The dam-break problem for viscous fluids in the high-capillary-number limit

Experiments were undertaken to investigate dam-break flows where a finite volume of highly viscous fluid (glucose with viscosity μ ≈ 350 Pa s) maintained behind a lock gate was released into a horizontal or inclined flume. The resulting sequence of flow-depth profiles was tracked using a three-dimensional visualization system. In the low-Reynolds-number and high-capillary-number limits, analytical solutions can be obtained from the Navier-Stokes equations using lubrication theory and matched asymptotic expansions. At shallow slopes, similarity solutions can also be worked out. While the variation in the front position scaled with time as predicted by theory for both horizontal and sloping flumes, there was a systematic delay in the front position observed. Moreover, taking a closer look at the experimental flow-depth profiles shows that they were similar, but they noticeably deviated from the theoretical similarity form for horizontal planes. For sloping beds, the flow-depth profile is correctly predicted provided that different scalings are used at shallow and large slope

The dam-break problem for concentrated suspensions of neutrally buoyant particles

This paper addresses the dam-break problem for particle suspensions, that is, the flow of a finite volume of suspension released suddenly down an inclined flume. We were concerned with concentrated suspensions made up of neutrally buoyant non-colloidal particles within a Newtonian fluid. Experiments were conducted over wide ranges of slope, concentration and mass. The major contributions of our experimental study are the simultaneous measurement of local flow properties far from the sidewalls (velocity profile and, with lower accuracy, particle concentration) and macroscopic features (front position, flow depth profile). To that end, the refractive index of the fluid was adapted to closely match that of the particles, enabling data acquisition up to particle volume fractions of 60 %. Particle migration resulted in the blunting of the velocity profile, in contrast to the parabolic profile observed in homogeneous Newtonian fluids. The experimental results were compared with predictions from lubrication theory and particle migration theory. For solids fractions as large as 45 %, the flow behaviour did not differ much from that of a homogeneous Newtonian fluid. More specifically, we observed that the velocity profiles were closely approximated by a parabolic form and there was little evidence of particle migration throughout the depth. For particle concentrations in the 52-56 % range, the flow depth and front position were fairly well predicted by lubrication theory, but taking a closer look at the velocity profiles revealed that particle migration had noticeable effects on the shape of the velocity profile (blunting), but had little impact on its strength, which explained why lubrication theory performed well. Particle migration theories (such as the shear-induced diffusion model) successfully captured the slow evolution of the velocity profiles. For particle concentrations in excess of 56 %, the macroscopic flow features were grossly predicted by lubrication theory (to within 20 % for the flow depth, 50 % for the front position). The flows seemed to reach a steady state, i.e. the shape of the velocity profile showed little time dependenc

Gas Exchange, Stem Water Potential and Xylem Flux on Some Grapevine Cultivars Affected by Esca Disease

The effect of esca disease on gas exchange, stem water potential and xylem flux of adult grapevines of CabernetSauvignon, Sangiovese and Trebbiano cultivars was studied over three growing seasons. Water relations weremeasured at véraison and cluster ripening on three types of vines: i) healthy (control); ii) symptomatic and iii)apparently healthy in the year of measurements but that had showed esca symptoms in the previous season. Xylemflux was determined on cane segments by perfusion using a tracing dye before and after the appearance of escasymptoms. Esca induced a marked reduction (about 70%) in carbon assimilation and stomatal conductance,especially in Cabernet Sauvignon and Sangiovese. Esca did not affect the stem water potential. Gas exchangeparameters measured before the symptoms appeared in plants affected by esca were similar to those of healthyplants. Measurements made one month before the appearance of the symptoms cannot be used as screening methodto determine whether the vine will show esca. No differences in dye translocation were found before the symptoms’appearance. However, a decrease in xylem flux was measured in symptomatic vines of Cabernet Sauvignon. Afterthe appearance of esca symptoms, only the Trebbiano had a lower xylem flux than the healthy vines

Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins

Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS). We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design

Calpionellid and calcareous nannofossil evolution and calcification across Tithonian-Berriasian interval (Tethys Ocean).

The Tithonian-Berriasian interval is characterized by the appearance of calpionellid and by a major calcareous nannofossil speciation episode: several genera and species first appear and evolve, showing an increase in diversity, abundance and calcification degree. Monte Pernice and Torre de Busi sections (Southern Alps, Italy) have been analyzed for calcareous nannofossil and calpionellid biostratigraphy, relative and absolute abundances and to reconstruct biogenic calcite palaeofluxes. Calcareous nannofossils have been investigated on simple smear slides and ultra-thin sections (7-8 \ub5m thick) calpionellids on the same thin sections (20-30 \u3bcm thick). All nannofossil specimens have been counted on 1 mm2 of ultra-thin section; all calpionellid specimens on 1 cm2 of thin sections to reconstruct paleofluxes. In the Tithonian- Berriasian interval all known calcareous nannofossil Zones and corresponding Subzones (Bralower et al., 1989) have been recognized. Chitinoidella, Crassicollaria and Calpionella Zones have been identified (Remane, 1986; Pop, 1994b; Reh\ue1kov\ue1 & Michal\uedk, 1997; Andreini et al., 2007). Quantitative calpionellid and nannofossil analyses point out major changes during the Tithonian \u2013 Berriasian interval: nannolith taxa (F.multicolumnatus, C.mexicana, P.beckmannii) increase in abundance, size and calcification degree in discrete steps across the Lower Tithonian, coeval with the occurrence of first calcified calpionellids (Tintinopsella). Nannoconids and calcified calpionellids (Crassicollaria, Calpionella, Remaniella) increase across the Tithonian/Berriasian boundary reaching lithogenetic abundances: the rise in high-calcified nannoconids roughly corresponds with the Acme of C. alpina spherical forms. The diversification and biomineralization of highly-calcified microplankton produced a major increase in pelagic carbonate sedimentation due to the onset of paleoenvrionmental conditions favorable to calcification

