104 research outputs found

    Intrusion and extrusion of water in hydrophobic mesopores

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    We present experimental and theoretical results on intrusion-extrusion cycles of water in hydrophobic mesoporous materials, characterized by independent cylindrical pores. The intrusion, which takes place above the bulk saturation pressure, can be well described using a macroscopic capillary model. Once the material is saturated with water, extrusion takes place upon reduction of the externally applied pressure; Our results for the extrusion pressure can only be understood by assuming that the limiting extrusion mechanism is the nucleation of a vapour bubble inside the pores. A comparison of calculated and experimental nucleation pressures shows that a proper inclusion of line tension effects is necessary to account for the observed values of nucleation barriers. Negative line tensions of order 10−11J.m−110^{-11} \mathrm{J.m}^{-1} are found for our system, in reasonable agreement with other experimental estimates of this quantity

    TreeKnit: Inferring ancestral reassortment graphs of influenza viruses

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    When two influenza viruses co-infect the same cell, they can exchange genome segments in a process known as reassortment. Reassortment is an important source of genetic diversity and is known to have been involved in the emergence of most pandemic influenza strains. However, because of the difficulty in identifying reassortment events from viral sequence data, little is known about their role in the evolution of the seasonal influenza viruses. Here we introduce TreeKnit, a method that infers ancestral reassortment graphs (ARG) from two segment trees. It is based on topological differences between trees, and proceeds in a greedy fashion by finding regions that are compatible in the two trees. Using simulated genealogies with reassortments, we show that TreeKnit performs well in a wide range of settings and that it is as accurate as a more principled bayesian method, while being orders of magnitude faster. Finally, we show that it is possible to use the inferred ARG to better resolve segment trees and to construct more informative visualizations of reassortments

    Propagation dynamics on networks featuring complex topologies

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    Analytical description of propagation phenomena on random networks has flourished in recent years, yet more complex systems have mainly been studied through numerical means. In this paper, a mean-field description is used to coherently couple the dynamics of the network elements (nodes, vertices, individuals...) on the one hand and their recurrent topological patterns (subgraphs, groups...) on the other hand. In a SIS model of epidemic spread on social networks with community structure, this approach yields a set of ODEs for the time evolution of the system, as well as analytical solutions for the epidemic threshold and equilibria. The results obtained are in good agreement with numerical simulations and reproduce random networks behavior in the appropriate limits which highlights the influence of topology on the processes. Finally, it is demonstrated that our model predicts higher epidemic thresholds for clustered structures than for equivalent random topologies in the case of networks with zero degree correlation.Comment: 10 pages, 5 figures, 1 Appendix. Published in Phys. Rev. E (mistakes in the PRE version are corrected here

    Limited Predictability of Amino Acid Substitutions in Seasonal Influenza Viruses

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    Seasonal influenza viruses repeatedly infect humans in part because they rapidly change their antigenic properties and evade host immune responses, necessitating frequent updates of the vaccine composition. Accurate predictions of strains circulating in the future could therefore improve the vaccine match. Here, we studied the predictability of frequency dynamics and fixation of amino acid substitutions. Current frequency was the strongest predictor of eventual fixation, as expected in neutral evolution. Other properties, such as occurrence in previously characterized epitopes or high Local Branching Index (LBI) had little predictive power. Parallel evolution was found to be moderately predictive of fixation. Although the LBI had little power to predict frequency dynamics, it was still successful at picking strains representative of future populations. The latter is due to a tendency of the LBI to be high for consensus-like sequences that are closer to the future than the average sequence. Simulations of models of adapting populations, in contrast, show clear signals of predictability. This indicates that the evolution of influenza HA and NA, while driven by strong selection pressure to change, is poorly described by common models of directional selection such as traveling fitness waves

    Propagation on networks: an exact alternative perspective

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    By generating the specifics of a network structure only when needed (on-the-fly), we derive a simple stochastic process that exactly models the time evolution of susceptible-infectious dynamics on finite-size networks. The small number of dynamical variables of this birth-death Markov process greatly simplifies analytical calculations. We show how a dual analytical description, treating large scale epidemics with a Gaussian approximations and small outbreaks with a branching process, provides an accurate approximation of the distribution even for rather small networks. The approach also offers important computational advantages and generalizes to a vast class of systems.Comment: 8 pages, 4 figure

    Localization of thermal packets and metastable states in Sinai model

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    We consider the Sinai model describing a particle diffusing in a 1D random force field. As shown by Golosov, this model exhibits a strong localization phenomenon for the thermal packet: the disorder average of the thermal distribution of the relative distance y=x-m(t), with respect to the (disorder-dependent) most probable position m(t), converges in the limit of infinite time towards a distribution P(y). In this paper, we revisit this question of the localization of the thermal packet. We first generalize the result of Golosov by computing explicitly the joint asymptotic distribution of relative position y=x(t)-m(t) and relative energy u=U(x(t))-U(m(t)) for the thermal packet. Next, we compute in the infinite-time limit the localization parameters Y_k, representing the disorder-averaged probabilities that k particles of the thermal packet are at the same place, and the correlation function C(l) representing the disorder-averaged probability that two particles of the thermal packet are at a distance l from each other. We moreover prove that our results for Y_k and C(l) exactly coincide with the thermodynamic limit of the analog quantities computed for independent particles at equilibrium in a finite sample of length L. Finally, we discuss the properties of the finite-time metastable states that are responsible for the localization phenomenon and compare with the general theory of metastable states in glassy systems, in particular as a test of the Edwards conjecture.Comment: 17 page

    Fast diffusion of a Lennard-Jones cluster on a crystalline surface

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    We present a Molecular Dynamics study of large Lennard-Jones clusters evolving on a crystalline surface. The static and the dynamic properties of the cluster are described. We find that large clusters can diffuse rapidly, as experimentally observed. The role of the mismatch between the lattice parameters of the cluster and the substrate is emphasized to explain the diffusion of the cluster. This diffusion can be described as a Brownian motion induced by the vibrationnal coupling to the substrate, a mechanism that has not been previously considered for cluster diffusion.Comment: latex, 5 pages with figure

    Glassy behaviour in disordered systems with non-relaxational dynamics

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    We show that a family of disordered systems with non-relaxational dynamics may exhibit ``glassy'' behavior at nonzero temperature, although such a behavior appears to be ruled out by a face-value application of mean-field theory. Nevertheless, the roots of this behavior can be understood within mean-field theory itself, properly interpreted. Finite systems belonging to this family have a dynamical regime with a self-similar pattern of alternating periods of fast motion and trapping.Comment: 4 pages, 4 figure
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