Non-meanfield deterministic limits in chemical reaction kinetics far from equilibrium

A general mechanism is proposed by which small intrinsic fluctuations in a system far from equilibrium can result in nearly deterministic dynamical behaviors which are markedly distinct from those realized in the meanfield limit. The mechanism is demonstrated for the kinetic Monte-Carlo version of the Schnakenberg reaction where we identified a scaling limit in which the global deterministic bifurcation picture is fundamentally altered by fluctuations. Numerical simulations of the model are found to be in quantitative agreement with theoretical predictions.Comment: 4 pages, 4 figures (submitted to Phys. Rev. Lett.

Mesh update techniques for free-surface flow solvers using spectral element method

This paper presents a novel mesh-update technique for unsteady free-surface Newtonian flows using spectral element method and relying on the arbitrary Lagrangian--Eulerian kinematic description for moving the grid. Selected results showing compatibility of this mesh-update technique with spectral element method are given

When Madagascar produced natural rubber: a brief, forgotten yet informative history.

From 1891 to 1914, Madagascar, like other western African countries, was a production zone for forest rubber destined for export to Europe when Asian plantations where not yet sufficiently developed . Numerous species endemic to the forests of the three major Malagasy ecosystems were exploited, often with a view to maximising short term productivity without any consideration for the sustainable management of the resource. This episode represents one of the first cases of industrial exploitation of Madagascar's biological resources. Although Madagascar occupies a modest position on the world rubber market at that time, the exploitation of rubber bore major consequences for the island's forestry resources and, moreover, influenced the vision and discourse of scientists and politicians concerning their management. It was one of the factors triggering awareness of the value of Madagascar's biodiversity and the threat to which it might be exposed through poorly-controlled human activity. As a result, highly repressive and forcible legislation was introduced aimed at containing the activity practiced by local populations considered to be mostly to blame. But from the early days of French colonial rule, naturalists judged the outcomes of political decisions too weak to offer any guarantee of an effective defence. They responded by adopting an intentionally alarmist and catastrophist discourse with the object of provoking a reaction from the politicians, considered too lax. This discourse, in fact, took an about-turn from 1942-45 when the war effort led to a revitalisation of the Malagasy rubber sector as Asian production was mainly out of reach. A second consequence came in 1927 with the creation of a network of protected areas managed by naturalists, making Madagascar at that time, a pioneer in Africa. There was a simultaneous flurry of activity to promote the domestication of Malagasy rubber species, combined with the introduction of new species with high potential (Hevea brasiliensis, Castilloa elastica). However, with the emergence of far more profitable Asian rubber, all attempts at cultivation in Madagascar were abandoned when exploitation ceased to be profitable, and thus the Malagasy forests were redeemed. This episode demonstrates how it was in fact economic reality, by condemning an unprofitable sector, that was the real vehicle by which the survival of Malagasy rubber species was secured, and not the naturalists' discourse, nor the creation of protected zones, nor the promulgation of repressive legislations. This case study is of more than purely historical interest, in that it still has currency where, for example, the exploitation of Prunus africana is concerned

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase

Refolding aggregated proteins is essential in combating cellular proteotoxic stress. Together with Hsp70, Hsp100 chaperones, including Escherichia coli ClpB, form a powerful disaggregation machine that threads aggregated polypeptides through the central pore of tandem adenosine triphosphatase (ATPase) rings. To visualize protein disaggregation, we determined cryo–electron microscopy structures of inactive and substrate-bound ClpB in the presence of adenosine 5′-O-(3-thiotriphosphate), revealing closed AAA+ rings with a pronounced seam. In the substrate-free state, a marked gradient of resolution, likely corresponding to mobility, spans across the AAA+ rings with a dynamic hotspot at the seam. On the seam side, the coiled-coil regulatory domains are locked in a horizontal, inactive orientation. On the opposite side, the regulatory domains are accessible for Hsp70 binding, substrate targeting, and activation. In the presence of the model substrate casein, the polypeptide threads through the entire pore channel and increased nucleotide occupancy correlates with higher ATPase activity. Substrate-induced domain displacements indicate a pathway of regulated substrate transfer from Hsp70 to the ClpB pore, inside which a spiral of loops contacts the substrate. The seam pore loops undergo marked displacements, along with ordering of the regulatory domains. These asymmetric movements suggest a mechanism for ATPase activation and substrate threading during disaggregation

Compositionality, stochasticity and cooperativity in dynamic models of gene regulation

