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J Ricardo G Mendonça, Yeva Gevorgyan
We investigate one-dimensional elementary probabilistic cellular automata (PCA) whose dynamics in first-order mean-field approximation yields discrete logisticlike growth models for a single-species unstructured population with nonoverlapping generations. Beginning with a general six-parameter model, we find constraints on the transition probabilities of the PCA that guarantee that the ensuing approximations make sense in terms of population dynamics and classify the valid combinations thereof. Several possible models display a negative cubic term that can be interpreted as a weak Allee factor...
May 2017: Physical Review. E
Yuan Gao, Chuanrong Zhang, Qingsong He, Yaolin Liu
Ecological security is an important research topic, especially urban ecological security. As highly populated eco-systems, cities always have more fragile ecological environments. However, most of the research on urban ecological security in literature has focused on evaluating current or past status of the ecological environment. Very little literature has carried out simulation or prediction of future ecological security. In addition, there is even less literature exploring the urban ecological environment at a fine scale...
June 15, 2017: International Journal of Environmental Research and Public Health
Andrew Adamatzky
We develop an excitable automata model of a protein verotoxin and demonstrate that logic gates and circuits are realised in the model via interacting patterns of excitation. By sampling potential input pairs of nodes, we calculate frequencies of logic gates which occurred in the verotoxin model for various parameters of node excitation rules. We show that overall the gates can be arranged in the following hierarchy of descending frequencies: AND>OR>AND-NOT>XOR. We demonstrate realisations of one-bit half-adder and controlled-not gates and estimate memory capacity of the verotoxin molecule...
June 13, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Amira Fatma Bennacer, Elmahdi Haffaf, Ghouti Kacimi, Brahim Oudjit, Elhadj-Ahmed Koceir
The interactions between fatty acids (FA) classes: polyunsaturated (PUFA-ω6, PUFA-ω3), saturated (SFA), EPA (eicosapentaenoic acid-ω3), DHA (docosahexaenoic-ω3) and cardiometabolic syndrome (CMS) clusters, thrombosis development and vascular inflammation are subtle. This relationship is mediated by insulin resistance (IR), endothelial dysfunction, platelet aggregation disorder and atherosclerosis. OBJECTIVES: We investigated whether PUFA/SFA - PUFA-ω6/PUFA-ω3 ratios and EPA + DHA can be associated with predictive atherothrombogenic biomarkers status in type 2 diabetes (T2D) patients with or without hypertension (HT)...
June 1, 2017: Annales de Biologie Clinique
Perrine Paul-Gilloteaux, Vincent Potiron, Grégory Delpon, Stéphane Supiot, Sophie Chiavassa, François Paris, Sylvain V Costes
The concept of hypofractionation is gaining momentum in radiation oncology centres, enabled by recent advances in radiotherapy apparatus. The gain of efficacy of this innovative treatment must be defined. We present a computer model based on translational murine data for in silico testing and optimization of various radiotherapy protocols with respect to tumour resistance and the microenvironment heterogeneity. This model combines automata approaches with image processing algorithms to simulate the cellular response of tumours exposed to ionizing radiation, modelling the alteration of oxygen permeabilization in blood vessels against repeated doses, and introducing mitotic catastrophe (as opposed to arbitrary delayed cell-death) as a means of modelling radiation-induced cell death...
May 23, 2017: Scientific Reports
Chen Chai, Yiik Diew Wong, Xuesong Wang
This paper proposes a simulation-based approach to estimate safety impact of driver cognitive failures and driving errors. Fuzzy Logic, which involves linguistic terms and uncertainty, is incorporated with Cellular Automata model to simulate decision-making process of right-turn filtering movement at signalized intersections. Simulation experiments are conducted to estimate the relationships between cognitive failures and driving errors with safety performance. Simulation results show Different types of cognitive failures are found to have varied relationship with driving errors and safety performance...
