相关论文: Types for BioAmbients

We introduce a family of deep-learning architectures for inter-sentence relation extraction, i.e., relations where the participants are not necessarily in the same sentence. We apply these architectures to an important use case in the…

We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…

Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific…

We propose a process calculus, named AbC, to study the behavioural theory of interactions in collective-adaptive systems by relying on attribute-based communication. An AbC system consists of a set of parallel components each of which is…

A spacially extended model of the collective behavior of a large number of locally acting organisms is proposed in which organisms move probabilistically between local cells in space, but with weights dependent on local morphogenetic…

We present the first session typing system guaranteeing request-response liveness properties for possibly non-terminating communicating processes. The types augment the branch and select types of the standard binary session types with a set…

Emerging network scenarios require the development of solid large-scale situated systems. Unfortunately, the diffusion/aggregation computational processes therein often introduce a source of complexity that hampers predictability of the…

In order to develop systems capable of modeling artificial life, we need to identify, which systems can produce complex behavior. We present a novel classification method applicable to any class of deterministic discrete space and time…

At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…

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…

Concurrent pattern calculus (CPC) drives interaction between processes by comparing data structures, just as sequential pattern calculus drives computation. By generalising from pattern matching to pattern unification, interaction becomes…

Bacteria possess diverse mechanisms to regulate their motility in response to environmental and physiological signals, enabling them to navigate complex habitats and adapt their behavior. Among these mechanisms, interspecies recognition…

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…

Living systems, from single cells to higher vertebrates, receive a continuous stream of non-stationary inputs that they sense, e.g., via cell surface receptors or sensory organs. Integrating these time-varying, multi-sensory, and often…

We introduce contextual behavioural metrics (CBMs) as a novel way of measuring the discrepancy in behaviour between processes, taking into account both quantitative aspects and contextual information. This way, process distances by…

Quantum collision models allow for the dynamics of open quantum systems to be described by breaking the environment into small segments, typically consisting of non-interacting harmonic oscillators or two-level systems. This work introduces…

Taha and Nielsen have developed a multi-stage calculus {\lambda}{\alpha} with a sound type system using the notion of environment classifiers. They are special identifiers, with which code fragments and variable declarations are annotated,…

What determines whether an organism or collective will survive under particular conditions? This question is asked across the life sciences when determining adaptive fit, developing efficacious treatments for diseases, and assessing the…

The Calculus of Wrapped Compartments (CWC) is a recently proposed modelling language for the representation and simulation of biological systems behaviour. Although CWC has no explicit structure modelling a spatial geometry, its compartment…

Virtually every biological function emerges through the organization of molecules in time and space. Consequently, a major challenge in statistical physics is to uncover the universal principles governing macromolecular self-organization…