The D-Grid Integration Project: How to Build a Grid for Different Communities

The Grid world is highly dynamic due to the appearance of new resources, easier access and new Grid applications. Moreover, an increasing number of scientific communities begins to realize that Grids will become an indispensable tool for modern science. However, the requirements of those communities often differ significantly from each other. Therefore, it is a particularly di±cult challenge to establish a national Grid infrastructure that serves as many communities as possible. To address this challenge, the German D-Grid has developed a concept that is based on development of independent Community Grids that are connected with a single integration project. Further, the process will involve several steps to consider dependencies between the various projects and their tasks. Presently, we are still at the beginning of the realization of a German Grid. Therefore in this paper, we first briefly explain this concept in this paper. Then we focus on the integration project and describe its tasks in more detail. This includes some first results and experiences that were achieved within the first year of the project. Finally, some plans for future steps are presented

Local Anisotropy of Fluids using Minkowski Tensors

Statistics of the free volume available to individual particles have previously been studied for simple and complex fluids, granular matter, amorphous solids, and structural glasses. Minkowski tensors provide a set of shape measures that are based on strong mathematical theorems and easily computed for polygonal and polyhedral bodies such as free volume cells (Voronoi cells). They characterize the local structure beyond the two-point correlation function and are suitable to define indices $0\leq \beta_\nu^{a,b}\leq 1$ of local anisotropy. Here, we analyze the statistics of Minkowski tensors for configurations of simple liquid models, including the ideal gas (Poisson point process), the hard disks and hard spheres ensemble, and the Lennard-Jones fluid. We show that Minkowski tensors provide a robust characterization of local anisotropy, which ranges from $\beta_\nu^{a,b}\approx 0.3$ for vapor phases to $\beta_\nu^{a,b}\to 1$ for ordered solids. We find that for fluids, local anisotropy decreases monotonously with increasing free volume and randomness of particle positions. Furthermore, the local anisotropy indices $\beta_\nu^{a,b}$ are sensitive to structural transitions in these simple fluids, as has been previously shown in granular systems for the transition from loose to jammed bead packs

Minkowski Tensors of Anisotropic Spatial Structure

This article describes the theoretical foundation of and explicit algorithms for a novel approach to morphology and anisotropy analysis of complex spatial structure using tensor-valued Minkowski functionals, the so-called Minkowski tensors. Minkowski tensors are generalisations of the well-known scalar Minkowski functionals and are explicitly sensitive to anisotropic aspects of morphology, relevant for example for elastic moduli or permeability of microstructured materials. Here we derive explicit linear-time algorithms to compute these tensorial measures for three-dimensional shapes. These apply to representations of any object that can be represented by a triangulation of its bounding surface; their application is illustrated for the polyhedral Voronoi cellular complexes of jammed sphere configurations, and for triangulations of a biopolymer fibre network obtained by confocal microscopy. The article further bridges the substantial notational and conceptual gap between the different but equivalent approaches to scalar or tensorial Minkowski functionals in mathematics and in physics, hence making the mathematical measure theoretic method more readily accessible for future application in the physical sciences

Gel-Electrophoresis and Diffusion of Ring-Shaped DNA

A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around the gel obstructions. This constitutes an extension of previous reptation tube treatments. It is shown that tension is essential for describing the dynamics in the presence of hernias. It is included in the model as long range interactions over stretched DNA regions. The mobility of ring-shaped DNA is found to saturate much as in the well-studied case of linear DNA. Experiments in polymer gels, however, show that the mobility drops exponentially with the DNA ring size. This is commonly attributed to dangling-ends in the gel that can impale the ring. The predictions of the present model are expected to apply to artificial 2D obstacle arrays (W.D. Volkmuth, R.H. Austin, Nature 358,600 (1992)) which have no dangling-ends. In the zero-field case an exact solution of the model steady-state is obtained, and quantities such as the average ring size are calculated. An approximate treatment of the ring dynamics is given, and the diffusion coefficient is derived. The model is also discussed in the context of spontaneous symmetry breaking in one dimension.Comment: 8 figures, LaTeX, Phys. Rev. E - in pres

