Geometric integrator for simulations in the canonical ensemble

In this work we introduce a geometric integrator for molecular dynamics simulations of physical systems in the canonical ensemble. In particular, we consider the equations arising from the so-called density dynamics algorithm with any possible type of thermostat and provide an integrator that preserves the invariant distribution. Our integrator thus constitutes a unified framework that allows the study and comparison of different thermostats and of their influence on the equilibrium and non-equilibrium (thermo-)dynamic properties of the system. To show the validity and the generality of the integrator, we implement it with a second-order, time-reversible method and apply it to the simulation of a Lennard-Jones system with three different thermostats, obtaining good conservation of the geometrical properties and recovering the expected thermodynamic results.Comment: 9 pages, 5 figure

A semantic deconstruction of session types

We investigate the semantic foundations of session types, by revisiting them in the abstract setting of labelled transition systems. The crucial insight is a simulation relation which generalises the usual syntax-directed notions of typing and subtyping, and encompasses both synchronous and asynchronous binary session types. This allows us to extend the session types theory to some common programming patterns which are not typically considered in the session types literature

Choreographies in Practice

Choreographic Programming is a development methodology for concurrent software that guarantees correctness by construction. The key to this paradigm is to disallow mismatched I/O operations in programs, called choreographies, and then mechanically synthesise distributed implementations in terms of standard process models via a mechanism known as EndPoint Projection (EPP). Despite the promise of choreographic programming, there is still a lack of practical evaluations that illustrate the applicability of choreographies to concrete computational problems with standard concurrent solutions. In this work, we explore the potential of choreographies by using Procedural Choreographies (PC), a model that we recently proposed, to write distributed algorithms for sorting (Quicksort), solving linear equations (Gaussian elimination), and computing Fast Fourier Transform. We discuss the lessons learned from this experiment, giving possible directions for the usage and future improvements of choreography languages

A Hierarchy of Scheduler Classes for Stochastic Automata

Stochastic automata are a formal compositional model for concurrent stochastic timed systems, with general distributions and non-deterministic choices. Measures of interest are defined over schedulers that resolve the nondeterminism. In this paper we investigate the power of various theoretically and practically motivated classes of schedulers, considering the classic complete-information view and a restriction to non-prophetic schedulers. We prove a hierarchy of scheduler classes w.r.t. unbounded probabilistic reachability. We find that, unlike Markovian formalisms, stochastic automata distinguish most classes even in this basic setting. Verification and strategy synthesis methods thus face a tradeoff between powerful and efficient classes. Using lightweight scheduler sampling, we explore this tradeoff and demonstrate the concept of a useful approximative verification technique for stochastic automata

Probabilistic Bisimulation: Naturally on Distributions

In contrast to the usual understanding of probabilistic systems as stochastic processes, recently these systems have also been regarded as transformers of probabilities. In this paper, we give a natural definition of strong bisimulation for probabilistic systems corresponding to this view that treats probability distributions as first-class citizens. Our definition applies in the same way to discrete systems as well as to systems with uncountable state and action spaces. Several examples demonstrate that our definition refines the understanding of behavioural equivalences of probabilistic systems. In particular, it solves a long-standing open problem concerning the representation of memoryless continuous time by memory-full continuous time. Finally, we give algorithms for computing this bisimulation not only for finite but also for classes of uncountably infinite systems

Behavioral types in programming languages

A recent trend in programming language research is to use behav- ioral type theory to ensure various correctness properties of large- scale, communication-intensive systems. Behavioral types encompass concepts such as interfaces, communication protocols, contracts, and choreography. The successful application of behavioral types requires a solid understanding of several practical aspects, from their represen- tation in a concrete programming language, to their integration with other programming constructs such as methods and functions, to de- sign and monitoring methodologies that take behaviors into account. This survey provides an overview of the state of the art of these aspects, which we summarize as the pragmatics of behavioral types

Using schedulers to test probabilistic distributed systems

This is the author's accepted manuscript. The final publication is available at Springer via http://dx.doi.org/10.1007/s00165-012-0244-5. Copyright © 2012, British Computer Society.Formal methods are one of the most important approaches to increasing the confidence in the correctness of software systems. A formal specification can be used as an oracle in testing since one can determine whether an observed behaviour is allowed by the specification. This is an important feature of formal testing: behaviours of the system observed in testing are compared with the specification and ideally this comparison is automated. In this paper we study a formal testing framework to deal with systems that interact with their environment at physically distributed interfaces, called ports, and where choices between different possibilities are probabilistically quantified. Building on previous work, we introduce two families of schedulers to resolve nondeterministic choices among different actions of the system. The first type of schedulers, which we call global schedulers, resolves nondeterministic choices by representing the environment as a single global scheduler. The second type, which we call localised schedulers, models the environment as a set of schedulers with there being one scheduler for each port. We formally define the application of schedulers to systems and provide and study different implementation relations in this setting

Tools and verification

This chapter presents different tools that have been developed inside the Sensoria project. Sensoria studied qualitative analysis techniques for verifying properties of service implementations with respect to their formal specifications. The tools presented in this chapter have been developed to carry out the analysis in an automated, or semi-automated, way. We present four different tools, all developed during the Sensoria project, exploiting new techniques and calculi from the Sensoria project itself

A tutorial on interactive Markov chains

Interactive Markov chains (IMCs) constitute a powerful sto- chastic model that extends both continuous-time Markov chains and labelled transition systems. IMCs enable a wide range of modelling and analysis techniques and serve as a semantic model for many industrial and scientific formalisms, such as AADL, GSPNs and many more. Applications cover various engineering contexts ranging from industrial system-on-chip manufacturing to satellite designs. We present a survey of the state-of-the-art in modelling and analysis of IMCs.\ud We cover a set of techniques that can be utilised for compositional modelling, state space generation and reduction, and model checking. The significance of the presented material and corresponding tools is highlighted through multiple case studies

Interaction of bone-dental implant with new ultra low modulus alloy using a numerical approach

International audienceAlthough mechanical stress is known as being a significant factor in bone remodeling, most implants are still made using materials that have a higher elastic stiffness than that of bones. Load transfer between the implant and the surrounding bones is much detrimental, and osteoporosis is often a consequence of such mechanical mismatch. The concept of mechanical biocompatibility has now been considered for more than a decade. However, it is limited by the choice of materials, mainly Ti-based alloys whose elastic properties are still too far from cortical bone. We have suggested using a bulk material in relation with the development of a new beta titanium-based alloy. Titanium is a much suitable biocompatible metal, and beta-titanium alloys such as metastable TiNb exhibit a very low apparent elastic modulus related to the presence of an orthorhombic martensite. The purpose of the present work has been to investigate the interaction that occurs between the dental implants and the cortical bone. 3D finite element models have been adopted to analyze the behaviour of the bone-implant system depending on the elastic properties of the implant, different types of implant geometry, friction force, and loading condition. The geometry of the bone has been adopted from a mandibular incisor and the surrounding bone. Occlusal static forces have been applied to the implants, and their effects on the bone-metal implant interface region have been assessed and compared with a cortical bone/ bone implant configuration. This work has shown that the low modulus implant induces a stress distribution closer to the actual physiological phenomenon, together with a better stress jump along the bone implant interface, regardless of the implant design