Platform Independent Specification of Engineering Model Transformations

Production machine engineering involves multiple engineering disciplines defining together the configuration of each machine. Each of these disciplines provides an engineering model, which influences engineering models from other disciplines and is itself influenced by other engineering models. Therefore, building a valid configuration of a production machine requires the reconciliation of engineering models of all involved engineering disciplines. Up to now, execution of model reconciliations by model transformation systems was mainly considered for desktop model transformation environments. The analysis of engineering processes and customer applications of production machines revealed that the industrial application of model transformations requires the execution of the same model transformation specification on different execution environments depending on the initiator of the model reconciliation. An electrical engineer runs the model transformation on his desktop between locally installed engineering applications for small organizations or on his field programming device for commissioning scenarios. For complex systems and bigger organizations, model transformations are executed on an enterprise product lifecycle management (PLM) server. A machine operator triggers model transformations on the real-time system of an automation controller for on-site reconfigurable machines, e.g. by physically connecting a modular device to a production machine. To tackle this scenario, this thesis presents a new application of the model driven architecture (MDA), which transforms a platform independent model transformation specifications (PIM-MT) to platform specific model transformation specifications (PSM-MT) by higher order transformations (HOT). For industrial usage, both the platform independent transformation specification and the platform specific execution reuse proven existing technology which is tailored and extended where needed. This allows for the stepwise introduction of model transformation technology in existing engineering and technology environments based on a classification scheme which was developed as part of this thesis. For the PIM-MT specification, the strict handling of references between engineering model elements from current model transformation specifications, which does not fit well the requirements of engineering models with temporarily violate references within the engineering workflow, was replaced by a weaker reference handling based on domain specific reference designators. An existing model transformation specification, the ATL language, has been tailored for PIM-MT specifications. For the PSM-MT desktop execution, the ATL desktop model transformation engine was reused. XSL transformations were adapted for enterprise model transformations executed on PLM servers. A PSM-MT engine for real-time IEC 61131 programmable logic controllers was developed as part of this thesis. With the results of this thesis it is now possible to build a customized engineering environment as an extension of the existing infrastructure of a machine builder, which automates the configuration of production machines by using model transformations generated from a common platform independent specification on multiple execution platforms

Support for Bidirectional Model-to-Text Transformations

In recent years, model-driven approaches and processes have established themselves as pragmatic and feasible solutions with tangible advantages. Transformations play a central role in any model-driven solution and, as interest in textual modelling grows, providing concepts and tools for supporting a high-level and declarative specification of bidirectional model-to-text transformations becomes a vital area of research. Our paper identifies important areas and scenarios for model-to-text transformations that are not or only partially supported by currently existing solutions. Based on the requirements of a real-world case study, we introduce a new concept that has been inspired by a successful bidirectional model-to-model transformation approach: Triple Graph Grammars

Topological Superconductivity in a Phase-Controlled Josephson Junction

Topological superconductors can support localized Majorana states at their boundaries. These quasi-particle excitations have non-Abelian statistics that can be used to encode and manipulate quantum information in a topologically protected manner. While signatures of Majorana bound states have been observed in one-dimensional systems, there is an ongoing effort to find alternative platforms that do not require fine-tuning of parameters and can be easily scalable to large numbers of states. Here we present a novel experimental approach towards a two-dimensional architecture. Using a Josephson junction made of HgTe quantum well coupled to thin-film aluminum, we are able to tune between a trivial and a topological superconducting state by controlling the phase difference $\phi$ across the junction and applying an in-plane magnetic field. We determine the topological state of the induced superconductor by measuring the tunneling conductance at the edge of the junction. At low magnetic fields, we observe a minimum in the tunneling spectra near zero bias, consistent with a trivial superconductor. However, as the magnetic field increases, the tunneling conductance develops a zero-bias peak which persists over a range of $\phi$ that expands systematically with increasing magnetic fields. Our observations are consistent with theoretical predictions for this system and with full quantum mechanical numerical simulations performed on model systems with similar dimensions and parameters. Our work establishes this system as a promising platform for realizing topological superconductivity and for creating and manipulating Majorana modes and will therefore open new avenues for probing topological superconducting phases in two-dimensional systems.Comment: Supplementary contains resized figures. Original files are available upon reques

Structural and Functional Characterization of PA14/Flo5-Like Adhesins From Komagataella pastoris

