    2014-01-01

    This work presents the result of a simultaneous measurement of pre-scission multiplicities and analysis using the statistical model code JOANNE2 which includes deformation effects. Evaporation residue cross-sections has also been measured for the same system and analyzed in a consistent manner. The neutron, charged particle, GDR γ-ray and ER data could be explained consistently. The emission of neutrons seems to be favored towards larger deformation as compared to charged particles. The pre-scission time scale is deduced as 0-2 x 10 -21 s whereas the saddle-to-scission time scale is 36-39 x 10 -21 s. The total fission time scale is deduced as 36-41 x 10 -21 s

  10. Cross-Scale Modelling of Subduction from Minute to Million of Years Time Scale

    Science.gov (United States)

    Sobolev, S. V.; Muldashev, I. A.

    2015-12-01

    Subduction is an essentially multi-scale process with time-scales spanning from geological to earthquake scale with the seismic cycle in-between. Modelling of such process constitutes one of the largest challenges in geodynamic modelling today.Here we present a cross-scale thermomechanical model capable of simulating the entire subduction process from rupture (1 min) to geological time (millions of years) that employs elasticity, mineral-physics-constrained non-linear transient viscous rheology and rate-and-state friction plasticity. The model generates spontaneous earthquake sequences. The adaptive time-step algorithm recognizes moment of instability and drops the integration time step to its minimum value of 40 sec during the earthquake. The time step is then gradually increased to its maximal value of 5 yr, following decreasing displacement rates during the postseismic relaxation. Efficient implementation of numerical techniques allows long-term simulations with total time of millions of years. This technique allows to follow in details deformation process during the entire seismic cycle and multiple seismic cycles. We observe various deformation patterns during modelled seismic cycle that are consistent with surface GPS observations and demonstrate that, contrary to the conventional ideas, the postseismic deformation may be controlled by viscoelastic relaxation in the mantle wedge, starting within only a few hours after the great (M>9) earthquakes. Interestingly, in our model an average slip velocity at the fault closely follows hyperbolic decay law. In natural observations, such deformation is interpreted as an afterslip, while in our model it is caused by the viscoelastic relaxation of mantle wedge with viscosity strongly varying with time. We demonstrate that our results are consistent with the postseismic surface displacement after the Great Tohoku Earthquake for the day-to-year time range. We will also present results of the modeling of deformation of the

  11. Late Miocene climate and time scale reconciliation: Accurate orbital calibration from a deep-sea perspective

    Science.gov (United States)

    Drury, Anna Joy; Westerhold, Thomas; Frederichs, Thomas; Tian, Jun; Wilkens, Roy; Channell, James E. T.; Evans, Helen; John, Cédric M.; Lyle, Mitch; Röhl, Ursula

    2017-10-01

    Accurate age control of the late Tortonian to early Messinian (8.3-6.0 Ma) is essential to ascertain the origin of benthic foraminiferal δ18O trends and the late Miocene carbon isotope shift (LMCIS), and to examine temporal relationships between the deep-sea, terrasphere and cryosphere. The current Tortonian-Messinian Geological Time Scale (GTS2012) is based on astronomically calibrated Mediterranean sections; however, no comparable non-Mediterranean stratigraphies exist for 8-6 Ma suitable for testing the GTS2012. Here, we present the first high-resolution, astronomically tuned benthic stable isotope stratigraphy (1.5 kyr resolution) and magnetostratigraphy from a single deep-sea location (IODP Site U1337, equatorial Pacific Ocean), which provides unprecedented insight into climate evolution from 8.3-6.0 Ma. The astronomically calibrated magnetostratigraphy provides robust ages, which differ by 2-50 kyr relative to the GTS2012 for polarity Chrons C3An.1n to C4r.1r, and eliminates the exceptionally high South Atlantic spreading rates based on the GTS2012 during Chron C3Bn. We show that the LMCIS was globally synchronous within 2 kyr, and provide astronomically calibrated ages anchored to the GPTS for its onset (7.537 Ma; 50% from base Chron C4n.1n) and termination (6.727 Ma; 11% from base Chron C3An.2n), confirming that the terrestrial C3:C4 shift could not have driven the LMCIS. The benthic records show that the transition into the 41-kyr world, when obliquity strongly influenced climate variability, already occurred at 7.7 Ma and further strengthened at 6.4 Ma. Previously unseen, distinctive, asymmetric saw-tooth patterns in benthic δ18O imply that high-latitude forcing played an important role in late Miocene climate dynamics from 7.7-6.9 Ma. This new integrated deep-sea stratigraphy from Site U1337 can act as a new stable isotope and magnetic polarity reference section for the 8.3-6.0 Ma interval.

  12. A rainfall disaggregation scheme for sub-hourly time scales: Coupling a Bartlett-Lewis based model with adjusting procedures

    Science.gov (United States)

    Kossieris, Panagiotis; Makropoulos, Christos; Onof, Christian; Koutsoyiannis, Demetris

    2018-01-01

    Many hydrological applications, such as flood studies, require the use of long rainfall data at fine time scales varying from daily down to 1 min time step. However, in the real world there is limited availability of data at sub-hourly scales. To cope with this issue, stochastic disaggregation techniques are typically employed to produce possible, statistically consistent, rainfall events that aggregate up to the field data collected at coarser scales. A methodology for the stochastic disaggregation of rainfall at fine time scales was recently introduced, combining the Bartlett-Lewis process to generate rainfall events along with adjusting procedures to modify the lower-level variables (i.e., hourly) so as to be consistent with the higher-level one (i.e., daily). In the present paper, we extend the aforementioned scheme, initially designed and tested for the disaggregation of daily rainfall into hourly depths, for any sub-hourly time scale. In addition, we take advantage of the recent developments in Poisson-cluster processes incorporating in the methodology a Bartlett-Lewis model variant that introduces dependence between cell intensity and duration in order to capture the variability of rainfall at sub-hourly time scales. The disaggregation scheme is implemented in an R package, named HyetosMinute, to support disaggregation from daily down to 1-min time scale. The applicability of the methodology was assessed on a 5-min rainfall records collected in Bochum, Germany, comparing the performance of the above mentioned model variant against the original Bartlett-Lewis process (non-random with 5 parameters). The analysis shows that the disaggregation process reproduces adequately the most important statistical characteristics of rainfall at wide range of time scales, while the introduction of the model with dependent intensity-duration results in a better performance in terms of skewness, rainfall extremes and dry proportions.

  13. Necessary and Sufficient Conditions for the Existence of Positive Solution for Singular Boundary Value Problems on Time Scales

    Directory of Open Access Journals (Sweden)

    Meiqiang Feng

    2009-01-01

    Full Text Available By constructing available upper and lower solutions and combining the Schauder's fixed point theorem with maximum principle, this paper establishes sufficient and necessary conditions to guarantee the existence of Cld[0,1]𝕋 as well as CldΔ[0,1]𝕋 positive solutions for a class of singular boundary value problems on time scales. The results significantly extend and improve many known results for both the continuous case and more general time scales. We illustrate our results by one example.

  14. Photoluminescence decay dynamics in γ-Ga2O3 nanocrystals: The role of exclusion distance at short time scales

    Science.gov (United States)

    Fernandes, Brian; Hegde, Manu; Stanish, Paul C.; Mišković, Zoran L.; Radovanovic, Pavle V.

    2017-09-01

    We developed a comprehensive theoretical model describing the photoluminescence decay dynamics at short and long time scales based on the donor-acceptor defect interactions in γ-Ga2O3 nanocrystals, and quantitatively determined the importance of exclusion distance and spatial distribution of defects. We allowed for donors and acceptors to be adjacent to each other or separated by different exclusion distances. The optimal exclusion distance was found to be comparable to the donor Bohr radius and have a strong effect on the photoluminescence decay curve at short times. The importance of the exclusion distance at short time scales was confirmed by Monte Carlo simulations.

  15. [Use of archival formalin-fixed, paraffin-embedded (FFPE) tissue samples for molecular genetic analysis in diffuse large B-cell lymphoma (DLBCL)].

