An NMF solution for the Flowgraphs case at the TTC 2013

Software systems are getting more and more complex. Model-driven engineering (MDE) offers ways to handle such increased complexity by lifting development to a higher level of abstraction. A key part in MDE are transformations that transform any given model into another. These transformations are used to generate all kinds of software artifacts from models. However, there is little consensus about the transformation tools. Thus, the Transformation Tool Contest (TTC) 2013 aims to compare different transformation engines. This is achieved through three different cases that have to be tackled. One of these cases is the Flowgraphs case. A solution has to transform a Java code model into a simplified version and has to derive control and data flow. This paper presents the solution for this case using NMF Transformations as transformation engine.Comment: In Proceedings TTC 2013, arXiv:1311.753

An NMF solution for the Petri Nets to State Charts case study at the TTC 2013

Software systems are getting more and more complex. Model-driven engineering (MDE) offers ways to handle such increased complexity by lifting development to a higher level of abstraction. A key part in MDE are transformations that transform any given model into another. These transformations are used to generate all kinds of software artifacts from models. However, there is little consensus about the transformation tools. Thus, the Transformation Tool Contest (TTC) 2013 aims to compare different transformation engines. This is achieved through three different cases that have to be tackled. One of these cases is the Petri Net to State Chart case. A solution has to transform a Petri Net to a State Chart and has to derive a hierarchical structure within the State Chart. This paper presents the solution for this case using NMF Transformations as transformation engine.Comment: In Proceedings TTC 2013, arXiv:1311.7536. arXiv admin note: substantial text overlap with arXiv:1312.034

Membrane computing with water

We introduce water tank systems as a new class of membrane systems inspired by a decentrally controlled circulation of water or other liquids throughout cells called tanks and capillaries called pipes. To our best knowledge, this is the first proposal addressing the behavioural principle of floating and stored water for modelling of information processing in terms of membrane computing. The volume of water within a tank stands for a non-negative rational value when acting in an analogue computation or it can be interpreted in a binary manner by distinction of “(nearly) full” or “(nearly) empty”. Water tanks might be interconnected by pipes for directed transport of water. Each pipe can be equipped with valves which in turn either fully open or fully close the hosting pipe according to permanent measurements whether the filling level in a dedicated water tank exceeds a certain threshold or not. We demonstrate dedicated water tank systems together with simulation case studies: a ring oscillator for generation of clock signals and for iteratively making available amounts of water in a cyclic scheme, analogue arithmetics by implementation of addition, non-negative subtraction, division, and multiplication complemented by systems in binary mode for implementation of selected logic gates

A novel screening protocol for the isolation of hydrogen producing Chlamydomonas reinhardtii strains

<p>Abstract</p> <p>Background</p> <p>Sealed <it>Chlamydomonas reinhardtii </it>cultures evolve significant amounts of hydrogen gas under conditions of sulfur depletion. However, the eukaryotic green alga goes through drastic metabolic changes during this nutritional stress resulting in cell growth inhibition and eventually cell death. This study aimed at isolating <it>C. reinhardtii </it>transformants which produce hydrogen under normal growth conditions to allow a continuous hydrogen metabolism without the stressful impact of nutrient deprivation.</p> <p>Results</p> <p>To achieve a steady photobiological hydrogen production, a screening protocol was designed to identify <it>C. reinhardtii </it>DNA insertional mutagenesis transformants with an attenuated photosynthesis to respiration capacity ratio (P/R ratio). The screening protocol entails a new and fast method for mutant strain selection altered in their oxygen production/consumption balance. Out of 9000 transformants, four strains with P/R ratios varying from virtually zero to three were isolated. Strain <it>apr</it>1 was found to have a slightly higher respiration rate and a significantly lower photosynthesis rate than the wild type. Sealed cultures of <it>apr</it>1 became anaerobic in normal growth medium (TAP) under moderate light conditions and induced [FeFe]-hydrogenase activity, yet without significant hydrogen gas evolution. However, Calvin-Benson cycle inactivation of anaerobically adapted <it>apr</it>1 cells in the light led to a 2-3-fold higher <it>in vivo </it>hydrogen production than previously reported for the sulfur-deprived <it>C. reinhardtii </it>wild type.</p> <p>Conclusion</p> <p>Attenuated P/R capacity ratio in microalgal mutants constitutes a platform for achieving steady state photobiological hydrogen production. Using this platform, algal hydrogen metabolism can be analyzed without applying nutritional stress. Furthermore, these strains promise to be useful for biotechnological hydrogen generation, since high <it>in vivo </it>hydrogen production rates are achievable under normal growth conditions, when the photosynthesis to respiration capacity ratio is lowered in parallel to down regulated assimilative pathways.</p

Lyophilization protects [FeFe]-hydrogenases against O2-induced H-cluster degradation

Nature has developed an impressive repertoire of metal-based enzymes that perform complex chemical reactions under moderate conditions. Catalysts that produce molecular hydrogen (H2) are particularly promising for renewable energy applications. Unfortunately, natural and chemical H2-catalysts are often irreversibly degraded by molecular oxygen (O2). Here we present a straightforward procedure based on freeze-drying (lyophilization), that turns [FeFe]-hydrogenases, which are excellent H2-producers, but typically extremely O2-sensitive in solution, into enzymes that are fully resistant against O2. Complete dryness protects and conserves both, the [FeFe]-hydrogenase proteins and their inorganic active-site cofactor (H-cluster), when exposed to 100% O2 for days. The full H2-formation capacity is restored after solvation of the lyophilized enzymes. However, even minimal moisturizing re-establishes O2-sensitivity. The dry [FeFe]-hydrogenase material is superior also for advanced spectroscopic investigations on the H-cluster reaction mechanism. Our method provides a convenient way for long-term storage and impacts on potential biotechnological hydrogen production applications of hydrogenase enzymes

