53 research outputs found
Finite volume approximation of a diffusion-dissolution model and application to nuclear waste storage
International audienceThe study of two phase flow in porous media under high capillary pressures, in the case where one phase is incompressible and the other phase is gaseous, shows complex phenomena. We present in this paper a numerical approximation method, based on a two pressures formulation in the case where both phases are miscible, which is shown to also handle the limit case of immiscible phases. The space discretization is performed using a finite volume method, which can handle general grids. The efficiency of the formulation is shown on three numerical examples related tounderground waste disposal situations
Order-of-magnitude speedup for steady states and traveling waves via Stokes preconditioning in Channelflow and Openpipeflow
Steady states and traveling waves play a fundamental role in understanding
hydrodynamic problems. Even when unstable, these states provide the
bifurcation-theoretic explanation for the origin of the observed states. In
turbulent wall-bounded shear flows, these states have been hypothesized to be
saddle points organizing the trajectories within a chaotic attractor. These
states must be computed with Newton's method or one of its generalizations,
since time-integration cannot converge to unstable equilibria. The bottleneck
is the solution of linear systems involving the Jacobian of the Navier-Stokes
or Boussinesq equations. Originally such computations were carried out by
constructing and directly inverting the Jacobian, but this is unfeasible for
the matrices arising from three-dimensional hydrodynamic configurations in
large domains. A popular method is to seek states that are invariant under
numerical time integration. Surprisingly, equilibria may also be found by
seeking flows that are invariant under a single very large Backwards-Euler
Forwards-Euler timestep. We show that this method, called Stokes
preconditioning, is 10 to 50 times faster at computing steady states in plane
Couette flow and traveling waves in pipe flow. Moreover, it can be carried out
using Channelflow (by Gibson) and Openpipeflow (by Willis) without any changes
to these popular spectral codes. We explain the convergence rate as a function
of the integration period and Reynolds number by computing the full spectra of
the operators corresponding to the Jacobians of both methods.Comment: in Computational Modelling of Bifurcations and Instabilities in Fluid
Dynamics, ed. Alexander Gelfgat (Springer, 2018
An ATP and Oxalate Generating Variant Tricarboxylic Acid Cycle Counters Aluminum Toxicity in Pseudomonas fluorescens
Although the tricarboxylic acid (TCA) cycle is essential in almost all aerobic organisms, its precise modulation and integration in global cellular metabolism is not fully understood. Here, we report on an alternative TCA cycle uniquely aimed at generating ATP and oxalate, two metabolites critical for the survival of Pseudomonas fluorescens. The upregulation of isocitrate lyase (ICL) and acylating glyoxylate dehydrogenase (AGODH) led to the enhanced synthesis of oxalate, a dicarboxylic acid involved in the immobilization of aluminum (Al). The increased activity of succinyl-CoA synthetase (SCS) and oxalate CoA-transferase (OCT) in the Al-stressed cells afforded an effective route to ATP synthesis from oxalyl-CoA via substrate level phosphorylation. This modified TCA cycle with diminished efficacy in NADH production and decreased CO2-evolving capacity, orchestrates the synthesis of oxalate, NADPH, and ATP, ingredients pivotal to the survival of P. fluorescens in an Al environment. The channeling of succinyl-CoA towards ATP formation may be an important function of the TCA cycle during anaerobiosis, Fe starvation and O2-limited conditions
Distinct Expression Profiles and Different Functions of Odorant Binding Proteins in Nilaparvata lugens StĂĄl
Background: Odorant binding proteins (OBPs) play important roles in insect olfaction. The brown planthopper (BPH), Nilaparvata lugens StaËšl (Delphacidae, Auchenorrhyncha, Hemiptera) is one of the most important rice pests. Its monophagy (only feeding on rice), wing form (long and short wing) variation, and annual long distance migration (seeking for rice plants of high nutrition) imply that the olfaction would play a central role in BPH behavior. However, the olfaction related proteins have not been characterized in this insect. Methodology/Principal Findings: Full length cDNA of three OBPs were obtained and distinct expression profiles were revealed regarding to tissue, developmental stage, wing form and gender for the first time for the species. The results provide important clues in functional differentiation of these genes. Binding assays with 41 compounds demonstrated that NlugOBP3 had markedly higher binding ability and wider binding spectrum than the other two OBPs. Terpenes and Ketones displayed higher binding while Alkanes showed no binding to the three OBPs. Focused on NlugOBP3, RNA interference experiments showed that NlugOBP3 not only involved in nymph olfaction on rice seedlings, but also had non-olfactory functions, as it was closely related to nymph survival. Conclusions: NlugOBP3 plays important roles in both olfaction and survival of BPH. It may serve as a potential target fo
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