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Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
Cellular self-assembly and organization are fundamental steps for the development of biological tissues. In this paper, within the framework of a cellular automata model, we address how an ordered tissue pattern spontaneously emerges from a…
Microbiological systems evolve to fulfill their tasks with maximal efficiency. The immune system is a remarkable example, where self-non self distinction is accomplished by means of molecular interaction between self proteins and antigens,…
Employing an effective cellular automata model, we investigate and analyze the build-up and erosion of soil. Depending on the strategy employed for handling agricultural production, in many cases we find a critical dependence on the…
Self-propelling bacteria are a dream of nano-technology. These unicellular organisms are not just capable of living and reproducing, but they can swim very efficiently, sense the environment and look for food, all packaged in a body…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
The composition of cellular metabolism is different across species. Empirical data reveal that bacterial species contain similar numbers of metabolic reactions but that the cross-species popularity of reactions is so heterogenous that some…
Some deterministic cellular automata have been observed to follow the pattern of the second law of thermodynamics: starting from a partially disordered state, the system evolves towards a state of equilibrium characterized by maximal…
Neuro-electronic hybrid promises to bring up a model architecture for computing. Such computing architecture could help to bring the power of biological connection and electronic circuits together for better computing paradigm. Such…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
We present a new kinetic equation for cell migration driven by mechanical interactions with the substrate, an effect not previously captured in kinetic models, and essential for explaining observed collective behaviors such as those in…
Cellular automata represent physical systems where both space and time are discrete, and the associated physical quantities assume a limited set of values. While previous research has applied cellular automata in modeling chemical,…
A mutualism is an interaction where the involved species benefit from each other. We study a two-dimensional hexagonal three-state cellular automaton model of a two-species mutualistic system. The simple model is characterized by four…
Understanding how growth induces form is a longstanding biological question. Many studies concentrated on the shapes of plant cells, fungi or bacteria. Some others have shown the importance of the mechanical properties of bacterial walls…
We quantify the amount of regulation required to control growth in living cells by a Maximum Entropy approach to the space of underlying metabolic states described by genome-scale models. Results obtained for E. coli and human cells are…
We introduce an agent-based model for the spreading of technological developments in socio-economic systems where the technology is mainly used for the collaboration/interaction of agents. Agents use products of different technologies to…
We present numerical results obtained from the modelling of a stochastic, highly connected and mobile community. The spread of attributes like health, disease among the community members is simulated using cellular automata on a planar 2…
We introduce bio-inspired artificial neural networks consisting of neurons that are additionally characterized by spatial positions. To simulate properties of biological systems we add the costs penalizing long connections and the proximity…
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses…
This paper is the second part of a series of two papers dealing with bulking: a way to define quasi-order on cellular automata by comparing space-time diagrams up to rescaling. In the present paper, we introduce three notions of simulation…