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At least 991 records · Page 55Linked to original sources

Supremacy distribution in evolving networks.

We study a supremacy distribution in evolving Barabasi-Albert networks. The supremacy s(i) of a node i is defined as the total number of all nodes that are not older than i and can be linked to it by a directed path (including the node i ). The nodes form a basin connected to the node i as its in-component. For a network with a characteristic parameter m=1,2,3,... , the supremacy of an individual node increases with the network age as t((1+m)/2) in an appropriate scaling region. It follows that there is a relation s(k) approximately k(m+1) between a node degree k and its supremacy s , and the supremacy distribution P(s) scales as s(-1-2/(1+m)) . Analytic calculations basing on a continuum theory of supremacy evolution and on a corresponding rate equation have been confirmed by numerical simulations.

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Properties of evolving e-mail networks.

Computer viruses spread by attaching to an e-mail message and sending themselves to users whose addresses are in the e-mail address book of the recipients. Here we investigate a simple model of an evolving e-mail network, with nodes as e-mail address books of users and links as the records of e-mail addresses in the address books. Within specific periods, some new links are generated and some old links are deleted. We study the statistical properties of this e-mail network and observe the effect of the evolution on the structure of the network. We also find that the balance between the generation procedure and deletion procedure is dependent on different parameters of the model.

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Steady light transport under flow: characterization of evolving dense random media.

We describe in this letter a new rheo-optical apparatus able to measure the photon transport length l* in an evolving random medium. First, the appropriate solution of the diffusion equation for oil in water, stable, micron-sized emulsions is compared successfully with the measured spatial distribution of incoherent backscattered light given by the new apparatus. Further validation is provided using stable samples of varying sizes and volume fractions (1% to 64%) and comparing measurements with Mie-Percus-Yevick calculations based on independent small-angle light scattering (SALS) measurements. As a typical example application of the system, the emulsification of a different oil in water system is studied in situ and dynamically. The continuous temporal measurements show the decrease of the average size versus time, in excellent quantitative agreement with independent SALS measurements. This evidences that this system is able to probe continuously and nonintrusively the microscopic and macroscopic flow-induced organization of suspensions.

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Evolving networks by merging cliques.

We propose a model for evolving networks by merging building blocks represented as complete graphs, reminiscent of modules in biological system or communities in sociology. The model shows power-law degree distributions, power-law clustering spectra, and high average clustering coefficients independent of network size. The analytical solutions indicate that a degree exponent is determined by the ratio of the number of merging nodes to that of all nodes in the blocks, demonstrating that the exponent is tunable, and are also applicable when the blocks are classical networks such as Erdös-Rényi or regular graphs. Our model becomes the same model as the Barabási-Albert model under a specific condition.

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Multifractal analysis of evolving noise associated with unstable plastic flow.

Plastic flow instability attracts increasing interest as a self-organization phenomenon showing various dynamical regimes, including deterministic chaos and self-organized criticality. The analysis of the associated nonrandom noise--drastic jumps of the mechanical stress--however, confronts the variation of the noise average parameters due to the evolution of the dislocation microstructure. The present paper examines some limitations of the multifractal approach to the study of the evolving noise. The applicability of the multifractal analysis to practical situations is proven using the example of discontinuous deformation curves observed under conditions of the Portevin-Le Châtelier effect in an A1Mg alloy, as well as model signals generated by stretching multifractal Cantor sets. It is found that the smooth trends in the stress serration parameters may narrow the range of the scale invariant behavior associated with the multifractal structure, but do not essentially mask it.

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Evolving Apollonian networks with small-world scale-free topologies.

We propose two types of evolving networks: evolutionary Apollonian networks (EANs) and general deterministic Apollonian networks (GDANs), established by simple iteration algorithms. We investigate the two networks by both simulation and theoretical prediction. Analytical results show that both networks follow power-law degree distributions, with distribution exponents continuously tuned from 2 to 3. The accurate expression of clustering coefficient is also given for both networks. Moreover, the investigation of the average path length of EAN and the diameter of GDAN reveals that these two types of networks possess small-world feature. In addition, we study the collective synchronization behavior on some limitations of the EAN.

