Dérivation des électrons photosynthétiques par des médiateurs de type quinone.

Photosynthesis can be views as the conversion of carbon dioxide and water into organic matter and dioxygen. Used by algae, plants or some bacteria, photosynthesis efficiency is limited because only 4% of light energy is converted into chemical energy. Under high light conditions, this can induce serious damages of the photosynthetic machinery. Besides, if considering the current environmental context, this limitation is an opportunity to use the part of not converted energy to generate some useable electricity. The aim of the work developed in this manuscript is thus to create an additional pathway for derivating the photosynthetic electrons flow. In this way, the system damages are expected to be reduced under hight light conditions as well as some photocurrent to be generated. This is why an experimental set-up involving carbon working electrode and some quinone type redox mediators has been developed. The quinone ability to accept some electrons from Photosystem II has been studied by the mean of fluorescence techniques. Their ability to be re-oxidised at the carbon electrode surface has been investigated by cyclic voltametry. As a conclusion, the best quinones (selected after the fluorescence investigations) are DCBQ and PPBQ and correspond to photocurrent values about several µA.cm-2. A correlation between experimental data and theoretical predictions helped us to best understand the photosynthetic electrons derivation pathway and to evidence concomitant phenomenon like poisoning and quinone partition effects.La photosynthèse consiste en la conversion photo-induite du dioxyde de carbone et de l'eau en matière organique et en dioxygène. Utilisée par les algues, les plantes ou certaines bactéries, la photosynthèse est pourtant intrinsèquement bridée puisque seulement 4 % de l'énergie lumineuse sont convertis en énergie chimique. Sous forte irradiation, ceci peut engendrer une dénaturation de l'appareil photosynthétique. Par ailleurs, dans le contexte environnemental actuel, cette limitation représente également une opportunité d'utiliser l'énergie non convertie sous forme d'énergie électrique. Le travail présenté dans ce manuscrit a donc pour but de créer une voie secondaire d'écoulement des électrons photosynthétiques excédentaires afin de réduire l'endommagement du système sous forte irradiation et de les transcrire sous la forme d'un photo-courant. C'est pourquoi un système impliquant une électrode collectrice de carbone et des médiateurs redox de type quinone a été envisagé. La capacité acceptrice de certaines quinones, connues pour être de bons accepteurs du Photosystème II, a été évaluée au moyen d'études de fluorescence. La facilité de restitution des électrons dérivés par les quinones réduites a été quant à elle étudiée par électrochimie. Au bilan, les meilleures quinones (DCBQ, PPBQ) permettent d'obtenir des photo-courants de l'ordre de quelques µA.cm-2. La corrélation entre données expérimentales et théorie a également permis de mieux cerner le mécanisme de dérivation des électrons photosynthétiques par les quinones exogènes mais aussi de mettre en évidence des effets d'empoisonnement et/ou de perte d'accepteur dans les membranes

FRET theoretical predictions concerning freely diffusive dyes inside spherical container: how to choose the best pair?

FRET has been massively used to see if biomolecules were bounded or not by labelling both biomolecules by one dye of a FRET pair. This should give a digital answer to the question (fluorescence of the acceptor: high FRET efficency: molecules associated, fluorescence of the donor: low FRET efficency: molecules dissociated). This has been used, inter alia, at the single-molecule scale in containers, such as liposomes. One perspective of the field is to reduce the container’s size to study the effect of confinement on binding. The problem is that if the two dyes are encapsulated inside a small liposome, they could have a significant probability to be close one from the other one (and thus to undergo a high FRET efficiency event without binding). This is why we suggest here a theoretical model which gives mean FRET efficiency as a function of liposome radius (the model applies to any spherical container) and Förster radius to help the experimentalist to choose their experimental set-up. Besides, the influence of side effect on mean FRET efficiency has been studied as well. We show here that if this “background FRET” is most of the time non-quantitative, it can remain significant and which makes data analysis trickier. We could show as well that if this background FRET obviously increases when liposome radius decreases, this variation was lower than the one which could be expected because of side effect. We show as well the FRET efficiency function distribution which let the experimentalist know the probability to get one FRET efficiency value

ANR BARESAFE Réduction des incertitudes sur les limites de stabilité de systèmes dynamiques complexes

Une méthode numérique précise et efficace est proposée pour la simulation de corps déformables interagissant avec un écoulement incompressible. Les équations de Navier-Stokes, sont discrétisées temporellement et spatialement à l'aide respectivement d'un schéma d'ordre quatre de Runge-Kutta et par des différences finies compactes. Grâce à l'utilisation d'un maillage uniforme, nous proposons un nouveau solveur direct au quatrième ordre pour l'équation de Poisson, permettant de garantir la contrainte d'incompressibilité au niveau du zéro machine sur une grille à pas d'espace optimale. L'introduction d'un corps déformable et mobile dans l'écoulement de fluide est réalisée au moyen d'une méthode de pénalisation de volume. Une loi de contrôle efficace de la courbure d'un poisson anguilliforme nageant vers un objectif prescrite est proposée. La méthode numérique développée prouve son efficacité et précision tant dans le cas de la nage du poisson mais aussi plus généralement dans le cas d'un grand nombre de problèmes d'interactions fluide-structure

Couplages de codes de calcul scientifique pour l’étude des interactions fluide structure en présence d’écoulements

L’appréhension de la complexité de certains phénomènes couplés multi-physiques constitue un défi à relever. La voie du couplage de codes qui consiste à faire communiquer entre eux des outils mono-disciplinaires semble prometteuse. Effectuer un calcul couplé revient à faire communiquer les deux milieux à travers une ou plusieurs interfaces communes. Le mécanisme d’un calcul couplé dynamique instationnaire est décrit puis illustré au travers de quelques exemples