    Science.gov (United States)

    Jarošová, Marie; Kučerová, Jana; Flodr, Patrik; Mikešová, Michaela; Procházka, Vít; Papajík, Tomáš

    2014-04-01

    The currently valid molecular genetic subclassification of patients with diffuse large B-cell lymphoma (DLBCL) into three prognostic subgroups based on expression profiling has been the objective of numerous genetic studies. In routine clinical practice, however, expression profiling technology remains unavailable for the most of centers. Apart from the technology, in some cases molecular genetic laboratories have problems obtaining high-quality material, i.e. fresh tissues, for RNA isolation to determine gene expression. One possibility is to determine the gene expression from RNA obtained by isolation from formalin-fixed, paraffin-embedded (FFPE) tissue. This pilot study aimed at isolating RNA from FFPE in patients diagnosed with DLBCL and verifying the potential use of such RNA for the expression analysis of 7 selected genes. Although the study showed that it is possible to isolate RNA and determine the expression of the selected genes from archival material, the values of relative expression of some genes in the set were too variable to be used for unambiguous prognostic classification. It was confirmed that retrospective analyses of selected genes may be performed with sufficient material obtained, and that properly archived blocks may be used for molecular biology analyses even after 8 years.

  16. Large-scale CO J = 1-0 observations of the giant molecular cloud associated with the infrared ring N35 with the Nobeyama 45 m telescope

    Science.gov (United States)

    Torii, Kazufumi; Fujita, Shinji; Matsuo, Mitsuhiro; Nishimura, Atsushi; Kohno, Mikito; Kuriki, Mika; Tsuda, Yuya; Minamidani, Tetsuhiro; Umemoto, Tomofumi; Kuno, Nario; Hattori, Yusuke; Yoshiike, Satoshi; Ohama, Akio; Tachihara, Kengo; Shima, Kazuhiro; Habe, Asao; Fukui, Yasuo

    2018-05-01

    We report an observational study of the giant molecular cloud (GMC) associated with the Galactic infrared ring-like structure N35 and two nearby H II regions G024.392+00.072 (H II region A) and G024.510-00.060 (H II region B), using the new CO J = 1-0 data obtained as a part of the FOREST Unbiased Galactic Plane Imaging survey with the Nobeyama 45 m telescope (FUGIN) project at a spatial resolution of 21″. Our CO data reveals that the GMC, with a total molecular mass of 2.1 × 106 M⊙, has two velocity components of over ˜10-15 km s-1. The majority of molecular gas in the GMC is included in the lower-velocity component (LVC) at ˜110-114 km s-1, while the higher-velocity components (HVCs) at ˜118-126 km s-1 consist of three smaller molecular clouds which are located near the three H II regions. The LVC and HVCs show spatially complementary distributions along the line-of-sight, despite large velocity separations of ˜5-15 km s-1, and are connected in velocity by the CO emission with intermediate intensities. By comparing the observations with simulations, we discuss a scenario where collisions of the three HVCs with the LVC at velocities of ˜10-15 km s-1 can provide an interpretation of these two observational signatures. The intermediate-velocity features between the LVC and HVCs can be understood as broad bridge features, which indicate the turbulent motion of the gas at the collision interfaces, while the spatially complementary distributions represent the cavities created in the LVC by the HVCs through the collisions. Our model indicates that the three H II regions were formed after the onset of the collisions, and it is therefore suggested that the high-mass star formation in the GMC was triggered by the collisions.

  17. A resource of large-scale molecular markers for monitoring Agropyron cristatum chromatin introgression in wheat background based on transcriptome sequences.

    Science.gov (United States)

    Zhang, Jinpeng; Liu, Weihua; Lu, Yuqing; Liu, Qunxing; Yang, Xinming; Li, Xiuquan; Li, Lihui

    2017-09-20

    Agropyron cristatum is a wild grass of the tribe Triticeae and serves as a gene donor for wheat improvement. However, very few markers can be used to monitor A. cristatum chromatin introgressions in wheat. Here, we reported a resource of large-scale molecular markers for tracking alien introgressions in wheat based on transcriptome sequences. By aligning A. cristatum unigenes with the Chinese Spring reference genome sequences, we designed 9602 A. cristatum expressed sequence tag-sequence-tagged site (EST-STS) markers for PCR amplification and experimental screening. As a result, 6063 polymorphic EST-STS markers were specific for the A. cristatum P genome in the single-receipt wheat background. A total of 4956 randomly selected polymorphic EST-STS markers were further tested in eight wheat variety backgrounds, and 3070 markers displaying stable and polymorphic amplification were validated. These markers covered more than 98% of the A. cristatum genome, and the marker distribution density was approximately 1.28 cM. An application case of all EST-STS markers was validated on the A. cristatum 6 P chromosome. These markers were successfully applied in the tracking of alien A. cristatum chromatin. Altogether, this study provided a universal method of large-scale molecular marker development to monitor wild relative chromatin in wheat.

  18. Association of clearance of middle- and large-molecular-weight substance with arterial stiffness and left ventricular mass in children receiving renal replacement therapy.

    Science.gov (United States)

    Özdemir, Kadriye; Yilmaz, Ebru; Dincel, Nida; Bozabali, Sibel; Apaydin, Sukriye; Gun, Zubeyr H; Sozeri, Betul; Mir, Sevgi

    2017-12-01

    The prominent cause of mortality in children receiving dialysis treatment is cardiovascular diseases. Risk factors related to chronic renal disease, are effective in the development of cardiovascular diseases. The aim of study was to investigate cardiovascular system (CVS) involvement for functional and structural alterations in children receiving dialysis, and display any association between cardiovascular morbidity and uremic toxins. 20 dialysis patients and 20 healthy controls were included to the study. Clearance of small, middle and large molecular-weight uremic toxins was evaluated in blood samples collected 30 minutes before (D0) and 2 hour after dialysis (D2), and change value was calculated as D0-D2/D0. Cardiovascular involvement was determined by comparing arterial stiffness, carotid intima-media thickness (CIMT) and Left Ventricular Mass Index (LVMI) with the control group. Four patients receiving hemodialysis and two patients in continuous ambulatory peritoneal dialysis (CAPD) group who have significant differences in all functional and structural parameters were detected. Four dialysis patients with detected cardiovascular disease have distinctively lower beta-2 microglobulin and homocysteine clearances compared to the patients with no CVS involvement. The clearance of middle and large molecular-weight substances should be closely monitored in children receiving dialysis.

  19. Climatic signals and frequencies in the Swedish Time Scale, River Aangermanaelven, Central Sweden

    Energy Technology Data Exchange (ETDEWEB)

    Sander, Mikkel

    2003-03-01

    Any future climate variation forced by human activities will be superimposed on the background of natural climate variation. Therefore, before interpreting the present climate and addressing future climate scenarios some knowledge of past climate is necessary. This thesis offers a rare glimpse into a long record of fluvial activity in Central Sweden and illuminates some of the possible forcing agent behind past (and future) discharge variation. Along the Swedish East Coast varved deposits of sand silt and clay couplets make up a chronology, which extend from the present into the Late Glacial. This chronology is known as the Swedish Time Scale (STS) and the c. 8000 varves were deposited in River Aangermanaelven, Central Sweden. Of these varves, the last c. 2000 years are considered secure in terms of coherent chronology and internal thickness variation. A 2000 year long geometric mean varve thickness series was calculated to account for the internal thickness variation, which is postulated to form a proxy for fluvial sediment transport. Geometric mean varve thickness was compared to observed maximum daily annual discharge Qmax (1909-1971 AD) and the relationship expressed in a power equation. Thus, a reconstruction of past discharge for the last 2000 years could be produced. Extreme reconstructed discharge events were shown to be reasonable, considering the range of the observed discharge. Observed Qmax normally occurs during the snow melt flood. Thus it is reasonable to attribute the variation in reconstructed Qmax to the snow melt flood and, therefore, to melt water generation. Accumulated observed winter precipitation data from eleven meteorological stations from within and in the vicinity of the Aangermanaelven catchment were compared to Qmax. Nine time series shared variation with Qmax and were complied into an average accumulated winter precipitation series. This series shares c. 40% of its variation with Qmax (observed and reconstructed) and it is reasonable

  20. [Multiple time scales analysis of spatial differentiation characteristics of non-point source nitrogen loss within watershed].

