Asymptotic Dynamics of High Dynamic Range Stratified Turbulence.

Direct numerical simulations of homogeneous sheared and stably stratified turbulence are considered to probe the asymptotic high dynamic range regime suggested by Gargett et al. J. Fluid Mech. 144, 231 (1984)10.1017/S0022112084001592 and Shih et al. J. Fluid Mech. 525, 193 (1999)10.1017/S0022112004002587. We consider statistically stationary configurations of the flow that span three decades in dynamic range defined by the separation between the Ozmidov length scale L_{O}=sqrt[ε/N^{3}] and the Kolmogorov length scale L_{K}=(ν^{3}/ε)^{1/4}, up to Re_{b}≡(L_{O}/L_{K})^{4/3}=ε/(νN^{2})∼O(1000), where ε is the mean turbulent kinetic energy dissipation rate, ν is the kinematic viscosity, and N is the buoyancy frequency. We isolate the effects of Re_{b}, particularly on irreversible mixing, from the effects of other flow parameters of stratified and sheared turbulence. Specifically, we evaluate the influence of dynamic range independent of initial conditions. We present evidence that the flow approaches an asymptotic state for Re_{b}⪆300, characterized both by an asymptotic partitioning between the potential and kinetic energies and by the approach of components of the dissipation rate to their expected values under the assumption of isotropy. As Re_{b} increases above 100, there is a slight decrease in the turbulent flux coefficient Γ=χ/ε, where χ is the dissipation rate of buoyancy variance, but, for this flow, there is no evidence of the commonly suggested Γ∝Re_{b}^{-1/2} dependence when 100≤Re_{b}≤1000.This work was funded by the U.S. Office of Naval Research via grant N00014-15-1-2248. High performance computing resources were provided through the U.S. Department of Defense High Performance Computing Modernization Program by the Army Engineer Research and Development Center, the Army Research Laboratory and the Navy DSRC under Frontier Project FP-CFD-FY14- 007. The research activity of C.P.C. is supported by EPSRC Programme Grant EP/K034529/1 entitled `Mathematical Underpinnings of Stratified Turbulence'

Testing the assumptions underlying ocean mixing methodologies using direct numerical simulations

AbstractDirect numerical simulations of stratified turbulence are used to test several fundamental assumptions involved in the Osborn, Osborn–Cox, and Thorpe methods commonly used to estimate the turbulent diffusivity from field measurements. The forced simulations in an idealized triply periodic computational domain exhibit characteristic features of stratified turbulence including intermittency and layer formation. When calculated using the volume-averaged dissipation rates from the simulations, the vertical diffusivities inferred from the Osborn and Osborn–Cox methods are within 40% of the value diagnosed using the volume-averaged buoyancy flux for all cases, while the Thorpe-scale method performs similarly well in the simulation with a relatively large buoyancy Reynolds number (Reb ≃ 240) but significantly overestimates the vertical diffusivity in simulations with Reb &lt; 60. The methods are also tested using a limited number of vertical profiles randomly selected from the computational volume. The Osborn, Osborn–Cox, and Thorpe-scale methods converge to their respective estimates based on volume-averaged statistics faster than the vertical diffusivity calculated directly from the buoyancy flux, which is contaminated with reversible contributions from internal waves. When applied to a small number of vertical profiles, several assumptions underlying the Osborn and Osborn–Cox methods are not well supported by the simulation data. However, the vertical diffusivity inferred from these methods compares reasonably well to the exact value from the simulations and outperforms the assumptions underlying these methods in terms of the relative error. Motivated by a recent theoretical development, it is speculated that the Osborn method might provide a reasonable approximation to the diffusivity associated with the irreversible buoyancy flux.</jats:p

