Truly modular (co)datatypes for Isabelle/HOL

We extended Isabelle/HOL with a pair of definitional commands for datatypes and codatatypes. They support mutual and nested (co)recursion through well-behaved type constructors, including mixed recursion–corecursion, and are complemented by syntaxes for introducing primitive (co)recursive functions and by a general proof method for reasoning coinductively. As a case study, we ported Isabelle’s Coinductive library to use the new commands, eliminating the need for tedious ad hoc constructions

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

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

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

Differential Hoare Logics and Refinement Calculi for Hybrid Systems with Isabelle/HOL

We present simple new Hoare logics and refinement calculi for hybrid systems in the style of differential dynamic logic. (Refinement) Kleene algebra with tests is used for reasoning about the program structure and generating verification conditions at this level. Lenses capture hybrid program stores in a generic algebraic way. The approach has been formalised with the Isabelle/HOL proof assistant. A number of examples explains the workflow with the resulting verification components

Foundational (co)datatypes and (co)recursion for higher-order logic

We describe a line of work that started in 2011 towards enriching Isabelle/HOL's language with coinductive datatypes, which allow infinite values, and with a more expressive notion of inductive datatype than previously supported by any system based on higher-order logic. These (co)datatypes are complemented by definitional principles for (co)recursive functions and reasoning principles for (co)induction. In contrast with other systems offering codatatypes, no additional axioms or logic extensions are necessary with our approach

Self-similar chain conformations in polymer gels

We use molecular dynamics simulations to study the swelling of randomly end-cross-linked polymer networks in good solvent conditions. We find that the equilibrium degree of swelling saturates at Q_eq = N_e**(3/5) for mean strand lengths N_s exceeding the melt entanglement length N_e. The internal structure of the network strands in the swollen state is characterized by a new exponent nu=0.72. Our findings are in contradiction to de Gennes' c*-theorem, which predicts Q_eq proportional N_s**(4/5) and nu=0.588. We present a simple Flory argument for a self-similar structure of mutually interpenetrating network strands, which yields nu=7/10 and otherwise recovers the classical Flory-Rehner theory. In particular, Q_eq = N_e**(3/5), if N_e is used as effective strand length.Comment: 4 pages, RevTex, 3 Figure

Many-Valued Institutions for Constraint Specification

We advance a general technique for enriching logical systems with soft constraints, making them suitable for specifying complex software systems where parts are put together not just based on how they meet certain functional requirements but also on how they optimise certain constraints. This added expressive power is required, for example, for capturing quality attributes that need to be optimised or, more generally, for formalising what are usually called service-level agreements. More specifically, we show how institutions endowed with a graded semantic consequence can accommodate soft-constraint satisfaction problems. We illustrate our approach by showing how, in the context of service discovery, one can quantify the compatibility of two specifications and thus formalise the selection of the most promising provider of a required resource.Peer Reviewe

Recent EUROfusion Achievements in Support of Computationally Demanding Multiscale Fusion Physics Simulations and Integrated Modeling

Integrated modeling (IM) of present experiments and future tokamak reactors requires the provision of computational resources and numerical tools capable of simulating multiscale spatial phenomena as well as fast transient events and relatively slow plasma evolution within a reasonably short computational time. Recent progress in the implementation of the new computational resources for fusion applications in Europe based on modern supercomputer technologies (supercomputer MARCONI-FUSION), in the optimization and speedup of the EU fusion-related first-principle codes, and in the development of a basis for physics codes/modules integration into a centrally maintained suite of IM tools achieved within the EUROfusion Consortium is presented. Physics phenomena that can now be reasonably modelled in various areas (core turbulence and magnetic reconnection, edge and scrape-off layer physics, radio-frequency heating and current drive, magnetohydrodynamic model, reflectometry simulations) following successful code optimizations and parallelization are briefly described. Development activities in support to IM are summarized. They include support to (1) the local deployment of the IM infrastructure and access to experimental data at various host sites, (2) the management of releases for sophisticated IM workflows involving a large number of components, and (3) the performance optimization of complex IM workflows.This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014 to 2018 under grant agreement 633053. The views and opinions expressed herein do not necessarily reflect those of the European Commission or ITER.Peer ReviewedPostprint (published version

Simulations of edge localised mode instabilities in MAST-U Super-X tokamak plasmas

The high heat fluxes to the divertor during edge localised mode (ELM) instabilities have to be reduced for a sustainable future tokamak reactor. A solution to reduce the heat fluxes could be the Super-X divertor, which will be tested on MAST-U. ELM simulations for MAST-U Super-X tokamak plasmas have been obtained, using JOREK. A factor 10 decrease in the peak heat flux to the outer target and almost a factor 8 decrease in the ELM energy fluence when comparing the Super-X to a conventional divertor configuration has been found. A detached MAST-U case, after the roll-over in the target parallel electron density flux, is used as a starting point for ELM burn-through simulations. The plasma burns through the neutrals front during the ELM causing the divertor plasma to re-attach. After the crash a transition back to detachment is indicated, where the recovery to pre-ELM divertor conditions occurs in a few milliseconds, when the neutral pressure is high in the divertor. Recovery times are shorter than the inter-ELM phase in previous MAST experiments. The peak ELM energy fluence obtained after the ELM burn-through is 0.82 kJ/m2, which is significantly lower than that predicted from the empirical scaling of the ELM energy fluence - indicating promising results for future MAST-U operations