Related papers: Bacteria inspired patterns grown with hyperbolic c…
We model an enclosed system of bacteria, whose motility-induced phase separation is coupled to slow population dynamics. Without noise, the system shows both static phase separation and a limit cycle, in which a rising global population…
Hybrid models of chemotaxis combine agent-based models of cells with partial differential equation models of extracellular chemical signals. In this paper, travelling wave properties of hybrid models of bacterial chemotaxis are…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
Biological evolution of a population is governed by the fitness landscape, which is a map from genotype to fitness. However, a fitness landscape depends on the organisms environment, and evolution in changing environments is still poorly…
We show that a behaviour analogous to degenerate hyperbolicity can occur in nearest-neighbour cellular automata (CA) with three states. We construct a 3-state rule by "lifting" elementary CA rule 140. Such "lifted" rule is equivalent to…
We consider the typical asymptotic behaviour of cellular automata of higher dimension (greater than 2). That is, we take an initial configuration at random according to a Bernoulli (i.i.d) probability measure, iterate some cellular…
Inspired by cellular growth and self-organization, Neural Cellular Automata (NCAs) have been capable of "growing" artificial cells into images, 3D structures, and even functional machines. NCAs are flexible and robust computational systems…
Immotile microbes inhabit nearly every environment on Earth, from soils and sediments to food matrices -- yet how they disperse through these physically confining environments is poorly understood. Here, we show that immotile microbial…
In this paper we propose an approach for measuring growth of complexity of emerging patterns in complex systems such as cellular automata. We discuss several ways how a metric for measuring the complexity growth can be defined. This…
This contribution belongs to a combinatorial approach to hyperbolic geometry and it is aimed at possible applications to computer simulations. It is based on the splitting method which was introduced by the author and which is reminded in…
Motivated by questions in biology and distributed computing, we investigate the behaviour of particular cellular automata, modelled as one-dimensional arrays of identical finite automata. We investigate what sort of self-stabilising…
An introduction to cellular automata (both deterministic and probabilistic) with examples. Definition of deterministic automata, dynamical properties, damage spreading and Lyapunov exponents; probabilistic automata and Markov processes,…
A transition from asymmetric to symmetric patterns in time-dependent extended systems is described. It is found that one dimensional cellular automata, started from fully random initial conditions, can be forced to evolve into complex…
We say that a Cellular Automata (CA) is coalescing when its execution on two distinct (random) initial configurations in the same asynchronous mode (the same cells are updated in each configuration at each time step) makes both…
This paper theoretically analyzes a phenomenological stochastic model for bacterial growth. This model comprises cell division and the linear growth of cells, where growth rates and cell cycles are drawn from lognormal distributions. We…
Cell tracking enables data extraction from time-lapse "cell movies" and promotes modeling biological processes at the single-cell level. We introduce a new fully automated computational strategy to track accurately cells across frames in…
We model the growth of a cell population using a piecewise deterministic Markov branching tree. In this model, each cell splits into two offspring at a division rate $B(x)$, which depends on its size $x$. The size of each cell increases…
The emergent spatial patterns generated by growing bacterial colonies have been the focus of intense study in physics during the last twenty years. Both experimental and theoretical investigations have made possible a clear qualitative…
In nature, microorganisms must often cope with hostile environmental conditions. To do so they have developed sophisticated cooperative behavior and intricate communication capabilities, such as: direct cell-cell physical interactions via…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…