    Science.gov (United States)

    Liu, Mei-bing; Chen, Xing-wei; Chen, Ying

    2015-07-01

    Identification of the critical source areas of non-point source pollution is an important means to control the non-point source pollution within the watershed. In order to further reveal the impact of multiple time scales on the spatial differentiation characteristics of non-point source nitrogen loss, a SWAT model of Shanmei Reservoir watershed was developed. Based on the simulation of total nitrogen (TN) loss intensity of all 38 subbasins, spatial distribution characteristics of nitrogen loss and critical source areas were analyzed at three time scales of yearly average, monthly average and rainstorms flood process, respectively. Furthermore, multiple linear correlation analysis was conducted to analyze the contribution of natural environment and anthropogenic disturbance on nitrogen loss. The results showed that there were significant spatial differences of TN loss in Shanmei Reservoir watershed at different time scales, and the spatial differentiation degree of nitrogen loss was in the order of monthly average > yearly average > rainstorms flood process. TN loss load mainly came from upland Taoxi subbasin, which was identified as the critical source area. At different time scales, land use types (such as farmland and forest) were always the dominant factor affecting the spatial distribution of nitrogen loss, while the effect of precipitation and runoff on the nitrogen loss was only taken in no fertilization month and several processes of storm flood at no fertilization date. This was mainly due to the significant spatial variation of land use and fertilization, as well as the low spatial variability of precipitation and runoff.

  1. Reducing Disparity in Radio-Isotopic and Astrochronology-Based Time Scales of the Late Eocene and Oligocene

    NARCIS (Netherlands)

    Sahy, Diana; Condon, Daniel J.; Hilgen, Frederik J.|info:eu-repo/dai/nl/102639876; Kuiper, Klaudia F.|info:eu-repo/dai/nl/258125772

    2017-01-01

    A significant discrepancy of up to 0.6 Myr exists between radio-isotopically calibrated and astronomically tuned time scales of the late Eocene-Oligocene. We explore the possible causes of this discrepancy through the acquisition of “high-precision” 206Pb/238U dating of zircons from 11 volcanic ash

  2. Time Scales of the European Surface Air Temperature Variability: The Role of the 7-8 Year Cycle

    Czech Academy of Sciences Publication Activity Database

    Jajcay, Nikola; Hlinka, Jaroslav; Kravtsov, S.; Tsonis, A.A.; Paluš, Milan

    2016-01-01

    Roč. 43, č. 2 (2016), s. 902-909 ISSN 0094-8276 R&D Projects: GA MŠk LH14001 Institutional support: RVO:67985807 Keywords : 7-8 year cycle * air temperature variability * annual cycle amplitude * cross-scale interactions * seasonality * time scales Subject RIV: DG - Athmosphere Sciences, Meteorology Impact factor: 4.253, year: 2016

  3. Ontology-aided annotation, visualization and generalization of geological time-scale information from online geological map services

    NARCIS (Netherlands)

    Ma, X.; Carranza, E.J.M.; Wu, C.; Meer, F.D. van der

    2012-01-01

    Geological maps are increasingly published and shared online, whereas tools and services supporting information retrieval and knowledge discovery are underdeveloped. In this study, we developed an ontology of geological time scale by using a RDF (Resource Description Framework) model to represent

  4. Ontology-aided annotation, visualization and generalization of geological time scale information from online geological map services

    NARCIS (Netherlands)

    Ma, Marshal; Ma, X.; Carranza, E.J.M; Wu, C.; van der Meer, F.D.

    2012-01-01

    Geological maps are increasingly published and shared online, whereas tools and services supporting information retrieval and knowledge discovery are underdeveloped. In this study, we developed an ontology of geological time scale by using a Resource Description Framework model to represent the

  5. Assessments of Drought Impacts on Vegetation in China with the Optimal Time Scales of the Climatic Drought Index

    Directory of Open Access Journals (Sweden)

    Zheng Li

    2015-07-01

    Full Text Available Drought is expected to increase in frequency and severity due to global warming, and its impacts on vegetation are typically extensively evaluated with climatic drought indices, such as multi-scalar Standardized Precipitation Evapotranspiration Index (SPEI. We analyzed the covariation between the SPEIs of various time scales and the anomalies of the normalized difference vegetation index (NDVI, from which the vegetation type-related optimal time scales were retrieved. The results indicated that the optimal time scales of needle-leaved forest, broadleaf forest and shrubland were between 10 and 12 months, which were considerably longer than the grassland, meadow and cultivated vegetation ones (2 to 4 months. When the optimal vegetation type-related time scales were used, the SPEI could better reflect the vegetation’s responses to water conditions, with the correlation coefficients between SPEIs and NDVI anomalies increased by 5.88% to 28.4%. We investigated the spatio-temporal characteristics of drought and quantified the different responses of vegetation growth to drought during the growing season (April–October. The results revealed that the frequency of drought has increased in the 21st century with the drying trend occurring in most of China. These results are useful for ecological assessments and adapting management steps to mitigate the impact of drought on vegetation. They are helpful to employ water resources more efficiently and reduce potential damage to human health caused by water shortages.

  6. The geopotential value W 0 for specifying the relativistic atomic time scale and a global vertical reference system

    Czech Academy of Sciences Publication Activity Database

    Burša, Milan; Kenyon, S.; Kouba, J.; Šíma, Zdislav; Vatrt, V.; Vítek, V.; Vojtíšková, M.

    2007-01-01

    Roč. 81, č. 2 (2007), s. 103-110 ISSN 0949-7714 R&D Projects: GA ČR GA205/05/2381 Institutional research plan: CEZ:AV0Z10030501 Keywords : geopotential * vertical datum unification * relativistic atomic time scale Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 1.636, year: 2007

  7. An astronomical time scale for the Maastrichtian at the Zumaia and Sopelana sections (Basque country, northern Spain)

    DEFF Research Database (Denmark)

    Batenburg, Sietske J.; Gale, Andy S.; Sprovieri, Mario

    2014-01-01

    The rhythmically bedded limestone–marl alternations in the coastal cliffs of Sopelana and Zumaia in the Basque country, northern Spain, permit testing and refining of existing Maastrichtian chronologies (latest Cretaceous). The recently established astronomical time scale for the late Maastrichtian...

  8. Multi-time scale analysis of the spatial representativeness of in situ soil moisture data within satellite footprints

    Science.gov (United States)

    We conduct a novel comprehensive investigation that seeks to prove the connection between spatial and time scales in surface soil moisture (SM) within the satellite footprint (~50 km). Modeled and measured point series at Yanco and Little Washita in situ networks are first decomposed into anomalies ...

  9. Native American Students' Understanding of Geologic Time Scale: 4th-8th Grade Ojibwe Students' Understanding of Earth's Geologic History

    Science.gov (United States)

    Nam, Younkyeong; Karahan, Engin; Roehrig, Gillian

    2016-01-01

    Geologic time scale is a very important concept for understanding long-term earth system events such as climate change. This study examines forty-three 4th-8th grade Native American--particularly Ojibwe tribe--students' understanding of relative ordering and absolute time of Earth's significant geological and biological events. This study also…

  10. A novel way to detect correlations on multi-time scales, with temporal evolution and for multi-variables

    Science.gov (United States)

    Yuan, Naiming; Xoplaki, Elena; Zhu, Congwen; Luterbacher, Juerg

    2016-06-01

    In this paper, two new methods, Temporal evolution of Detrended Cross-Correlation Analysis (TDCCA) and Temporal evolution of Detrended Partial-Cross-Correlation Analysis (TDPCCA), are proposed by generalizing DCCA and DPCCA. Applying TDCCA/TDPCCA, it is possible to study correlations on multi-time scales and over different periods. To illustrate their properties, we used two climatological examples: i) Global Sea Level (GSL) versus North Atlantic Oscillation (NAO); and ii) Summer Rainfall over Yangtze River (SRYR) versus previous winter Pacific Decadal Oscillation (PDO). We find significant correlations between GSL and NAO on time scales of 60 to 140 years, but the correlations are non-significant between 1865-1875. As for SRYR and PDO, significant correlations are found on time scales of 30 to 35 years, but the correlations are more pronounced during the recent 30 years. By combining TDCCA/TDPCCA and DCCA/DPCCA, we proposed a new correlation-detection system, which compared to traditional methods, can objectively show how two time series are related (on which time scale, during which time period). These are important not only for diagnosis of complex system, but also for better designs of prediction models. Therefore, the new methods offer new opportunities for applications in natural sciences, such as ecology, economy, sociology and other research fields.