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Analysis of an evolving email network.

In this paper we study an evolving email network model first introduced by Wang and De Wilde, to the best of our knowledge. The model is analyzed by formulating the network topology as a random process and studying the dynamics of the process. Our analytical results show a number of steady state properties about the email traffic between different nodes and the aggregate networking behavior (i.e., degree distribution, clustering coefficient, average path length, and phase transition), and also confirm the empirical results obtained by Wang and De Wilde. We also conducted simulations confirming the analytical results. Extensive simulations were run to evaluate email traffic behavior at the link and network levels, phase transition phenomena, and also studying the behavior of email traffic in a hierarchical network. The methods established here are also applicable to many other practical networks including sensor networks and social networks.

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Topology of evolving networks: local events and universality

Networks grow and evolve by local events, such as the addition of new nodes and links, or rewiring of links from one node to another. We show that depending on the frequency of these processes two topologically different networks can emerge, the connectivity distribution following either a generalized power law or an exponential. We propose a continuum theory that predicts these two regimes as well as the scaling function and the exponents, in good agreement with numerical results. Finally, we use the obtained predictions to fit the connectivity distribution of the network describing the professional links between movie actors.

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The first law for slowly evolving horizons.

We study the mechanics of Hayward's trapping horizons, taking isolated horizons as equilibrium states. Zeroth and second laws of dynamic horizon mechanics come from the isolated and trapping horizon formalisms, respectively. We derive a dynamical first law by introducing a new perturbative formulation for dynamic horizons in which "slowly evolving" trapping horizons may be viewed as perturbatively nonisolated.

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Evolving dark energy with w not = -1.

Theories of evolving quintessence are constructed that generically lead to deviations from the w = -1 prediction of nonevolving dark energy. The small mass scale that governs evolution, m(phi) approximately = 10(-33) eV, is radiatively stable, and the "Why now?" problem is solved. These results rest on seesaw cosmology: Fundamental physics and cosmology can be broadly understood from only two mass scales, the weak scale nu and the Planck scale M. Requiring a scale of dark energy rho(DE)(1/4) governed by nu2/M and a radiatively stable evolution rate m(phi) given by nu4/M3 leads to a distinctive form for the equation of state w(z). Dark energy resides in the potential of a hidden axion field that is generated by a new QCD-like force that gets strong at the scale lambda approximately = nu2/M approximately = rho(DE)(1/4). The evolution rate is given by a second seesaw that leads to the axion mass m(phi) approximately = lambda2/f, with f approximately = M.

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Volatile Products of the Lipoxygenase Pathway Evolved from Phaseolus vulgaris (L.) Leaves Inoculated with Pseudomonas syringae pv phaseolicola.

Activation of the "lipoxygenase pathway" in plants gives rise to a series of products derived from fatty acids. Analysis by gas chromatography-mass spectroscopy of volatile products produced by Phaseolus vulgaris (L.) cv Red Mexican leaves during a hypersensitive resistance response (HR) to the plant pathogenic bacterium Pseudomonas syringae pv phaseolicola showed evolution of several lipid-derived volatiles, including cis-3-hexenol and trans-2-hexenal, which arise from the 13-hydroperoxide of linolenic acid. These compounds were not produced in detectable amounts by buffer-inoculated leaves, nor did they evolve to such a high degree during comparable stages of the susceptible response. The absence of trans-2,cis-6-nonadienal, a product expected from 9-hydroperoxide of linolenic acid, suggests that lipid peroxidation during the HR proceeded primarily enzymically via bean lipoxygenase, which produces the 13-hydroperoxide, and not via autoxidative processes. The effects of trans-2-hexenal, cis-3-hexenol, and traumatic acid on P.s pv phaseolicola were investigaed. trans-2-Hexenal appeared to be highly bactericidal at low concentrations, whereas cis-3-hexenol was bactericidal only at much higher concentrations. Traumatic acid appeared to have no effect on P.s. pv. phaseolicola at the concentrations tested. These results demonstrate that during plant defense responses against microbial attack, several lipid-derived compounds are produced by the plant, some of which possess antimicrobial activity and conceivably are involved in plant disease resistance. The time of production of these substances, in amounts that would be expected to be antibacterial in vitro, correlated with a slowing down of the growth rate of bacteria in the leaves and was seen at a time before the accumulation of isoflavonoid phytoalexins in the host.

