| 1. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
- Atzori, Marco, 1992-, et al.
(author)
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A new perspective on skin-friction contributions in adverse-pressure-gradient turbulent boundary layers
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Other publication (other academic/artistic)abstract
- For adverse-pressure-gradient turbulent boundary layers, the study of integral skin-friction contributions still poses significant challenges. Beyond questions related to the integration boundaries and the derivation procedure, which have been thoroughly investigated in the literature, an important issue is how different terms should be aggregated. The nature of these flows, which exhibit significant in-homogeneity in the streamwise direction, usually results in cancellation between several contributions with high absolute values. We propose a formulation of the identity derived by Fukagata, Iwamoto \& Kasagi (Phys. Fluids, vol. 14, 2002, pp. 73--76), which we obtained from the convective form of the governing equations. A new skin-friction contribution is defined, considering wall-tangential convection and pressure gradient together. This contribution is related to the evolution of the dynamic pressure in the mean flow. The results of the decomposition are examined for a broad range of pressure-gradient conditions and different flow-control strategies. We found that the new formulation of the identity allows to readily identify the different regimes of near-equilibrium conditions and approaching separation. It also provides a more effective description of control effects. A similar aggregation between convection and pressure-gradient terms is also possible for any other decomposition where in-homogeneity contributions are considered explicitly.
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| 3. |
- Atzori, Marco, et al.
(author)
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A new perspective on skin-friction contributions in adverse-pressure-gradient turbulent boundary layers
- 2023
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In: International Journal of Heat and Fluid Flow. - : Elsevier BV. - 0142-727X .- 1879-2278. ; 101
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Journal article (peer-reviewed)abstract
- For adverse-pressure-gradient turbulent boundary layers, the study of integral skin-friction contributions still poses significant challenges. Beyond questions related to the integration boundaries and the derivation procedure, which have been thoroughly investigated in the literature, an important issue is how different terms should be aggregated. The nature of these flows, which exhibit significant in-homogeneity in the streamwise direction, usually results in cancellation between several contributions with high absolute values. We propose a formulation of the identity derived by Fukagata et al. (2002), which we obtained from the convective form of the governing equations. A new skin-friction contribution is defined, considering wall-tangential convection and pressure gradient together. This contribution is related to the evolution of the dynamic pressure in the mean flow. The results of the decomposition are examined for a broad range of pressure-gradient conditions and different flow-control strategies. We found that the new formulation of the identity allows to readily identify the different regimes of near-equilibrium conditions and approaching separation. It also provides a more effective description of control effects. A similar aggregation between convection and pressure-gradient terms is also possible for any other decomposition where in-homogeneity contributions are considered explicitly.
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| 4. |
- Fan, Yitong, et al.
(author)
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Decomposition of the mean friction drag in adverse-pressure-gradient turbulent boundary layers
- 2020
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In: Physical Review Fluids. - : American Physical Society (APS). - 2469-990X. ; 5:11
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Journal article (peer-reviewed)abstract
- In this study, we exploit the Renard-Deck identity [J. Fluid Mech. 790, 339 (2016)] to decompose the mean friction drag in adverse-pressure-gradient turbulent boundary layers (APG-TBLs) into three components, associated with viscous dissipation, turbulence kinetic energy production, and spatial growth of the flow, respectively. We consider adverse-pressure-gradient turbulent boundary layers developing on flat plates and airfoils, with friction Reynolds numbers in the range 200 < Re-tau < 2000, and with Rotta-Clauser pressure-gradient parameters (beta) ranging from 0 to 50. The effects of Reynolds number, adverse pressure gradient, and the pressure-gradient history on the contributing components are individually investigated, and special attention is paid to the comparisons with zero-pressure-gradient turbulent boundary layers (ZPG-TBLs). Our results indicate that the inner peaks of the dissipation and production terms are located at y(+) approximate to 6 and y(+) approximate to 16.5, respectively, and their outer peaks scale with the 99% boundary-layer thickness (delta(99)), i.e., y/delta(99) approximate to 0.7 and 0.53, respectively. These results are independent of the friction Reynolds number, the magnitude of beta, and its development history. Moreover, the spatial-growth component is negative in the investigated APG-TBLs, and its magnitude increases with beta.