  11. Molecular analysis of recombination in a family with Duchenne muscular dystrophy and a large pericentric X chromosome inversion

    Energy Technology Data Exchange (ETDEWEB)

    Shashi, V.; Golden, W.L.; Allinson, P.S. [Univ. of Virginia Health Sciences Center, Charlottesville, VA (United States)] [and others

    1996-06-01

    It has been demonstrated in animal studies that, in animals heterozygous for pericentric chromosomal inversions, loop formation is greatly reduced during meiosis. This results in absence of recombination within the inverted segment, with recombination seen only outside the inversion. A recent study in yeast has shown that telomeres, rather than centromeres, lead in chromosome movement just prior to meiosis and may be involved in promoting recombination. We studied by cytogenetic analysis and DNA polymorphisms the nature of meiotic recombination in a three-generation family with a large pericentric X chromosome inversion, inv(X)(p21.1q26), in which Duchenne muscular dystrophy (DMD) was cosegregating with the inversion. On DNA analysis there was no evidence of meiotic recombination between the inverted and normal X chromosomes in the inverted segment. Recombination was seen at the telomeric regions, Xp22 and Xq27-28. No deletion or point mutation was found on analysis of the DMD gene. On the basis of the FISH results, we believe that the X inversion is the mutation responsible for DMD in this family. Our results indicate that (1) pericentric X chromosome inversions result in reduction of recombination between the normal and inverted X chromosomes; (2) meiotic X chromosome pairing in these individuals is likely initiated at the telomeres; and (3) in this family DMD is caused by the pericentric inversion. 50 refs., 7 figs., 1 tab.

  12. Predictability and environmental drivers of chlorophyll fluctuations vary across different time scales and regions of the North Sea

    Science.gov (United States)

    Blauw, Anouk N.; Benincà, Elisa; Laane, Remi W. P. M.; Greenwood, Naomi; Huisman, Jef

    2018-02-01

    Phytoplankton concentrations display strong temporal variability at different time scales. Recent advances in automated moorings enable detailed investigation of this variability. In this study, we analyzed phytoplankton fluctuations at four automated mooring stations in the North Sea, which measured phytoplankton abundance (chlorophyll) and several environmental variables at a temporal resolution of 12-30 min for two to nine years. The stations differed in tidal range, water depth and freshwater influence. This allowed comparison of the predictability and environmental drivers of phytoplankton variability across different time scales and geographical regions. We analyzed the time series using wavelet analysis, cross correlations and generalized additive models to quantify the response of chlorophyll fluorescence to various environmental variables (tidal and meteorological variables, salinity, suspended particulate matter, nitrate and sea surface temperature). Hour-to-hour and day-to-day fluctuations in chlorophyll fluorescence were substantial, and mainly driven by sinking and vertical mixing of phytoplankton cells, horizontal transport of different water masses, and non-photochemical quenching of the fluorescence signal. At the macro-tidal stations, these short-term phytoplankton fluctuations were strongly driven by the tides. Along the Dutch coast, variation in salinity associated with the freshwater influence of the river Rhine played an important role, while in the central North Sea variation in weather conditions was a major determinant of phytoplankton variability. At time scales of weeks to months, solar irradiance, nutrient conditions and thermal stratification were the dominant drivers of changes in chlorophyll concentrations. These results show that the dominant drivers of phytoplankton fluctuations differ across marine environments and time scales. Moreover, our findings show that phytoplankton variability on hourly to daily time scales should not be

  13. Time scales of associating food and odor by predator communities in the field

    NARCIS (Netherlands)

    Janssen, A.; Fonseca, J.O.; Colares, F.; Silva, L.; Pedrosa, A.R.P.; Lima, E.R.; van Wijk, M.; Pallini, A.; Oliveira, C.M.; Sabelis, M.W.; Lesna, I.

    2014-01-01

    Many animals use volatile chemicals to detect and locate their food, but they frequently have to cope with a large variation in volatile blends associated with food. It has often been suggested that they do this by learning the association between odors and the presence of food. Indeed, associative

  14. Time scales for spinodal decomposition in nuclear matter with pseudo-particle model

    Energy Technology Data Exchange (ETDEWEB)

    Idier, D.; Benhassine, B.; Farine, M.; Remaud, B.; Sebille, F.

    1993-12-31

    Dynamical instabilities arising from fluctuations in the spinodal zone for nuclear matter are studied using a large variety of zero range interactions in the frame of a pseudo-particle model. Scale times for spinodal decomposition are extracted and a possible link with decomposition in real heavy-ion collisions is discussed. (author) 12 refs.; 6 figs.; 1 tab.

  15. Time scales for spinodal decomposition in nuclear matter with pseudo-particle model

    International Nuclear Information System (INIS)

    Idier, D.; Benhassine, B.; Farine, M.; Remaud, B.; Sebille, F.

    1993-01-01

    Dynamical instabilities arising from fluctuations in the spinodal zone for nuclear matter are studied using a large variety of zero range interactions in the frame of a pseudo-particle model. Scale times for spinodal decomposition are extracted and a possible link with decomposition in real heavy-ion collisions is discussed. (author) 12 refs.; 6 figs.; 1 tab

  16. Time scales for spinodal decomposition in nuclear matter with pseudoparticle models

    International Nuclear Information System (INIS)

    Idier, D.; Benhassine, B.; Farine, M.; Remaud, B.; Sebille, F.

    1993-01-01

    Dynamical instabilities arising from fluctuations in the spinodal zone for nuclear matter are studied using a large variety of zero range interactions in the frame of a pseudoparticle model. Scale times for spinodal decomposition are extracted and a possible link with decomposition in real heavy-ion collisions is discussed

  17. Time scales for spinodal decomposition in nuclear matter with pseudoparticle models

    Energy Technology Data Exchange (ETDEWEB)

    Idier, D.; Benhassine, B.; Farine, M.; Remaud, B.; Sebille, F. (Laboratoire de Physique Nucleaire CNRS/IN2P3, Universite de Nantes, 2, rue de la Houssiniere, 44072 Nantes (France))

    1993-08-01

    Dynamical instabilities arising from fluctuations in the spinodal zone for nuclear matter are studied using a large variety of zero range interactions in the frame of a pseudoparticle model. Scale times for spinodal decomposition are extracted and a possible link with decomposition in real heavy-ion collisions is discussed.

