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Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
Cellular automata provide a fascinating class of dynamical systems capable of diverse complex behavior. These include simplified models for many phenomena seen in nature. Among other things, they provide insight into self-organized…
Cellular automata are a set of computational models in discrete space that have a discrete time evolution defined by neighbourhood rules. They are used to simulate many complex systems in physics and science in general. In this work,…
The periodic swarming of bacteria is one of the simplest examples for pattern formation produced by the self-organized collective behavior of a large number of organisms. In the spectacular colonies of Proteus mirabilis (the most common…
Biological systems excel at building spatial structures on scales ranging from nanometers to kilometers and exhibit temporal patterning from milliseconds to years. One approach that nature has taken to accomplish this relies on the…
State-of-the-art review of cellular automata, cellular automata for partial differential equations, differential equations for cellular automata and pattern formation in biology and engineering.
In this paper I describe a cellular automaton model of a multi-species ecosystem, suitable for the study of emergent properties of macroevolution. Unlike majority of ecological models, the number of coexisting species is not fixed. Starting…
In this paper we present two interesting properties of stochastic cellular automata that can be helpful in analyzing the dynamical behavior of such automata. The first property allows for calculating cell-wise probability distributions over…
Here I describe a view of the evolution of cellular automata that allows to operate on larger structures. Instead of calculating the next state of all cells in one step, the method here developed uses a time slice that can proceed at…
We construct a two dimensional Cellular Automata based model for the description of pedestrian dynamics. Wide range of complicated pattern formation phenomena in pedestrian dynamics are described in the model, e.g. lane formation, jams in a…
Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits.…
Eukaryotic cells and intracellular pathogens such as bacteria or viruses utilize the actin polymerization machinery to propel themselves forward. Thereby, the onset of motion and choice of direction may be the result of a spontaneous…
Models based on surfactant driven instabilities have been employed to describe pattern formation by swarming bacteria. However, by definition, such models cannot account for the effect of bacterial sensing and decision making. Here we…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
A simulation approach to the stochastic growth of bacterial towers is presented, in which a non-uniform and finite nutrient supply essentially determines the emerging structure through elementary chemotaxis. The method is based on cellular…
We study colonies of non-motile, rod-shaped bacteria growing on solid substrates. In our model, bacteria interact purely mechanically, by pushing each other away as they grow, and consume a diffusing nutrient. We show that mechanical…
We study the growth of a population of bacteria in a dynamical hostile environment corresponding to the immune system of the colonised organism. The immune cells evolve as subcritical open clusters of oriented percolation and are…
The effect of mechanical interactions between cells in the spreading of bacterial populations was investigated in one-dimensional space. A continuum-mechanics approach, comprising cell migration, proliferation, and exclusion processes, was…
The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in…
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to…