Rotating Rayleigh–Bénard convection, the flow in a rotating fluid layer heated from below and cooled from above, is used to analyse the transition to the geostrophic regime of thermal convection. In ...the geostrophic regime, which is of direct relevance to most geo- and astrophysical flows, the system is strongly rotating while maintaining a sufficiently large thermal driving to generate turbulence. We directly simulate the Navier–Stokes equations for two values of the thermal forcing, i.e.
$Ra=10^{10}$
and
$Ra=5\times 10^{10}$
, at constant Prandtl number
$Pr=1$
, and vary the Ekman number in the range
$Ek=1.3\times 10^{-7}$
to
$Ek=2\times 10^{-6}$
, which satisfies both requirements of supercriticality and strong rotation. We focus on the differences between the application of no-slip versus stress-free boundary conditions on the horizontal plates. The transition is found at roughly the same parameter values for both boundary conditions, i.e. at
$Ek\approx 9\times 10^{-7}$
for
$Ra=1\times 10^{10}$
and at
$Ek\approx 3\times 10^{-7}$
for
$Ra=5\times 10^{10}$
. However, the transition is gradual and it does not exactly coincide in
$Ek$
for different flow indicators. In particular, we report the characteristics of the transitions in the heat-transfer scaling laws, the boundary-layer thicknesses, the bulk/boundary-layer distribution of dissipations and the mean temperature gradient in the bulk. The flow phenomenology in the geostrophic regime evolves differently for no-slip and stress-free plates. For stress-free conditions, the formation of a large-scale barotropic vortex with associated inverse energy cascade is apparent. For no-slip plates, a turbulent state without large-scale coherent structures is found; the absence of large-scale structure formation is reflected in the energy transfer in the sense that the inverse cascade, present for stress-free boundary conditions, vanishes.
Many geophysical and astrophysical phenomena are driven by turbulent fluid dynamics, containing behaviors separated by tens of orders of magnitude in scale. While direct simulations have made large ...strides toward understanding geophysical systems, such models still inhabit modest ranges of the governing parameters that are difficult to extrapolate to planetary settings. The canonical problem of rotating Rayleigh-Bénard convection provides an alternate approach - isolating the fundamental physics in a reduced setting. Theoretical studies and asymptotically-reduced simulations in rotating convection have unveiled a variety of flow behaviors likely relevant to natural systems, but still inaccessible to direct simulation. In lieu of this, several new large-scale rotating convection devices have been designed to characterize such behaviors. It is essential to predict how this potential influx of new data will mesh with existing results. Surprisingly, a coherent framework of predictions for extreme rotating convection has not yet been elucidated. In this study, we combine asymptotic predictions, laboratory and numerical results, and experimental constraints to build a heuristic framework for cross-comparison between a broad range of rotating convection studies. We categorize the diverse field of existing predictions in the context of asymptotic flow regimes. We then consider the physical constraints that determine the points of intersection between flow behavior predictions and experimental accessibility. Applying this framework to several upcoming devices demonstrates that laboratory studies may soon be able to characterize geophysically-relevant flow regimes. These new data may transform our understanding of geophysical and astrophysical turbulence, and the conceptual framework developed herein should provide the theoretical infrastructure needed for meaningful discussion of these results.
We propose that the collision rates of non-spherical particles settling in a turbulent environment are significantly higher than those of spherical particles of the same mass and volume. The ...theoretical argument is based on the dependence of the particle drag force on the particle orientation, thus varying gravitational settling velocities, which can remain different until contact due to the particle inertia. Therefore, non-spherical particles can collide with large relative velocities. Direct numerical simulations (DNS) of streamwise decaying isotropic turbulence seeded with small, heavy, rotationally symmetric ellipsoids of five different aspect ratios are performed to confirm these arguments. The motion of 21 million ellipsoids is tracked by a Lagrangian particle solver assuming creeping flow conditions and neglecting the influence of the particles on the flow. We find that ellipsoids collide considerably more often than spherical particles of the same volume and mass due to a drastically increased mean relative velocity at contact.