  18. High-Resolution Imaging of Dense Gas Structure and Kinematics in Nearby Molecular Clouds with the CARMA Large Area Star Formation Survey

    Science.gov (United States)

    Storm, Shaye

    This thesis utilizes new observations of dense gas in molecular clouds to develop an empirical framework for how clouds form structures which evolve into young cores and stars. Previous observations show the general turbulent and hierarchical nature of clouds. However, current understanding of the star formation pathway is limited by existing data that do not combine angular resolution needed to resolve individual cores with area coverage required to capture entire star-forming regions and with tracers that can resolve gas motions. The original contributions of this thesis to astrophysical research are the creation and analysis of the largest-area high-angular-resolution maps of dense gas in molecular clouds to-date, and the development of a non-binary dendrogram algorithm to quantify the hierarchical nature and three-dimensional morphology of cloud structure. I first describe the CARMA Large Area Star Formation Survey, which provides spectrally imaged N2H+, HCO+, and HCN (J = 1→0) emission across diverse regions of the Perseus and Serpens Molecular Clouds. I then present a detailed analysis of the Barnard 1 and L1451 regions in Perseus. A non-binary dendrogram analysis of Barnard 1 N2H emission and all L1451 emission shows that the most hierarchically complex gas corresponds with sub-regions actively forming young stars. I estimate the typical depth of molecular emission in each region using the spatial and kinematic properties of dendrogram-identified structures. Barnard 1 appears to be a sheet-like region at the largest scales with filamentary substructure, while the L1451 region is composed of more spatially distinct ellipsoidal structures. I then do a uniform comparison of the hierarchical structure and young stellar content of all five regions. The more evolved regions with the most young stellar objects (YSOs) and strongest emission have formed the most hierarchical levels. However, all regions show similar mean branching properties at each level

  19. Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach.

    Directory of Open Access Journals (Sweden)

    Simon Boitard

    2016-03-01

    Full Text Available Inferring the ancestral dynamics of effective population size is a long-standing question in population genetics, which can now be tackled much more accurately thanks to the massive genomic data available in many species. Several promising methods that take advantage of whole-genome sequences have been recently developed in this context. However, they can only be applied to rather small samples, which limits their ability to estimate recent population size history. Besides, they can be very sensitive to sequencing or phasing errors. Here we introduce a new approximate Bayesian computation approach named PopSizeABC that allows estimating the evolution of the effective population size through time, using a large sample of complete genomes. This sample is summarized using the folded allele frequency spectrum and the average zygotic linkage disequilibrium at different bins of physical distance, two classes of statistics that are widely used in population genetics and can be easily computed from unphased and unpolarized SNP data. Our approach provides accurate estimations of past population sizes, from the very first generations before present back to the expected time to the most recent common ancestor of the sample, as shown by simulations under a wide range of demographic scenarios. When applied to samples of 15 or 25 complete genomes in four cattle breeds (Angus, Fleckvieh, Holstein and Jersey, PopSizeABC revealed a series of population declines, related to historical events such as domestication or modern breed creation. We further highlight that our approach is robust to sequencing errors, provided summary statistics are computed from SNPs with common alleles.

  20. Large scale genotype comparison of human papillomavirus E2-host interaction networks provides new insights for e2 molecular functions.

    Directory of Open Access Journals (Sweden)

    Mandy Muller

    Full Text Available Human Papillomaviruses (HPV cause widespread infections in humans, resulting in latent infections or diseases ranging from benign hyperplasia to cancers. HPV-induced pathologies result from complex interplays between viral proteins and the host proteome. Given the major public health concern due to HPV-associated cancers, most studies have focused on the early proteins expressed by HPV genotypes with high oncogenic potential (designated high-risk HPV or HR-HPV. To advance the global understanding of HPV pathogenesis, we mapped the virus/host interaction networks of the E2 regulatory protein from 12 genotypes representative of the range of HPV pathogenicity. Large-scale identification of E2-interaction partners was performed by yeast two-hybrid screenings of a HaCaT cDNA library. Based on a high-confidence scoring scheme, a subset of these partners was then validated for pair-wise interaction in mammalian cells with the whole range of the 12 E2 proteins, allowing a comparative interaction analysis. Hierarchical clustering of E2-host interaction profiles mostly recapitulated HPV phylogeny and provides clues to the involvement of E2 in HPV infection. A set of cellular proteins could thus be identified discriminating, among the mucosal HPV, E2 proteins of HR-HPV 16 or 18 from the non-oncogenic genital HPV. The study of the interaction networks revealed a preferential hijacking of highly connected cellular proteins and the targeting of several functional families. These include transcription regulation, regulation of apoptosis, RNA processing, ubiquitination and intracellular trafficking. The present work provides an overview of E2 biological functions across multiple HPV genotypes.

  1. Molecular Mechanisms of Disease Progression in Primary Cutaneous Diffuse Large B-Cell Lymphoma, Leg Type during Ibrutinib Therapy

    Directory of Open Access Journals (Sweden)

    Lucy C. Fox

    2018-06-01

    Full Text Available Primary cutaneous diffuse large B-cell lymphoma, leg type (PCDLBCL-LT is one of the well-recognized extranodal lymphomas commonly addicted to the B-cell receptor-MYD88 superpathway. We aimed to describe the genomic changes in a patient who progressed through treatment with ibrutinib, a Bruton’s tyrosine kinase (BTK inhibitor. An 80-year-old woman presented with multiply relapsed PCDLBCL-LT after multiple lines of chemoimmunotherapy and radiotherapy. Pre-treatment testing of the localized cutaneous tumor lesion on a lymphoid amplicon panel demonstrated an MYD88 p.L265P mutation. Ibrutinib therapy was subsequently commenced, resulting in complete resolution of the skin disease. Despite an ongoing skin response, the patient developed progressive nodal disease at two months. Genomic analysis of the cutaneous tumor sample at baseline was compared to that of the inguinal lymph node upon progression, and revealed the acquisition of multiple genomic changes. These included several aberrations expected to bypass BTK inhibition, including two CARD11-activating mutations, and a deleterious mutation in the nuclear factor kappa B (NF-κB negative regulator, NFKBIE. In addition, an IgH-IRF8 translocation was detected (which brings the IRF8 transcription factor under control of the immunoglobulin heavy chain locus, representing a third plausible mechanism contributing to ibrutinib resistance. Several copy-number changes occurred in both samples, including an amplification of 18q, which encodes the anti-apoptotic protein BCL2. We describe the first case of novel genomic changes of PCDLBCL-LT that occurred while on ibrutinib, providing important mechanistic insights into both pathogenesis and drug resistance.

  2. Molecular Characterization and Biological Effects of a C-Type Lectin-Like Receptor in Large Yellow Croaker (Larimichthys crocea).

    Science.gov (United States)

    Ao, Jingqun; Ding, Yang; Chen, Yuanyuan; Mu, Yinnan; Chen, Xinhua

    2015-12-10

    The C-type lectin-like receptors (CTLRs) play important roles in innate immunity as one type of pattern recognition receptors. Here, we cloned and characterized a C-type lectin-like receptor (LycCTLR) from large yellow croaker Larimichthys crocea. The full-length cDNA of LycCTLR is 880 nucleotides long, encoding a protein of 215 amino acids. The deduced LycCTLR contains a C-terminal C-type lectin-like domain (CTLD), an N-terminal cytoplasmic tail, and a transmembrane region. The CTLD of LycCTLR possesses six highly conserved cysteine residues (C1-C6), a conserved WI/MGL motif, and two sugar binding motifs, EPD (Glu-Pro-Asp) and WYD (Trp-Tyr-Asp). Ca(2+) binding site 1 and 2 were also found in the CTLD. The LycCTLR gene consists of five exons and four introns, showing the same genomic organization as tilapia (Oreochromis niloticus) and guppy (Poecilia retitculata) CTLRs. LycCTLR was constitutively expressed in various tissues tested, and its transcripts significantly increased in the head kidney and spleen after stimulation with inactivated trivalent bacterial vaccine. Recombinant LycCTLR (rLycCTLR) protein produced in Escherichia coli BL21 exhibited not only the hemagglutinating activity and a preference for galactose, but also the agglutinating activity against two food-borne pathogenic bacteria E. coli and Bacillus cereus in a Ca(2+)-dependent manner. These results indicate that LycCTLR is a potential galactose-binding C-type lectin that may play a role in the antibacterial immunity in fish.

