Micrometric particles twodimensional self-assembly during drying of liquid film

We computed the self-organisation process of a monodisperse collection of spherical micrometric particles trapped in a two-dimensional (2D) thin liquid film isothermally dried on a chemically inert substrate. The substrate is either flat or indented to create linear stripes on its surface. The numerical results are illustrated and discussed in the light of experimental ones obtained from the drying of diamond particles water based suspension ($d_{50} = 10 \mu m$) on a glass substrate. The drying of the suspension on a flat substrate leads to the formation of linear patterns and small clusters of micrometric particles distributed over the whole surface of the substrate, whereas the drying of the suspension on a indented substrate leads to the aggregation of the particles along one side of the stripe which has a higher roughness than the other side of the stripe. This is an easy experimental way to obtain colloidal selforganized patterns.Comment: 16 pages 7 figure

A Short Counterexample Property for Safety and Liveness Verification of Fault-tolerant Distributed Algorithms

Distributed algorithms have many mission-critical applications ranging from embedded systems and replicated databases to cloud computing. Due to asynchronous communication, process faults, or network failures, these algorithms are difficult to design and verify. Many algorithms achieve fault tolerance by using threshold guards that, for instance, ensure that a process waits until it has received an acknowledgment from a majority of its peers. Consequently, domain-specific languages for fault-tolerant distributed systems offer language support for threshold guards. We introduce an automated method for model checking of safety and liveness of threshold-guarded distributed algorithms in systems where the number of processes and the fraction of faulty processes are parameters. Our method is based on a short counterexample property: if a distributed algorithm violates a temporal specification (in a fragment of LTL), then there is a counterexample whose length is bounded and independent of the parameters. We prove this property by (i) characterizing executions depending on the structure of the temporal formula, and (ii) using commutativity of transitions to accelerate and shorten executions. We extended the ByMC toolset (Byzantine Model Checker) with our technique, and verified liveness and safety of 10 prominent fault-tolerant distributed algorithms, most of which were out of reach for existing techniques.Comment: 16 pages, 11 pages appendi

A model checking approach to the parameter estimation of biochemical pathways

Model checking has historically been an important tool to verify models of a wide variety of systems. Typically a model has to exhibit certain properties to be classed ‘acceptable’. In this work we use model checking in a new setting; parameter estimation. We characterise the desired behaviour of a model in a temporal logic property and alter the model to make it conform to the property (determined through model checking). We have implemented a computational system called MC2(GA) which pairs a model checker with a genetic algorithm. To drive parameter estimation, the fitness of set of parameters in a model is the inverse of the distance between its actual behaviour and the desired behaviour. The model checker used is the simulation-based Monte Carlo Model Checker for Probabilistic Linear-time Temporal Logic with numerical constraints, MC2(PLTLc). Numerical constraints as well as the overall probability of the behaviour expressed in temporal logic are used to minimise the behavioural distance. We define the theory underlying our parameter estimation approach in both the stochastic and continuous worlds. We apply our approach to biochemical systems and present an illustrative example where we estimate the kinetic rate constants in a continuous model of a signalling pathway

Real-Time Synthesis is Hard!

We study the reactive synthesis problem (RS) for specifications given in Metric Interval Temporal Logic (MITL). RS is known to be undecidable in a very general setting, but on infinite words only; and only the very restrictive BRRS subcase is known to be decidable (see D'Souza et al. and Bouyer et al.). In this paper, we precise the decidability border of MITL synthesis. We show RS is undecidable on finite words too, and present a landscape of restrictions (both on the logic and on the possible controllers) that are still undecidable. On the positive side, we revisit BRRS and introduce an efficient on-the-fly algorithm to solve it

Using Flow Specifications of Parameterized Cache Coherence Protocols for Verifying Deadlock Freedom

We consider the problem of verifying deadlock freedom for symmetric cache coherence protocols. In particular, we focus on a specific form of deadlock which is useful for the cache coherence protocol domain and consistent with the internal definition of deadlock in the Murphi model checker: we refer to this deadlock as a system- wide deadlock (s-deadlock). In s-deadlock, the entire system gets blocked and is unable to make any transition. Cache coherence protocols consist of N symmetric cache agents, where N is an unbounded parameter; thus the verification of s-deadlock freedom is naturally a parameterized verification problem. Parametrized verification techniques work by using sound abstractions to reduce the unbounded model to a bounded model. Efficient abstractions which work well for industrial scale protocols typically bound the model by replacing the state of most of the agents by an abstract environment, while keeping just one or two agents as is. However, leveraging such efficient abstractions becomes a challenge for s-deadlock: a violation of s-deadlock is a state in which the transitions of all of the unbounded number of agents cannot occur and so a simple abstraction like the one above will not preserve this violation. In this work we address this challenge by presenting a technique which leverages high-level information about the protocols, in the form of message sequence dia- grams referred to as flows, for constructing invariants that are collectively stronger than s-deadlock. Efficient abstractions can be constructed to verify these invariants. We successfully verify the German and Flash protocols using our technique