Renal epithelial cells are exposed to mechanical forces due to flow‐induced shear stress within the nephrons. Shear stress is altered in renal diseases caused by tubular dilation, obstruction, and ...hyperfiltration, which occur to compensate for lost nephrons. Fundamental in regulation of shear stress are primary cilia and other mechano‐sensors, and defects in cilia formation and function have profound effects on development and physiology of kidneys and other organs. We applied RNA sequencing to get a comprehensive overview of fluid‐shear regulated genes and pathways in renal epithelial cells. Functional enrichment‐analysis revealed TGF‐β, MAPK, and Wnt signaling as core signaling pathways up‐regulated by shear. Inhibitors of TGF‐β and MAPK/ERK signaling modulate a wide range of mechanosensitive genes, identifying these pathways as master regulators of shear‐induced gene expression. However, the main down‐regulated pathway, that is, JAK/STAT, is independent of TGF‐β and MAPK/ERK. Other up‐regulated cytokine pathways include FGF, HB‐EGF, PDGF, and CXC. Cellular responses to shear are modified at several levels, indicated by altered expression of genes involved in cell‐matrix, cytoskeleton, and glycocalyx remodeling, as well as glycolysis and cholesterol metabolism. Cilia ablation abolished shear induced expression of a subset of genes, but genes involved in TGF‐β, MAPK, and Wnt signaling were hardly affected, suggesting that other mechano‐sensors play a prominent role in the shear stress response of renal epithelial cells. Modulations in signaling due to variations in fluid shear stress are relevant for renal physiology and pathology, as suggested by elevated gene expression at pathological levels of shear stress compared to physiological shear.
In this study we applied RNA sequencing to get a comprehensive overview of fluid‐shear stress regulated genes and pathways in renal epithelial cells. Our results indicate that shear stress alters expression of genes involved in several cytokine signaling and cellular remodeling pathways, as well as glycolysis and cholesterol metabolism, which indicates that the cellular response to shear is modified at several levels.
When the classical Rayleigh–Bénard (RB) system is rotated about its vertical axis roughly three regimes can be identified. In regime I (weak rotation) the large-scale circulation (LSC) is the ...dominant feature of the flow. In regime II (moderate rotation) the LSC is replaced by vertically aligned vortices. Regime III (strong rotation) is characterized by suppression of the vertical velocity fluctuations. Using results from experiments and direct numerical simulations of RB convection for a cell with a diameter-to-height aspect ratio equal to one at $\mathit{Ra}\ensuremath{\sim} 1{0}^{8} \text{{\ndash}} 1{0}^{9} $ ($\mathit{Pr}= 4\text{{\ndash}} 6$) and $0\lesssim 1/ \mathit{Ro}\lesssim 25$ we identified the characteristics of the azimuthal temperature profiles at the sidewall in the different regimes. In regime I the azimuthal wall temperature profile shows a cosine shape and a vertical temperature gradient due to plumes that travel with the LSC close to the sidewall. In regimes II and III this cosine profile disappears, but the vertical wall temperature gradient is still observed. It turns out that the vertical wall temperature gradient in regimes II and III has a different origin than that observed in regime I. It is caused by boundary layer dynamics characteristic for rotating flows, which drives a secondary flow that transports hot fluid up the sidewall in the lower part of the container and cold fluid downwards along the sidewall in the top part.
We perform direct numerical simulations of rotating Rayleigh-Bénard convection (RRBC) of fluids with low (Pr = 0.1) and high (Pr ≈ 5) Prandtl numbers in a horizontally periodic layer with no-slip ...bottom and top boundaries. No-slip boundaries are known to actively promote the formation of plumelike vertical disturbances, through so-called Ekman pumping, that control the ambient flow at sufficiently high rotation rates. At both Prandtl numbers, we demonstrate the presence of competing large-scale vortices (LSVs) in the bulk. Strong buoyant forcing and rotation foster the quasi-two-dimensional turbulent state of the flow that leads to the upscale transfer of kinetic energy that forms the domain-filling LSV condensate. The Ekman plumes from the boundary layers are sheared apart by the large-scale flow, yet we find that their energy feeds the upscale transfer. Our results of RRBC simulations substantiate the emergence of large-scale flows in nature regardless of the specific details of the boundary conditions.