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The polygalacturonase-inhibiting protein PGIP2 of Phaseolus vulgaris has evolved a mixed mode of inhibition of endopolygalacturonase PG1 of Botrytis cinerea.

Botrytis cinerea is a phytopathogenic fungus that causes gray mold in >1,000 plant species. During infection, it secretes several endopolygalacturonases (PGs) to degrade cell wall pectin, and among them, BcPG1 is constitutively expressed and is an important virulence factor. To counteract the action of PGs, plants express polygalacturonase-inhibiting proteins (PGIPs) that have been shown to inhibit a variety of PGs with different inhibition kinetics, both competitive and noncompetitive. The PG-PGIP interaction promotes the accumulation of oligogalacturonides, fragments of the plant cell wall that are general elicitors of plant defense responses. Here, we characterize the enzymatic activity of BcPG1 and investigate its interaction with PGIP isoform 2 from Phaseolus vulgaris (PvPGIP2) by means of inhibition assays, homology modeling, and molecular docking simulations. Our results indicate a mixed mode of inhibition. This is compatible with a model for the interaction where PvPGIP2 binds the N-terminal portion of BcPG1, partially covering its active site and decreasing the enzyme affinity for the substrate. The structural framework provided by the docking model is confirmed by site-directed mutagenesis of the residues that distinguish PvPGIP2 from the isoform PvPGIP1. The finding that PvPGIP2 inhibits BcPG1 with a mixed-type kinetics further indicates the versatility of PGIPs to evolve different recognition specificities.

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Identification of a Role for an Azide-Sensitive Factor in the Thylakoid Transport of the 17-Kilodalton Subunit of the Photosynthetic Oxygen-Evolving Complex

We have examined the transport of the precursor of the 17-kD subunit of the photosynthetic O2-evolving complex (OE17) in intact chloroplasts in the presence of inhibitors that block two protein-translocation pathways in the thylakoid membrane. This precursor uses the transmembrane pH gradient-dependent pathway into the thylakoid lumen, and its transport across the thylakoid membrane is thought to be independent of ATP and the chloroplast SecA homolog, cpSecA. We unexpectedly found that azide, widely considered to be an inhibitor of cpSecA, had a profound effect on the targeting of the photosynthetic OE17 to the thylakoid lumen. By itself, azide caused a significant fraction of mature OE17 to accumulate in the stroma of intact chloroplasts. When added in conjunction with the protonophore nigericin, azide caused the maturation of a fraction of the stromal intermediate form of OE17, and this mature protein was found only in the stroma. Our data suggest that OE17 may use the sec-dependent pathway, especially when the transmembrane pH gradient-dependent pathway is inhibited. Under certain conditions, OE17 may be inserted across the thylakoid membrane far enough to allow removal of the transit peptide, but then may slip back out of the translocation machinery into the stromal compartment.

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A Highly Active Oxygen-Evolving Photosystem II Preparation from the Cyanobacterium Anacystis nidulans.

A highly active O(2)-evolving Photosystem (PS)-II fraction has been isolated from the cyanobacterium, Anacystis nidulans R2, using an isolation buffer containing high concentrations of sucrose and salts and subsequent solubilization of the thylakoid membranes with the detergent Triton X-100. The isolated fraction had very high PSII activity (2500 micromoles O(2) per milligram chlorophyll per hour) and was largely depleted of PSI activity. Fluorescence emission spectra (77 K) and polypeptide analysis indicated that this preparation is highly enriched in PSII, but almost completely devoid of Cyt b(6)-f and PSI complexes.