  3. Molecular Characterization and Biological Effects of a C-Type Lectin-Like Receptor in Large Yellow Croaker (Larimichthys crocea

    Directory of Open Access Journals (Sweden)

    Jingqun Ao

    2015-12-01

    Full Text Available The C-type lectin-like receptors (CTLRs play important roles in innate immunity as one type of pattern recognition receptors. Here, we cloned and characterized a C-type lectin-like receptor (LycCTLR from large yellow croaker Larimichthys crocea. The full-length cDNA of LycCTLR is 880 nucleotides long, encoding a protein of 215 amino acids. The deduced LycCTLR contains a C-terminal C-type lectin-like domain (CTLD, an N-terminal cytoplasmic tail, and a transmembrane region. The CTLD of LycCTLR possesses six highly conserved cysteine residues (C1–C6, a conserved WI/MGL motif, and two sugar binding motifs, EPD (Glu-Pro-Asp and WYD (Trp-Tyr-Asp. Ca2+ binding site 1 and 2 were also found in the CTLD. The LycCTLR gene consists of five exons and four introns, showing the same genomic organization as tilapia (Oreochromis niloticus and guppy (Poecilia retitculata CTLRs. LycCTLR was constitutively expressed in various tissues tested, and its transcripts significantly increased in the head kidney and spleen after stimulation with inactivated trivalent bacterial vaccine. Recombinant LycCTLR (rLycCTLR protein produced in Escherichia coli BL21 exhibited not only the hemagglutinating activity and a preference for galactose, but also the agglutinating activity against two food-borne pathogenic bacteria E. coli and Bacillus cereus in a Ca2+-dependent manner. These results indicate that LycCTLR is a potential galactose-binding C-type lectin that may play a role in the antibacterial immunity in fish.

  4. Large scale genotype comparison of human papillomavirus E2-host interaction networks provides new insights for e2 molecular functions.

    Science.gov (United States)

    Muller, Mandy; Jacob, Yves; Jones, Louis; Weiss, Amélie; Brino, Laurent; Chantier, Thibault; Lotteau, Vincent; Favre, Michel; Demeret, Caroline

    2012-01-01

    Human Papillomaviruses (HPV) cause widespread infections in humans, resulting in latent infections or diseases ranging from benign hyperplasia to cancers. HPV-induced pathologies result from complex interplays between viral proteins and the host proteome. Given the major public health concern due to HPV-associated cancers, most studies have focused on the early proteins expressed by HPV genotypes with high oncogenic potential (designated high-risk HPV or HR-HPV). To advance the global understanding of HPV pathogenesis, we mapped the virus/host interaction networks of the E2 regulatory protein from 12 genotypes representative of the range of HPV pathogenicity. Large-scale identification of E2-interaction partners was performed by yeast two-hybrid screenings of a HaCaT cDNA library. Based on a high-confidence scoring scheme, a subset of these partners was then validated for pair-wise interaction in mammalian cells with the whole range of the 12 E2 proteins, allowing a comparative interaction analysis. Hierarchical clustering of E2-host interaction profiles mostly recapitulated HPV phylogeny and provides clues to the involvement of E2 in HPV infection. A set of cellular proteins could thus be identified discriminating, among the mucosal HPV, E2 proteins of HR-HPV 16 or 18 from the non-oncogenic genital HPV. The study of the interaction networks revealed a preferential hijacking of highly connected cellular proteins and the targeting of several functional families. These include transcription regulation, regulation of apoptosis, RNA processing, ubiquitination and intracellular trafficking. The present work provides an overview of E2 biological functions across multiple HPV genotypes.

  5. Refining the Early and Middle Eocene Geomagnetic Polarity Time Scale: new results from ODP Leg 208 (Walvis Ridge)

    Science.gov (United States)

    Westerhold, T.; Roehl, U.; Frederichs, T.; Bohaty, S. M.; Florindo, F.; Zachos, J. C.; Raffi, I.; Agnini, C.

    2015-12-01

    Astronomical calibration of the Geomagnetic Polarity Time Scale (GPTS) for the Eocene (34-56 Ma) has advanced tremendously in recent years. Combining a cyclostratigraphic approach based on the recognition of the stable 405-kyr eccentricity cycle of Earth's orbit with high-resolution bio- and magnetostratigraphy from deep-sea sedimentary records (ODP Legs 171B, 189 and 207; IODP Exp. 320/321) resulted in a new calibration of the middle-to-late Eocene GPTS spanning Chrons C12r to C19n (30.9-41.3 Ma). A fully astronomically calibrated GPTS for the Eocene was established recently by integrating cyclo-bio-magnetostratigraphy from ODP Sites 702 and 1263 records spanning the middle Eocene with Site 1258 records covering the early Eocene. Comparison of this deep sea-derived GPTS with GTS2012 and GPTS calibration points from terrestrial successions show overall consistent results, but there are still major offsets for the duration of Chrons C20r, C22r and C23n.2n. Because of the relatively large uncertainty of the calibration point, a radioisotopic dated ash layer in DSDP 516F, at C21n.75 (46.24±0.5 Ma) the duration of C20r in GPTS2012 (2.292 myr) is uncertain. Offsets in durations of C22r and C23n.2n between GPTS2012 and the new astronomical GPTS (~400-kyr longer C22r; ~400-kyr shorter C23n.2n) could be due to uncertainties in the interpretation of Site 1258 magnetostratigraphic data. Here we present new results toward establishing a more accurate and complete bio-, magneto- and chemostratigraphy for South Atlantic Leg 208 sites encompassing magnetochrons C13 to C24 (33 to 56 Ma). Our study aims to integrate paleomagnetic records from multiple drilled sites with physical property data, stable isotope data and XRF core scanning data to construct an astronomically calibrated framework for refining GPTS age estimates. This effort will complete the Early-to-Middle Eocene GPTS and allow evaluation of the relative position of calcareous nannofossil events to magnetostratigraphy.

  6. Ultrahigh Molecular Weight Linear Block Copolymers: Rapid Access by Reversible-Deactivation Radical Polymerization and Self- Assembly into Large Domain Nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Mapas, Jose Kenneth D.; Thomay, Tim; Cartwright, Alexander N.; Ilavsky, Jan; Rzayev, Javid

    2016-05-05

    Block copolymer (BCP) derived periodic nanostructures with domain sizes larger than 150 nm present a versatile platform for the fabrication of photonic materials. So far, the access to such materials has been limited to highly synthetically involved protocols. Herein, we report a simple, “user-friendly” method for the preparation of ultrahigh molecular weight linear poly(solketal methacrylate-b-styrene) block copolymers by a combination of Cu-wire-mediated ATRP and RAFT polymerizations. The synthesized copolymers with molecular weights up to 1.6 million g/mol and moderate dispersities readily assemble into highly ordered cylindrical or lamella microstructures with domain sizes as large as 292 nm, as determined by ultra-small-angle x-ray scattering and scanning electron microscopy analyses. Solvent cast films of the synthesized block copolymers exhibit stop bands in the visible spectrum correlated to their domain spacings. The described method opens new avenues for facilitated fabrication and the advancement of fundamental understanding of BCP-derived photonic nanomaterials for a variety of applications.

  7. Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?

    Science.gov (United States)

    Mellis, Ian A; Raj, Arjun

    2015-10-01

    Small-scale molecular systems biology, by which we mean the understanding of a how a few parts work together to control a particular biological process, is predicated on the assumption that cellular regulation is arranged in a circuit-like structure. Results from the omics revolution have upset this vision to varying degrees by revealing a high degree of interconnectivity, making it difficult to develop a simple, circuit-like understanding of regulatory processes. We here outline the limitations of the small-scale systems biology approach with examples from research into genetic algorithms, genetics, transcriptional network analysis, and genomics. We also discuss the difficulties associated with deriving true understanding from the analysis of large data sets and propose that the development of new, intelligent, computational tools may point to a way forward. Throughout, we intentionally oversimplify and talk about things in which we have little expertise, and it is likely that many of our arguments are wrong on one level or another. We do believe, however, that developing a true understanding via molecular systems biology will require a fundamental rethinking of our approach, and our goal is to provoke thought along these lines. © 2015 Mellis and Raj; Published by Cold Spring Harbor Laboratory Press.

