310 research outputs found
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
Group synthesis for alternating-time temporal logic
We present an extension of Alternating-time Temporal Logic ATL, called ATLP (Parametric ATL), where parameters are allowed in place of concrete groups of agents. We devise a procedure to nd all instantiations for the parameters in a given formula of ATLP so that is true in a given model. We propose a formalisation of the problem and symbolic algorithms for its solution. We discuss an experimental implementation of the approach on top of the open-source model checker mcmas and demonstrate the bene ts of the technique through experimental results
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
Structural insights into RNA processing by the human RISC-loading complex.
Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Dicer and the RNA-binding protein TRBP to form a RISC-loading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and miRNAs from Dicer to AGO2. Here, using single-particle EM analysis, we show that human Dicer has an L-shaped structure. The RLC Dicer's N-terminal DExH/D domain, located in a short 'base branch', interacts with TRBP, whereas its C-terminal catalytic domains in the main body are proximal to AGO2. A model generated by docking the available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction suggests a mechanism for siRNA transfer from Dicer to AGO2
Towards Independent Particle Reconstruction from Cryogenic Transmission Electron Microscopy
Coronary heart disease is the single largest killer of Americans so improved means of detecting risk factors before arterial obstructions appear are expected to lead to a improvement in quality of life with a reduced cost. This paper introduces a new approach to 3-D reconstruction of individual particles based on statistical modeling from a sparse set of 2-D projection images. This paper introduces a new approach to 3-D reconstruction of individual particles based on statistical modeling from a sparse set of 2-D projection images. The method is in contrast to the current state of practice where reconstruction is performed via signal processing or Bayesian methods that use averaged images acquired from an ensemble of particles. As such, this new approach has its impetus in use for novel diagnostic tests such as LDL and HDL particle shape characterization. The approach is also expected to have uses in areas such as quality assurance for drug delivery nano-technologies and for general proteomic studies.
The individual particle reconstruction algorithm is based on a hidden Markov model. Higher order Markov chain statistics, which are generated from the a priori model of the target of interest, can be derived from traditional methods such as single particle reconstruction and/or the underlying physical properties of the particle. By placing the reconstruction voxel space at a 45° angle to the projection image, 4-passes of the HMM processing can be performed from a single image. Reconstruction results from a simple model and a single projection image resulted in better than 98% reconstruction accuracy as compared to the original target
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
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
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