We present an approach for constructing dynamic models for the simulation of gene regulatory networks from simple computational elements. Each element is called a ``gene gate'' and defines an input/output-relationship corresponding to the binding and production of transcription factors. The proposed reaction kinetics of the gene gates can be mapped onto stochastic processes and the standard ode-description. While the ode-approach requires fixing the system's topology before its correct implementation, expressing them in stochastic pi-calculus leads to a fully compositional scheme: network elements become autonomous and only the input/output relationships fix their wiring. The modularity of our approach allows to pass easily from a basic first-level description to refined models which capture more details of the biological system. As an illustrative application we present the stochastic repressilator, an artificial cellular clock, which oscillates readily without any cooperative effects.Comment: 15 pages, 8 figures. Accepted by the HFSP journal (13/09/07

Progress report and first operation of the GANIL injector

http://accelconf.web.cern.ch/AccelConf/c81/papers/abp-07.pdfInternational audienc

Quantitative Stability of Linear Infinite Inequality Systems under Block Perturbations with Applications to Convex Systems

The original motivation for this paper was to provide an efficient quantitative analysis of convex infinite (or semi-infinite) inequality systems whose decision variables run over general infinite-dimensional (resp. finite-dimensional) Banach spaces and that are indexed by an arbitrary fixed set $J$. Parameter perturbations on the right-hand side of the inequalities are required to be merely bounded, and thus the natural parameter space is $l_{\infty}(J)$. Our basic strategy consists of linearizing the parameterized convex system via splitting convex inequalities into linear ones by using the Fenchel-Legendre conjugate. This approach yields that arbitrary bounded right-hand side perturbations of the convex system turn on constant-by-blocks perturbations in the linearized system. Based on advanced variational analysis, we derive a precise formula for computing the exact Lipschitzian bound of the feasible solution map of block-perturbed linear systems, which involves only the system's data, and then show that this exact bound agrees with the coderivative norm of the aforementioned mapping. In this way we extend to the convex setting the results of [3] developed for arbitrary perturbations with no block structure in the linear framework under the boundedness assumption on the system's coefficients. The latter boundedness assumption is removed in this paper when the decision space is reflexive. The last section provides the aimed application to the convex case

Mobility of the SecA 2-helix-finger is not essential for polypeptide translocation via the SecYEG complex

The bacterial ATPase SecA and protein channel complex SecYEG form the core of an essential protein translocation machinery. The nature of the conformational changes induced by each stage of the hydrolytic cycle of ATP and how they are coupled to protein translocation are not well understood. The structure of the SecA–SecYEG complex revealed a 2-helix-finger (2HF) of SecA in an ideal position to contact the substrate protein and push it through the membrane. Surprisingly, immobilization of this finger at the edge of the protein channel had no effect on translocation, whereas its imposition inside the channel blocked transport. This analysis resolves the stoichiometry of the active complex, demonstrating that after the initiation process translocation requires only one copy each of SecA and SecYEG. The results also have important implications on the mechanism of energy transduction and the power stroke driving transport. Evidently, the 2HF is not a highly mobile transducing element of polypeptide translocation

On Distributive Subalgebras of Qualitative Spatial and Temporal Calculi

Qualitative calculi play a central role in representing and reasoning about qualitative spatial and temporal knowledge. This paper studies distributive subalgebras of qualitative calculi, which are subalgebras in which (weak) composition distributives over nonempty intersections. It has been proven for RCC5 and RCC8 that path consistent constraint network over a distributive subalgebra is always minimal and globally consistent (in the sense of strong $n$-consistency) in a qualitative sense. The well-known subclass of convex interval relations provides one such an example of distributive subalgebras. This paper first gives a characterisation of distributive subalgebras, which states that the intersection of a set of $n\geq 3$ relations in the subalgebra is nonempty if and only if the intersection of every two of these relations is nonempty. We further compute and generate all maximal distributive subalgebras for Point Algebra, Interval Algebra, RCC5 and RCC8, Cardinal Relation Algebra, and Rectangle Algebra. Lastly, we establish two nice properties which will play an important role in efficient reasoning with constraint networks involving a large number of variables.Comment: Adding proof of Theorem 2 to appendi

Physical examination for lumbar radiculopathy due to disc herniation in patients with low-back pain (Protocol)

This is the protocol for a review and there is no abstract. The objectives are as follows: The general aim of our review is to provide information that may assist the clinician in making decisions about appropriate management in patients with low-back pain and leg pain suspected of having radicular pain and radiculopathy due to disc herniation. More specifically, the objective of this systematic review is to assess the diagnostic performance of tests performed during physical examination in the identification of radicular pain and radiculopathy due to lumbar disc herniation in patients with low-back and leg pain. The secondary objective of this review is to assess the influence of sources of heterogeneity on the diagnostic accuracy of tests performed during physical examination, in particular the type of reference standard, health care setting, spectrum of disease, and study design