Vortex-induced vibrations of an elasticallymounted cylinderwith lowmass-ratio at RE=3900

The present paper deals with the numerical study of vortex-induced vibrations (VIV) of an elastically mounted cylinder in a cross flow with uniform inflow. It is well known that, in the case of low mass-damping, three distinct types of transverse amplitude response can be observed depending on the range of the reduced velocity. However, the accurate numerical simulation of the VIV amplitudes at the lock-in upper branch remains a great challenge. Moreover, few studies deal with the investigation of the hysteretic loop due to the jump between the initial excitation branch and the upper branch. Here, we propose to compute the transverse motion of the structure at a Reynolds number equal to 3900 Large Eddy Simulation. The Navier-Stokes equations are solved on a moving and deforming grid by means of an Arbitrary Lagrangian Eulerian (ALE) co-located finite volume method for unstructured meshes. An iterative algorithm is used at each time step based on Newton’s or fixed point method. This algorithm uses convergent explicit predictions of the coupled fluid structure system and sub-cycling is involved to get convergence towards the implicit solution of the fully coupled system. A criterion based on the structure velocity is used to stop the numerical sub-cycling process. First, we compare the transverse amplitude response of the cylinder for various reduced velocities with the DNS results obtained by Lucor et al. (2005) for zero structural damping and a mass ration equal to 2. Next, the experimental data of Hover et al. (1998) are considered to demonstrate the ability of the present solver to predict the VIV response for lowmass-damping

Biomolecular Binding under Confinement: Statistical Predictions of Steric Influence in Absence of Long-Distance Interactions

We propose a theoretical model for the influence of confinement on biomolecular binding at the single-molecule scale at equilibrium, based on the change of the number of microstates (localization and orientation) upon reaction. Three cases are discussed: DNA sequences shorter and longer than the single strain DNA Kuhn length and spherical proteins, confined into a spherical container (liposome, droplet, etc.). The influence of confinement is found to be highly dependent on the molecular structure and significant for large molecules (relative to container size)

LES of cross flow induced vibrations in square normal cylinder array

Large eddy simulations (LES) of a single phase water flow through square normal tube bundle at Reynolds numbers from 2000 to 6000 is performed to investigate the fluid-elastic instability. A single cylinder is allowed to oscillate in one degree of freedom (1-DOF) in flow normal direction, similar as in experiments. The fluid-structure coupling is simulated using the Arbitrary Lagrangian-Eulerian (ALE) apporach. The sub-grid scale turbulence is modeled using standard Smagorinsky's eddy-viscosity model. The LES results show good agreement with experimental results in terms of the response frequency and damping ratio of the cylinder. The dynamic case simulations are compared with static cases over the range of Reynolds numbers by means of the probe velocity spectra and pressure profiles on the cylinder surface

Impact of the Coverage of Aptamers on a Nanoparticle on the Binding Equilibrium and Kinetics between Aptamer and Protein

Knowledge of the interaction between aptamer and protein is integral to the design and development of aptamer-based biosensors. Nanoparticles functionalized with aptamers are commonly used in these kinds of sensors. As such, studies into how the number of aptamers on the nanoparticle surface influence both kinetics and thermodynamics of the binding interaction are required. In this study, aptamers specific for interferon gamma (IFN-γ) were immobilized on the surface of gold nanoparticles (AuNPs), and the effect of surface coverage of aptamer on the binding interaction with its target was investigated using fluorescence spectroscopy. The number of aptamers were adjusted from an average of 9.6 to 258 per particle. The binding isotherm between AuNPs-aptamer conjugate and protein was modeled with the Hill-Langmuir equation, and the determined equilibrium dissociation constant (K′D) decreased 10-fold when increasing the coverage of aptamer. The kinetics of the reaction as a function of coverage of aptamer were also investigated, including the association rate constant (kon) and the dissociation rate constant (koff). The AuNPs-aptamer conjugate with 258 aptamers per particle had the highest kon, while the koff was similar for AuNPs-aptamer conjugates with different surface coverages. Therefore, the surface coverage of aptamers on AuNPs affects both the thermodynamics and the kinetics of the binding. The AuNPs-aptamer conjugate with the highest surface coverage is the most favorable in biosensors considering the limit of detection, sensitivity, and response time of the assay. These findings deepen our understanding of the interaction between aptamer and target protein on the particle surface, which is important to both improve the scientific design and increase the application of aptamer-nanoparticle based biosensor

Vibrations d'un cylindre induites par détachement tourbillonnaire en régime sous-critique

Les vibrations induites par le sillage d'un cylindre seul oscillant librement sous l'effet d'un écoulement transverse en régime sous-critique sont modélisées par simulation des grandes échelles. Le système couplé fluide structure est résolu par une méthode itérative. La branche supérieure de réponse ainsi que l'intermittence vers la branche inférieure et l'hysteresis vers la branche initiale sont examinées pour différents nombres de Scruton, vitesses réduites et rapports de masse. Des comparaisons sont effectuées avec des données numériques et expérimentales de la littérature

Couplage de codes appliqué à la simulation de l’accrochage

La présente étude est consacrée à la simulation des oscillations transverses d’un cylindre rigide, non amorti, monté sur supports élastiques et soumis à un écoulement à faible nombre de Reynolds. Des calculs couplés fluide structure basés sur une procédure de couplage de codes sont réalisés pour caractériser le comportement du cylindre au voisinage de l’accrochage et les résultats des simulations sont comparés à des données de la littérature obtenues dans des configurations similaires