S-Net for multi-memory multicores

Copyright ACM, 2010. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in Proceedings of the 5th ACM SIGPLAN Workshop on Declarative Aspects of Multicore Programming: http://doi.acm.org/10.1145/1708046.1708054S-Net is a declarative coordination language and component technology aimed at modern multi-core/many-core architectures and systems-on-chip. It builds on the concept of stream processing to structure dynamically evolving networks of communicating asynchronous components. Components themselves are implemented using a conventional language suitable for the application domain. This two-level software architecture maintains a familiar sequential development environment for large parts of an application and offers a high-level declarative approach to component coordination. In this paper we present a conservative language extension for the placement of components and component networks in a multi-memory environment, i.e. architectures that associate individual compute cores or groups thereof with private memories. We describe a novel distributed runtime system layer that complements our existing multithreaded runtime system for shared memory multicores. Particular emphasis is put on efficient management of data communication. Last not least, we present preliminary experimental data

Comparing BDD and SAT based techniques for model checking Chaum's Dining Cryptographers Protocol

We analyse different versions of the Dining Cryptographers protocol by means of automatic verification via model checking. Specifically we model the protocol in terms of a network of communicating automata and verify that the protocol meets the anonymity requirements specified. Two different model checking techniques (ordered binary decision diagrams and SAT-based bounded model checking) are evaluated and compared to verify the protocols

Rich Counter-Examples for Temporal-Epistemic Logic Model Checking

Model checking verifies that a model of a system satisfies a given property, and otherwise produces a counter-example explaining the violation. The verified properties are formally expressed in temporal logics. Some temporal logics, such as CTL, are branching: they allow to express facts about the whole computation tree of the model, rather than on each single linear computation. This branching aspect is even more critical when dealing with multi-modal logics, i.e. logics expressing facts about systems with several transition relations. A prominent example is CTLK, a logic that reasons about temporal and epistemic properties of multi-agent systems. In general, model checkers produce linear counter-examples for failed properties, composed of a single computation path of the model. But some branching properties are only poorly and partially explained by a linear counter-example. This paper proposes richer counter-example structures called tree-like annotated counter-examples (TLACEs), for properties in Action-Restricted CTL (ARCTL), an extension of CTL quantifying paths restricted in terms of actions labeling transitions of the model. These counter-examples have a branching structure that supports more complete description of property violations. Elements of these counter-examples are annotated with parts of the property to give a better understanding of their structure. Visualization and browsing of these richer counter-examples become a critical issue, as the number of branches and states can grow exponentially for deeply-nested properties. This paper formally defines the structure of TLACEs, characterizes adequate counter-examples w.r.t. models and failed properties, and gives a generation algorithm for ARCTL properties. It also illustrates the approach with examples in CTLK, using a reduction of CTLK to ARCTL. The proposed approach has been implemented, first by extending the NuSMV model checker to generate and export branching counter-examples, secondly by providing an interactive graphical interface to visualize and browse them.Comment: In Proceedings IWIGP 2012, arXiv:1202.422

A Logic with Reverse Modalities for History-preserving Bisimulations

We introduce event identifier logic (EIL) which extends Hennessy-Milner logic by the addition of (1) reverse as well as forward modalities, and (2) identifiers to keep track of events. We show that this logic corresponds to hereditary history-preserving (HH) bisimulation equivalence within a particular true-concurrency model, namely stable configuration structures. We furthermore show how natural sublogics of EIL correspond to coarser equivalences. In particular we provide logical characterisations of weak history-preserving (WH) and history-preserving (H) bisimulation. Logics corresponding to HH and H bisimulation have been given previously, but not to WH bisimulation (when autoconcurrency is allowed), as far as we are aware. We also present characteristic formulas which characterise individual structures with respect to history-preserving equivalences.Comment: In Proceedings EXPRESS 2011, arXiv:1108.407

Terminology of polymers and polymerization processes in dispersed systems (IUPAC Recommendations 2011)

A large group of industrially important polymerization processes is carried out in dispersed systems. These processes differ with respect to their physical nature, mechanism of particle formation, particle morphology, size, charge, types of interparticle interactions, and many other aspects. Polymer dispersions, and polymers derived from polymerization in dispersed systems, are used in diverse areas such as paints, adhesives, microelectronics, medicine, cosmetics, biotechnology, and others. Frequently, the same names are used for different processes and products or different names are used for the same processes and products. The document contains a list of recommended terms and definitions necessary for the unambiguous description of processes, products, parameters, and characteristic features relevant to polymers in dispersed systems

Molecular Architecture of the Human Mediator–RNA Polymerase II–TFIIF Assembly

The authors perform a cryo-EM study of the 1.9 MDa human Mediator-RNA polymerase II-TFIIF assembly, which reveals the structural organization of the human transcription initiation apparatus

MCMAS: an open-source model checker for the verification of multi-agent systems

We present MCMAS, a model checker for the verification of multi-agent systems. MCMAS supports efficient symbolic techniques for the verification of multi-agent systems against specifications representing temporal, epistemic and strategic properties. We present the underlying semantics of the specification language supported and the algorithms implemented in MCMAS, including its fairness and counterexample generation features. We provide a detailed description of the implementation. We illustrate its use by discussing a number of examples and evaluate its performance by comparing it against other model checkers for multi-agent systems on a common case study

Conformational Reorganization of the SARS Coronavirus Spike Following Receptor Binding: Implications for Membrane Fusion

The SARS coronavirus (SARS-CoV) spike is the largest known viral spike molecule, and shares a similar function with all class 1 viral fusion proteins. Previous structural studies of membrane fusion proteins have largely used crystallography of static molecular fragments, in isolation of their transmembrane domains. In this study we have produced purified, irradiated SARS-CoV virions that retain their morphology, and are fusogenic in cell culture. We used cryo-electron microscopy and image processing to investigate conformational changes that occur in the entire spike of intact virions when they bind to the viral receptor, angiotensin-converting enzyme 2 (ACE2). We have shown that ACE2 binding results in structural changes that appear to be the initial step in viral membrane fusion, and precisely localized the receptor-binding and fusion core domains within the entire spike. Furthermore, our results show that receptor binding and subsequent membrane fusion are distinct steps, and that each spike can bind up to three ACE2 molecules. The SARS-CoV spike provides an ideal model system to study receptor binding and membrane fusion in the native state, employing cryo-electron microscopy and single-particle image analysis