Related papers: A Process Calculus for Spatially-explicit Ecologic…
In this paper we extend PALPS, a process calculus proposed for the spatially-explicit individual-based modeling of ecological systems, with the notion of a policy. A policy is an entity for specifying orderings between the different…
We define a mean-field semantics for S-PALPS, a process calculus for spatially-explicit, individual-based modeling of ecological systems. The new semantics of S-PALPS allows an interpretation of the average behavior of a system as a set of…
Ecology studies the interactions between individuals, species and the environment. The ability to predict the dynamics of ecological systems would support the design and monitoring of control strategies and would help to address pressing…
We propose a variant of the CCS process algebra with new features aiming at allowing multiscale modelling of biological systems. In the usual semantics of process algebras for modelling biological systems actions are instantaneous. When…
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…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of Ordinary Differential Equations. Alternative approaches based on formal calculi, often derived from process algebras or term…
We propose a hybrid probabilistic process calculus for modelling and reasoning on cyber-physical systems (CPSs). The dynamics of the calculus is expressed in terms of a probabilistic labelled transition system in the SOS style of Plotkin.…
The Shape Calculus is a bio-inspired calculus for describing 3D shapes moving in a space. A shape forms a 3D process when combined with a behaviour. Behaviours are specified with a timed CCS-like process algebra using a notion of channel…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Mathematical models of spatial population dynamics typically focus on the interplay between dispersal events and birth/death processes. However, for many animal communities, significant arrangement in space can occur on shorter timescales,…
This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
We define BioScapeL, a stochastic pi-calculus in 3D-space. A novel aspect of BioScapeL is that entities have programmable locations. The programmer can specify a particular location where to place an entity, or a location relative to the…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
We study the spatial patterns formed by a system of interacting particles where the mobility of any individual is determined by the population crowding at two different spatial scales. In this way we model the behavior of some biological…
Various formal languages have been proposed in the literature for the individual-based modelling of ecological systems. These languages differ in their treatment of time and space. Each modelling language offers a distinct view and…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…
Spatial information is often expressed using qualitative terms such as natural language expressions instead of coordinates; reasoning over such terms has several practical applications, such as bus routes planning. Representing and…
This paper deals with the probabilistic behaviours of distributed systems described by a process calculus considering both probabilistic internal choices and nondeterministic external choices. For this calculus we define and study a typing…
Population protocols are a model of distributed computation intended for the study of networks of independent computing agents with dynamic communication structure. Each agent has a finite number of states, and communication opportunities…