Related papers: Types for BioAmbients

In this paper we derive and analyse mean-field models for the dynamics of groups of individuals undergoing a random walk. The random motion of individuals is only influenced by the perceived densities of the different groups present as well…

From flocking birds to schooling fish, organisms interact to form collective dynamics across the natural world. Self-organization is present at smaller scales as well: cells interact and move during development to produce patterns in fish…

Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about…

The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Measurements of microbial abundances are key to learning the intricate network of interactions amongst microbes.…

When cells measure concentrations of chemical signals, they may average multiple measurements over time in order to reduce noise in their measurements. However, when cells are in a environment that changes over time, past measurements may…

We investigate the correspondence between classical noise and quantum environments. Although it has been known that the classical noise can be mapped to the quantum environments only for pure dephasing and infinite-temperature dissipation…

Living organisms process information to interact and adapt to their changing environment with the goal of finding food, mates or averting hazards. The structure of their niche has profound repercussions by both selecting their internal…

This essay provides a critical overview of the mathematical kinetic theory of active particles, which is used to model and study collective systems consisting of interacting living entities, such as those involved in behavior and evolution.…

Species sampling processes have long served as the fundamental framework for modeling random discrete distributions and exchangeable sequences. However, data arising from distinct but related sources require a broader notion of…

The biological hierarchy and the differences between living and non-living systems are considered from the standpoint of quantum mechanics. The hierarchical organization of biological systems requires hierarchical organization of quantum…

We argue that the analysis of agent/environment interactions should be extended to include the conventions and invariants maintained by agents throughout their activity. We refer to this thicker notion of environment as a lifeworld and…

The density matrix formalism which is widely used in the theory of measurements, quantum computing, quantum description of chemical and biological systems always imply the averaging over the states of the environment. In practice this is…

We introduce a minimal model of multilevel selection on structured populations, considering the interplay between game theory and population dynamics. Through a bottleneck process, finite groups are formed with cooperators and defectors…

Given a group action on a simplicial complex such that each simplex stabiliser admits a cocompact model of classifying space for proper actions, we give conditions implying the existence of a cocompact model of classifying space for proper…

Motivated by a model of an area-wide integrated pest management, we develop an interacting particle system evolving in a random environment. It is a generalised contact process in which the birth rate takes two possible values, determined…

Predicting where people can walk in a scene is important for many tasks, including autonomous driving systems and human behavior analysis. Yet learning a computational model for this purpose is challenging due to semantic ambiguity and a…

We review canonical experiments on systems that have pushed the boundary between the quantum and classical worlds towards much larger scales, and discuss their unique features that enable quantum coherence to survive. Because the types of…

Multistability is a phenomenon prevalent in many natural systems. In climate, for example, it allows the possibility of irreversible consequences on planetary scale as a result of climate change. Indeed, a climate ``tipping element'' is a…

In this paper we introduced an algebraic semantics for process algebra in form of abstract data types. For that purpose, we developed a particular type of algebra, the seed algebra, which describes exactly the behavior of a process within a…

In open systems, i.e. systems operating in an environment that they cannot control and with components that may join or leave, behaviors can arise as side effects of intensive components interaction. Finding ways to understand and design…