Cell–cell and cell-substrate based adhesion of yeasts are major determinants of their adoption of different life styles. Genome-mining of ascomycetous GPI-anchored cell wall proteins with lectin-like PA14 domains identified a unique class of putative adhesins in the clade of methylotrophic Komagataella yeasts, many of which are known to colonize plants and insects involving yet unknown adhesion mechanisms. Here, we report the functional and structural analysis of two of its members: KpFlo1 (=Cea1), that is highly specific for terminal N-acetylglucosamine moieties, and KpFlo2, which represents an orphan lectin with intact binding site but unknown specificity. Crystal structures of the Cea1 adhesion domain complexed to N-acetylglucosamine and N,N′-diacetylchitobiose reveal a Ca2+-dependent binding mode that differs from other members of the PA14/Flo5 adhesin family. Heterologous expression of Cea1A in Saccharomyces cerevisiae promotes cellular adhesion to non-reducing ends of non-crystalline chitin. Overall, our data suggest that high-affinity recognition of β-GlcNAc-capped glycans by Cea1 enable Komagataella species to interact with surface cues present in fungi and insects

The lipoxygenase-dependent oxygenation of lipid body membranes is promoted by a patatin-type phospholipase in cucumber cotyledons

Oilseed germination is characterized by the mobilization of storage lipids as a carbon and energy source for embryonic growth. In addition to storage lipid degradation in germinating oilseeds via the direct action of a triacylglycerol lipase (TGL) on the storage lipids, a second degradation pathway that is dependent on a specific lipid body trilinoleate 13-lipoxygenase (13-LOX) has been proposed in several plant species. The activity of this specific 13-LOX leads first to the formation of ester lipid hydroperoxides. These hydroperoxy fatty acids are then preferentially cleaved off by a TGL and serve as a substrate for glyoxysomal β-oxidation. As a prerequisite for triacylglycerol (TAG) mobilization, a partial degradation of the phospholipid monolayer and/or membrane proteins of the oil body has been discussed. Evidence has now been found for both processes: partial degradation of the proteins caleosin and oleosin was observed and simultaneously a patatin-like protein together with transient phospholipase (PLase) activity could be detected at the oil body membranes during germination. Moreover, in vitro experiments with isolated oil bodies from mature seeds revealed that the formation of 13-LOX-derived lipid peroxides in lipid body membranes is increased after incubation with the purified recombinant patatin-like protein. These experiments suggest that in vivo the degradation of storage lipids in cucumber cotyledons is promoted by the activity of a specific oil body PLase, which leads to an increased decomposition of the oil body membrane by the 13-LOX and thereby TAGs may be better accessible to LOX and TGL

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.Peer reviewe

Platform Independent Specification of Engineering Model Transformations

Production machine engineering involves multiple engineering disciplines defining together the configuration of each machine. Each of these disciplines provides an engineering model, which influences engineering models from other disciplines and is itself influenced by other engineering models. Therefore, building a valid configuration of a production machine requires the reconciliation of engineering models of all involved engineering disciplines. Up to now, execution of model reconciliations by model transformation systems was mainly considered for desktop model transformation environments. The analysis of engineering processes and customer applications of production machines revealed that the industrial application of model transformations requires the execution of the same model transformation specification on different execution environments depending on the initiator of the model reconciliation. An electrical engineer runs the model transformation on his desktop between locally installed engineering applications for small organizations or on his field programming device for commissioning scenarios. For complex systems and bigger organizations, model transformations are executed on an enterprise product lifecycle management (PLM) server. A machine operator triggers model transformations on the real-time system of an automation controller for on-site reconfigurable machines, e.g. by physically connecting a modular device to a production machine. To tackle this scenario, this thesis presents a new application of the model driven architecture (MDA), which transforms a platform independent model transformation specifications (PIM-MT) to platform specific model transformation specifications (PSM-MT) by higher order transformations (HOT). For industrial usage, both the platform independent transformation specification and the platform specific execution reuse proven existing technology which is tailored and extended where needed. This allows for the stepwise introduction of model transformation technology in existing engineering and technology environments based on a classification scheme which was developed as part of this thesis. For the PIM-MT specification, the strict handling of references between engineering model elements from current model transformation specifications, which does not fit well the requirements of engineering models with temporarily violate references within the engineering workflow, was replaced by a weaker reference handling based on domain specific reference designators. An existing model transformation specification, the ATL language, has been tailored for PIM-MT specifications. For the PSM-MT desktop execution, the ATL desktop model transformation engine was reused. XSL transformations were adapted for enterprise model transformations executed on PLM servers. A PSM-MT engine for real-time IEC 61131 programmable logic controllers was developed as part of this thesis. With the results of this thesis it is now possible to build a customized engineering environment as an extension of the existing infrastructure of a machine builder, which automates the configuration of production machines by using model transformations generated from a common platform independent specification on multiple execution platforms