Cell shape analysis of random tessellations based on Minkowski tensors

To which degree are shape indices of individual cells of a tessellation characteristic for the stochastic process that generates them? Within the context of stochastic geometry and the physics of disordered materials, this corresponds to the question of relationships between different stochastic models. In the context of image analysis of synthetic and biological materials, this question is central to the problem of inferring information about formation processes from spatial measurements of resulting random structures. We address this question by a theory-based simulation study of shape indices derived from Minkowski tensors for a variety of tessellation models. We focus on the relationship between two indices: an isoperimetric ratio of the empirical averages of cell volume and area and the cell elongation quantified by eigenvalue ratios of interfacial Minkowski tensors. Simulation data for these quantities, as well as for distributions thereof and for correlations of cell shape and volume, are presented for Voronoi mosaics of the Poisson point process, determinantal and permanental point processes, and Gibbs hard-core and random sequential absorption processes as well as for Laguerre tessellations of polydisperse spheres and STIT- and Poisson hyperplane tessellations. These data are complemented by mechanically stable crystalline sphere and disordered ellipsoid packings and area-minimising foam models. We find that shape indices of individual cells are not sufficient to unambiguously identify the generating process even amongst this limited set of processes. However, we identify significant differences of the shape indices between many of these tessellation models. Given a realization of a tessellation, these shape indices can narrow the choice of possible generating processes, providing a powerful tool which can be further strengthened by density-resolved volume-shape correlations.Comment: Chapter of the forthcoming book "Tensor Valuations and their Applications in Stochastic Geometry and Imaging" in Lecture Notes in Mathematics edited by Markus Kiderlen and Eva B. Vedel Jense

Lactic acid production from lime-treated wheat straw by Bacillus coagulans: neutralization of acid by fed-batch addition of alkaline substrate

Conventional processes for lignocellulose-to-organic acid conversion requires pretreatment, enzymatic hydrolysis, and microbial fermentation. In this study, lime-treated wheat straw was hydrolyzed and fermented simultaneously to lactic acid by an enzyme preparation and Bacillus coagulans DSM 2314. Decrease in pH because of lactic acid formation was partially adjusted by automatic addition of the alkaline substrate. After 55 h of incubation, the polymeric glucan, xylan, and arabinan present in the lime-treated straw were hydrolyzed for 55%, 75%, and 80%, respectively. Lactic acid (40.7 g/l) indicated a fermentation efficiency of 81% and a chiral l(+)-lactic acid purity of 97.2%. In total, 711 g lactic acid was produced out of 2,706 g lime-treated straw, representing 43% of the overall theoretical maximum yield. Approximately half of the lactic acid produced was neutralized by fed-batch feeding of lime-treated straw, whereas the remaining half was neutralized during the batch phase with a Ca(OH)2 suspension. Of the lime added during the pretreatment of straw, 61% was used for the neutralization of lactic acid. This is the first demonstration of a process having a combined alkaline pretreatment of lignocellulosic biomass and pH control in fermentation resulting in a significant saving of lime consumption and avoiding the necessity to recycle lime

Influence of very low doses of mediators on fungal laccase activity - nonlinearity beyond imagination

Laccase, an enzyme responsible for aerobic transformations of natural phenolics, in industrial applications requires the presence of low-molecular substances known as mediators, which accelerate oxidation processes. However, the use of mediators is limited by their toxicity and the high costs of exploitation. The activation of extracellular laccase in growing fungal culture with highly diluted mediators, ABTS and HBT is described. Two high laccase-producing fungal strains, Trametes versicolor and Cerrena unicolor, were used in this study as a source of enzyme. Selected dilutions of the mediators significantly increased the activity of extracellular laccase during 14 days of cultivation what was distinctly visible in PAGE technique and in colorimetric tests. The same mediator dilutions increased demethylation properties of laccase, which was demonstrated during incubation of enzyme with veratric acid. It was established that the activation effect was assigned to specific dilutions of mediators. Our dose-response dilution process smoothly passes into the range of action of homeopathic dilutions and is of interest for homeopaths