Surface-sampled simulations of turbulent flow at high Reynolds number

A new approach to turbulence simulation, based on a combination of large-eddy simulation (LES) for the whole flow and an array of non-space-filling quasi-direct numerical simulations (QDNS), which sample the response of near-wall turbulence to large-scale forcing, is proposed and evaluated. The technique overcomes some of the cost limitations of turbulence simulation, since the main flow is treated with a coarse-grid LES, with the equivalent of wall functions supplied by the near-wall sampled QDNS. Two cases are tested, at friction Reynolds number Re$_\tau$=4200 and 20,000. The total grid node count for the first case is less than half a million and less than two million for the second case, with the calculations only requiring a desktop computer. A good agreement with published DNS is found at Re$_\tau$=4200, both in terms of the mean velocity profile and the streamwise velocity fluctuation statistics, which correctly show a substantial increase in near-wall turbulence levels due to a modulation of near-wall streaks by large-scale structures. The trend continues at Re$_\tau$=20,000, in agreement with experiment, which represents one of the major achievements of the new approach. A number of detailed aspects of the model, including numerical resolution, LES-QDNS coupling strategy and sub-grid model are explored. A low level of grid sensitivity is demonstrated for both the QDNS and LES aspects. Since the method does not assume a law of the wall, it can in principle be applied to flows that are out of equilibrium.Comment: Author accepted version. Accepted for publication in the International Journal for Numerical Methods in Fluids on 26 April 201

Integrating Research Data Management into Geographical Information Systems

Ocean modelling requires the production of high-fidelity computational meshes upon which to solve the equations of motion. The production of such meshes by hand is often infeasible, considering the complexity of the bathymetry and coastlines. The use of Geographical Information Systems (GIS) is therefore a key component to discretising the region of interest and producing a mesh appropriate to resolve the dynamics. However, all data associated with the production of a mesh must be provided in order to contribute to the overall recomputability of the subsequent simulation. This work presents the integration of research data management in QMesh, a tool for generating meshes using GIS. The tool uses the PyRDM library to provide a quick and easy way for scientists to publish meshes, and all data required to regenerate them, to persistent online repositories. These repositories are assigned unique identifiers to enable proper citation of the meshes in journal articles.Comment: Accepted, camera-ready version. To appear in the Proceedings of the 5th International Workshop on Semantic Digital Archives (http://sda2015.dke-research.de/), held in Pozna\'n, Poland on 18 September 2015 as part of the 19th International Conference on Theory and Practice of Digital Libraries (http://tpdl2015.info/

Decolorization of synthetic dyes by laccase immobilized on epoxy-activated carriers

The Myceliophthora thermophila laccase was covalently immobilized on polymethacrylate-based polymers (Sepabeads EC-EP3 and Dilbeads NK) activated with epoxy groups. The enzyme immobilized on Sepabeads EC-EP3 exhibited notable activity (203 U/g) along with remarkably improved stability towards pH, temperature and storage time, but no increased resistance to organic solvents. In addition, the immobilized laccase also showed good operational stability, maintaining 84% of its initial activity after 17 cycles of oxidation of ABTS. The immobilized biocatalyst was applied to the decolorization of six synthetic dyes. Immobilized laccase retained 41% activity in the decolorization of Methyl Green in a fixed-bed reactor after five cycles. The features of these biocatalysts are very attractive for their application on the decolorization of dyes in the textile industry in batch and continuous fixed-bed bioreactors. To our knowledge, this is the first report on immobilization of laccase on Sepabeads carriers and its efficient dyes decolorization.We thank Drs. Moreno Daminati and Paolo Caimi (Resindion) and Vyasa Rajasekar (DilComplex) for providing us Sepabeads EC-EP3 and Dilbeads NK polymers, respectively. We are grateful to Ramiro Martínez (Novozymes A/S, Spain) for DeniLite II S samples. This material is based upon work founded by Spanish MEC (Projects VEM2004-08559 and CTQ2005-08925-C02-02/PPQ); European Union (Project NMP2-CT-2006-026456) and CSIC (Project 200580M121). Spanish MEC is also thanked for the post-doctoral fellowship (SB2004-0011) of Dr. A. Kunamneni and for the Ramon y Cajal contracts of Drs. S. Camarero and M. Alcalde.This material is based upon work financed by Spanish MEC (Projects VEM2004-08559 and CTQ2005-08925-C02-02/PPQ); European Union (Project NMP2-CT-2006-026456) and CSIC (Project 200580M121). Spanish MEC is also thanked for the post-doctoral fellowship (SB2004-0011) of Dr. A. Kunamneni and for the Ramon y Cajal contracts of Drs. S. Camarero and M. Alcalde.Peer reviewe