July 2017: Accident; Analysis and Prevention
Mohammad Mahdi Jaghoori, Frank de Boer, Delphine Longuet, Tom Chothia, Marjan Sirjani
We present an extension of the actor model with real-time, including deadlines associated with messages, and explicit application-level scheduling policies, e.g.,"earliest deadline first" which can be associated with individual actors. Schedulability analysis in this setting amounts to checking whether, given a scheduling policy for each actor, every task is processed within its designated deadline. To check schedulability, we introduce a compositional automata-theoretic approach, based on maximal use of model checking combined with testing...
2017: Acta Informatica
Javier Vera
Traditionally, the formation of vocabularies has been studied by agent-based models (primarily, the naming game) in which random pairs of agents negotiate word-meaning associations at each discrete time step. This article proposes a first approximation to a novel question: To what extent is the negotiation of word-meaning associations influenced by the order in which agents interact? Automata networks provide the adequate mathematical framework to explore this question. Computer simulations suggest that on two-dimensional lattices the typical features of the formation of word-meaning associations are recovered under random schemes that update small fractions of the population at the same time; by contrast, if larger subsets of the population are updated, a periodic behavior may appear...
2017: Artificial Life
S Lilienthal, M Klein, R Orbach, I Willner, F Remacle, R D Levine
The concentration of molecules can be changed by chemical reactions and thereby offer a continuous readout. Yet computer architecture is cast in textbooks in terms of binary valued, Boolean variables. To enable reactive chemical systems to compute we show how, using the Cox interpretation of probability theory, one can transcribe the equations of chemical kinetics as a sequence of coupled logic gates operating on continuous variables. It is discussed how the distinct chemical identity of a molecule allows us to create a common language for chemical kinetics and Boolean logic...
March 1, 2017: Chemical Science
João Guilherme Ferreira Campos, Ariadne de Andrade Costa, Mauro Copelli, Osame Kinouchi
In a recent work, mean-field analysis and computer simulations were employed to analyze critical self-organization in networks of excitable cellular automata where randomly chosen synapses in the network were depressed after each spike (the so-called annealed dynamics). Calculations agree with simulations of the annealed version, showing that the nominal branching ratio σ converges to unity in the thermodynamic limit, as expected of a self-organized critical system. However, the question remains whether the same results apply to the biological case where only the synapses of firing neurons are depressed (the so-called quenched dynamics)...
April 2017: Physical Review. E
Vladimir García-Morales, José A Manzanares, Salvador Mafe
We present a weakly coupled map lattice model for patterning that explores the effects exerted by weakening the local dynamic rules on model biological and artificial networks composed of two-state building blocks (cells). To this end, we use two cellular automata models based on (i) a smooth majority rule (model I) and (ii) a set of rules similar to those of Conway's Game of Life (model II). The normal and abnormal cell states evolve according to local rules that are modulated by a parameter κ. This parameter quantifies the effective weakening of the prescribed rules due to the limited coupling of each cell to its neighborhood and can be experimentally controlled by appropriate external agents...
April 2017: Physical Review. E
Michail-Antisthenis I Tsompanas, Andrew Adamatzky, Georgios Ch Sirakoulis, John Greenman, Ioannis Ieropoulos
The Microbial Fuel Cell (MFC) is a bio-electrochemical transducer converting waste products into electricity using microbial communities. Cellular Automaton (CA) is a uniform array of finite-state machines that update their states in discrete time depending on states of their closest neighbors by the same rule. Arrays of MFCs could, in principle, act as massive-parallel computing devices with local connectivity between elementary processors. We provide a theoretical design of such a parallel processor by implementing CA in MFCs...
