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  1. Hedi Ben Amor, Fabien Corblin, Eric Fanchon, Adrien Elena, Laurent Trilling, Jacques Demongeot & Nicolas Glade (forthcoming). Formal Methods for Hopfield-Like Networks. Acta Biotheoretica.
    Building a meaningful model of biological regulatory network is usually done by specifying the components (e.g. the genes) and their interactions, by guessing the values of parameters, by comparing the predicted behaviors to the observed ones, and by modifying in a trial-error process both architecture and parameters in order to reach an optimal fitness. We propose here a different approach to construct and analyze biological models avoiding the trial-error part, where structure and dynamics are represented as formal constraints. We apply (...)
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  2. Abdessalem Chekhchoukh & Nicolas Glade (forthcoming). Influence of Sparkle and Saccades on Tongue Electro-Stimulation-Based Vision Substitution of 2D Vectors. Acta Biotheoretica.
    Abstract Vision substitution by electro-stimulation has been studied since the 60s beginning with P. Bach-y-Rita. Camera pictures or movies encoded in gray levels are displayed using an electro-stimulation display device on the surface of a body part, such as the skin or the tongue. Medical-technical devices have been developed on this principle to compensate for sensory-motor disabilities such as blindness or loss of balance, or to guide specific actions, such as surgery. However, the electrical signals of stationary or moving slowly (...)
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  3. Jacques Demongeot, Nicolas Glade & Andrés Moreira (forthcoming). Evolution and RNa Relics. A Systems Biology View. Acta Biotheoretica.
    The genetic code has evolved from its initial non-degenerate wobble version until reaching its present state of degeneracy. By using the stereochemical hypothesis, we revisit the problem of codon assignations to the synonymy classes of amino-acids. We obtain these classes with a simple classifier based on physico-chemical properties of nucleic bases, like hydrophobicity and molecular weight. Then we propose simple RNA (or more generally XNA, with X for D, P or R) ring structures that present, overlap included, one and only (...)
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  4. Nicolas Glade (forthcoming). On the Nature and Shape of Tubulin Trails: Implications on Microtubule Self-Organization. Acta Biotheoretica.
    Abstract Microtubules, major elements of the cell skeleton are, most of the time, well organized in vivo, but they can also show self-organizing behaviors in time and/or space in purified solutions in vitro. Theoretical studies and models based on the concepts of collective dynamics in complex systems, reaction–diffusion processes and emergent phenomena were proposed to explain some of these behaviors. In the particular case of microtubule spatial self-organization, it has been advanced that microtubules could behave like ants, self-organizing by ‘talking (...)
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  5. Nicolas Glade, Jacques Demongeot & James Tabony (2002). Numerical Simulations of Microtubule Self-Organisation by Reaction and Diffusion. Acta Biotheoretica 50 (4).
    This article addresses the physical chemical processes underlying biological self-organisation by which a homogenous solution of reacting chemicals spontaneously self-organises. Theoreticians have predicted that self-organisation can arise from a coupling of reactive processes with molecular diffusion. In addition, the presence of an external field, such as gravity, at a critical moment early in the process may determine the morphology that subsequently develops. The formation, in-vitro, of microtubules, a constituent of the cellular skeleton, shows this type of behaviour. The preparations spontaneously (...)
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