Fungal Automata

2020 ◽  
Vol 29 (4) ◽  
pp. 759-778
Author(s):  
Andrew Adamatzky ◽  
◽  
Eric Goles ◽  
Genaro J. Martínez ◽  
Michail-Antisthenis Tsompanas ◽  
...  
Keyword(s):  
Cellular Automaton ◽  
State Transition ◽  
Fungal Mycelium ◽  
Information Dynamics ◽  
Binary State ◽  
Eca Rules ◽  
Previous State ◽  
Single Hypha ◽  
Elementary Cellular Automaton ◽  
The One

We study a cellular automaton (CA) model of information dynamics on a single hypha of a fungal mycelium. Such a filament is divided in compartments (here also called cells) by septa. These septa are invaginations of the cell wall and their pores allow for the flow of cytoplasm between compartments and hyphae. The septal pores of the fungal phylum of the Ascomycota can be closed by organelles called Woronin bodies. Septal closure is increased when the septa become older and when exposed to stress conditions. Thus, Woronin bodies act as informational flow valves. The one-dimensional fungal automaton is a binary-state ternary neighborhood CA, where every compartment follows one of the elementary cellular automaton (ECA) rules if its pores are open and either remains in state 0 (first species of fungal automata) or its previous state (second species of fungal automata) if its pores are closed. The Woronin bodies closing the pores are also governed by ECA rules. We analyze a structure of the composition space of cell-state transition and pore-state transition rules and the complexity of fungal automata with just a few Woronin bodies, and exemplify several important local events in the automaton dynamics.

Classifying elementary cellular automata using compressibility, diversity and sensitivity measures

2014 ◽  
Vol 25 (03) ◽  
pp. 1350098 ◽  
Author(s):  
Shigeru Ninagawa ◽  
Andrew Adamatzky
Keyword(s):  
Cellular Automata ◽  
Cellular Automaton ◽  
Initial Conditions ◽  
Morphological Diversity ◽  
Compression Algorithm ◽  
One Dimensional ◽  
Elementary Cellular Automata ◽  
Eca Rules ◽  
Substantial Correlation ◽  
Elementary Cellular Automaton

An elementary cellular automaton (ECA) is a one-dimensional, synchronous, binary automaton, where each cell update depends on its own state and states of its two closest neighbors. We attempt to uncover correlations between the following measures of ECA behavior: compressibility, sensitivity and diversity. The compressibility of ECA configurations is calculated using the Lempel–Ziv (LZ) compression algorithm LZ78. The sensitivity of ECA rules to initial conditions and perturbations is evaluated using Derrida coefficients. The generative morphological diversity shows how many different neighborhood states are produced from a single nonquiescent cell. We found no significant correlation between sensitivity and compressibility. There is a substantial correlation between generative diversity and compressibility. Using sensitivity, compressibility and diversity, we uncover and characterize novel groupings of rules.

scholarly journals Modeling of fungal mycelium growth by fourth-class continuous stochastic cellular automaton with continuously defined growth conditions

2017 ◽  
Vol 6 (4) ◽  
pp. 98-102
Author(s):  
Anatoliy Sergeevich Shumilov ◽  
Sergey Alexandrovich Blagodatsky
Keyword(s):  
Spatial Structure ◽  
Cellular Automaton ◽  
Colony Growth ◽  
Growth Conditions ◽  
Growth Patterns ◽  
Fungal Mycelium ◽  
Mycelium Growth ◽  
Proposed Model ◽  
Area Unit ◽  
Fungal Colony

The aim of this work was to simulate the growth and spatial structure of the fungal mycelium using a cellular automaton based on the synthesis of various model approaches. The spatial structure of the mycelium is described in the structural submodel of the cellular automaton, which determines the growth rate in the direction of larger resource amount and the number of branches of the mycelium per area unit. The amount of available substrate determines the probability of unidirectional apical growth. Another, biochemical part of the model allows us to describe the rate of transport of resources into the cell, their transport within the mycelium, and also their excretion, and is intended to describe the vertical and horizontal migration in the soil of two nutrients. The proposed model makes it possible to quantitatively describe such a feature of fungal colony growth as more active absorption of resources by external cells, compared to central ones due to separation of transport resources into active and passive resources. The active transport was described using the Michaelis-Menten kinetics. We were able to simulate the stockpiling of surplus resources and their redistribution over the mycelium after the exhaustion of reserves in the external environment, and also to simulate typical growth patterns of mycelial colonies that were observed in experiments published in the literature.

A 3D Cellular Automaton for Cell Differentiation in a Solid Tumor with Plasticity

2018 ◽  
Vol 13 (01) ◽  
pp. 19-28 ◽  
Author(s):  
David H. Margarit ◽  
Lilia Romanelli ◽  
Alejandro J. Fendrik
Keyword(s):  
Stem Cells ◽  
Cell Differentiation ◽  
Cancer Stem Cells ◽  
Cellular Automaton ◽  
Solid Tumor ◽  
Spherical Symmetry ◽  
Differentiated Cells ◽  
Previous State

A model with spherical symmetry is proposed. We analyze the appropriate parameters of cell differentiation for different kinds of cells (Cancer Stem Cells (CSC) and Differentiated Cells (DC)). The plasticity (capacity to return from a DC to its previous state of CSC) is taken into account. Following this hypothesis, the dissemination of CSCs to another organ is analyzed. The location of the cells in the tumor and the plasticity range for possible metastasis is discussed.

