Some Atmospheric Processes Governing the Large-Scale Tropical Circulation in Idealized Aquaplanet Simulations

International audienceThe large-scale tropical atmospheric circulation is analyzed in idealized aquaplanet simulations using an atmospheric general circulation model. Idealized sea surface temperatures (SSTs) are used as lower-boundary conditions to provoke modifications of the atmospheric general circulation. Results show that 1) an increase in the meridional SST gradients of the tropical region drastically strengthens the Hadley circulation intensity, 2) the presence of equatorial zonal SST anomalies weakens the Hadley cells and reinforces the Walker circulation, and 3) a uniform SST warming causes small and nonsystematic changes of the Hadley and Walker circulations. In all simulations, the jet streams strengthen and move equatorward as the Hadley cells strengthen and become narrower.Some relevant mechanisms are then proposed to interpret the large range of behaviors obtained from the simulations. First, the zonal momentum transport by transient and stationary eddies is shown to modulate the eddy-driven jets, which causes the poleward displacements of the jet streams. Second, it is found that the Hadley circulation adjusts to the changes of the poleward moist static energy flux and gross moist static stability, associated with the geographical distribution of convection and midlatitude eddies. The Walker circulation intensity corresponds to the zonal moist static energy transport induced by the zonal anomalies of the turbulent fluxes and radiative cooling. These experiments provide some hints to understand a few robust changes of the atmospheric circulation simulated by ocean–atmosphere coupled models for future and past climates

Some Atmospheric Processes Governing the Large-Scale Tropical Circulation in Idealized Aquaplanet Simulations

International audienceThe large-scale tropical atmospheric circulation is analyzed in idealized aquaplanet simulations using an atmospheric general circulation model. Idealized sea surface temperatures (SSTs) are used as lower-boundary conditions to provoke modifications of the atmospheric general circulation. Results show that 1) an increase in the meridional SST gradients of the tropical region drastically strengthens the Hadley circulation intensity, 2) the presence of equatorial zonal SST anomalies weakens the Hadley cells and reinforces the Walker circulation, and 3) a uniform SST warming causes small and nonsystematic changes of the Hadley and Walker circulations. In all simulations, the jet streams strengthen and move equatorward as the Hadley cells strengthen and become narrower.Some relevant mechanisms are then proposed to interpret the large range of behaviors obtained from the simulations. First, the zonal momentum transport by transient and stationary eddies is shown to modulate the eddy-driven jets, which causes the poleward displacements of the jet streams. Second, it is found that the Hadley circulation adjusts to the changes of the poleward moist static energy flux and gross moist static stability, associated with the geographical distribution of convection and midlatitude eddies. The Walker circulation intensity corresponds to the zonal moist static energy transport induced by the zonal anomalies of the turbulent fluxes and radiative cooling. These experiments provide some hints to understand a few robust changes of the atmospheric circulation simulated by ocean–atmosphere coupled models for future and past climates

A high-resolution flux-matrix model describes the spread of diseases in a spatial network and the effect of mitigation strategies

Propagation of an epidemic across a spatial network of communities is described by a variant of the SIR model accompanied by an intercommunity infectivity matrix. This matrix is estimated from fluxes between communities, obtained from cell-phone tracking data recorded in the USA between March 2020 and February 2021. We apply this model to the SARS-CoV-2 pandemic by fitting just one global parameter representing the frequency of interaction between individuals. We find that the predicted infections agree reasonably well with the reported cases. We clearly see the effect of “shelter-in-place” policies introduced at the onset of the pandemic. Interestingly, a model with uniform transmission rates produces similar results, suggesting that the epidemic transmission was deeply influenced by air travel. We then study the effect of alternative mitigation policies, in particular restricting long-range travel. We find that this policy is successful in decreasing the epidemic size and slowing down the spread, but less effective than the shelter-in-place policy. This policy can result in a pulled wave of infections. We express its velocity and characterize the shape of the traveling front as a function of the epidemiological parameters. Finally, we discuss a policy of selectively constraining travel based on an edge-betweenness criterion.journal articl

Modèles de l'architecture du chromosome et lien avec la régulation de l'expression génétique

