A generic length-scale equation for geophysical turbulence models

A generalization of a class of differential length-scale equations typically used in second-order turbulence models for oceanic flows is suggested. Commonly used models, like the k-ε model and the Mellor-Yamada model, can be recovered as special cases of this generic model, and thus can be rationally compared. In addition, a method is proposed that yields a generalized framework for the calibration of the most frequently used class of differential length-scale equations. The generic model, calibrated with this method, exhibits a greater range of applicability than any of the traditional models. Stratified flows, plane mixing layers, and turbulence introduced by breaking surface waves are considered besides some classical test cases

Validation and intercomparison of two vertical-mixing schemes in the Mediterranean Sea

International audienceIn this study, two types of vertical turbulence closure models are tested in the Mediterranean Sea in a one-dimensional configuration. The numerical experiments are performed at different locations in the Mediterranean for which the year 2004 is simulated. The model results are then compared and validated with in-situ temperature observations. For the model simulations, initial profiles of temperature and salinity come from the ARGO (Array for Real-time Geostrophic Oceanography) profiles. The surface forcing (momentum, heat) is calculated from bulk formulae using 6-hourly atmospheric data from the European Center for Medium Range Weather Forecast (ECMWF). The vertical mixing schemes tested in this study are a second-order statistical model (k-?) and the non-local K-profile parameterization (KPP). Both schemes yield similar results in terms of reproducing the water column dynamics. A major source of discrepancy between model and observations comes from the uncertainties in the atmospheric forcing parameterization. At this point, net shortwave radiation data from NCEP atmospheric reanalysis has been used obtaining a more realistic Sea Surface Temperature (SST) compared with satellite observations for the summer months

A second-order, unconditionally positive, mass-conserving integration scheme for biochemical systems.

Biochemical systems are bound by two mathematically-relevant restrictions. First, state variables in such systems represent non-negative quantities, such as concentrations of chemical compounds. Second, biochemical systems conserve mass and energy. Both properties must be reflected in results of an integration scheme applied to biochemical models. This paper first presents a mathematical framework for biochemical problems, which includes an exact definition of biochemical conservation: elements and energy, rather than state variable units, are conserved. We then analyze various fixed-step integration schemes, including traditional Euler-based schemes and the recently published modified Patankar schemes, and conclude that none of these deliver unconditional positivity and biochemical conservation in combination with higher-order accuracy. Finally, we present two new fixed-step integration schemes, one first-order and one second-order accurate, which do guarantee positivity and (biochemical) conservatio

Global Regulation on microRNA in Hepatitis B Virus-Associated Hepatocellular Carcinoma

Recent work has revealed the causative links between deregulation of microRNAs (miRNAs) and cancer development. In hepatocellular carcinoma (HCC), aberrant expression of miRNAs has been observed, but the molecular mechanisms that contribute to such changes remains to be elucidated. Here, we reported the analysis of miRNA expression in 94 pairs of tumor and adjacent nontumor tissues from HBV-associated HCC in Chinese patients. We found miRNAs were aberrantly expressed in HCC tissues. To investigate the cause of such deregulation, we detected changes in DNA copy number by measuring locus-specific hybridization intensity, and found changes in expression of several miRNAs are correlated with genomic amplification or deletion. For example, the genomic regions of miR-30d and miR-151 were amplified in ∼50% of HCC tumor tissues, and the expressions of these miRNAs are significantly correlated with DNA copy number. We also employed cDNA microarray data, and provide evidence that key regulators of the miRNA biosynthetic pathway, including DROSHA, DGCR8, AGO1, and AGO2, are frequently overexpressed in HCC. This study provides molecular clues that may contribute to the global changes of miRNA expression in HCC. Copyright © 2011, Mary Ann Liebert, Inc.published_or_final_versio

Identification of Ag-acceptors in 111 ⁣^{111}\!Ag 111 ⁣^{111}\!Cd doped ZnTe and CdTe

Nominally undoped ZnTe and CdTe crystals were implanted with radioactive $^{111}\!$Ag, which decays to $^{111}\!$Cd, and investigated by photoluminescence spectroscopy (PL). In ZnTe, the PL lines caused by an acceptor level at 121 meV are observed: the principal bound exciton (PBE) line, the donor-acceptor pair (DAP) band, and the two-hole transition lines. In CdTe, the PBE line and the DAP band that correspond to an acceptor level at 108 meV appear. Since the intensities of all these PL lines decrease in good agreement with the half-life of $^{111}\!$Ag of 178.8 h, both acceptor levels are concluded to be associated with defects containing a single Ag atom. Therefore, the earlier assignments to substitutional Ag on Zn- and Cd-lattice sites in the respective II-VI semiconductors are confirmed. The assignments in the literature of the S$_1$, S$_2$, and S$_3$ lines in ZnTe and the X$\scriptstyle^\textrm{Ag}_{1}\,\,,$ X$\scriptstyle^\textrm{Ag}_{2}$/ C$\scriptstyle^\textrm{Ag}_{1}\,$ and C$\scriptstyle^\textrm{Ag}_{2}\,$ lines in CdTe to Ag-related defect complexes are not confirmed

