3-D chemistry-transport model Polair: numerical issues, validation and automatic-differentiation strategy

International audienceWe briefly present in this short paper some issues related to the development and the validation of the three-dimensional chemistry-transport model Polair. Numerical studies have been performed in order to let Polair be an efficient and robust solver. This paper summarizes and comments choices that were made in this respect. Simulations of relevant photochemical episodes were led to assess the validity of the model. The results can be considered as a validation, which allows next studies to focus on fine modeling issues. A major feature of Polair is the availability of a tangent linear mode and an adjoint mode entirely generated by automatic differentiation. Tangent linear and adjoint modes grant the opportunity to perform detailed sensitivity analyses and data assimilation. This paper shows how inverse modeling is achieved with Polair

Polyphemus : une plate-forme multimodèles pour la pollution atmosphérique et l'évaluation des risques

National audienceCet article présente le système de modélisation de la qualité de l'air Polyphemus, ses principales fonctionnalités et quelques applications. Polyphemus est dédié à la modélisation de la dispersion atmosphérique de traceurs passifs ou d'espèces réactives aux échelles locale, régionale et continentale. Polyphemus est développé au CEREA, laboratoire commun entre EDF R&D et lʼÉcole des Ponts et au sein dʼun projet commun avec lʼInstitut national de recherche en informatique et automatique (INRIA), avec le soutien de lʼIRSN et de lʼINERIS. Polyphemus est un système dʼun type nouveau qui se distingue de lʼapproche classique du " modèle tout en un " par sa construction modulaire, notamment fondée sur des bibliothèques et des pilotes manipulant les modèles de dispersion. Accueillant plusieurs modèles, Polyphemus est une plate-forme et non un modèle. Une de ses fonctionnalités notables est sa capacité à effectuer des simulations multimodèles, ce qui permet d'évaluer des incertitudes. Plusieurs méthodes dʼassimilation de données font aussi partie du système afin de pouvoir intégrer des données fournies par des réseaux de mesure

Dominant aerosol processes during high-pollution episodes over Greater Tokyo

This paper studies two high-pollution episodes over Greater Tokyo: 9 and 10 December 1999, and 31 July and 1 August 2001. Results obtained with the chemistry-transport model (CTM) Polair3D are compared to measurements of inorganic PM2.5. To understand to which extent the aerosol processes modeled in Polair3D impact simulated inorganic PM2.5, Polair3D is run with different options in the aerosol module, e.g. with/without heterogeneous reactions. To quantify the impact of processes outside the aerosol module, simulations are also done with another CTM (CMAQ). In the winter episode, sulfate is mostly impacted by condensation, coagulation, long-range transport, and deposition to a lesser extent. In the summer episode, the effect of long-range transport largely dominates. The impact of condensation/evaporation is dominant for ammonium, nitrate and chloride in both episodes. However, the impact of the thermodynamic equilibrium assumption is limited. The impact of heterogeneous reactions is large for nitrate and ammonium, and taking heterogeneous reactions into account appears to be crucial in predicting the peaks of nitrate and ammonium. The impact of deposition is the same for all inorganic PM2.5. It is small compared to the impact of other processes although it is not negligible. The impact of nucleation is negligible in the summer episode, and small in the winter episode. The impact of coagulation is larger in the winter episode than in the summer episode, because the number of small particles is higher in the winter episode as a consequence of nucleation.Comment: Journal of Geophysical Research D: Atmospheres (15/05/2007) in pres

Technical Note: The air quality modeling system Polyphemus

International audiencePolyphemus is an air quality modeling platform which aims at covering the scope and the abilities of modern air quality systems. It deals with applications from local scale to continental scale, using two Gaussian models and two Eulerian models. It manages passive tracers, radioactive decay, photochemistry and aerosol dynamics. The structure of the system includes four independent levels with data management, physical parameterizations, numerical solvers and high-level methods such as data assimilation. This enables sensitivity and uncertainty analysis, primarily through multimodel approaches. On top of the models, drivers implement advanced methods such as model coupling or data assimilation

Expression of LIM kinase 1 is associated with reversible G1/S phase arrest, chromosomal instability and prostate cancer

