257 research outputs found
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
SMT-Solvers in Action: Encoding and Solving Selected Problems in NP and EXPTIME
We compare the efficiency of seven modern SMT-solvers for several decision and combinatorial problems: the bounded Post correspondence problem (BPCP), the extended string correction problem (ESCP), and the Towers of Hanoi (ToH) of exponential solutions. For this purpose, we define new original reductions to SMT for all the above problems, and show their complexity. Our extensive experimental results allow for drawing quite interesting conclusions on efficiency and applicability of SMT-solvers depending on the theory used in the encoding
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
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
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Consistency and Standardization of Color in Medical Imaging: a Consensus Report
This article summarizes the consensus reached at the Summit on Color in Medical Imaging held at the Food and Drug Administration (FDA) on May 8–9, 2013, co-sponsored by the FDA and ICC (International Color Consortium). The purpose of the meeting was to gather information on how color is currently handled by medical imaging systems to identify areas where there is a need for improvement, to define objective requirements, and to facilitate consensus development of best practices. Participants were asked to identify areas of concern and unmet needs. This summary documents the topics that were discussed at the meeting and recommendations that were made by the participants. Key areas identified where improvements in color would provide immediate tangible benefits were those of digital microscopy, telemedicine, medical photography (particularly ophthalmic and dental photography), and display calibration. Work in these and other related areas has been started within several professional groups, including the creation of the ICC Medical Imaging Working Group
Automata for true concurrency properties
We present an automata-theoretic framework for the model checking of true concurrency properties. These are specified in a fixpoint logic, corresponding to history-preserving bisimilarity, capable of describing events in computations and their dependencies. The models of the logic are event structures or any formalism which can be given a causal semantics, like Petri nets. Given a formula and an event structure satisfying suitable regularity conditions we show how to construct a parity tree automaton whose language is non-empty if and only if the event structure satisfies the formula. The automaton, due to the nature of event structure models, is usually infinite. We discuss how it can be quotiented to an equivalent finite automaton, where emptiness can be checked effectively. In order to show the applicability of the approach, we discuss how it instantiates to finite safe Petri nets. As a proof of concept we provide a model checking tool implementing the technique
Definitions of basic terms relating to polymer liquid crystals (IUPAC Recommendations 2001)
The document first gives definitions of basic terms related to liquid-crystalline and mesomorphic states of matter and then terms specific to the classification of liquid-crystal polymers. The terms have been restricted to those most commonly encountered in the structural description of the latter class of materials. The terms have been selected from the recently published comprehensive document "Definitions of basic terms relating to low-molar-mass and polymer liquid crystals" [Pure and Applied Chemistry 73 (5), 845-895 (2001)] and are intended to form a readily usable guide for the reader interested in the structural description of polymer liquid crystals. The more comprehensive document should be used for terminology associated with types of mesophases and the optical and physical characteristics of liquid-crystalline materials. The advice given by representatives of the International Liquid Crystal Society for the preparation of this document is gratefully acknowledged.Fil:Barón, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina
SecM-Stalled Ribosomes Adopt an Altered Geometry at the Peptidyl Transferase Center
A structure of a ribosome stalled during translation of the SecM peptide provides insight into the mechanism by which the large subunit active site is inactivated
Labeled EF-Tus for rapid kinetic studies of pretranslocation complex formation
The universally conserved translation elongation factor EF-Tu delivers aminoacyl(aa)-tRNA in the form of an aa-tRNA·EF-Tu·GTP ternary complex (TC) to the ribosome where it binds to the cognate mRNA codon within the ribosomal A-site, leading to formation of a pretranslocation (PRE) complex. Here we describe preparation of QSY9 and Cy5 derivatives of the variant E348C-EF-Tu that are functional in translation elongation. Together with fluorophore derivatives of aa-tRNA and of ribosomal protein L11, located within the GTPase associated center (GAC), these labeled EF-Tus allow development of two new FRET assays that permit the dynamics of distance changes between EF-Tu and both L11 (Tu-L11 assay) and aa-tRNA (Tu-tRNA assay) to be determined during the decoding process. We use these assays to examine: (i) the relative rates of EF-Tu movement away from the GAC and from aa-tRNA during decoding, (ii) the effects of the misreading-inducing antibiotics streptomycin and paromomycin on tRNA selection at the A-site, and (iii) how strengthening the binding of aa-tRNA to EF-Tu affects the rate of EF-Tu movement away from L11 on the ribosome. These FRET assays have the potential to be adapted for high throughput screening of ribosomal antibiotics
Mechanism of eIF6 release from the nascent 60S ribosomal subunit.
SBDS protein (deficient in the inherited leukemia-predisposition disorder Shwachman-Diamond syndrome) and the GTPase EFL1 (an EF-G homolog) activate nascent 60S ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eIF6 from nascent 60S ribosomal subunits. However, the mechanism is completely unknown. Here, we present cryo-EM structures of human SBDS and SBDS-EFL1 bound to Dictyostelium discoideum 60S ribosomal subunits with and without endogenous eIF6. SBDS assesses the integrity of the peptidyl (P) site, bridging uL16 (mutated in T-cell acute lymphoblastic leukemia) with uL11 at the P-stalk base and the sarcin-ricin loop. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit. Our data reveal the conserved mechanism of eIF6 release, which is corrupted in both inherited and sporadic leukemias.Supported by a Federation of European Biochemical Societies Long term Fellowship (to FW), Specialist Programme from Bloodwise [12048] (AJW), the Medical Research Council [MC_U105161083] (AJW) and [U105115237] (RRK), Wellcome Trust strategic award to the Cambridge Institute for Medal Research [100140], Tesni Parry Trust (AJW), Ted’s Gang (AJW) and the Cambridge NIHR Biomedical Research Centre.This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nsmb.311
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