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Reproducible Boolean model analyses and simulations with the CoLoMoTo software suite: a tutorial
No full textInternational audienceThis tutorial provides stepwise instructions to install over 20 tools, written in multiple languages. Their integration in the CoLoMoTo software suite makes them accessible with a single popular language (Python), thereby enabling reproducible and sophisticated dynamical analyses of logical models of complex cellular networks. The tutorial specifically focuses on the analysis of a previously published model of the regulatory network controlling mammalian cell proliferation. It includes chunks of Python code to reproduce several of the results and figures published in the original article, and further extends these results with the help of selected tools included in the CoLoMoTo suite. The tutorial covers the visualization of the network with the tool GINsim, an attractor analysis with bioLQM, the computation of synchronous attractors with BNS, the extraction of modules from the full model, stochastic simulations of the wild-type model and of selected perturbations with MaBoSS and finally the delineation of compressed probabilistic state transition graphs. The integration of all these analyses in an executable Jupyter Notebook greatly eases their reproducibility, as well as the inclusion of further extensions. The notebook provided along with this tutorial further constitutes a template, which can be enriched with other ColoMoTo tools, to develop comprehensive dynamical analyses of various biological network models
Exploiting outcomes of life cycle costing to conduct coherent screening social life cycle assessments of emerging systems: a case study of microalgae biorefineries
No full textInternational audienceAbstract Purpose Microalgae are considered a promising source of bioenergy and high value-added products that could help face the rising demand for energy and raw materials. However, microalgae systems entail consumption of materials and energy, with potential environmental, economic, and social costs. While environmental and economic impacts have been analyzed in the literature, the social dimension has been barely explored. In this article, social life cycle assessment (S-LCA) is applied to identify the main contributors to social risks. Methodology In this paper, an approach is proposed and applied to exploit outcomes of a Life Cycle Costing (LCC) study as the input data to model and evaluate the potential social impacts of microalgae biorefinery schemes. Such approach helps ensure the consistency between the economic and social assessments, while facilitating data gathering in a context of data scarcity typical of an emerging technology. Priority levels for stakeholder categories and impact subcategories have been assigned based on the literature. Workers and local communities were identified as the stakeholders with the highest priority, related to impact subcategories such as health and safety issues and fair salary for the former and local employment for the latter. An inventory model was built, using PSILCA database v2.0 Starter and openLCA software, together with cost estimates from an LCC using real data from experiments at lab and pilot scale. Results According to the results, the main contribution to social risks of the biogas production is expected to be linked to the anaerobic digestion. Some contributors, both from the cultivation and the anaerobic digestion, are basic chemicals production and market public sewage activities, together with civil engineering and construction, and metal products and machinery production. The geographical distribution of risks depends on the stakeholder category and impact subcategory. Since many activities of the value chain are assumed to happen in Spain, a non-negligible part of social risks take place there. However, other countries with minor contributions to total working time are found to have the highest social risk for subcategories and indicators such as fatal accidents. Finally, three scenarios have been compared, considering production in a Chinese, French, or Spanish context, which lead to significant differences. Conclusions This study aims to highlight the importance of assessing the different dimensions of sustainability in a coherent manner. Furthermore, it provides useful information and hints on main contributors to potential social impacts in the microalgae-based sector based on available information and generic S-LCA databases, and their dependence on geographical locations of the life cycle activities. Despite limitations, conducting such social assessments with available tools is key to better understand the need for widening the scope of sustainability studies
Flux-pump induced degradation of for dissipative cat qubits
No full text24 pages, 13 figuresInternational audienceDissipative stabilization of cat qubits autonomously corrects for bit flip errors by ensuring that reservoir-engineered two-photon losses dominate over other mechanisms inducing phase flip errors. To describe the latter, we derive an effective master equation for an asymmetrically threaded SQUID based superconducting circuit used to stabilize a dissipative cat qubit. We analyze the dressing of relaxation processes under drives in time-dependent Schrieffer-Wolff perturbation theory for weakly anharmonic bosonic degrees of freedom, and in numerically exact Floquet theory. We find that spurious single-photon decay rates can increase under the action of the parametric pump that generates the required interactions for cat-qubit stabilization. Our analysis feeds into mitigation strategies that can inform current experiments, and the methods presented here can be extended to other circuit implementations