Robust identification of dynamically distinct regions in stratified turbulence

We present a new robust method for identifying three dynamically distinct regions in a stratified turbulent flow, which we characterise as quiescent flow, intermittent layers and turbulent patches. The method uses the cumulative filtered distribution function of the local density gradient to identify each region. We apply it to data from direct numerical simulations of homogeneous stratified turbulence, with unity Prandtl number, resolved on up to $8192\times 8192\times 4096$ grid points. In addition to classifying regions consistently with contour plots of potential enstrophy, our method identifies quiescent regions as regions where \unicode[STIX]{x1D716}/\unicode[STIX]{x1D708}N^{2}\sim O(1), layers as regions where \unicode[STIX]{x1D716}/\unicode[STIX]{x1D708}N^{2}\sim O(10) and patches as regions where \unicode[STIX]{x1D716}/\unicode[STIX]{x1D708}N^{2}\sim O(100). Here, \unicode[STIX]{x1D716} is the dissipation rate of turbulence kinetic energy, \unicode[STIX]{x1D708} is the kinematic viscosity and $N$ is the (overall) buoyancy frequency. By far the highest local dissipation and mixing rates, and the majority of dissipation and mixing, occur in patch regions, even when patch regions occupy only 5 % of the flow volume. We conjecture that treating stratified turbulence as an instantaneous assemblage of these different regions in varying proportions may explain some of the apparently highly scattered flow dynamics and statistics previously reported in the literature.The research activities of G.D.P. and S.dB.K. were funded by the US Office of Naval Research via grant N00014-15-1-2248. Additional support to G.D.P. and S.dB.K. was provided from the UK Engineering and Physical Sciences Research Council grant EP/K034529/1 entitled ‘Mathematical Underpinnings of Stratified Turbulence’, which also funds the research activity of J.R.T. and C.P.C. H.S. gratefully acknowledges the award of a Crighton Fellowship at the Department of Applied Mathematics & Theoretical Physics, University of Cambridge. High-performance computing resources were provided through the US Department of Defense High Performance Computing Modernization Program by the Army Engineer Research and Development Center and the Army Research Laboratory under Frontier Project FP-CFD-FY14-007.This is the author accepted manuscript. The final version is available from Cambridge University Press via https://doi.org/10.1017/jfm.2016.61

Circumcision for prevention against HIV: marked seasonal variation in demand and potential public sector readiness in Soweto, South Africa

The public sector delivery of male circumcision in the only public sector hospital in Soweto, South Africa was examined to gauge local capacity to deliver this procedure as an intervention for prevention of HIV acquisition. During the period from July 1998 to March 2006, approximately 360 procedures were performed per annum. Striking seasonal variations and the relatively few procedures performed may create challenges for program planning, if male circumcision is increased to a level required to have an impact on the incidence of HIV among this population

Desmodium mottle virus, the first legumovirus (genus Begomovirus) from East Africa

A novel bipartite legumovirus (genus Begomovirus, family Geminiviridae), that naturally infects the wild leguminous plant Desmodium sp. in Uganda, was molecularly characterized and named Desmodium mottle virus. The highest nucleotide identities for DNA-A, obtained from two field-collected samples, were 79.9% and 80.1% with the legumovirus, soybean mild mottle virus. DNA-B had the highest nucleotide identities (65.4% and 66.4%) with a typical non-legumovirus Old World begomovirus, African cassava mosaic virus. This is the first report of a legumovirus in East Africa and extends the known diversity of begomoviruses found infecting wild plants in this continent

Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax

The complex climatic and geological history of Southeast Asia has shaped this region’s high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods

SHANK proteins limit integrin activation by directly interacting with Rap1 and R-Ras

SHANK3, a synaptic scaffold protein and actin regulator, is widely expressed outside of the central nervous system with predominantly unknown function. Solving the structure of the SHANK3 N-terminal region revealed that the SPN domain is an unexpected Ras-association domain with high affinity for GTP-bound Ras and Rap G-proteins. The role of Rap1 in integrin activation is well established but the mechanisms to antagonize it remain largely unknown. Here, we show that SHANK1 and SHANK3 act as integrin activation inhibitors by sequestering active Rap1 and R-Ras via the SPN domain and thus limiting their bioavailability at the plasma membrane. Consistently, SHANK3 silencing triggers increased plasma membrane Rap1 activity, cell spreading, migration and invasion. Autism-related mutations within the SHANK3 SPN domain (R12C and L68P) disrupt G-protein interaction and fail to counteract integrin activation along the Rap1-RIAM-talin axis in cancer cells and neurons. Altogether, we establish SHANKs as critical regulators of G-protein signalling and integrin-dependent processes

Optimal Uses of Antiretrovirals for Prevention in HIV-1 Serodiscordant Heterosexual Couples in South Africa: A Modelling Study

Hallett et al use a mathematical model to examine the long-term impact and cost-effectiveness of different pre-exposure prophylaxis (PrEP) strategies for HIV prevention in serodiscordant couples

Short-Lived Trace Gases in the Surface Ocean and the Atmosphere

The two-way exchange of trace gases between the ocean and the atmosphere is important for both the chemistry and physics of the atmosphere and the biogeochemistry of the oceans, including the global cycling of elements. Here we review these exchanges and their importance for a range of gases whose lifetimes are generally short compared to the main greenhouse gases and which are, in most cases, more reactive than them. Gases considered include sulphur and related compounds, organohalogens, non-methane hydrocarbons, ozone, ammonia and related compounds, hydrogen and carbon monoxide. Finally, we stress the interactivity of the system, the importance of process understanding for modeling, the need for more extensive field measurements and their better seasonal coverage, the importance of inter-calibration exercises and finally the need to show the importance of air-sea exchanges for global cycling and how the field fits into the broader context of Earth System Science