A dynamic neural model of localization of brief successive stimuli in saltation

Somatosensory saltation is an illusion robustly generated using short tactile stimuli [1,2]. There is a perceived displacement of a first stimulus if followed by a subsequent nearby stimulus with a short stimulus onset asynchrony (SOA). Experimental reports suggest that this illusion results from spatiotemporal integration in early processing stages, but the exact neural mechanism is unknown. The neuronal mechanism involved is probably quite generic as similar phenomena occur in other modalities, audition for example [3]

Adapting Quality Assurance to Adaptive Systems: The Scenario Coevolution Paradigm

From formal and practical analysis, we identify new challenges that self-adaptive systems pose to the process of quality assurance. When tackling these, the effort spent on various tasks in the process of software engineering is naturally re-distributed. We claim that all steps related to testing need to become self-adaptive to match the capabilities of the self-adaptive system-under-test. Otherwise, the adaptive system's behavior might elude traditional variants of quality assurance. We thus propose the paradigm of scenario coevolution, which describes a pool of test cases and other constraints on system behavior that evolves in parallel to the (in part autonomous) development of behavior in the system-under-test. Scenario coevolution offers a simple structure for the organization of adaptive testing that allows for both human-controlled and autonomous intervention, supporting software engineering for adaptive systems on a procedural as well as technical level.Comment: 17 pages, published at ISOLA 201

Coupling JOREK and STARWALL for Non-linear Resistive-wall Simulations

The implementation of a resistive-wall extension to the non-linear MHD-code JOREK via a coupling to the vacuum-field code STARWALL is presented along with first applications and benchmark results. Also, non-linear saturation in the presence of a resistive wall is demonstrated. After completion of the ongoing verification process, this code extension will allow to perform non-linear simulations of MHD instabilities in the presence of three-dimensional resistive walls with holes for limited and X-point plasmas.Comment: Contribution for "Theory Of Fusion Plasmas, Joint Varenna - Lausanne International Workshop, Villa Monastero, Varenna, Italy (27.-31.8.2012)", accepted for publication in Journal of Physics Conference Serie

Adaptable transition systems

We present an essential model of adaptable transition systems inspired by white-box approaches to adaptation and based on foundational models of component based systems. The key feature of adaptable transition systems are control propositions, imposing a clear separation between ordinary, functional behaviours and adaptive ones. We instantiate our approach on interface automata yielding adaptable interface automata, but it may be instantiated on other foundational models of component-based systems as well. We discuss how control propositions can be exploited in the specification and analysis of adaptive systems, focusing on various notions proposed in the literature, like adaptability, control loops, and control synthesis

Activation of the human anaphase-promoting complex by proteins of the CDC20/Fizzy family

AbstractThe initiation of anaphase and exit from mitosis depend on the activation of the cyclosome/anaphase-promoting complex (APC) that ubiquitinates regulatory proteins such as anaphase inhibitors and mitotic cyclins [1–4]. Genetic experiments have demonstrated that two related WD40-repeat proteins – called Cdc20p and Hct1p/Cdh1p in budding yeast and Fizzy and Fizzy-related in Drosophila – are essential for APC-dependent proteolysis [5–11]. Human orthologs of these proteins – hCDC20/p55CDC[12] and hCDH1 – have recently been found to associate with APC in a cell-cycle-dependent manner [13,14]. Here, we show that the amount of hCDC20 and hCDH1 bound to APC correlates with a high ubiquitination activity of APC and that binding of recombinant hCDC20 and hCDH1 can activate APC in vitro. Our results suggest that the association between hCDH1 and APC is regulated by post-translational mechanisms, whereas the amount of hCDC20 bound to APC may in addition be controlled by hCDC20 synthesis and destruction [15]. The temporally distinct association of hCDC20 and hCDH1 with APC suggests that these proteins are, respectively, mitosis-specific and G1-specific activating subunits of APC

A Component-oriented Framework for Autonomous Agents

The design of a complex system warrants a compositional methodology, i.e., composing simple components to obtain a larger system that exhibits their collective behavior in a meaningful way. We propose an automaton-based paradigm for compositional design of such systems where an action is accompanied by one or more preferences. At run-time, these preferences provide a natural fallback mechanism for the component, while at design-time they can be used to reason about the behavior of the component in an uncertain physical world. Using structures that tell us how to compose preferences and actions, we can compose formal representations of individual components or agents to obtain a representation of the composed system. We extend Linear Temporal Logic with two unary connectives that reflect the compositional structure of the actions, and show how it can be used to diagnose undesired behavior by tracing the falsification of a specification back to one or more culpable components