2017: PloS One
Estefanía Caballero-Ruiz, Gema García-Sáez, Mercedes Rigla, María Villaplana, Belen Pons, M Elena Hernando
BACKGROUND: The growth of diabetes prevalence is causing an increasing demand in health care services which affects the clinicians' workload as medical resources do not grow at the same rate as the diabetic population. Decision support tools can help clinicians with the inspection of monitoring data, providing a preliminary analysis to ease their interpretation and reduce the evaluation time per patient. This paper presents Sinedie, a clinical decision support system designed to manage the treatment of patients with gestational diabetes...
June 2017: International Journal of Medical Informatics
Christoph Leberecht, Florian Heinke, Dirk Labudde
A variety of mathematical models is used to describe and simulate the multitude of natural processes examined in life sciences. In this paper we present a scalable and adjustable foundation for the simulation of natural systems. Based on neighborhood relations in graphs and the complex interactions in cellular automata, the model uses recurrence relations to simulate changes on a mesoscopic scale. This implicit definition allows for the manipulation of every aspect of the model even during simulation. The definition of value rules ω facilitates the accumulation of change during time steps...
April 29, 2017: In Silico Biology
Lina Meinecke, Markus Eriksson
Mathematical models are important tools to study the excluded volume effects on reaction-diffusion systems, which are known to play an important role inside living cells. Detailed microscopic simulations with off-lattice Brownian dynamics become computationally expensive in crowded environments. In this study, the authors therefore investigate to which extent on-lattice approximations, the so-called cellular automata models, can be used to simulate reactions and diffusion in the presence of crowding molecules...
April 2017: IET Systems Biology
Martín Gutiérrez, Paula Gregorio-Godoy, Guillermo Pérez Del Pulgar, Luis E Muñoz, Sandra Sáez, Alfonso Rodríguez-Patón
gro is a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It is used as a synthetic biology prototyping tool for simulating multicellular biocircuits and microbial consortia. In this work, we present several extensions made to gro that improve the performance of the simulator, make it easier to use, and provide new functionalities. The new version of gro is between 1 and 2 orders of magnitude faster than the original version. It is able to grow microbial colonies with up to 10(5) cells in less than 10 min...
May 8, 2017: ACS Synthetic Biology
Sebastian Sakowski, Tadeusz Krasiński, Joanna Sarnik, Janusz Blasiak, Jacek Waldmajer, Tomasz Poplawski
Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e...
April 22, 2017: Zeitschrift Für Naturforschung. C, A Journal of Biosciences
Leonardo Banchi, Joaquín Fernández-Rossier, Cyrus F Hirjibehedin, Sougato Bose
The development of communication channels at the ultimate size limit of atomic scale physical dimensions will make the use of quantum entities an imperative. In this regime, quantum fluctuations naturally become prominent and are generally considered to be detrimental. Here, we show that for spin-based information processing, these fluctuations can be uniquely exploited to gate the flow of classical binary information across a magnetic chain in thermal equilibrium. Moreover, this information flow can be controlled with a modest external magnetic field that drives the system through different many-body quantum phases in which the orientation of the final spin does or does not reflect the orientation of the initial input...
April 7, 2017: Physical Review Letters
Alyssa Adams, Hector Zenil, Paul C W Davies, Sara Imari Walker
Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an isolated system, and innovation as trajectories not observed in isolated systems...
April 20, 2017: Scientific Reports
Liana Manukyan, Sophie A Montandon, Anamarija Fofonjka, Stanislav Smirnov, Michel C Milinkovitch
In vertebrates, skin colour patterns emerge from nonlinear dynamical microscopic systems of cell interactions. Here we show that in ocellated lizards a quasi-hexagonal lattice of skin scales, rather than individual chromatophore cells, establishes a green and black labyrinthine pattern of skin colour. We analysed time series of lizard scale colour dynamics over four years of their development and demonstrate that this pattern is produced by a cellular automaton (a grid of elements whose states are iterated according to a set of rules based on the states of neighbouring elements) that dynamically computes the colour states of individual mesoscopic skin scales to produce the corresponding macroscopic colour pattern...
April 12, 2017: Nature
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