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| 5. |
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| 6. |
- Pozuelo, Ramon, et al.
(author)
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An adverse-pressure-gradient turbulent boundary layer with nearly constant beta similar or equal to 1.4 up to Re-theta similar or equal to 8700
- 2022
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In: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 939
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Journal article (peer-reviewed)abstract
- In this study, a new well-resolved large-eddy simulation of an incompressible near-equilibrium adverse-pressure-gradient (APG) turbulent boundary layer (TBL) over a flat plate is presented. In this simulation, we have established a near-equilibrium APG over a wide Reynolds-number range. In this so-called region of interest, the Rotta-Clauser pressure-gradient parameter beta exhibits an approximately constant value of around 1.4, and the Reynolds number based on momentum thickness reaches Re-theta = 8700. To the best of the authors' knowledge, this is to date the highest Re-theta achieved for a near-equilibrium APG TBL under an approximately constant moderate APG. We evaluated the self-similarity of the outer region using two scalings, namely the Zagarola-Smits and an alternative scaling based on edge velocity and displacement thickness. Our results reveal that outer-layer similarity is achieved, and the viscous scaling collapses the near-wall region of the mean flow in agreement with classical theory. Spectral analysis reveals that the APG displaces some small-scale energy from the near-wall to the outer region, an effect observed for all the components of the Reynolds-stress tensor, which becomes more evident at higher Reynolds numbers. In general, the effects of the APG are more noticeable at lower Reynolds numbers. For instance, the outer peak of turbulent-kinetic-energy (TKE) production is less prominent at higher Re. Although the scale separation increases with Re in zero-pressure-gradient TBLs, this effect becomes accentuated by the APG. Despite the reduction of the outer TKE production at higher Reynolds numbers, the mechanisms of energisation of large scales are still present.
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| 7. |
- Pozuelo, Ramon, 1991-, et al.
(author)
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New Insight Into The Spectra Of Turbulent Boundary Layers With Pressure Gradients.
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Other publication (other academic/artistic)abstract
- In this study, a new well-resolved large-eddy-simulation (LES) of an incompressible near-equilibrium adverse-pressure-gradient (APG) turbulent boundary layer (TBL) over a flat plate is presented. In this simulation, we have established a near-equilibrium APG over a wide Reynolds-number range. In this so-called region of interest (ROI), the Clauser–Rotta pressure-gradient parameter β exhibits an approximately constant value of around 1.4, and the Reynolds number based on momentum thickness reaches Reθ = 8700. To the authors’ knowledge, this is to date the highest Reθ achieved for a near-equilibrium APG TBL under an approximately constant moderate APG. We evaluated the self-similarity of the outer region using two scalings, namely the Zagarola–Smits and an alternative one based on edge velocity and displacement thickness. Our results reveal that outer-layer similarity is achieved, and the viscous scaling collapses the near-wall region of the mean flow in agreement with classical theory. Spectral analysis reveals that the APG displaces some small-scale energy from the near-wall to the outer region, an effect observed for all the components of the Reynolds-stress tensor, which becomes more evident at higher Reynolds numbers. Generally, the effects of the APG are more noticeable at lower Reynolds numbers. For instance, the outer peak of turbulent-kinetic-energy (TKE) production is less prominent at higher Re. While the scale separation increases with Re in zero-pressure-gradient (ZPG) TBLs, this effect becomes accentuated by the APG. Despite the reduction of the outer TKE production at higher Reynolds numbers, the mechanisms of energization of large scales are still present.
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| 8. |
- Pozuelo, Ramon, 1991-, et al.