Nanopore Sequencing as a Cutting-Edge Technology for Medulloblastoma Classification
No full textInternational audienceBackground: Medulloblastoma (MB) is one of the most prevalent embryonal malignant brain tumors. Current classification organizes these tumors into four molecular subgroups (WNT, SHH, Group 3, and Group 4 MB). Recently, a comprehensive classification has been established, identifying numerous subtypes, some of which exhibit a poor prognosis. It is critical to establish effective subtyping methods for accurate diagnosis and patient's management that strikes a delicate balance between improving outcomes and minimizing the risk of comorbidities.Methods: We evaluated the ability of Nanopore sequencing to provide clinically relevant methylation and copy number profiles of MB. Nanopore sequencing was applied to an EPIC cohort of 44 frozen MB, benchmarked against the gold standard EPIC array, and further evaluated on an integrated diagnosis cohort of 116 MB.Results: Most MB of both cohorts (42/44; 95.5% and 106/116; 91.4% respectively) were accurately subgrouped by Nanopore sequencing. Employing Flongle flow cells for 18 MB allowed a more rapid and cost-effective analysis, with 94.4% (17/18) being correctly classified. Nanopore sequencing enabled us to accurately subtype 28/30 (93.3%) MB.Conclusion: This study, conducted on the largest cohort of MB analyzed with Nanopore sequencing to date, establishes the proof of concept that this modern and innovative technology is well-suited for MB classification. Nanopore sequencing demonstrates a robust capacity for precise subtyping of MB, a critical advancement that holds significant potential for enhancing patient stratification in future clinical trials. Its ability to deliver quick and cost-effective results firmly establishes it as a game-changer in the field of MB classification
Phase Equilibrium Study of Ethane + Perfluorohexane System across Temperatures from (292.89 to 317.92) K and Pressures from (0.513 to 4.913) MPa
No full textInternational audienceThis study provides comprehensive experimental vapour-liquid equilibrium data for a system composed of perfluorohexane and ethane at four temperatures (292.89 to 317.92) K and pressures spanning from (0.513 to 4.913) MPa. The experimental investigation was achieved using a "static-analytic" equipment fitted with a capillary sampler for the equilibrium phases.The expanded uncertainties in the measurement of temperatures, pressures and mole fractions were determined to be within 0.04 K, 0.003 MPa and less than 0.03, respectively. The phase equilibrium data were successfully modelled via the phi-phi approach using two sets of thermodynamic models, i.e., the Peng-Robinson equation of state with the Wong-Sandler mixing rule or the Soave-Redlich-Kwong equation of state with the predictive Soave-Redlich-Kwong mixing rule. The parameters of both models were adjusted using the ordinary least-squares objective function. The PR-MC-WS-NRTL model slightly outperforms the SRK-MC-PSRK-NRTL model in representing experimental data, with both models showing minor differences and Bias P, Bias y and AAD y values within 1%, while AAD P values exceed 1% but remain nearly identical for both. A comparison of the VLE data for the C₂ H₆ + C₆ F₁₄ and the CO 2 + C 6 F 14 systems reveals that C₆ F₁₄ exhibits strong selectivity for C₂ H₆ over CO₂ at high pressures.</p
Impact of cathode contamination by sulfur dioxide on proton exchange membrane fuel cell performance: Experimental and modeling study
No full textInternational audienc
Stabilisation de qubits de chats avec des jonctions Josephson polarisées en tension dc
No full textA central challenge in quantum computing is realizing qubits with long coherence times and fast operations. This requires isolating the quantum system from its environment to prevent decoherence while enabling precise external control, two seemingly conflicting requirements. Driven-dissipative bosonic qubits challenge the idea that qubits must be isolated from their environment. In particular, by carefully engineering the drive and dissipation of a harmonic oscillator to mediate the exchange of photon pairs with its environment, we can encode quantum information in the oscillator's two metastable states. This approach dissipatively stabilizes the so-called cat qubit, which provides intrinsic exponential suppression of bit-flip errors with increasing number of photons, at the modest cost of a linear deterioration of phase flips. A key parameter in this strategy is the two-photon dissipation rate, which sets an upper bound on cat qubit gate speeds and must be large relative to any parasitic processes. In this thesis, we propose and theoretically study of a novel superconducting circuit design for the implementation of the dissipative cat qubit, the DC cat qubit. The proposed circuit replaces the perturbative effect of a periodic parametric pump to mediate the two-photon exchange, by the natural periodic evolution of a DC voltage biased Josephson junction. Compared to more conventional approaches based on parametric pumps, our simple design is predicted to showcase a two-photon dissipation rate larger than that of the pump-based cat qubit implementation, while dynamically averaging the usually resonant parasitic terms such as Kerr and cross Kerr nonlinearities. A key challenge in using DC-biased Josephson junctions is their susceptibility to unavoidable DC voltage noise, which is detrimental for the encoded cat states by causing long-term drifts