scholarly journals A transcriptional roadmap for 2C-like–to–pluripotent state transition

2020 ◽  
Vol 6 (22) ◽  
pp. eaay5181 ◽  
Author(s):  
Xudong Fu ◽  
Mohamed Nadhir Djekidel ◽  
Yi Zhang
Keyword(s):  
Intermediate State ◽  
State Transition ◽  
Embryonic Stem ◽  
Mouse Embryonic Stem Cell ◽  
Small Cell ◽  
Molecular Event ◽  
Cell Stage ◽  
Pluripotent State ◽  
Transcriptional Dynamics ◽  
The One

In mouse embryonic stem cell (ESC), a small cell population displays totipotent features by expressing a set of genes that are transiently active in 2-cell–stage embryos. These 2-cell–like (2C-like) cells spontaneously transit back into the pluripotent state. We previously dissected the transcriptional dynamics of the transition from pluripotency to the totipotent 2C-like state and identified factors that modulate the process. However, how 2C-like cells transit back into the pluripotent state remains largely unknown. In this study, we analyzed the transcriptional dynamics from the 2C-like state to pluripotent ESCs and identified an intermediate state. The intermediate state characterized by two-wave step up-regulation of pluripotent genes is different from the one observed during the 2C-like entry transition. Nonsense-mediated Dux mRNA decay plays an important role in the 2C-like state exit. Thus, our study not only provides a transcriptional roadmap for 2C-like–to–pluripotent state transition but also reveals a key molecular event driving the transition.

scholarly journals Characterization of the Evolution of Nonlinear Uniform Cellular Automata in the Light of Deviant States

2011 ◽  
Vol 2011 ◽  
pp. 1-16 ◽  
Author(s):  
Pabitra Pal Choudhury ◽  
Sudhakar Sahoo ◽  
Mithun Chakraborty
Keyword(s):  
Cellular Automata ◽  
Cellular Automaton ◽  
Boolean Functions ◽  
State Transition ◽  
The State ◽  
Transition Diagram ◽  
One Dimensional ◽  
State Transition Diagram ◽  
Linear Rule

Dynamics of a nonlinear cellular automaton (CA) is, in general asymmetric, irregular, and unpredictable as opposed to that of a linear CA, which is highly systematic and tractable, primarily due to the presence of a matrix handle. In this paper, we present a novel technique of studying the properties of the State Transition Diagram of a nonlinear uniform one-dimensional cellular automaton in terms of its deviation from a suggested linear model. We have considered mainly elementary cellular automata with neighborhood of size three, and, in order to facilitate our analysis, we have classified the Boolean functions of three variables on the basis of number and position(s) of bit mismatch with linear rules. The concept of deviant and nondeviant states is introduced, and hence an algorithm is proposed for deducing the State Transition Diagram of a nonlinear CA rule from that of its nearest linear rule. A parameter called the proportion of deviant states is introduced, and its dependence on the length of the CA is studied for a particular class of nonlinear rules.

Short Time Dynamics of an Irreversible Probabilistic Cellular Automaton

1998 ◽  
Vol 12 (21) ◽  
pp. 873-879 ◽  
Author(s):  
T. Tomé ◽  
J. R. Drugowich de Fel Icio
Keyword(s):  
Ising Model ◽  
Cellular Automaton ◽  
Early Time ◽  
Universality Class ◽  
Kinetic Ising Model ◽  
Time Dynamics ◽  
Probabilistic Cellular Automaton ◽  
Time Regime ◽  
The One ◽  
Short Time

We study the short-time dynamics of a three-state probabilistic cellular automaton. This automaton, termed TD model, possess "up-down" symmetry similar to Ising models, and displays continuous kinetic phase transitions belonging to the Ising model universality class. We perform Monte Carlo simulations on the early time regime of the two-dimensional TD model at criticality and obtain the dynamic exponent θ associated to this regime, and the exponents β/ν and z. Our results indicate that, although the model do not possess microscopic reversibility, it presents short-time universality which is consistent with the one of the kinetic Ising model.

COMPLEX DYNAMICS OF THE ELEMENTARY CELLULAR AUTOMATON RULE 54

2012 ◽  
Vol 23 (07) ◽  
pp. 1250052
Author(s):  
JUNBIAO GUAN
Keyword(s):  
Boundary Conditions ◽  
Cellular Automaton ◽  
Periodic Boundary ◽  
Complex Dynamics ◽  
Bernoulli Shift ◽  
Periodic Boundary Conditions ◽  
Self Similarity ◽  
Symbolic Sequences ◽  
Topologically Mixing ◽  
Elementary Cellular Automaton

This work deals with a discussion of complex dynamics of the elementary cellular automaton rule 54. An equation which shows some degree of self-similarity is obtained. It is shown that rule 54 exhibits Bernoulli shift and is topologically mixing on its closed invariant subsystem. Finally, many complex Bernoulli shifts are explored for the finite symbolic sequences with periodic boundary conditions.

Elementary cellular automaton Rule 110 explained as a block substitution system

Computing ◽  
2010 ◽  
Vol 88 (3-4) ◽  
pp. 193-205
Author(s):  
Juan C. Seck-Tuoh-Mora ◽  
Genaro J. Martínez ◽  
Norberto Hernández-Romero ◽  
Joselito Medina-Marín
Keyword(s):  
Cellular Automaton ◽  
Substitution System ◽  
Elementary Cellular Automaton
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