<p>Abstract</p> <p>Background</p> <p>LIM kinase 1 (LIMK1), a LIM domain containing serine/threonine kinase, modulates actin dynamics through inactivation of the actin depolymerizing protein cofilin. Recent studies have indicated an important role of LIMK1 in growth and invasion of prostate and breast cancer cells; however, the molecular mechanism whereby LIMK1 induces tumor progression is unknown. In this study, we investigated the effects of ectopic expression of LIMK1 on cellular morphology, cell cycle progression and expression profile of LIMK1 in prostate tumors.</p> <p>Results</p> <p>Ectopic expression of LIMK1 in benign prostatic hyperplasia cells (BPH), which naturally express low levels of LIMK1, resulted in appearance of abnormal mitotic spindles, multiple centrosomes and smaller chromosomal masses. Furthermore, a transient G1/S phase arrest and delayed G2/M progression was observed in BPH cells expressing LIMK1. When treated with chemotherapeutic agent Taxol, no metaphase arrest was noted in these cells. We have also noted increased nuclear staining of LIMK1 in tumors with higher Gleason Scores and incidence of metastasis.</p> <p>Conclusion</p> <p>Our results show that increased expression of LIMK1 results in chromosomal abnormalities, aberrant cell cycle progression and alteration of normal cellular response to microtubule stabilizing agent Taxol; and that LIMK1 expression may be associated with cancerous phenotype of the prostate.</p

Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca2+ Release Patterns in Cardiomyocytes

Spatio-temporal dynamics of intracellular calcium, [Ca2+]i, regulate the contractile function of cardiac muscle cells. Measuring [Ca2+]i flux is central to the study of mechanisms that underlie both normal cardiac function and calcium-dependent etiologies in heart disease. However, current imaging techniques are limited in the spatial resolution to which changes in [Ca2+]i can be detected. Using spatial point process statistics techniques we developed a novel method to simulate the spatial distribution of RyR clusters, which act as the major mediators of contractile Ca2+ release, upon a physiologically-realistic cellular landscape composed of tightly-packed mitochondria and myofibrils.We applied this method to computationally combine confocal-scale (~ 200 nm) data of RyR clusters with 3D electron microscopy data (~ 30 nm) of myofibrils and mitochondria, both collected from adult rat left ventricular myocytes. Using this hybrid-scale spatial model, we simulated reaction-diffusion of [Ca2+]i during the rising phase of the transient (first 30 ms after initiation). At 30 ms, the average peak of the simulated [Ca2+]i transient and of the simulated fluorescence intensity signal, F/F0, reached values similar to that found in the literature ([Ca2+]i 1 μM; F/F0 5.5). However, our model predicted the variation in [Ca2+]i to be between 0.3 and 12.7 μM (~3 to 100 fold from resting value of 0.1 μM) and the corresponding F/F0 signal ranging from 3 to 9.5. We demonstrate in this study that: (i) heterogeneities in the [Ca2+]i transient are due not only to heterogeneous distribution and clustering of mitochondria; (ii) but also to heterogeneous local densities of RyR clusters. Further, we show that: (iii) these structureinduced heterogeneities in [Ca2+]i can appear in line scan data. Finally, using our unique method for generating RyR cluster distributions, we demonstrate the robustness in the [Ca2+]i transient to differences in RyR cluster distributions measured between rat and human cardiomyocytes

A note on operator splitting in a stiff linear case

This note is concerned with the numerical technique of operator splitting for initial value problems. Using a stiff linear ODE system as model problem, error bounds are derived for standard 1st- and 2nd-order splitting methods. The analysis focuses on deriving bounds independent of stiffness. The aim is to study the influence of stiffness on accuracy. Attention is paid to the influence of the splitting sequence on the splitting error and to the order reduction phenomenon

Some reduction techniques for simplifying atmospheric chemical kinetics

International audienceWe review in this article some issues related to reduction techniques for atmospheric chemical kinetics. There is indeed a wide range of characteristic timescales for atmospheric chemistry and the time evolution is characterized by a slow-fast behaviour. We present here some related points: the existence of an underlying reduced model, the partitioning techniques to build reduced models, time integration of the reduced models and finally the application of Proper Orthogonal Decomposition (POD) method for reducing chemical systems