GridLabs: Facilitating collaborative access to remote laboratories

eScience is usually characterized by the cooperation of distributed groups of researchers who share data and computing environments and perform experiments together. Often immense data sets that were produced by expensive equipments need to be accessed and evaluated. Such eScience scenarios require both, support for collaboration of researchers at distant locations and also the remote control of the shared laboratory devices. However, this type of remote experimentation and collaboration must be taught during university education. In this paper, we propose a framework that supports the training of above practices through the provision of a dedicated collaboration environment. It extends current approaches with support for a life cycle of remote labs, including scheduling the access to remote labs as well as defining access permissions. Our experiences in teaching lab courses suggest that the approach is also applicable in eScience scenarios

Loss of APC induces polyploidy as a result of a combination of defects in mitosis and apoptosis

Mutations in the adenomatous polyposis coli (APC) tumor suppressor gene initiate a majority of colorectal cancers. Acquisition of chromosomal instability is an early event in these tumors. We provide evidence that the loss of APC leads to a partial loss of interkinetochore tension at metaphase and alters mitotic progression. Furthermore, we show that inhibition of APC in U2OS cells compromises the mitotic spindle checkpoint. This is accompanied by a decrease in the association of the checkpoint proteins Bub1 and BubR1 with kinetochores. Additionally, APC depletion reduced apoptosis. As expected from this combination of defects, tetraploidy and polyploidy are consequences of APC inhibition in vitro and in vivo. The removal of APC produced the same defects in HCT116 cells that have constitutively active β-catenin. These data show that the loss of APC immediately induces chromosomal instability as a result of a combination of mitotic and apoptotic defects. We suggest that these defects amplify each other to increase the incidence of tetra- and polyploidy in early stages of tumorigenesis

Eigenfunctions of GL(N,\RR) Toda chain: The Mellin-Barnes representation

The recurrent relations between the eigenfunctions for GL(N,\RR) and GL(N-1,\RR) quantum Toda chains is derived. As a corollary, the Mellin-Barnes integral representation for the eigenfunctions of a quantum open Toda chain is constructed for the $N$-particle case.Comment: Latex+amssymb.sty, 7 pages; corrected some typos published in Pis'ma v ZhETF (2000), vol. 71, 338-34

A zeolitic imidazolate framework with conformational variety: Conformational polymorphs versus frameworks with static conformational disorder

We show via structural considerations and DFT calculations that for a zeolitic imidazolate framework (ZIF) with sodalite (SOD) topology, [Zn(dcim)2]-SOD (dcim = 4,5-dichloroimidazolate), structural models of an infinite number of hypothetical conformational polymorphs with distinct linker orientations can be generated, which can be interconverted most likely only via reconstructive structural transitions. The relative total energies suggest that some of those polymorphs might be synthetically accessible. Efforts in that direction led to the synthesis of new trigonal 1 and previously known cubic 2 with improved crystallinity. According to structural analyses based on powder X-ray diffraction (PXRD) methods supported by NMR spectroscopy, 1 is the most stable of the theoretically predicted SOD-type framework conformers (isostructural to ZIF-7), whereas 2, at variance to a recent proposal, is a SOD-type material with a high degree of orientational disorder of the dcim linker units. The statistics of the linker orientations in 2 is close to that in 1, indicating that the disorder in 2 is not random. Rather crystals of 2 are likely twins consisting of nanoscopic domains of trigonal 1 that are deformed to a cubic metric, with linker disorder being located in the domain interfaces. As structural differences appear to be more related to characteristics of the real as opposed to the ideal crystal structures, we propose to not consider 1 and 2 as true conformational polymorphs. Systematic investigations of solvent mixtures led to the discovery of intermediate materials of 1 and 2. The PXRD patterns and SEM images indicate that they belong to a complete series of structural intermediates. Differences in the Ar adsorption/desorption behaviours reveal that 1, in contrast to 2, is a flexible ZIF framework

Particle interactions and lattice dynamics: Scenarios for efficient bidirectional stochastic transport?

Intracellular transport processes driven by molecular motors can be described by stochastic lattice models of self-driven particles. Here we focus on bidirectional transport models excluding the exchange of particles on the same track. We explore the possibility to have efficient transport in these systems. One possibility would be to have appropriate interactions between the various motors' species, so as to form lanes. However, we show that the lane formation mechanism based on modified attachment/detachment rates as it was proposed previously is not necessarily connected to an efficient transport state and is suppressed when the diffusivity of unbound particles is finite. We propose another interaction mechanism based on obstacle avoidance that allows to have lane formation for limited diffusion. Besides, we had shown in a separate paper that the dynamics of the lattice itself could be a key ingredient for the efficiency of bidirectional transport. Here we show that lattice dynamics and interactions can both contribute in a cooperative way to the efficiency of transport. In particular, lattice dynamics can decrease the interaction threshold beyond which lanes form. Lattice dynamics may also enhance the transport capacity of the system even when lane formation is suppressed.Comment: 25 pages, 17 figures, 2 table

An Experimental and Simulation Study of Early Flame Development in a Homogeneous-Charge Spark-Ignition Engine

An integrated experimental and Large-Eddy Simulation (LES) study is presented for homogeneous premixed combustion in a spark-ignition engine. The engine is a single-cylinder two-valve optical research engine with transparent liner and piston: the Transparent Combustion Chamber (TCC) engine. This is a relatively simple, open engine configuration that can be used for LES model development and validation by other research groups. Pressure-based combustion analysis, optical diagnostics and LES have been combined to generate new physical insight into the early stages of combustion. The emphasis has been on developing strategies for making quantitative comparisons between high-speed/high-resolution optical diagnostics and LES using common metrics for both the experiments and the simulations, and focusing on the important early flame development period. Results from two different LES turbulent combustion models are presented, using the same numerical methods and computational mesh. Both models yield Cycle-to-Cycle Variations (CCV) in combustion that are higher than what is observed in the experiments. The results reveal strengths and limitations of the experimental diagnostics and the LES models, and suggest directions for future diagnostic and simulation efforts. In particular, it has been observed that flame development between the times corresponding to the laminar-to-turbulent transition and 1% mass-burned fraction are especially important in establishing the subsequent combustion event for each cycle. This suggests a range of temporal and spatial scales over which future experimental and simulation efforts should focus

The double Ringel-Hall algebra on a hereditary abelian finitary length category

In this paper, we study the category $\mathscr{H}^{(\rho)}$ of semi-stable coherent sheaves of a fixed slope $\rho$ over a weighted projective curve. This category has nice properties: it is a hereditary abelian finitary length category. We will define the Ringel-Hall algebra of $\mathscr{H}^{(\rho)}$ and relate it to generalized Kac-Moody Lie algebras. Finally we obtain the Kac type theorem to describe the indecomposable objects in this category, i.e. the indecomposable semi-stable sheaves.Comment: 29 page

Phase diagram of two-lane driven diffusive systems

We consider a large class of two-lane driven diffusive systems in contact with reservoirs at their boundaries and develop a stability analysis as a method to derive the phase diagrams of such systems. We illustrate the method by deriving phase diagrams for the asymmetric exclusion process coupled to various second lanes: a diffusive lane; an asymmetric exclusion process with advection in the same direction as the first lane, and an asymmetric exclusion process with advection in the opposite direction. The competing currents on the two lanes naturally lead to a very rich phenomenology and we find a variety of phase diagrams. It is shown that the stability analysis is equivalent to an `extremal current principle' for the total current in the two lanes. We also point to classes of models where both the stability analysis and the extremal current principle fail