Visualizing transport structures of time-dependent flow fields

This article focuses on the transport characteristics of physical properties in fluids-in particular, visualizing the finite-time transport structure of property advection. Applied to a well-chosen set of property fields, the proposed approach yields structures giving insights into the underlying flow's dynamic processes.     

Probabilistic Marching Cubes

In this paper we revisit the computation and visualization of equivalents to isocontours in uncertain scalar fields. We model uncertainty by discrete random fields and, in contrast to previous methods, also take arbitrary spatial correlations into account. Starting with joint distributions of the random variables associated to the sample locations, we compute level crossing probabilities for cells of the sample grid. This corresponds to computing the probabilities that the well‐known symmetry‐reduced marching cubes cases occur in random field realizations. For Gaussian random fields, only marginal density functions that correspond to the vertices of the considered cell need to be integrated. We compute the integrals for each cell in the sample grid using a Monte Carlo method. The probabilistic ansatz does not suffer from degenerate cases that usually require case distinctions and solutions of ill‐conditioned problems. Applications in 2D and 3D, both to synthetic and real data from ensemble simulations in climate research, illustrate the influence of spatial correlations on the spatial distribution of uncertain isocontours.     

Eicosapentaenoic and docosahexaenoic acid affect mitochondrial and peroxisomal fatty acid oxidation in relation to substrate preference

Decreased triacylglycerol synthesis within hepatocytes due to decreased diacylglycerol acyltransferase (DGAT) activity has been suggested to be an important mechanism by which diets rich in fish oil lower plasma triacylglycerol levels. New findings suggest that eicosapentaenoic acid (EPA), and not docosahexaenoic acid (DHA), lowers plasma triacylglycerol by increased mitochondrial fatty acid oxidation and decreased availability of fatty acids for triacylglycerol synthesis. To contribute to the understanding of the triacylglycerol-lowering mechanism of fish oil, the different metabolic properties of EPA and DHA were studied in rat liver parenchymal cells and isolated rat liver organelles. EPA-CoA was a poorer substrate than DHA-CoA for DGAT in isolated rat liver microsomes, and in the presence of EPA, a markedly lower value for the triacyl[³H]glycerol/diacyl[³H]glycerol ratio was observed. The distribution of [1-¹⁴C]palmitic acid was shifted from incorporation into secreted glycerolipids toward oxidation in the presence of EPA (but not DHA) in rat liver parenchymal cells. [1-¹⁴C]EPA was oxidized to a much greater extent than [1-¹⁴C]DHA in rat liver parenchymal cells, isolated peroxisomes, and especially in purified mitochondria. As the oxidation of EPA was more effective and sensitive to the CPT-I inhibitor, etomoxir, when measured in a combination of both mitochondria and peroxisomes, we hypothesized that both are involved in EPA oxidation, whereas DHA mainly is oxidized in peroxisomes. In rats, EPA treatment lowered plasma triacylglycerol and increased hepatic mitochondrial fatty acid oxidation and carnitine palmitoyltransferase (CPT)-I activity in both the presence and absence of malonyl-CoA. Whereas only EPA treatment increased the mRNA levels of CPT-I, DHA treatment increased the mRNA levels of peroxisomal fatty acyl-CoA oxidase and fatty acid binding protein more effectively than EPA treatment. In conclusion, EPA and DHA affect cellular organelles in relation to their substrate preference. The present study strongly supports the hypothesis that EPA, and not DHA, lowers plasma triacylglycerol by increased mitochondrial fatty acid oxidation.     

Evaluation of polycaprolactone − poly‐D,L‐lactide copolymer as biomaterial for breast tissue engineering

The potential of the copolymer polycaprolactone‐co‐ poly‐d ,l ‐lactic acid (PCLLA ) as a biomaterial for scaffold‐based therapy for breast tissue engineering applications was assessed. First, the synthesized PCLLA was evaluated for its processability by means of additive manufacturing (AM ). We found that the synthesized PCLLA could be fabricated into scaffolds with an overall gross morphology and porosity similar to that of polycaprolactone. The PCLLA scaffolds possessed a compressive Young's modulus (ca 46 kPa ) similar to that of native breast (0.5 ? 25 kPa ), but lacked thermal stability and underwent thermal degradation during the fabrication process. The PCLLA scaffolds underwent rapid degradation in vitro which was characterized by loss of the scaffolds' mechanical integrity and a drastic decrease in mass‐average molar mass (M _w) and number‐average molar mass (M _n) after 4 weeks of immersion in phosphate buffer solution maintained at 37 °C. The tin‐catalysed PCLLA scaffold was also found to have cytotoxic effects on cells. Although the initial mechanical properties of the PCLLA scaffolds generally showed potential for applications in breast tissue regeneration, the thermal stability of the copolymer for AM processes, biocompatibility towards cells and degradation rate is not satisfactory at this stage. Therefore, we conclude that research efforts should be geared towards fine‐tuning the copolymer synthesizing methods. © 2016 Society of Chemical Industry     