Drug-induced liver injury (DILI) is an adverse reaction caused by the intake of drugs of common use that produces liver damage. The impact of DILI is estimated to affect around 20 in 100,000 ...inhabitants worldwide each year. Despite being one of the main causes of liver failure, the pathophysiology and mechanisms of DILI are poorly understood. In the present study, we developed an ensemble learning approach based on different features (CMap gene expression, chemical structures, drug targets) to predict drugs that might cause DILI and gain a better understanding of the mechanisms linked to the adverse reaction.
We searched for gene signatures in CMap gene expression data by using two approaches: phenotype-gene associations data from DisGeNET, and a non-parametric test comparing gene expression of DILI-Concern and No-DILI-Concern drugs (as per DILIrank definitions). The average accuracy of the classifiers in both approaches was 69%. We used chemical structures as features, obtaining an accuracy of 65%. The combination of both types of features produced an accuracy around 63%, but improved the independent hold-out test up to 67%. The use of drug-target associations as feature obtained the best accuracy (70%) in the independent hold-out test.
When using CMap gene expression data, searching for a specific gene signature among the landmark genes improves the quality of the classifiers, but it is still limited by the intrinsic noise of the dataset. When using chemical structures as a feature, the structural diversity of the known DILI-causing drugs hampers the prediction, which is a similar problem as for the use of gene expression information. The combination of both features did not improve the quality of the classifiers but increased the robustness as shown on independent hold-out tests. The use of drug-target associations as feature improved the prediction, specially the specificity, and the results were comparable to previous research studies.
The force balance of rotating Rayleigh–Bénard convection regimes is investigated using direct numerical simulation on a laterally periodic domain, vertically bounded by no-slip walls. We provide a ...comprehensive view of the interplay between governing forces both in the bulk and near the walls. We observe, as in other prior studies, regimes of cells, convective Taylor columns, plumes, large-scale vortices (LSVs) and rotation-affected convection. Regimes of rapidly rotating convection are dominated by geostrophy, the balance between Coriolis and pressure-gradient forces. The higher-order interplay between inertial, viscous and buoyancy forces defines a subdominant balance that distinguishes the geostrophic states. It consists of viscous and buoyancy forces for cells and columns, inertial, viscous and buoyancy forces for plumes, and inertial forces for LSVs. In rotation-affected convection, inertial and pressure-gradient forces constitute the dominant balance; Coriolis, viscous and buoyancy forces form the subdominant balance. Near the walls, in geostrophic regimes, force magnitudes are larger than in the bulk; buoyancy contributes little to the subdominant balance of cells, columns and plumes. Increased force magnitudes denote increased ageostrophy near the walls. Nonetheless, the flow is geostrophic as the bulk. Inertia becomes increasingly more important compared with the bulk, and enters the subdominant balance of columns. As the bulk, the near-wall flow loses rotational constraint in rotation-affected convection. Consequently, kinetic boundary layers deviate from the expected behaviour from linear Ekman boundary layer theory. Our findings elucidate the dynamical balances of rotating thermal convection under realistic top/bottom boundary conditions, relevant to laboratory settings and large-scale natural flows.
We perform three-dimensional particle tracking measurements on droplets in a turbulent airflow. The droplets display the well-known preferential concentration of inertial particles, with an ...additional extreme clustering at the smallest scales. We explain this additional clustering phenomenon theoretically based on a Stokes-flow description of two spheres including their mutual hydrodynamic interaction and a perturbative small-inertia expansion.
PDF