Engineered spider silk-based 2D and 3D materials prevent microbial infestation

Biofilm formation, especially of antimicrobiotic-resistant microbial strains, are a major problem in health care. Therefore, there is great interest in developing advanced materials that are selectively inhibiting microbial adhesion to surfaces, but at the same time promoting mammalian cell growth. In nature, some spider silks have evolved to repel microbes, a feature that could be used in biomaterials. To unravel how microbe repellence can be achieved in engineered spider silk, different recombinant spider silk proteins based on the consensus sequences of Araneus diadematus dragline silk proteins (fibroin 3 and 4) were processed into 2D-patterned films and 3D-hydrogels. Strikingly, protein structure characteristics on the nanoscale are the basis for the detected microbe-repellence. Designed spider silk materials promoted mammalian cell attachment and proliferation while inhibiting microbial infestation, demonstrating the great potential of these engineered spider silk-based materials as bio-selective microbial-resistant coatings in biomedical as well as technical applications

An improved quantitative measure of the tendency for volcanic ash plumes to form in water: implications for the deposition of marine ash beds

Laboratory experiments and numerical simulations have shown that volcanic ash particles immersed in water can either settle slowly and individually, or rapidly and collectively as particle-laden plumes. The ratio of timescales for individual and collective settling, in the form of analytical expressions, provides a dimensionless quantitative measure of the tendency for such plumes to grow and persist which has important implications for determining particle residence times and deposition rates. However, existing measures in the literature assume that collective settling obeys Stokes' law and is therefore controlled by the balance between gravitational forces and viscous drag, despite plume development actually being controlled by the balance between gravitational forces and inertial drag even in the absence of turbulence during early times. This paper presents a new measure for plume onset which takes into account the inertial drag-controlled (rather than viscous drag-controlled) nature of plume growth and descent. A parameter study comprising a set of numerical simulations of small-scale volcanic ash particle settling experiments highlights the effectiveness of the new measure and, by comparison with an existing measure in the literature, also demonstrates that the timescale of collective settling is grossly under-estimated when assuming that plume development is slowed by viscous drag. Furthermore, the formulation of the new measure means that the tendency for plumes to form can be estimated from the thickness and concentration of the final deposit; the magnitude and duration of particle flux across the water's surface do not need to be known. The measure therefore permits the residence times of particles in a large body of water to be more accurately and practically determined, and allows the improved interpretation of layers of volcaniclastic material deposited at the seabed

Alternative Oxidase Attenuates Cigarette Smoke-induced Lung Dysfunction and Tissue Damage

Cigarette smoke (CS) exposure is the predominant risk factor for the development of chronic obstructive pulmonary disease (COPD) and the third leading cause of death worldwide. We aimed to elucidate whether mitochondrial respiratory inhibition and oxidative stress are triggers in its etiology. In different models of CS exposure, we investigated the effect onlung remodeling and cell signaling of restoring mitochondrial respiratory electron flow using alternative oxidase (AOX), which bypasses the cytochrome segment of the respiratory chain. AOX attenuated CS-induced lung tissue destruction and loss of function in mice exposed chronically to CS for 9 months. It preserved the cell viability of isolated mouse embryonic fibroblasts treated with CS condensate, limited the induction of apoptosis, and decreased the production of reactive oxygen species (ROS). In contrast, the earlyphase inflammatory response induced by acute CS exposure of mouse lung, i.e., infiltration by macrophages and neutrophils and adverse signaling, was unaffected. The use of AOX allowed us to obtain novel pathomechanistic insights into CS-induced cell damage,mitochondrial ROS production, and lung remodeling. Our findings implicate mitochondrial respiratory inhibition as a key pathogenicmechanism of CS toxicity in the lung. We propose AOX as a novel tool to study CS-related lung remodeling and potentially to counteract CS-induced ROS production and cell damage

Soundness and completeness proofs by coinductive methods

We show how codatatypes can be employed to produce compact, high-level proofs of key results in logic: the soundness and completeness of proof systems for variations of first-order logic. For the classical completeness result, we first establish an abstract property of possibly infinite derivation trees. The abstract proof can be instantiated for a wide range of Gentzen and tableau systems for various flavors of first-order logic. Soundness becomes interesting as soon as one allows infinite proofs of first-order formulas. This forms the subject of several cyclic proof systems for first-order logic augmented with inductive predicate definitions studied in the literature. All the discussed results are formalized using Isabelle/HOL’s recently introduced support for codatatypes and corecursion. The development illustrates some unique features of Isabelle/HOL’s new coinductive specification language such as nesting through non-free types and mixed recursion–corecursion