Increasing evidences suggest that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space. Furthermore, functional structures can result from the particular folding of the chromosome. These can be rather compact bundle-like aggregates that prevent the access to DNA, or in contrast, open coil configurations with several (presumably) globular clusters like transcription factories. Such phenomena have in common to result from the binding of divalent proteins that can bridge regions sometimes far away on the DNA sequence. The physical system consisting of the chromosome interacting with divalent proteins can be very complex. As such, most of the mechanisms responsible for chromosome folding and for the formation of functional structures have remained elusive.Using methods from statistical physics, we investigated models of chromosome architecture. A common denominator of our approach has been to represent the chromosome as a polymer with bending rigidity and consider its interaction with a solution of DNA-binding proteins. Structures entailed by the binding of such proteins were then characterized at the thermodynamical equilibrium. Furthermore, we complemented theoretical results with Brownian dynamics simulations, allowing to reproduce more of the biological complexity.The main contributions of this thesis have been: (i) to provide a model for the existence of transcrip- tion factories characterized in vivo with fluorescence microscopy; (ii) to propose a physical basis for a conjectured regulatory mechanism of the transcription involving the formation of DNA hairpin loops by the H-NS protein as characterized with atomic-force microscopy experiments; (iii) to propose a physical model of the chromosome that reproduces contacts measured in chromosome conformation capture (CCC) experiments. Consequences on the regulation of transcription are discussed in each of these studies.Plusieurs indices suggèrent que le repliement du chromosome et la régulation de l’expression génétique sont étroitement liés. Par exemple, la co-expression d’un grand nombre de gènes est favorisée par leur rapprochement dans l’espace cellulaire. En outre, le repliement du chromosome permet de faire émerger des structures fonctionnelles. Celles-ci peuvent être des amas condensés et fibrillaires, interdisant l’accès à l’ADN, ou au contraire des configurations plus ouvertes de l’ADN avec quelques amas globulaires, comme c’est le cas avec les usines de transcription. Bien que dissemblables au premier abord, de telles structures sont rendues possibles par l’existence de protéines bivalentes, capable d’apparier des régions parfois très éloignées sur la séquence d’ADN. Le système physique ainsi constitué du chromosome et de protéines bivalentes peut être très complexe. C’est pourquoi les mécanismes régissant le repliement du chromosome sont restés majoritairement incompris.Nous avons étudié des modèles d’architecture du chromosome en utilisant le formalisme de la physique statistique. Notre point de départ est la représentation du chromosome sous la forme d’un polymère rigide, pouvant interagir avec une solution de protéines liantes. Les structures résultant de ces interactions ont été caractérisées à l’équilibre thermodynamique. De plus, nous avons utilisé des simulations de dynamique Brownienne en complément des méthodes théoriques, car elles permettent de prendre en considération une plus grande complexité dans les phénomènes biologiques étudiés.Les principaux aboutissements de cette thèse ont été : (i) de fournir un modèle pour l’existence des usines de transcriptions caractérisées in vivo à l’aide de microscopie par fluorescence ; (ii) de proposer une explication physique pour une conjecture portant sur un mécanisme de régulation de la transcription impliquant la formation de boucles d’ADN en tête d’épingle sous l’effet de la protéine H-NS, qui a été émise suite à l’observation de ces boucles au microscope à force atomique ; (iii) de proposer un modèle du chromosome qui reproduise les contacts mesurés à l’aide des techniques Hi-C. Les conséquences de ces mécanismes sur la régulation de la transcription ont été systématiquement discutées

Les changements de la circulation atmosphérique tropicale et conséquences lors du changement climatique

Les variations de la circulation tropicale de grande échelle lors du changement climatique peuvent avoir d'importantes conséquences en terme d'impact sur les activités humaines. Dans un premier temps nous étudions la circulation atmosphérique tropicale méridienne, dans les différents modèles climatiques couplés. Lors du réchauffement climatique, nous trouvons que les circulations méridiennes de Hadley et les jets subtropicaux sont significativement déplacés vers les pôles, et que l'intensité de ces circulations diminue faiblement lors du changement climatique. Dans une seconde partie, des simulations utilisant le GCM LMDZ4 dans différentes configurations, montrent que l'intensité et le déplacement des cellules de Hadley sont reliés au changement uniforme de température de mer mais aussi au changement des gradients méridionaux de température. Enfin, on montre que les changements de circulation de Hadley peuvent alors avoir un impact significatif sur la rétroaction de la vapeur d'eau.PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Sci.Terre recherche (751052114) / SudocSudocFranceF

Phase Behavior of DNA in the Presence of DNA-Binding Proteins

International audienc

Phase behaviour of DNA in presence of DNA-binding proteins

20 pages, 9 figures, accepted for publication at The Biophysical JournalInternational audienceTo characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of the DNA collapse. For physiologically relevant values of the DNA-protein affinity, this collapse gives rise to a biphasic regime with a dense and a dilute phase; the corresponding phase diagram was computed. Using an approach based on Hamiltonian paths, we show that the dense phase has either a molten globule or a crystalline structure, depending on the DNA bending rigidity, which is influenced by the ionic strength. These results are valid at the thermodynamical equilibrium and should therefore be consistent with many biological processes, whose characteristic timescales range typically from 1 ms to 10 s. Our model may thus be applied to biological phenomena that involve DNA-binding proteins, such as DNA condensation with crystalline order, which occurs in some bacteria to protect their chromosome from detrimental factors; or transcription initiation, which occurs in clusters called transcription factories that are reminiscent of the dense phase characterized in this study