Duality in Perturbation Theory and the Quantum Adiabatic Approximation

Duality is considered for the perturbation theory by deriving, given a series solution in a small parameter, its dual series with the development parameter being the inverse of the other. A dual symmetry in perturbation theory is identified. It is then shown that the dual to the Dyson series in quantum mechanics is given by a recent devised series having the adiabatic approximation as leading order. A simple application of this result is given by rederiving a theorem for strongly perturbed quantum systems.Comment: 9 pages, revtex. Improved english and presentation. Final version accepted for publication by Physical Review

Incremental bounded model checking for embedded software

Program analysis is on the brink of mainstream usage in embedded systems development. Formal verification of behavioural requirements, finding runtime errors and test case generation are some of the most common applications of automated verification tools based on bounded model checking (BMC). Existing industrial tools for embedded software use an off-the-shelf bounded model checker and apply it iteratively to verify the program with an increasing number of unwindings. This approach unnecessarily wastes time repeating work that has already been done and fails to exploit the power of incremental SAT solving. This article reports on the extension of the software model checker CBMC to support incremental BMC and its successful integration with the industrial embedded software verification tool BTC EMBEDDED TESTER. We present an extensive evaluation over large industrial embedded programs, mainly from the automotive industry. We show that incremental BMC cuts runtimes by one order of magnitude in comparison to the standard non-incremental approach, enabling the application of formal verification to large and complex embedded software. We furthermore report promising results on analysing programs with arbitrary loop structure using incremental BMC, demonstrating its applicability and potential to verify general software beyond the embedded domain

Epigenetic regulation of 5α reductase-1 underlies adaptive plasticity of reproductive function and pubertal timing

Women facing increased energetic demands in childhood commonly have altered adult ovarian activity and shorter reproductive lifespan, possibly comprising a strategy to optimize reproductive success. Here we sought to understand the mechanisms of early-life programming of reproductive function, by integrating analysis of reproductive tissues in an appropriate mouse model with methylation analysis of proxy tissue DNA in a well-characterized population of Bangladeshi migrants in the UK. Bangladeshi women whose childhood was in Bangladesh were found to have later pubertal onset and lower age-matched ovarian reserve than Bangladeshi women who grew-up in England. Subsequently we aimed to explore the potential relevance to the altered reproductive phenotype of one of the genes that emerged from the screens. Results: Of the genes associated with differential methylation in the Bangladeshi women whose childhood was in Bangladesh as compared to Bangladeshi women who grew up in the UK, 13 correlated with altered expression of the orthologous gene in the mouse model ovaries. These mice had delayed pubertal onset and a smaller ovarian reserve compared to controls. The most relevant of these genes for reproductive function appeared to be SRD5A1, which encodes the steroidogenic enzyme 5α reductase-1. SRD5A1 was more methylated at the same transcriptional enhancer in mice ovaries as in the women’s buccal DNA, and its expression was lower in the hypothalamus of the mice as well, suggesting a possible role in the central control of reproduction. The expression of Kiss1 and Gnrh was also lower in these mice compared to controls, and inhibition of 5α reductase-1 reduced Kiss1 and Gnrh mRNA levels and blocked GnRH release in GnRH neuronal cell cultures. Crucially, we show that inhibition of this enzyme in female mice in vivo delayed pubertal onset. Conclusions: SRD5A1/5α reductase-1 responds epigenetically to the environment and its down-regulation appears to alter the reproductive phenotype. These findings help to explain diversity in reproductive characteristics and how they are shaped by early-life environment, and reveal novel pathways that might be targeted to mitigate health issues caused by life-history trade-offs

Distributed Synthesis in Continuous Time

We introduce a formalism modelling communication of distributed agents strictly in continuous-time. Within this framework, we study the problem of synthesising local strategies for individual agents such that a specified set of goal states is reached, or reached with at least a given probability. The flow of time is modelled explicitly based on continuous-time randomness, with two natural implications: First, the non-determinism stemming from interleaving disappears. Second, when we restrict to a subclass of non-urgent models, the quantitative value problem for two players can be solved in EXPTIME. Indeed, the explicit continuous time enables players to communicate their states by delaying synchronisation (which is unrestricted for non-urgent models). In general, the problems are undecidable already for two players in the quantitative case and three players in the qualitative case. The qualitative undecidability is shown by a reduction to decentralized POMDPs for which we provide the strongest (and rather surprising) undecidability result so far