The Geometry of the Catalytic Active Site in [FeFe]-hydrogenases is Determined by Hydrogen Bonding and Proton Transfer

[FeFe]-hydrogenases are efficient metalloenzymes that catalyze the oxidation and evolution of molecular hydrogen, H2. They serve as a blueprint for the design of synthetic H2-forming catalysts. [FeFe]-hydrogenases harbor a six-iron cofactor that comprises a [4Fe-4S] cluster and a unique diiron site with cyanide, carbonyl, and hydride ligands. To address the ligand dynamics in catalytic turnover and upon carbon monoxide (CO) inhibition, we replaced the native aminodithiolate group of the diiron site by synthetic dithiolates, inserted into wild-type and amino acid variants of the [FeFe]-hydrogenase HYDA1 from Chlamydomonas reinhardtii. The reactivity with H2 and CO was characterized using in situ and transient infrared spectroscopy, protein crystallography, quantum chemical calculations, and kinetic simulations. All cofactor variants adopted characteristic populations of reduced species in the presence of H2 and showed significant changes in CO inhibition and reactivation kinetics. Differences were attributed to varying interactions between polar ligands and the dithiolate head group and/or the environment of the cofactor (i.e., amino acid residues and water molecules). The presented results show how catalytically relevant intermediates are stabilized by inner-sphere hydrogen bonding suggesting that the role of the aminodithiolate group must not be restricted to proton transfer. These concepts may inspire the design of improved enzymes and biomimetic H2-forming catalysts

Cyanide Binding to [FeFe]-Hydrogenase Stabilizes the Alternative Configuration of the Proton Transfer Pathway

Hydrogenases are H2 converting enzymes that harbor catalytic cofactors in which iron (Fe) ions are coordinated by biologically unusual carbon monoxide (CO) and cyanide (CN−) ligands. Extrinsic CO and CN−, however, inhibit hydrogenases. The mechanism by which CN− binds to [FeFe]-hydrogenases is not known. Here, we obtained crystal structures of the CN−-treated [FeFe]-hydrogenase CpI from Clostridium pasteurianum. The high resolution of 1.39 Å allowed us to distinguish intrinsic CN− and CO ligands and to show that extrinsic CN− binds to the open coordination site of the cofactor where CO is known to bind. In contrast to other inhibitors, CN− treated crystals show conformational changes of conserved residues within the proton transfer pathway which could allow a direct proton transfer between E279 and S319. This configuration has been proposed to be vital for efficient proton transfer, but has never been observed structurally

Electronic and molecular structures of the active-site H-cluster in [FeFe]-hydrogenase determined by site-selective X-ray spectroscopy and quantum chemical calculations

The [FeFe]-hydrogenase (HydA1) from green algae is the minimal enzyme for efficient biological hydrogen (H2) production. Its active-site six-iron center (H-cluster) consists of a cubane, [4Fe4S]H, cysteine-linked to a diiron site, [2Fe]H. We utilized the spin-polarization of the iron Kβ X-ray fluorescence emission to perform site-selective X-ray absorption experiments for spectral discrimination of the two sub-complexes. For the H-cluster in reduced HydA1 protein, XANES and EXAFS spectra, Kβ emission lines (3p → 1s transitions), and core-to-valence (pre-edge) absorption (1s → 3d) and valence-to-core (Kβ2,5) emission (3d → 1s) spectra were obtained, individually for [4Fe4S]H and [2Fe]H. Iron–ligand bond lengths and intermetal distances in [2Fe]H and [4Fe4S]H were resolved, as well as fine structure in the high-spin iron containing cubane. Density functional theory calculations reproduced the X-ray spectral features and assigned the molecular orbital configurations, emphasizing the asymmetric d-level degeneracy of the proximal (Fep) and distal (Fed) low-spin irons in [2Fe]H in the non-paramagnetic state. This yielded a specific model structure of the H-cluster with a bridging carbon monoxide ligand and an apical open coordination site at Fed in [2Fe]H. The small HOMO–LUMO gap ([similar]0.3 eV) enables oxidation and reduction of the active site at similar potentials for reversible H2 turnover by HydA1, the LUMO spread over [4Fe4S]H supports its role as an electron transfer relay, and Fed carrying the HOMO is prepared for transient hydride binding. These features and the accessibility of Fed from the bulk phase can account for regio- specific redox transitions as well as H2-formation and O2-inhibition at the H-cluster. We provide a conceptual and experimental framework for site- selective studies on catalytic mechanisms in inhomogeneous materials

Extraction de chroniques discriminantes

International audienceL'extraction de motifs séquentiels vise à extraire des comportements récurrents dans un ensemble de séquences. Lorsque ces séquences sont étiquetées, l'extraction de motifs discriminants engendre des motifs caractéristiques de chaque classe de séquences. Cet article s'intéresse à l'extraction des chroniques discriminantes où une chronique est un type de motif temporel représentant des durées inter-évènements quantitatives. L'article présente l'algorithme DCM dont l'originalité réside dans l'utilisation de méthodes d'apprentissage automatique pour extraire les intervalles temporels. Les performances computationnelles et le pouvoir discriminant des chroniques extraites sont évalués sur des données synthétiques et réelles