of the cat qubit angle. In addition to addressing qubit stabilization, we propose a synchronization technique via injection locking, that can be seen as another type of driven dissipative mechanism, in an adapted version compatible with DC cat qubits. We demonstrate that introducing a weak injection AC signal to provide a phase reference to which the cat can lock, can effectively counteract the detrimental effects of DC voltage noise. The whole scheme is simulated without rotating-wave approximations, highlighting for the first time the amplitude of related oscillatory effects in cat-qubit stabilization schemes. This study lays the groundwork for the experimental realization of such a circuit. Beyond cat qubit stabilization, this thesis drives progress in employing driven-dissipative stabilization mechanisms and DC-biased Josephson junctions to engineer parametric interactions in superconducting circuits and autonomously correct for noise.Un défi central en informatique quantique est la réalisation de qubits avec des temps de cohérence longs et des opérations rapides. Cela nécessite d'isoler le système quantique de son environnement pour éviter la décohérence tout en permettant un contrôle externe précis, deux exigences apparemment contradictoires. Les qubits bosoniques dissipatifs pompés remettent en question l'idée selon laquelle les qubits doivent être isolés de leur environnement. En particulier, en concevant soigneusement l'excitation et la dissipation d'un oscillateur harmonique pour permettre un échange de paires de photons avec son environnement, il est possible d'encoder l'information quantique dans les deux états métastables de l'oscillateur. Cette approche stabilise de manière dissipative les qubits de chat, ce qui permet une suppression exponentielle intrinsèque du taux de bit-flip avec le nombre de photons, au prix modéré d'une détérioration linéaire du taux de phase-flip. Un paramètre clé dans cette stratégie est le taux de dissipation à deux photons, qui définit une limite supérieure pour la vitesse des portes du qubit-chat et doit être élevé par rapport à tout processus parasite. Dans cette thèse, nous proposons et étudions théoriquement un nouveau design de circuit supraconducteur pour la mise en œuvre du qubit chat dissipatif, le qubit de chat DC. Le circuit proposé remplace l'effet perturbatif d'une pompe paramétrique périodique pour médiatiser l'échange de deux photons, par l'évolution périodique naturelle d'une jonction Josephson biaisée en tension continu DC. Comparé aux approches plus conventionnelles basées sur des pompes paramétriques, notre conception simple devrait présenter un taux de dissipation à deux photons plus élevé que celui de la mise en œuvre du qubit-chat basé sur une pompe, tout en moyennant dynamiquement les termes parasites habituellement résonants tels que les non-linéarités de Kerr et de cross-Kerr. Un défi majeur lié à l'utilisation de jonctions Josephson polarisées en tension DC est leur sensibilité au bruit inévitable de la tension DC, qui est nuisible aux états du qubit chat en provoquant des dérives à long terme de l'angle de ce qubit. En plus d'adresser la stabilisation du qubit, nous proposons une technique de synchronisation par verrouillage d'injection, qui peut être vue comme un autre type de mécanisme dissipatif pompé, dans une version adaptée compatible avec les qubits de chat DC. Nous démontrons que l'introduction d'un faible signal AC d'injection afin de fournir une référence de phase à laquelle le chat peut se verrouiller, peut efficacement contrer les effets nuisibles du bruit de tension DC. L'ensemble du schéma est simulé sans approximations d'onde tournante, mettant en évidence pour la première fois l'amplitude des effets oscillatoires associés dans les schémas de stabilisation des qubits de chat. Cette étude pose les bases de la réalisation expérimentale d'un tel circuit. Au-delà de la stabilisation du qubit de chat, cette thèse fait progresser l'utilisation des mécanismes de stabilisation dissipative pompés et de jonctions Josephson polarisées en tension DC dans la conception des interactions paramétriques dans les circuits supraconducteurs et la correction autonome du bruit
Mise en scène hydrologique d'un deuxième abri gravé du bassin parisien : émergence de nouveaux symboles paléolithiques
No full textInternational audienceA second female sexual figuration has been found in a cramped cavity shelter in a quartzitic sandstone megaclast at Courdimanche, some 10 km from that recently described in the La Ségognole 3 shelter at Noisy-sur-Ecole. As in the latter, modifications to the quartzitic sandstone hosting the figuration had been undertaken to deliver water flows on demand, presumably to enhance its ‘power’. The Courdimanche figuration is a spectacular, annular, essentially natural structure with a sandstone protrusion at its centre. The encompassing shelter is engraved with a large motif of neat and deep grooves which evoke a phallus and several smaller convergent grooves evoking vulvar features: almost all point to the annulus.The proximity of the Courdimanche shelter to the La Ségognole shelter, both featuring modifications that enhance natural structures to form a sexual figuration, is noteworthy. The two sites are likely to have a cultural link (technological and possibly also spiritual) and thereby the same Magdalenian age as that attributed to the Ségognole 3 shelter by the style of the horse engraving associated with the sexual feature. Staging the sexual figuration by hydrological modifications, as at Ségognole 3, connects femininity with water. This is funda-mentally different from the engraved or sculpted