A multiscale subgrid model for both free vortex flows and wall-bounded flows

A new subgrid-scale (SGS) model which has an adequate behavior in both vortical flows and wall-bounded flows is proposed. In wall-bounded flows with "wall-resolved" large eddy simulation (LES), the theory predicts that the SGS dissipation should vanish as y(+3) near the wall. In free vortex flows, one needs to have models which do not dissipate energy in the strongly vortical and essentially laminar part of the flow, e. g., in the vortex core regions. The wall adapting local eddy (WALE) viscosity model of Nicoud and Ducros (Flow, Turbul. Combust. 62, 183 (1999)] has the correct near-wall behavior. It is, however, demonstrated here that it produces values of effective eddy viscosity which are too high in vortical flows: this constitutes a major drawback for LES of vortex flows. On the other hand, the regularized variational multiscale models are suitable to simulate vortical flows as demonstrated by Cocle et al. [Complex Effects in LES (Springer, New York, 2007), p. 56], but they do not have a correct behavior in wall-bounded flows as shown by Jeanmart and Winckelmans [Phys. Fluids 19, 055110 (2007)]. The model presented here aims at combining the strengths of the two models: it is a multiscale model, thus acting on the high pass filtered LES field, and for which the SGS viscosity is evaluated using the WALE model, itself also computed using the high pass filtered field. Hence, this model is only active when there is locally a significant high wavenumber content in the flow and it has a natural near-wall damping behavior. The ability of this model to simulate vortex and wall-bounded flows is demonstrated on three test cases. The first case is the turbulent channel flow at Re-tau=395 and Re-tau=590. The second test concerns a counter-rotating four-vortex system at Re-Gamma=20 000. The third case concerns a two-vortex system in ground effect at Re-Gamma=20 000. It is shown that the model allows to perform successfully the LES of these flows with the proper dissipative behavior in both the near-wall and the vortical regions. (C) 2009 American Institute of Physics. [doi:10.1063/1.3241991

The use of thioglycolate to distinguish between 3' AP (apurinic/apyrimidinic) endonucleases and AP lyases.

Addition of thioglycolate and DEAE-Sephadex chromatography were used to analyze the cleavage of the C(3')-O-P bond 3' to AP (apurinic/apyrimidinic) sites in DNA and to distinguish between a mechanism of hydrolysis (which would allow the nicking enzyme to be called 3' AP endonuclease) or beta-elimination (so that the nicking enzyme should be called AP lyase). For this purpose, DNA labelled in the AP sites was first cleaved by rat-liver AP endonuclease, then with the 3' nicking catalyst in the presence of thioglycolate and the reaction products were analyzed on DEAE-Sephadex: deoxyribose-5-phosphate (indicating a 3' cleavage by hydrolysis) and the thioglycolate:unsaturated sugar-5-phosphate adduct (indicating a cleavage by beta-elimination) are well separated allowing to eventually easily discard the hypothesis of a hydrolytic process and the appellation of 3' AP endonuclease. We have shown that addition of thioglycolate to the unsaturated sugar resulting from nicking the C(3')-O-P bond 3' to AP sites by beta-elimination is an irreversible reaction. We have also shown that the thioglycolate must be present from the beginning of the reaction with the nicking catalyst to prevent the primary 5' product of the beta-elimination reaction from undergoing other modifications that complicate the interpretation of the results

The sampling-based dynamic procedure for LES : investigations using finite differences

The dynamic procedure for LES performed solely in physical space (i.e.,no Fourier transform) is considered. It amounts to a procedure working at the force (vector) level that is natural and quite general: it only requires a numerical tool for restriction of the discrete LES field and forces to a coarser level. It is here investigated using finite differences and with restriction done by sampling. It gives good results on flows with homogenous directions: Burger’s turbulence and homogeneous isotropic turbulence. Preliminary results on the turbulent channel flow are also presented: they are encouraging but not yet satisfactory (velocity profile underpredicted). The obtained profile of CΔ2 is found to have the proper near and far wall behaviors,but with too low amplitude. Further improvements are required: they might include some filtering (using tensor-product stencil-3 discrete filters, also iterated) prior to the sampling, to mitigate the aliasing effects due to the sampling; they might also require to modify the procedure itself, following what was done by others when using the classical procedure expressed at the force level

Scale dependence and asymptotic very high Reynolds number spectral behavior of multiscale subgrid models

This paper investigates the spectral response of recent multiscale subgrid models, all of eddy viscosity type, in large-eddy simulation (LES) of fully developed turbulence, from moderate to very high Reynolds (Re) number. The objective of this work is to provide useful results about the behavior of the subgrid scale (SGS) models and, in particular, their asymptotic behavior. Such information is indeed important for practitioners using LES to simulate truly high Reynolds number flows. Specifically, we consider LES of homogeneous isotropic turbulence at very high Re and where the LES cutoff (here the grid Delta) is taken well into the inertial range (i.e., Delta/eta >= 100 with eta the Kolmogorov scale). Large LES grids (128(3) and 256(3)) are also used in order to compare and attain the true asymptotic behavior of each SGS model, something not fully observable in LES on smaller grids. An analysis is also carried out to obtain the scale dependence of each model coefficient in the viscous range of turbulence using LES run on several grids and compared to direct numerical simulation. The results provide C for each model and for various Delta/eta. A convenient fit then also provides C/C-infinity. as a function of Delta/eta, where C-infinity is the asymptotic coefficient. The comparisons are supported using the evolution of resolved energy (global and spectrum), resolved enstrophy, and effective dissipation. It is shown that the multiscale models acting on the high wavenumber part of the LES field are indeed able to provide a significant kappa(-5/3) inertial subrange, yet it is always followed by an energy pileup effect also called "bottleneck." This effect is also characterized for the various models. (C) 2009 American Institute of Physics. [DOI:10.1063/1.3194302

Intranucleosomal localization of the AP endodeoxyribonuclease of rat liver chromatin

AbstractThe chromatin AP endodeoxyribonuclease of rat liver cells is located in the cores as well as in the linkers of the nucleosomes