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-nn,δ\delta 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 $\delta$, and to the depth $n$ of the observation along traces. Essentially, our soundness theorem establishes that, when a state $q$ satisfies a given formula up-to error $\delta$ and steps $n$, and $q$ is bisimilar to $q'$ up-to error $\delta'$ and enough steps, we prove that $q'$ also satisfies the formula up-to a suitable error $\delta"$ and steps $n$. The new error $\delta"$ is computed from $\delta$, $\delta'$ and the formula, and only depends linearly on $n$. 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