static Palaeolithic feminine representations throughout southwestern Europe. We explore a territorial cultural identity that links water to the symbol of fertility: a semiological change that could indicate changes in the socio-economic functioning of regional groups.Une deuxième figuration sexuelle féminine a été découverte dans un abri exiguë à Courdimanche-sur-Essonne, à une dizaine de kilomètres de celle récemment décrite dans l'abri de La Ségognole 3 à Noisy-sur-École. La figuration de Courdimanche est une spectaculaire structure annulaire, essentiellement naturelle, avec une saillie de grès en son centre. Comme à La Ségognole, des modifications ont été apportées au grès quartzitique de l’abri pour créer un écoulement d'eau de la figuration et qui peut être provoqué par apport d’eau. Cet écoulement ajoute probablement une signification et une puissance supplémentaire à la figuration sexuelle. L'abri est gravé d'un motif de sillons profonds évoquant un grand phallus et de plusieurs sillons convergents moins profonds évoquant des figurations vulvaires : presque toutes ces gravures pointent vers la structure annulaire. L'abri de Courdimanche et La Ségognole sont remarquables pour avoir été modifiés pour mettre en valeur les structures naturelles d’une figuration sexuelle et favoriser un écoulement vulvaire. Les deux sites sont susceptibles d'avoir un lien culturel (technologique et peut-être aussi spirituel) et datent probablement du Magdalénien, âge attribué à l'abri de Ségognole 3 par le style de la gravure du cheval associée à l'élément sexuel. Les mises en scène des figurations sexuelles par des modifications hydrologiques relient la féminité à l'eau. Ces représentations sont fondamentalement différentes des représentations féminines statiques paléolithiques gravées ou sculptées dans toute l'Europe du Sud-Ouest. Nous explorons dans cette note une identité culturelle territoriale qui lie l'eau au symbole de la fertilité : une évolution sémiologique qui pourrait indiquer des changements dans le fonctionnement socio-économique des groupes régionaux
Identification de lois de comportement plasticité cristalline par jumeau numérique et apprentissage statistique
No full textStudying the plastic deformation of polycrystalline materials, such as commercially pure alpha-phase titanium, presents a significant challenge in materials mechanics. The mechanical properties of these materials are strongly influenced by their grain-scale microstructure, making it essential to develop models that can accurately capture local plastic deformation heterogeneities. To address the challenges associated with identifying these models using high-resolution local data, an innovative methodology is proposed, integrating multi-scale and multi-modal experimental data with numerical simulations in crystal plasticity.Advanced imaging techniques, such as X-ray Diffraction Contrast Tomography (DCT), enable the acquisition of accu-rate volumetric representations of the actual microstructure of polycrystalline materials. These data are subsequently employed in FFT-based simulations, allowing for the prediction of plastic deformation heterogeneities at micrometric res-olution. Unlike traditional approaches that rely on macroscopic predictions, this method directly compares numerical predictions with local experimental data obtained from techniques such as High-Resolution Digital Image Correlation (HR-DIC), Electron Backscatter Diffraction (EBSD), and DCT. This direct comparison of microscopic predictions within acceptable simulation times facilitates the identification process.Furthermore, the integration of statistical learning methods aims to accelerate these simulations by leveraging the image-based nature of the numerical predictions. This framework opens new perspectives for the identification of crystal plasticitylaws, taking into account the deformation heterogeneities within polycrystalline materials.L’étude de la déformation des matériaux polycristallins, à l’échelle fine, constitue un enjeu majeur en mécanique des matériaux. Les propriétés mécaniques de ces matériaux sont fortement influencées par la microstructure à l’échelle des grains, rendant essentiel le développement de modèles capables de capturer les hétérogénéités locales de déformation plastique. Pour répondre à ces défis, une méthodologie innovante est proposée, intégrant des données expérimentales multi-échelles et multimodales avec des simulations numériques en plasticité cristalline, avec une application de la méthode au titane commercialement pur de phase alpha.En utilisant des techniques d’imagerie avancées comme la tomographie par contraste de diffraction (DCT) par rayons X, il est possible d’obtenir une représentation volumique précise de la microstructure réelle des matériaux. Ce jumeau numérique de la microstructure peut être utilisé dans des simulations FFT, permettant de prédire les hétérogénéités de déformation plastique à une résolution micrométrique. Contrairement aux approches classiques, cette méthode repose sur une comparaison directe entre les prédictions numériques et les données expérimentales locales issues de tech-niques comme la Corrélation d’Images Numériques à Haute Résolution, l’imagerie EBSD et DCT, en termes de rotations de réseau cristallin et de déformations axiales.De plus, l’intégration de méthodes d’apprentissage statistique permet d’accélérer ces simulations en exploitant le caractère d’image des prédictions numériques. Ce cadre ouvre ainsi de nouvelles perspectives pour l’identification des lois deplasticité cristalline, en tenant compte des hétérogénéités de déformation au sein des matériaux polycristallins