  8. A massively parallel algorithm for the solution of constrained equations of motion with applications to large-scale, long-time molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fijany, A. [Jet Propulsion Lab., Pasadena, CA (United States); Coley, T.R. [Virtual Chemistry, Inc., San Diego, CA (United States); Cagin, T.; Goddard, W.A. III [California Institute of Technology, Pasadena, CA (United States)

    1997-12-31

    Successful molecular dynamics (MD) simulation of large systems (> million atoms) for long times (> nanoseconds) requires the integration of constrained equations of motion (CEOM). Constraints are used to eliminate high frequency degrees of freedom (DOF) and to allow the use of rigid bodies. Solving the CEOM allows for larger integration time-steps and helps focus the simulation on the important collective dynamics of chemical, biological, and materials systems. We explore advances in multibody dynamics which have resulted in O(N) algorithms for propagating the CEOM. However, because of their strictly sequential nature, the computational time required by these algorithms does not scale down with increased numbers of processors. We then present the new constraint force algorithm for solving the CEOM and show that this algorithm is fully parallelizable, leading to a computational cost of O(N/P+IogP) for N DOF on P processors.

  9. Computational issues in complex water-energy optimization problems: Time scales, parameterizations, objectives and algorithms

    Science.gov (United States)

    Efstratiadis, Andreas; Tsoukalas, Ioannis; Kossieris, Panayiotis; Karavokiros, George; Christofides, Antonis; Siskos, Alexandros; Mamassis, Nikos; Koutsoyiannis, Demetris

    2015-04-01

    Modelling of large-scale hybrid renewable energy systems (HRES) is a challenging task, for which several open computational issues exist. HRES comprise typical components of hydrosystems (reservoirs, boreholes, conveyance networks, hydropower stations, pumps, water demand nodes, etc.), which are dynamically linked with renewables (e.g., wind turbines, solar parks) and energy demand nodes. In such systems, apart from the well-known shortcomings of water resources modelling (nonlinear dynamics, unknown future inflows, large number of variables and constraints, conflicting criteria, etc.), additional complexities and uncertainties arise due to the introduction of energy components and associated fluxes. A major difficulty is the need for coupling two different temporal scales, given that in hydrosystem modeling, monthly simulation steps are typically adopted, yet for a faithful representation of the energy balance (i.e. energy production vs. demand) a much finer resolution (e.g. hourly) is required. Another drawback is the increase of control variables, constraints and objectives, due to the simultaneous modelling of the two parallel fluxes (i.e. water and energy) and their interactions. Finally, since the driving hydrometeorological processes of the integrated system are inherently uncertain, it is often essential to use synthetically generated input time series of large length, in order to assess the system performance in terms of reliability and risk, with satisfactory accuracy. To address these issues, we propose an effective and efficient modeling framework, key objectives of which are: (a) the substantial reduction of control variables, through parsimonious yet consistent parameterizations; (b) the substantial decrease of computational burden of simulation, by linearizing the combined water and energy allocation problem of each individual time step, and solve each local sub-problem through very fast linear network programming algorithms, and (c) the substantial

  10. Early science with the large millimeter telescope: exploring the effect of AGN activity on the relationships between molecular gas, dust, and star formation

    Energy Technology Data Exchange (ETDEWEB)

    Kirkpatrick, Allison; Pope, Alexandra; Calzetti, Daniela; Narayanan, Gopal; Schloerb, F. Peter; Yun, Min S. [Department of Astronomy, University of Massachusetts, Amherst, MA 01002 (United States); Aretxaga, Itziar; Montaña, Alfredo; Vega, Olga [Instituto Nacional de Astrofísica, Optica y Electrónica, Apdos. Postales 51 y 216, C.P. 72000 Puebla, Pue. (Mexico); Armus, Lee [Spitzer Science Center, California Institute of Technology, MS 220-6, Pasadena, CA 91125 (United States); Helou, George [Infrared Processing and Analysis Center, California Institute of Technology, Pasadena, CA 91125 (United States); Shi, Yong, E-mail: kirkpatr@astro.umass.edu [School of Astronomy and Space Science, Nanjing University, Nanjing, 210093 (China)

    2014-12-01

    The molecular gas, H{sub 2}, that fuels star formation in galaxies is difficult to observe directly. As such, the ratio of L {sub IR} to L{sub CO}{sup ′} is an observational estimate of the star formation rate compared with the amount of molecular gas available to form stars, which is related to the star formation efficiency and the inverse of the gas consumption timescale. We test what effect an IR luminous active galactic nucleus (AGN) has on the ratio L{sub IR}/L{sub CO}{sup ′} in a sample of 24 intermediate redshift galaxies from the 5 mJy Unbiased Spitzer Extragalactic Survey (5MUSES). We obtain new CO(1-0) observations with the Redshift Search Receiver on the Large Millimeter Telescope. We diagnose the presence and strength of an AGN using Spitzer IRS spectroscopy. We find that removing the AGN contribution to L{sub IR}{sup tot} results in a mean L{sub IR}{sup SF}/L{sub CO}{sup ′} for our entire sample consistent with the mean L{sub IR}/L{sub CO}{sup ′} derived for a large sample of star forming galaxies from z ∼ 0-3. We also include in our comparison the relative amount of polycyclic aromatic hydrocarbon emission for our sample and a literature sample of local and high-redshift ultra luminous infrared galaxies and find a consistent trend between L{sub 6.2}/L{sub IR}{sup SF} and L{sub IR}{sup SF}/L{sub CO}{sup ′}, such that small dust grain emission decreases with increasing L{sub IR}{sup SF}/L{sub CO}{sup ′} for both local and high-redshift dusty galaxies.

  11. A large-scale superhydrophobic surface-enhanced Raman scattering (SERS) platform fabricated via capillary force lithography and assembly of Ag nanocubes for ultratrace molecular sensing.

    Science.gov (United States)

    Tan, Joel Ming Rui; Ruan, Justina Jiexin; Lee, Hiang Kwee; Phang, In Yee; Ling, Xing Yi

    2014-12-28

    An analytical platform with an ultratrace detection limit in the atto-molar (aM) concentration range is vital for forensic, industrial and environmental sectors that handle scarce/highly toxic samples. Superhydrophobic surface-enhanced Raman scattering (SERS) platforms serve as ideal platforms to enhance detection sensitivity by reducing the random spreading of aqueous solution. However, the fabrication of superhydrophobic SERS platforms is generally limited due to the use of sophisticated and expensive protocols and/or suffers structural and signal inconsistency. Herein, we demonstrate a high-throughput fabrication of a stable and uniform superhydrophobic SERS platform for ultratrace molecular sensing. Large-area box-like micropatterns of the polymeric surface are first fabricated using capillary force lithography (CFL). Subsequently, plasmonic properties are incorporated into the patterned surfaces by decorating with Ag nanocubes using the Langmuir-Schaefer technique. To create a stable superhydrophobic SERS platform, an additional 25 nm Ag film is coated over the Ag nanocube-decorated patterned template followed by chemical functionalization with perfluorodecanethiol. Our resulting superhydrophobic SERS platform demonstrates excellent water-repellency with a static contact angle of 165° ± 9° and a consequent analyte concentration factor of 59-fold, as compared to its hydrophilic counterpart. By combining the analyte concentration effect of superhydrophobic surfaces with the intense electromagnetic "hot spots" of Ag nanocubes, our superhydrophobic SERS platform achieves an ultra-low detection limit of 10(-17) M (10 aM) for rhodamine 6G using just 4 μL of analyte solutions, corresponding to an analytical SERS enhancement factor of 10(13). Our fabrication protocol demonstrates a simple, cost- and time-effective approach for the large-scale fabrication of a superhydrophobic SERS platform for ultratrace molecular detection.

  12. Short-time-scale Doppler and intensity variations in the spectrum of SS 433

    International Nuclear Information System (INIS)

    Wagner, R.M.; Newsom, G.H.; Foltz, C.B.; Byard, P.L.

