Related papers: A Calculus of Located Entities
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…
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…
The hippocampus supports spatial navigation by encoding cognitive maps through collective place cell activity. We model the place cell population as non-negative spatial embeddings derived from the spectral decomposition of multi-step…
We describe a process calculus featuring high level constructs for component-oriented programming in a distributed setting. We propose an extension of the higher-order pi-calculus intended to capture several important mechanisms related to…
We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the…
Bigraphs are a universal computational modelling formalism for the spatial and temporal evolution of a system in which entities can be added and removed. We extend bigraphs to probablistic bigraphs, and then again to action bigraphs, which…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
We introduce a modified model of random walk, and then develop two novel clustering algorithms based on it. In the algorithms, each data point in a dataset is considered as a particle which can move at random in space according 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…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
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…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
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…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
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…
We describe a novel approach to statistical learning from particles tracked while moving in a random environment. The problem consists in inferring properties of the environment from recorded snapshots. We consider here the case of a fluid…
In this paper physical multi-scale processes governed by their own principles for evolution or equilibrium on each scale are coupled by matching the stored and dissipated energy, in line with the Hill-Mandel principle. In our view the…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
We propose that a quantum particle in a potential in one space dimension can be described by a probabilistic cellular automaton. While the simple updating rule of the automaton is deterministic, the probabilistic description is introduced…
Discrete time, spatially extended models play an important role in ecology, modelling population dynamics of species ranging from micro-organisms to birds. An important question is how 'bottom up', individual-based models can be…