Conformation of a Polyelectrolyte Complexed to a Like-Charged Colloid

We report results from a molecular dynamics (MD) simulation on the conformations of a long flexible polyelectrolyte complexed to a charged sphere, \textit{both negatively charged}, in the presence of neutralizing counterions in the strong Coulomb coupling regime. The structure of this complex is very sensitive to the charge density of the polyelectrolyte. For a fully charged polyelectrolyte the polymer forms a dense two-dimensional "disk", whereas for a partially charged polyelectrolyte the monomers are spread over the colloidal surface. A mechanism involving the \textit{overcharging} of the polyelectrolyte by counterions is proposed to explain the observed conformations.Comment: 4 pages, 4 figures (6 EPS files

A Negative Result on Inductive Inference of Extended Pattern Languages

A negative result on inductive inference of extended pattern language

Extended Computation Tree Logic

We introduce a generic extension of the popular branching-time logic CTL which refines the temporal until and release operators with formal languages. For instance, a language may determine the moments along a path that an until property may be fulfilled. We consider several classes of languages leading to logics with different expressive power and complexity, whose importance is motivated by their use in model checking, synthesis, abstract interpretation, etc. We show that even with context-free languages on the until operator the logic still allows for polynomial time model-checking despite the significant increase in expressive power. This makes the logic a promising candidate for applications in verification. In addition, we analyse the complexity of satisfiability and compare the expressive power of these logics to CTL* and extensions of PDL

Formal Analysis of the ACE Specification for Cache Coherent Systems-on-Chip

Abstract. System-on-Chip (SoC) architectures integrate now many different components, such as processors, accelerators, memory, and I/O blocks, some but not all of which may have caches. Because the validation effort with simulation-based validation techniques, as currently used in industry, grows exponentially with the complexity of the SoC, we investigate in this paper the use of formal verification techniques. More precisely, we use the CADP toolbox to develop and validate a generic formal model of an SoC compliant with the recent ACE specification proposed by ARM to implement system-level coherency.

Distributed on-the-fly model checking and test case generation

Abstract. The explicit-state analysis of concurrent systems must handle large state spaces, which correspond to realistic systems containing many parallel processes and complex data structures. In this paper, we combine the on-the-fly approach (incremental construction of the state space) and the distributed approach (state space exploration using several machines connected by a network) in order to increase the computing power of analysis tools. To achieve this, we propose Mb-DSolve, a new algorithm for distributed on-the-fly resolution of multiple block, alternation-free boolean equation systems (Bess). First, we apply Mb-DSolve to perform distributed on-the-fly model checking of alternation-free modal µ-calculus, using the standard encoding of the problem as a Bes resolution. The speedup and memory consumption obtained on large state spaces improve over previously published approaches based on game graphs. Next, we propose an encoding of the conformance test case generation problem as a Bes resolution from which a diagnostic representing the complete test graph (Ctg) is built. By applying Mb-DSolve, we obtain a distributed on-the-fly test case generator whose capabilities scale up smoothly w.r.t. well-established existing sequential tools.

Learning Linearly Separable Languages

Abstract. This paper presents a novel paradigm for learning languages that consists of mapping strings to an appropriate high-dimensional feature space and learning a separating hyperplane in that space. It initiates the study of the linear separability of automata and languages by examining the rich class of piecewise-testable languages. It introduces a high-dimensional feature map and proves piecewise-testable languages to be linearly separable in that space. The proof makes use of word combinatorial results relating to subsequences. It also shows that the positive definite kernel associated to this embedding can be computed in quadratic time. It examines the use of support vector machines in combination with this kernel to determine a separating hyperplane and the corresponding learning guarantees. It also proves that all languages linearly separable under a regular finite cover embedding, a generalization of the embedding we used, are regular.

Precise Parameter Synthesis for Stochastic Biochemical Systems

We consider the problem of synthesising rate parameters for stochastic biochemical networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of quantitative properties, the probability of satisfying the property is maximised/minimised. We develop algorithms based on the computation of lower and upper bounds of the probability, in conjunction with refinement and sampling, which yield answers that are precise to within an arbitrarily small tolerance value. Our methods are efficient and improve on existing approximate techniques that employ discretisation and refinement. We evaluate the usefulness of the methods by synthesising rates for two biologically motivated case studies, including the reliability analysis of a DNA walker

Precise Parameter Synthesis for Stochastic Biochemical Systems

We consider the problem of synthesising rate parameters for stochastic biochemical networks so that a given time-bounded CSL property is guaranteed to hold, or, in the case of quantitative properties, the probability of satisfying the property is maximised/minimised. We develop algorithms based on the computation of lower and upper bounds of the probability, in conjunction with refinement and sampling, which yield answers that are precise to within an arbitrarily small tolerance value. Our methods are efficient and improve on existing approximate techniques that employ discretisation and refinement. We evaluate the usefulness of the methods by synthesising rates for two biologically motivated case studies, including the reliability analysis of a DNA walker