135 research outputs found
Efficient Finite Difference Method for Computing Sensitivities of Biochemical Reactions
Sensitivity analysis of biochemical reactions aims at quantifying the
dependence of the reaction dynamics on the reaction rates. The computation of
the parameter sensitivities, however, poses many computational challenges when
taking stochastic noise into account. This paper proposes a new finite
difference method for efficiently computing sensitivities of biochemical
reactions. We employ propensity bounds of reactions to couple the simulation of
the nominal and perturbed processes. The exactness of the simulation is
reserved by applying the rejection-based mechanism. For each simulation step,
the nominal and perturbed processes under our coupling strategy are
synchronized and often jump together, increasing their positive correlation and
hence reducing the variance of the estimator. The distinctive feature of our
approach in comparison with existing coupling approaches is that it only needs
to maintain a single data structure storing propensity bounds of reactions
during the simulation of the nominal and perturbed processes. Our approach
allows to computing sensitivities of many reaction rates simultaneously.
Moreover, the data structure does not require to be updated frequently, hence
improving the computational cost. This feature is especially useful when
applied to large reaction networks. We benchmark our method on biological
reaction models to prove its applicability and efficiency.Comment: 29 pages with 6 figures, 2 table
Primitives for Contract-based Synchronization
We investigate how contracts can be used to regulate the interaction between
processes. To do that, we study a variant of the concurrent constraints
calculus presented in [1], featuring primitives for multi-party synchronization
via contracts. We proceed in two directions. First, we exploit our primitives
to model some contract-based interactions. Then, we discuss how several models
for concurrency can be expressed through our primitives. In particular, we
encode the pi-calculus and graph rewriting.Comment: In Proceedings ICE 2010, arXiv:1010.530
Contract agreements via logic
We relate two contract models: one based on event structures and game theory,
and the other one based on logic. In particular, we show that the notions of
agreement and winning strategies in the game-theoretic model are related to
that of provability in the logical model.Comment: In Proceedings ICE 2013, arXiv:1310.401
Jalapa: Securing Java with Local Policies Tool Demonstration
AbstractWe present Jalapa, a tool for securing Java bytecode programs with history-based usage policies. Policies are defined by usage automata, that recognize the forbidden execution histories. Usage automata are expressive enough to allow programmers specify of many real-world usage policies; yet, they are simple enough to permit formal reasoning. Programmers can sandbox untrusted pieces of code with usage policies. The Jalapa tool rewrites the Java bytecode by adding the hooks for the mechanism that enforces the given policies at run-time
A Sound Up-to-, Bisimilarity for PCTL
We tackle the problem of establishing the soundness of approximate
bisimilarity with respect to PCTL and its relaxed semantics. To this purpose,
we consider a notion of bisimilarity similar to the one introduced by
Desharnais, Laviolette, and Tracol, which is parametric with respect to an
approximation error , and to the depth of the observation along
traces. Essentially, our soundness theorem establishes that, when a state
satisfies a given formula up-to error and steps , and is
bisimilar to up-to error and enough steps, we prove that
also satisfies the formula up-to a suitable error and steps . The
new error is computed from , and the formula, and
only depends linearly on . We provide a detailed overview of our soundness
proof
Chromosome analysis and rDNA FISH in the stag beetle Dorcus parallelipipedus L. (Coleoptera: Scarabaeoidea: Lucanidae).
In the present work the chromosome complement (2n = 18; 8AA + XY) of the stag beetle Dorcus parallelipipedus L. (Scarabaeoidea: Lucanidae) is analyzed using conventional Giemsa staining, banding techniques and ribosomal fluorescent in situ hybridization (rDNA FISH). rDNA FISH remains the unique tool for providing a clear-cut identification of Nucleolar Organizer Regions (NORs) when conventional banding methods such as silver- and CMA3-staining proved to be inadequate. The dull, homogeneous CMA3 fluorescence of all chromosomes indicates the absence of markedly GC rich compartmentalized regions in D. parallelipipedus genome. Silver impregnation inadequacy in detecting NOR regions is to be sought in the unusual extensive silver stainability of heterochromatic material which, on the contrary of what stated for vertebrates, seems to be a common feature in Scarabaeoidea species
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