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Characterization of Reachable Attractors Using Petri Net Unfoldings
No full textInternational audienceAttractors of network dynamics represent the long-term behaviours of the modelled system. Their characterization is therefore crucial for understanding the response and differentiation capabilities of a dynamical system. In the scope of qualitative models of interaction networks, the computation of attractors reachable from a given state of the network faces combinatorial issues due to the state space explosion. In this paper, we present a new algorithm that exploits the concurrency between transitions of parallel acting components in order to reduce the search space. The algorithm relies on Petri net unfoldings that can be used to compute a compact representation of the dynamics. We illustrate the applicability of the algorithm with Petri net models of cell signalling and regulation networks, Boolean and multi-valued. The proposed approach aims at being complementary to existing methods for deriving the attractors of Boolean models, while being %so far more generic since it applies to any safe Petri net
An Overview of Electrostatic Free Energy Computations for Solutions and Proteins
No full textInternational audienceFree energy simulations for electrostatic and charging processes in complex molecular systems encounter specific difficulties owing to the long-range, 1/r Coulomb interaction. To calculate the solvation free energy of a simple ion, it is essential to take into account the polarization of nearby solvent but also the electrostatic potential drop across the liquid-gas boundary, however distant. The latter does not exist in a simulation model based on periodic boundary conditions because there is no physical boundary to the system. An important consequence is that the reference value of the electrostatic potential is not an ion in a vacuum. Also, in an infinite system, the electrostatic potential felt by a perturbing charge is conditionally convergent and dependent on the choice of computational conventions. Furthermore, with Ewald lattice summation and tinfoil conducting boundary conditions, the charges experience a spurious shift in the potential that depends on the details of the simulation system such as the volume fraction occupied by the solvent. All these issues can be handled with established computational protocols, as reviewed here and illustrated for several small ions and three solvated proteins
Experimental control of natural perturbations in channel flow
No full textInternational audienceA combined approach using system identification and feed-forward control design has been applied to experimental laminar channel flow in an effort to reduce the naturally occurring disturbance level. A simple blowing/suction strategy was capable of reducing the standard deviation of the measured sensor signal by 45 %, which markedly exceeds previously obtained results under comparable conditions. A comparable reduction could be verified over a significant streamwise extent, implying an improvement over previous, more localized disturbance control. The technique is effective, flexible, and robust, and the obtained results encourage further explorations of experimental control of convection-dominated flows
Explosions at the water surface
No full textInternational audienceWe study the shape and dynamics of cavities created by the explosion of firecrackers at the surface of a large pool of water. Without confinement, the explosion generates a hemispherical air cavity which grows, reaches a maximum size and collapses in a generic w-shape to form a final central jet. When a rigid open tube confines the firecracker, the explosion produces a cylindrical cavity that expands without ever escaping the free end of the tube. We discuss a potential flow model, which captures most of these feature
The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond.
No full textInternational audienceBrown algae (stramenopiles) are key players in intertidal ecosystems, and represent a source of biomass with several industrial applications. Ectocarpus siliculosus is a model to study the biology of these organisms. Its genome has been sequenced and a number of post-genomic tools have been implemented. Based on this knowledge, we report the reconstruction and analysis of a genome-scale metabolic network for E. siliculosus, EctoGEM (http://ectogem.irisa.fr). This atlas of metabolic pathways consists of 1866 reactions and 2020 metabolites, and its construction was performed by means of an integrative computational approach for identifying metabolic pathways, gap filling and manual refinement. The capability of the network to produce biomass was validated by flux balance analysis. EctoGEM enabled the reannotation of 56 genes within the E. siliculosus genome, and shed light on the evolution of metabolic processes. For example, E. siliculosus has the potential to produce phenylalanine and tyrosine from prephenate and arogenate, but does not possess a phenylalanine hydroxylase, as is found in other stramenopiles. It also possesses the complete eukaryote molybdenum co-factor biosynthesis pathway, as well as a second molybdopterin synthase that was most likely acquired via horizontal gene transfer from cyanobacteria by a common ancestor of stramenopiles. EctoGEM represents an evolving community resource to gain deeper understanding of the biology of brown algae and the diversification of physiological processes. The integrative computational method applied for its reconstruction will be valuable to set up similar approaches for other organisms distant from biological benchmark models