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Changes in Protein Composition and Mn Abundance in Photosystem II Particles on Photoactivation of the Latent O(2)-Evolving System in Flash-Grown Wheat Leaves.

Protein composition and Mn abundance were compared between the two photosystem II (PSII) particle preparations obtained before and after photoactivation of the latent O(2)-evolving system in intermittently flashed wheat leaves. The following results have been obtained: (a) nonphotoactivated PSII particles were devoid of two extrinsic proteins which corresponded to the 24 and 16 kilodalton proteins in spinach particles, although the particles contained all the intrinsic proteins and the 33 kilodalton extrinsic protein. (b) The two extrinsic proteins absent in nonphotoactivated PSII particles were present in nonphotoactivated thylakoids, but were easily removed by a hypotonic shock followed by brief sonication. Such removal of the proteins did not occur in photoactivated thylakoids. (c) Nonphotoactivated PSII particles contained 1.5 Mn/400 chlorophyll, while photoactivated particles contained 8 Mn/400 chlorophyll. (d) Nonphotoactivated thylakoids contained 6 Mn/400 chlorophyll, but most of them were removed from thylakoids by a hypotonic shock in the presence of ethylenediaminetetraacetate. Such removal of Mn did not occur in photoactivated thylakoids.

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Oxygen-evolving activity of thylakoids from barley plants cultivated on different concentrations of jasmonic Acid.

The kinetics characteristics of oxygen evolution in thylakoids prepared from barley (Horeum vulgare) seedlings grown in the presence of different jasmonic acid (JA) concentrations were studied. In comparison to control preparations, 100 micromolar JA-treated samples show an inhibition of the Hill activity (46%) and of O(2)-flash yields to above 70%. A damping in the oscillations of O(2) yields, induced by a flash train, increases with increasing growth regulator concentration. After these treatments, the value of the total number of oxygen-evolving centers (S(0) + S(1)), estimated according to the Kok scheme, shows a considerable decrease. In 100 micromolar JA-treated preparations, the turnover half-time of S(1)-states increases and the stability of the S(2)- and S(3)-states decreases.

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Cause for dark, chilling-induced inactivation of photosynthetic oxygen-evolving system in cucumber leaves.

Effects on oxygen evolution of the storage of detached cucumber (Cucumis sativus) leaves at 0 degrees C in the dark were investigated with thylakoids and oxygen-evolving photosystem II membranes isolated from stored leaves. The cold and dark treatment of leaves selectively inactivated electron transport on the oxidizing side of photosystem II. Photosystem II membranes isolated from treated leaves were largely depleted of two proteins of 20 and 14 kilodaltons, which correspond to the extrinsic 23- and 17- kilodalton proteins of spinach functioning in oxygen evolution. The manganese content of photosystem II membranes was also markedly reduced by the treatment. Thus, the inactivation of oxygen evolution induced by the dark, chilling treatment is ascribed to solubilization of the 20- and 14-kilodalton proteins and extraction of manganese.

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Crystallization and preliminary crystallographic studies on the extrinsic 23 kDa protein in the oxygen-evolving complex of photosystem II.

The extrinsic 23 kDa protein in the oxygen-evolving complex (OEC23 or PsbP) of photosystem II (PS II) helps to retain calcium and chloride ions, which are essential cofactors for the photosynthetic evolution of oxygen. OEC23 is found in the PS II complex from higher plants and green algae, but not in that from cyanobacteria or other ancestral photosynthetic organisms. In order to elucidate the three-dimensional structure and its molecular evolution, OEC23 was crystallized by the hanging-drop vapour-diffusion technique with PEG 4000 as a precipitant. Diffraction data to a resolution of 2.0 A were collected from a native crystal belonging to space group P2(1)2(1)2, with unit-cell parameters a = 91.36, b = 74.15, c = 52.16 A.

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