Towards the Formal Reliability Analysis of Oil and Gas Pipelines

It is customary to assess the reliability of underground oil and gas pipelines in the presence of excessive loading and corrosion effects to ensure a leak-free transport of hazardous materials. The main idea behind this reliability analysis is to model the given pipeline system as a Reliability Block Diagram (RBD) of segments such that the reliability of an individual pipeline segment can be represented by a random variable. Traditionally, computer simulation is used to perform this reliability analysis but it provides approximate results and requires an enormous amount of CPU time for attaining reasonable estimates. Due to its approximate nature, simulation is not very suitable for analyzing safety-critical systems like oil and gas pipelines, where even minor analysis flaws may result in catastrophic consequences. As an accurate alternative, we propose to use a higher-order-logic theorem prover (HOL) for the reliability analysis of pipelines. As a first step towards this idea, this paper provides a higher-order-logic formalization of reliability and the series RBD using the HOL theorem prover. For illustration, we present the formal analysis of a simple pipeline that can be modeled as a series RBD of segments with exponentially distributed failure times.Comment: 15 page

The Interplay of Methyl-Group Distribution and Hydration Pattern of Isomeric Amphiphilic Osmolytes

© 2018 American Chemical Society. The intermolecular interactions and dynamics of aqueous 1,1-dimethyurea (1,1-DMU) solutions were studied by examining the concentration dependence of the solvent and solute relaxations detected by dielectric spectroscopy. Molecular dynamics simulations were carried out to facilitate interpretation of the dielectric data and to get a deeper insight into the behavior of the system components at the microscopic level. In particular, the simulations allowed for explaining the main differences between the dielectric spectra of aqueous solutions of 1,1-DMU and of its structural isomer 1,3-DMU. Similar to the previously studied compounds urea and 1,3-DMU, 1,1-DMU forms rather stable hydrates. This is evidenced by an effective solute dipole moment that significantly exceeds the value of a neat 1,1-DMU molecule, indicating pronounced parallel alignment of the solute dipole with two to three H2O moments. The MD simulations revealed that the involved water molecules form strong hydrogen bonds with the carbonyl group. However, in contrast to 1,3-DMU, it was not possible to resolve a "slow-water" mode in the dielectric spectra, suggesting rather different hydration-shell dynamics for 1,1-DMU as confirmed by the simulations. In contrast to aqueous urea and 1,3-DMU, addition of 1,1-DMU to water leads to a weak decrease of the static permittivity. This is explained by the emergence of antiparallel dipole-dipole correlations among 1,1-DMU hydrates with rising concentration

Bioink properties before, during and after 3D bioprinting

Bioprinting is a process based on additive manufacturing from materials containing living cells. These materials, often referred to as bioink, are based on cytocompatible hydrogel precursor formulations, which gel in a manner compatible with different bioprinting approaches. The bioink properties before, during and after gelation are essential for its printability, comprising such features as achievable structural resolution, shape fidelity and cell survival. However, it is the final properties of the matured bioprinted tissue construct that are crucial for the end application. During tissue formation these properties are influenced by the amount of cells present in the construct, their proliferation, migration and interaction with the material. A calibrated computational framework is able to predict the tissue development and maturation and to optimize the bioprinting input parameters such as the starting material, the initial cell loading and the construct geometry. In this contribution relevant bioink properties are reviewed and discussed on the example of most popular bioprinting approaches. The effect of cells on hydrogel processing and vice versa is highlighted. Furthermore, numerical approaches were reviewed and implemented for depicting the cellular mechanics within the hydrogel as well as for prediction of mechanical properties to achieve the desired hydrogel construct considering cell density, distribution and material-cell interaction

Exploiting the Hierarchical Structure of Rule-Based Specifications for Decision Planning

Rule-based specifications have been very successful as a declarative approach in many domains, due to the handy yet solid foundations offered by rule-based machineries like term and graph rewriting. Realistic problems, however, call for suitable techniques to guarantee scalability. For instance, many domains exhibit a hierarchical structure that can be exploited conveniently. This is particularly evident for composition associations of models. We propose an explicit representation of such structured models and a methodology that exploits it for the description and analysis of model- and rule-based systems. The approach is presented in the framework of rewriting logic and its efficient implementation in the rewrite engine Maude and is illustrated with a case study.