Numerical issues of the Total Exchange Flow (TEF) analysis framework for quantifying estuarine circulation

For more than a century, estuarine exchange flow has been quantified by means of the Knudsen relations which connect bulk quantities such as inflow and outflow volume fluxes and salinities. These relations are closely linked to estuarine mixing. The recently developed Total Exchange Flow (TEF) analysis framework, which uses salinity coordinates to calculate these bulk quantities, allows an exact formulation of the Knudsen relations in realistic cases. There are however numerical issues, since the original method does not converge to the TEF bulk values for an increasing number of salinity classes. In the present study, this problem is investigated and the method of dividing salinities, described by MacCready et al. (2018), is mathematically introduced. A challenging yet compact analytical scenario for a well-mixed estuarine exchange flow is investigated for both methods, showing the proper convergence of the dividing salinity method. Furthermore, the dividing salinity method is applied to model results of the Baltic Sea to demonstrate the analysis of realistic exchange flows and exchange flows with more than two layers.</p

Baroclinic Interleaving Instability: A Second-Moment Closure Approach

Interleaving motions on a wide, baroclinic front are modeled using a second-moment closure to represent unresolved fluxes by turbulence and salt fingering. A linear perturbation analysis reveals two broad classes of unstable modes. First are scale-selective modes comparable with interleaving as observed in oceanic fronts. These correspond well with observations in some respects but grow by a very different mechanism, which ought to be easily distinguished in hydrographic profiles. The second mode type is the so-called ultraviolet catastrophe, which is expected to lead to steppy profiles even in the absence of interleaving. Both modes are driven by positive feedbacks between interleaving and the underlying small-scale mixing processes. Contrary to expectations, use of the second-moment closure in place of earlier empirical mixing models does not lead to improved agreement with observations.Keywords: Mixing, Diapycnal mixing, Instabilit

Seasonal adaptation of the thermal‐based two‐source energy balance model for estimating evapotranspiration in a semiarid tree‐grass ecosystem

© 2020 by the authors.The thermal-based two-source energy balance (TSEB) model has accurately simulated energy fluxes in a wide range of landscapes with both remote and proximal sensing data. However, tree-grass ecosystems (TGE) have notably complex heterogeneous vegetation mixtures and dynamic phenological characteristics presenting clear challenges to earth observation and modeling methods. Particularly, the TSEB modeling structure assumes a single vegetation source, making it difficult to represent the multiple vegetation layers present in TGEs (i.e., trees and grasses) which have different phenological and structural characteristics. This study evaluates the implementation of TSEB in a TGE located in central Spain and proposes a new strategy to consider the spatial and temporal complexities observed. This was based on sensitivity analyses (SA) conducted on both primary remote sensing inputs (local SA) and model parameters (global SA). The model was subsequently modified considering phenological dynamics in semi-arid TGEs and assuming a dominant vegetation structure and cover (i.e., either grassland or broadleaved trees) for different seasons (TSEB-2S). The adaptation was compared against the default model and evaluated against eddy covariance (EC) flux measurements and lysimeters over the experimental site. TSEB-2S vastly improved over the default TSEB performance decreasing the mean bias and root-mean-square-deviation (RMSD) of latent heat (LE) from 40 and 82 W m−2 to −4 and 59 W m−2, respectively during 2015. TSEB-2S was further validated for two other EC towers and for different years (2015, 2016 and 2017) obtaining similar error statistics with RMSD of LE ranging between 57 and 63 W m−2. The results presented here demonstrate a relatively simple strategy to improve water and energy flux monitoring over a complex and vulnerable landscape, which are often poorly represented through remote sensing models.The research received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 721995. It was also funded by Ministerio de Economía y Competitividad through FLUXPEC CGL2012-34383 and SynerTGE CGL2015-G9095-R (MINECO/FEDER, UE) projects. The research infrastructure at the measurement site in Majadas de Tiétar was partly funded through the Alexander von Humboldt Foundation, ELEMENTAL (CGL 2017-83538-C3-3-R, MINECO-FEDER) and IMAGINA (PROMETEU 2019; Generalitat Valenciana).Peer reviewe