Calcareous Nannofossil and Calpionellid calcification events across Tithonian \u2013 Berriasian time interval and low latitudes paleoceanographic implications.

The Tithonian-Berriasian time interval is characterized by a major calcareous nannofossil speciation episode and by the appearance of calpionellid group: several genera and species first appear and evolve, showing an increase in diversity, abundance and particularly in calcification degree. This time interval is also characterized by a significant low latitudes increase of carbonate-rich sediments (Rosso ad Aptici fm. toward Maiolica fm.). Calcareous nannofossil and calpionellid biostratigraphy and absolute abundances have been performed on low latitudes selected sections in order to reconstruct biogenic calcite palaeofluxes. Calpionellid has been investigated on thin sections (25\u3bcm thick), while calcareous nannofossil on the same thinnered thin sections (up to 7\ub5m thick) used for calpionellid. All specimens have been counted on 1 cm2 of thin section or 1 mm2 of ultra-thin section respectively for calpionellid and calcareous nannofossil. Paleofluxes have been obtained integrating absolute abundance with single speciment mass weigh (10-12gr of calcareous carbonate) per area unit (cm2) per time unit (yr). Calcareous biogenic paleofluxes point out a link between the lithologic changes and calcified plankton evolution across the Tithonian \u2013 Berriasian interval. During Lower Tithonian (Rosso ad Aptici Fm.) a first calcification event is characterized by nannolith (F.multicolumnatus, C.mexicana, P.beckmannii) increase in abundance, size and calcification degree, followed by the occurrence of first calcified calpionellid (Tintinopsella). Across Upper Tithonian to Lower Berriasian (Rosso ad Aptici fm. \u2013 Maiolica transition and Maiolica fm.) a second bigger calcification event is characterized by a dramatic increase of nannoconid abundance and calcification degree reaching lithogenetic amounts, concomitant with a moderate abundance increase of calcified calpionellid (genera Crassicollaria, Calpionella, Remaniella). Linkages between calcareous nannofossil and calpionellid evolutions with geologic, palaeoceanographic or palaeoclimatic events are inferred. The diversification and biomineralization of high-calcified plankton produced a major increase in pelagic carbonate sedimentation due to the onset of paleoenvrionmental conditions favorable to calcification. The diversification and proliferation of nannolith and nannoconid, interpreted as inhabitants of the lower photic zone, might indicate the establishment of a thermocline/nutricline in the deep photic zone, suggesting the develope of oligotrophic and stable oceanic conditions. It is also suggested that Tithonian-Berriasian calcified plankton evolution could be controlled by a decrease in pCO2, due to decreased spreading rate and/or increased weathering rate (87Sr/86Sr) and cool climatic conditions, concomitant with a decrease in oceanic Mg/Ca ratio values. Both factors thermodynamically promoted low Mg-CaCO3 and CaCO3 biomineralization supporting calpionellid and calcareous nannofossil abundance and calcification rate increases

Predicting zinc binding at the proteome level

BACKGROUND: Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, for regulation of their activities or for structural purposes. Metal-binding properties remain difficult to predict as well as to investigate experimentally at the whole-proteome level. Consequently, the current knowledge about metalloproteins is only partial. RESULTS: The present work reports on the development of a machine learning method for the prediction of the zinc-binding state of pairs of nearby amino-acids, using predictors based on support vector machines. The predictor was trained using chains containing zinc-binding sites and non-metalloproteins in order to provide positive and negative examples. Results based on strong non-redundancy tests prove that (1) zinc-binding residues can be predicted and (2) modelling the correlation between the binding state of nearby residues significantly improves performance. The trained predictor was then applied to the human proteome. The present results were in good agreement with the outcomes of previous, highly manually curated, efforts for the identification of human zinc-binding proteins. Some unprecedented zinc-binding sites could be identified, and were further validated through structural modelling. The software implementing the predictor is freely available at: CONCLUSION: The proposed approach constitutes a highly automated tool for the identification of metalloproteins, which provides results of comparable quality with respect to highly manually refined predictions. The ability to model correlations between pairwise residues allows it to obtain a significant improvement over standard 1D based approaches. In addition, the method permits the identification of unprecedented metal sites, providing important hints for the work of experimentalists