    1981-01-01

    Spectroscopic observations of SS 433 were obtained on ten consecutive nights in 1981 May. Measurements of the equivalent widths of the spectral lines and Doppler shifts of the moving lines are presented. Not only does the 6-day period in the wavelengths of the moving lines appear quite clearly, but the data strongly suggest that this period is decreasing at a rate of (3.0 +- 1.1) x 10 -5 days/day. In addition, large equivalent width variations of the stationary lines are observed

  13. Comparison of the Mercury and earth magnetospheres - electron measurements and substorm time scales

    International Nuclear Information System (INIS)

    Christon, S.P.

    1987-01-01

    The present search for similarities between earth and Mercury plasma electron distribution and large-scale dynamics notes that both spectral shapes are similar to a kappa-distribution. A model distribution of this type which incorporates convective flow is used to simulate the observed plasma electron spectral variations near the Mariner 10-Mercury 1 A event; convection appears to be stronger before, rather than during, the A event, in contradiction to the Baker (1986) convective injection model for Mercury's two relativistic electron flux enhancements. Mercury's postmidnight energetic electron B and B-prime events seem to be multiple onsets in the course of a substorm. 65 references

  14. The time scale for the transition to turbulence in a high Reynolds number, accelerated flow

    International Nuclear Information System (INIS)

    Robey, H.F.; Zhou Ye; Buckingham, A.C.; Keiter, P.; Remington, B.A.; Drake, R.P.

    2003-01-01

    An experiment is described in which an interface between materials of different density is subjected to an acceleration history consisting of a strong shock followed by a period of deceleration. The resulting flow at this interface, initiated by the deposition of strong laser radiation into the initially well characterized solid materials, is unstable to both the Richtmyer-Meshkov (RM) and Rayleigh-Taylor (RT) instabilities. These experiments are of importance in their ability to access a difficult experimental regime characterized by very high energy density (high temperature and pressure) as well as large Reynolds number and Mach number. Such conditions are of interest, for example, in the study of the RM/RT induced mixing that occurs during the explosion of a core-collapse supernova. Under these experimental conditions, the flow is in the plasma state and given enough time will transition to turbulence. By analysis of the experimental data and a corresponding one-dimensional numerical simulation of the experiment, it is shown that the Reynolds number is sufficiently large (Re>10 5 ) to support a turbulent flow. An estimate of three key turbulence length scales (the Taylor and Kolmogorov microscales and a viscous diffusion scale), however, shows that the temporal duration of the present flow is insufficient to allow for the development of a turbulent inertial subrange. A methodology is described for estimating the time required under these conditions for the development of a fully turbulent flow

  15. Poleward energy transport: is the standard definition physically relevant at all time scales?

    Science.gov (United States)

    Liang, Minyi; Czaja, Arnaud; Graversen, Rune; Tailleux, Remi

    2018-03-01

    Poleward energy transport in the atmosphere and oceans constitutes an important branch of the global energy budget, and its role in the climate system has been the subject of many studies. In the atmosphere, the transport is affected by "eddies" and large scale meridional cells, both with zero net mass transport across latitude circles, but also partly by processes associated with a net transport of mass across latitude circles. The latter must cease to operate in steady state, but they may be significant when time variability of the heat budget is considered. Indeed, examination of reanalysis data on short (daily to monthly) timescales shows that mass variations on these timescales result in surprisingly large fluctuations (in excess of 10^{15} W = 1 PW) in the poleward heat transport. These fluctuations are referred to as "extensive", for they primarily alter the mass integrated energy of the region considered, but not its averaged value. It is suggested that extensive fluctuations mask more meaningful climate signals present in the heat transport variability on monthly and interannual timescales, and a new formulation is proposed to isolate the latter. This new formulation is applied successfully to reanalysis data and climate model simulations.

  16. Non-equilibrium dynamics of disordered systems: understanding the broad continuum of relevant time scales via a strong-disorder RG in configuration space

    International Nuclear Information System (INIS)

    Monthus, Cecile; Garel, Thomas

    2008-01-01

    We show that an appropriate description of the non-equilibrium dynamics of disordered systems is obtained through a strong disorder renormalization procedure in configuration space that we define for any master equation with transitions rates W(C→C') between configurations. The idea is to eliminate iteratively the configuration with the highest exit rate W out (C)+Σ C' W(C→C') to obtain renormalized transition rates between the remaining configurations. The multiplicative structure of the new generated transition rates suggests that for a very broad class of disordered systems, the distribution of renormalized exit barriers defined as B out (C)≡-ln W out (C) will become broader and broader upon iteration, so that the strong disorder renormalization procedure should become asymptotically exact at large time scales. We have checked numerically this scenario for the non-equilibrium dynamics of a directed polymer in a two-dimensional random medium

  17. Reference evapotranspiration models using different time scales in the Jaboticabal region of São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    Natália Buzinaro Caporusso

    2014-11-01

    Full Text Available The aim of this paper is to compare 18 reference evapotranspiration models to the standard Penman-Monteith model in the Jaboticabal, São Paulo, region for the following time scales: daily, 5-day, 15-day and seasonal. A total of 5 years of daily meteorological data was used for the following analyses: accuracy (mean absolute percentage error, Mape, precision (R2 and tendency (bias (systematic error, SE. The results were also compared at the 95% probability level with Tukey’s test. The Priestley-Taylor (1972 method was the most accurate for all time scales, the Tanner-Pelton (1960 method was the most accurate in the winter, and the Thornthwaite (1948 method was the most accurate of the methods that only used temperature data in the equations.

  18. Consensus for linear multi-agent system with intermittent information transmissions using the time-scale theory

    Science.gov (United States)

    Taousser, Fatima; Defoort, Michael; Djemai, Mohamed

    2016-01-01

    This paper investigates the consensus problem for linear multi-agent system with fixed communication topology in the presence of intermittent communication using the time-scale theory. Since each agent can only obtain relative local information intermittently, the proposed consensus algorithm is based on a discontinuous local interaction rule. The interaction among agents happens at a disjoint set of continuous-time intervals. The closed-loop multi-agent system can be represented using mixed linear continuous-time and linear discrete-time models due to intermittent information transmissions. The time-scale theory provides a powerful tool to combine continuous-time and discrete-time cases and study the consensus protocol under a unified framework. Using this theory, some conditions are derived to achieve exponential consensus under intermittent information transmissions. Simulations are performed to validate the theoretical results.

  19. Full-scale and time-scale heating experiments at Stripa: preliminary results. Technical project report No. 11

    International Nuclear Information System (INIS)

    Cook, N.G.W.; Hood, M.

    1978-12-01

    Two full-scale heating experiments and a time-scale heating experiment have recently been started in granite 340 meters below surface. The purpose of the full-scale heating experiments is to assess the near-field effects of thermal loading for the design of an underground repository of nuclear wastes. That of the time-scale heating experiments is to obtain field data of the interaction between heaters and its effect on the rock mass during a period of about two years, which corresponds to about twenty years of full-scale operation. Geological features of the rock around each experiment have been mapped carefully, and temperatures, stresses and displacements induced in the rock by heating have been calculated in advance of the experiments. Some 800 different measurements are recorded at frequent intervals by a computer system situated underground. These data can be compared at any time with predictions made earlier on video display units underground

  20. ''The ambipolar diffusion time scale and the location of star formation in magnetic interstellar clouds'': Setting the record straight

    International Nuclear Information System (INIS)

    Mouschovias, T.C.

    1984-01-01

    The point of a recent (1983) paper by Scott is that a previous paper (1979) by Mouschovias has concluded ''erroneously'' that star formation takes place off center in a cloud because of the use of an ''improver'' definition of a time scale for ambipolar diffusion. No such conclusion, Scott claims, follows from a ''proper'' definition, such as the ''traditional'' one by Spitzer. (i) Scott misrepresents the reasoning that led to the conclusion in the paper which he criticized. (ii) He is also wrong: both the ''traditional'' and the ''improper'' definitions vary similarly with radius, and both can have an off-center minimum; the spatial variation of the degree of ionization is the determining factor: not the specific value of the time scale at the origin, as Scott claims