Related papers: A Type System for a Stochastic CLS
The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. We enrich this calculus with a type discipline to guarantee the soundness of reduction rules with respect…
In this paper we present a variant of the Calculus of Looping Sequences (CLS for short) with global and local rewrite rules. While global rules, as in CLS, are applied anywhere in a given term, local rules can only be applied in the…
The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
Stochastic processes offer a flexible mathematical formalism to model and reason about systems. Most analysis tools, however, start from the premises that models are fully specified, so that any parameters controlling the system's dynamics…
Modelling is an essential procedure in analyzing and controlling a given logical dynamic system (LDS). It has been proved that deterministic LDS can be modeled as a linear-like system using algebraic state space representation. However, due…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
The Calculus of Wrapped Compartments (CWC) is a variant of the Calculus of Looping Sequences (CLS). While keeping the same expressiveness, CWC strongly simplifies the development of automatic tools for the analysis of biological systems.…
The Stochastic Calculus of Looping Sequences (SCLS) is a recently proposed modelling language for the representation and simulation of biological systems behaviour. It has been designed with the aim of combining the simplicity of notation…
An approach to analyse the properties of a particle system is to compare it with different processes to understand when one of them is larger than other ones. The main technique for that is coupling, which may not be easy to construct. We…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
Stochastic Spatio-Temporal processes are prevalent across domains ranging from modeling of plasma to the turbulence in fluids to the wave function of quantum systems. This letter studies a measure-theoretic description of such systems by…
We propose PALPS, a Process Algebra with Locations for Population Systems. PALPS allows us to produce spatially-explicit, individual-based models and to reason about their behavior. Our calculus has two levels: at the first level we may…
We describe stochastic calculus in the context of processes that are driven by an adapted point process of locally finite intensity and are differentiable between jumps. This includes Markov chains as well as non-Markov processes. By…
We present a calculus that models a form of process interaction based on copyless message passing, in the style of Singularity OS. The calculus is equipped with a type system ensuring that well-typed processes are free from memory faults,…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…
A syntactic model is presented for the specification of finite-state synchronous digital logic systems with complex input/output interfaces, which control the flow of data between opaque computational elements, and for the composition of…