Related papers: Embedding arbitrary Boolean circuits into fungal a…
We propose a general approach to compute the seed sensitivity, that can be applied to different definitions of seeds. It treats separately three components of the seed sensitivity problem - a set of target alignments, an associated…
We study a two-dimensional semi-totalistic binary cell-state cellular automaton, which imitates a reversible precipitation in an abstract chemical medium. The systems exhibits a non-trivial growth and nucleation. We demonstrate how basic…
This paired article aims to develop an automated and programmable biochemical fully connected neural network (BFCNN) with solid theoretical support. In Part I, a concrete design for BFCNN is presented, along with the validation of the…
For a class of one-dimensional cellular automata, we review and complete the characterization of the invariant measures (in particular, all invariant phase separation measures), the rate of convergence to equilibrium, and the derivation of…
Starting from integrable cellular automata we present a novel form of Painlev\'e equations. These equations are discrete in both the independent variable and the dependent one. We show that they capture the essence of the behavior of the…
The fixed point construction is a method for designing tile sets and cellular automata with highly nontrivial dynamical and computational properties. It produces an infinite hierarchy of systems where each layer simulates the next one. The…
A ``sandpile'' cellular automaton achieves complex temporal correlations, like a $1/f$ spectrum, if the position where it is perturbed diffuses slowly rather than changing completely at random, showing that the spatial correlations of the…
It is shown that for the N-neighbor and K-state cellular automata, the class II, class III and class IV patterns coexist at least in the range $\frac{1}{K} \le \lambda \le 1-\frac{1}{K} $. The mechanism which determines the difference…
Complex systems in a wide variety of areas such as biological modeling, image processing, and language recognition can be modeled using networks of very simple machines called finite automata. Connecting subsystems modeled using finite…
Fungal electronics is a family of living electronic devices made of mycelium bound composites or pure mycelium. Fungal electronic devices are capable of changing their impedance and generating spikes of electrical potential in response to…
We present a method to eliminate redundancy in the transition tables of Boolean automata: schema redescription with two symbols. One symbol is used to capture redundancy of individual input variables, and another to capture permutability in…
This paper studies three classes of cellular automata from a computational point of view: freezing cellular automata where the state of a cell can only decrease according to some order on states, cellular automata where each cell only makes…
We study the problem of determinizing $\omega$-automata whose acceptance condition is defined on the transitions using Boolean formulas, also known as transition-based Emerson-Lei automata (TELA). The standard approach to determinize TELA…
The class of Boolean combinations of tree languages recognized by deterministic top-down tree automata (also known as deterministic root-to-frontier automata) is studied. The problem of determining for a given regular tree language whether…
The Tile Automata (TA) model describes self-assembly systems in which monomers can build structures and transition with an adjacent monomer to change their states. This paper shows that seeded TA is a non-committal intrinsically universal…
A Boolean network model of the cell-cycle regulatory network of fission yeast (Schizosaccharomyces Pombe) is constructed solely on the basis of the known biochemical interaction topology. Simulating the model in the computer, faithfully…
Wheeler automata were introduced in 2017 as a tool to generalize existing indexing and compression techniques based on the Burrows-Wheeler transform. Intuitively, an automaton is said to be Wheeler if there exists a total order on its…
Let $E$ be a virtually central extension of the group $G$ by a finitely generated abelian group $A$. We show that $E$ carries a biautomatic structure if and only if $G$ has a biautomatic structure $L$ for which the cohomology class of the…
The work introduces a 3D cellular automaton model for the spatial and crystallographic prediction of spherulite growth phenomena in polymers at the mesoscopic scale. The automaton is discrete in time, real space, and orientation space. The…
The goal of this tutorial is to promote interest in the study of random Boolean networks (RBNs). These can be very interesting models, since one does not have to assume any functionality or particular connectivity of the networks to study…