Search for pair production of third-generation scalar leptoquarks and top squarks in proton-proton collisions at sqrt(s) = 8 TeV
No full textSubmitted to Phys. Lett. B ; see paper for full list of authorsA search for pair production of third-generation scalar leptoquarks and supersymmetric top quark partners, top squarks, in final states involving tau leptons and bottom quarks is presented. The search uses events from a data sample of proton-proton collisions corresponding to an integrated luminosity of 19.7 inverse femtobarns, collected with the CMS detector at the LHC with sqrt(s)=8 TeV. The number of observed events is found to be in agreement with the expected standard model background. Third-generation scalar leptoquarks with masses below 740 GeV are excluded at 95% confidence level, assuming a 100% branching fraction for the leptoquark decay to a tau lepton and a bottom quark. In addition, this mass limit applies directly to top squarks decaying via an R-parity violating coupling lambda'[333]. The search also considers a similar signature from top squarks undergoing a chargino-mediated decay involving the R-parity violating coupling lambda'[3jk]. Each top squark decays to a tau lepton, a bottom quark, and two light quarks. Top squarks in this model with masses below 580 GeV are excluded at 95% confidence level. The constraint on the leptoquark mass is the most stringent to date, and this is the first search for top squarks decaying via lambda'[3jk]
Investigating the Cell Membrane via Single Particle Tracking, Bayesian Inference and Hydrodynamic Force Application
No full textInternational audienceWe investigate the potential felt by membrane receptors inside membrane microdomains via tracking of single receptors labelled with rare-earth doped luminescent nanoparticles and Bayesian inference analysis of the recorded trajectories. We demonstrated that the potential felt by peptidic toxin receptors confined in lipid rafts is well described by a second-order polynomial potential, possibly due to an inhomogeneous lipid and protein distribution [Türkcan et al., Biophys. J. 2012] In contrast, the potential experienced by transferrin receptors in cytoskeleton-delimited microdomains is localized at the border of the confinement domain
Spectral conditions for the controllability of the Schroedinger equation
No full textParallel sessionInternational audienceSpectral conditions for the controllability of the Schroedinger equatio
Timelike deeply virtual Compton scattering with a linearly polarized real (or quasi-real) photon beam
No full textTo appear in the proceedings XXII. International Workshop on Deep Inelastic Scattering and Related Subjects (DIS 2014), 28 April - 2 May 2014, Warsaw, PolandWe calculate timelike virtual Compton scattering amplitudes in the generalized Bjorken scaling regime and focus on a new polarization asymmetry in the scattering process with a linearly polarized photon beam in the medium energy range, which will be studied intensely at JLab12 experiments. We demonstrate that new observables help us to access the polarized quark and gluon generalized parton distributions Htilde(x, xi, t) and Etilde(x, xi, t)
Validity of some asymptotic models for eddy current inspection of highly conducting thin deposits
No full textHighly conducting thin deposits may blind eddy current probes in non-destructive testing of steam generator tubes and thus should be identified. In this report, various asymptotic models are studied to model the axisymmetric thin conducting layers by effective transmission conditions depending on re-scaling parameter and asymptotic expansion order, so as to avoid the high computational cost in a full model due to those thin layers. We also select the most adapted models for practical configurations via numerical comparisons in a simplified case.Des couches minces hautement conductrices peuvent masquer des défauts problématiques lors d'un contrôle non-destructif des tubes dans un générateur de vapeur via des sondes courant de Foucault. Ainsi il est essentiel de pouvoir en tenir compte. Dans ce rapport, on étudie des modèles asymptotiques avec différentes conditions de transmission effectives ayant pour objectif de modéliser une couche mince axis-symétrique afin de réduire le coût de calcul numérique. Parmi des conditions de transmission qui dépendent d'un paramètre de redimensionnement et de l'ordre du développement asymptotique, on en sélectionne les plus pertinentes pour les applications pratiques via des tests numériques dans des configurations simplifiées