(author)
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Spectra of near-equilibrium adverse-pressure-gradient turbulent boundary layers
- 2023
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In: Physical Review Fluids. - : American Physical Society (APS). - 2469-990X. ; 8:2
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Journal article (peer-reviewed)abstract
- With the availability of new high-Reynolds-number (Re) databases of turbulent bound-ary layers (TBLs) it has been possible to identify in detail certain regions of the boundary layer with more complex behavior. In this study we consider a unique database at moderately-high Re, with a nearconstant adverse pressure gradient (APG) [Pozuelo et al., J. Fluid Mech. 939, A34 (2022)], and perform spectral analysis of the Reynolds stresses, focusing on the streamwise component. We assess different regions of the APG TBL, comparing this case with the zero-pressure-gradient (ZPG) TBL, and identify the relevant scaling parameters as well as the contribution of the scales of different sizes. The small scales in the near-wall region up to the near-wall spectral peak have been found to scale using viscous units. In APG TBLs, the largest scales close to the wall have a better scaling with the boundary-layer thickness (899), and they are significantly affected by the APG. In the overlap and wake regions of the boundary layer, the small energetic scales exhibit a good scaling with the displacement thickness (8*) while the larger scales and the outer spectral peak are better scaled with the boundary-layer thickness. Also, note that the wall-normal location of the spectral outer peak scales with the displacement thickness rather than the boundary layer thickness. The various scalings exhibited by the spectra in APG TBLs are reported here, and shed light on the complex phenomena present in these flows of great scientific and technological importance.
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| 9. |
- Pozuelo, Ramón, 1991-
(author)
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Study of adverse-pressure-gradient effects on a flat-plate boundary layer at high Reynolds numbers
- 2022
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Doctoral thesis (other academic/artistic)abstract
- Turbulent boundary layers are present in many aspects of life, from the weather and wind currents to transportation, production of energy or mixing processes. Understanding turbulent motions can allow for an improvement and development of technical devices, techniques or diagnosis of phenomena where a fluid flow is in the turbulent regime. From the economical and environmental perspectives, knowledge of turbulent boundary layers may help to reduce the drag on aerodynamic surfaces in transportation, thus leading to a reduction in fuel consumption and emissions. It is also possible to enhance the production of energy from wind sources or the harvest of tidal energy. Otherturbulent motions that have recently impacted society are those related to diffusion such as the transport of aerial diseases, or the motions of air in the respiratory system. In all those examples, external pressure gradients or those produced by the curvature of wall surfaces affect the turbulent structures and thus, the outputs that we study such as drag, transport of substances, energetic output, etc. A relevant case is that of adverse pressure gradient, which enhances the wall-normal convection and redistributes the turbulent energy across the turbulent boundary later. In this work, we study a canonical case of an adverse-pressure-gradient turbulent boundary layer, which is the flow over a flat plate, under near-equilibrium adverse-pressure-gradient conditions. We have extended the previous datasets on flat-plate boundary layers under adverse pressure gradients which were obtained at low Reynolds numbers, with a new numerical simulation reaching high Reynolds numbers, comparable to those of experimental campaigns. This new data set allowed us to study both adverse-pressure-gradient and Reynolds-number effects, where the thicker boundary layer exhibits a clear separation of turbulent scales. The influence of the size of the domain and the wider turbulent scales are analyzed through a set of turbulent channel-flow simulations and the spectral analysis of the Reynolds stresses in high Reynolds numbers turbulent boundary layers. The impact of the wider scales was analyzed and scaling factors were found for different regions of the spectra of the Reynolds stresses. In particular, we propose a new scaling for the energy of the small scales that have been advected to the outer region of the boundary layer.
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| 10. |
- Pozuelo, Ramon, et al.
(author)
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Widest scales in channel flow at Reτ = 550
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Other publication (other academic/artistic)abstract
- The widest scales in turbulent channel flows are studied through the use of three periodic channel-flow simulations at friction Reynolds number Reτ=550. The length and height of the channels are the same in all cases (Lx/h=8π and Ly/h=2 respectively), while the width is progressively doubled: Lz/h = {4π, 8π, 16π}. The domain width has an effect on the turbulence statistics of a similar order as the error of convergence. Note that a channel flow similar to the smaller one from Del Álamo, Jiménez, Zandonade & Moser (J.~Fluid Mech., vol. 500, 2004, pp. 135--144), which was averaged over a very long time, was used for the comparison of the results. The one-dimensional spanwise spectrum of the streamwise velocity is performed with the aim of assessing the domain-size effect on the widest scales. Our results indicate that 90% of the total streamwise energetic fluctuations is recovered without a significant influence of the size of the domain. The remaining 10% of the energy reflects that the widest scales in the outer layer are the ones most significantly affected by the spanwise length of the domain.
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