Accelerated Visualization of Dynamic Molecular Surfaces

Molecular surfaces play an important role in studying the interactions between molecules. Visualizing the dynamic behavior of molecules is particularly interesting to gain insights into a molecular system. Only recently it has become possible to interactively visualize dynamic molecular surfaces using ray casting techniques. In this paper, we show how to further accelerate the construction and the rendering of the solvent excluded surface (SES) and the molecular skin surface (MSS). We propose several improvements to reduce the update times for displaying these molecular surfaces. First, we adopt a parallel approximate Voronoi diagram algorithm to compute the MSS. This accelerates the MSS computation by more than one order of magnitude on a single core. Second, we demonstrate that the contour‐buildup algorithm is ideally suited for computing the SES due to its inherently parallel structure. For both parallel algorithms, we observe good scalability up to 8 cores and, thus, obtain interactive frame rates for molecular dynamics trajectories of up to twenty thousand atoms for the SES and up to a few thousand atoms for the MSS. Third, we reduce the rendering time for the SES using tight‐fitting bounding quadrangles as rasterization primitives. These primitives also accelerate the rendering of the MSS. With these improvements, the interactive visualization of the MSS of dynamic trajectories of a few thousand atoms becomes for the first time possible. Nevertheless, the SES remains a few times faster than the MSS.     

Electro-oxidative abatement of low-salinity reverse osmosis membrane concentrates

The present study encompasses the application of electrolysis as novel treatment technique for the abatement of low-salinity concentrates generated from the filtrative treatment of water and wastewater. Four different materials have been tested as anode for a number of brine samples in a one-compartment electrolytic cell in galvanostatic mode. It was found that PbO(2) and SnO(2) anodes initiated electrochemical precipitation through an increase of the pH. Boron-doped diamond (BDD) and RuO(2) anodes successfully oxidised the pollutants in the brine and a linear removal of total ammonia nitrogen (TAN) and chemical oxygen demand (COD) was observed during the first phase of oxidation. Oxidation was predominantly achieved through indirect hypochlorite bulk oxidation; the higher oxidation rate and extent for the BDD anode was attributed to the higher selectivity and activity of the latter. Overall performance of the BDD electrode was higher than for RuO(2): higher rates for TAN (17.9 vs. 13.5mg/Ah) and COD (74.5 vs. 20.0mg/Ah) removal as well as higher overall current efficiencies (35.2% vs. 14.5%). Extensive colour removal was observed for both anodes (>90% decrease in absorbency at 455 nm).     

Stabilization of a chitinase from Serratia marcescens by Gly->Ala and Xxx->Pro mutations

This paper describes attempts to increase the kinetic stabilityof chitinase B from Serratia marcescens (ChiB) by the introductionof semi-automatically designed rigidifying mutations of theGlyAla and XxxPro type. Of 15 single mutants, several displayedsignificant increases in thermal stability, whereas most mutantsshowed minor effects. All mutations with non-marginal effectson stability clustered in a limited, surface-exposed regionof the enzyme, indicating that this region is involved in apartial unfolding process that triggers irreversible thermalinactivation (aggregation). A double mutant containing two stabilizingmutations in this region (G188A, A234P) displayed a 10-foldincrease in half-life at 57°C and a 4.2°C increase inapparent T_m. These results show that entropic stabilizationworks well for ChiB and they pinpoint a region whose unfoldingmay be crucial for the kinetic stability of this enzyme. Received June 18, 2003; revised September 3, 2003; accepted September 12, 2003.     

Zinc and cadmium accumulation among and within populations of the pseudometalophytic species Arrhenatherum elatius: implications for phytoextraction

The purpose of this study was to investigate, under standard conditions, the bioaccumulation of zinc and cadmium in Arrhenatherum elatius, a perennial grass with a high biomass production. Nine populations of three different origins were tested: three metallicolous populations (mpop); three non-metallicolous populations (nmpop) and three populations developing on soils moderately metal polluted (medpop). We have found that bioaccumulation differs among these populations, with nmpop accumulating significantly more zinc (p<0.0001) and cadmium (p<0.0001) than mpop. Indeed, we have observed a concentration of 325 mg kg(-1) of zinc and 52 mg kg(-1) of cadmium in A. elatius shoots from mpop, whereas in nmpop, the concentration reached on average 524 mg kg(-1) zinc and 83 mg kg(-1) cadmium. In the same way, medpop accumulated as much zinc but more cadmium than nmpop. Moreover, the standard deviation of medpop was larger than the one for mpop and nmpop. Indeed, some A. elatius samples from medpop presented a high metal content whereas, others presented low concentrations in their shoots (ranging from 60 to 210 mg kg(-1) cadmium). Hence, these medpop exhibited a large variability among and within populations in accumulating zinc and cadmium in their shoots. Based on these results, the possibility of selecting A. elatius plants with the best accumulating capacity from medpop was proposed. We concluded that if the accumulation capacity is genetically controlled in A. elatius, this species fulfils this necessary condition for efficiently increasing species bioaccumulation by crossbreeding A. elatius plants with the higher accumulation capacity.