12 found
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  1.  4
    Angélique Stéphanou & Nicolas Glade (2015). SMT or TOFT? How the Two Main Theories of Carcinogenesis Are Made Incompatible. Acta Biotheoretica 63 (3):257-267.
    The building of a global model of carcinogenesis is one of modern biology’s greatest challenges. The traditional somatic mutation theory is now supplemented by a new approach, called the Tissue Organization Field Theory. According to TOFT, the original source of cancer is loss of tissue organization rather than genetic mutations. In this paper, we study the argumentative strategy used by the advocates of TOFT to impose their view. In particular, we criticize their claim of incompatibility used to justify the necessity (...)
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  2.  6
    Angélique Stéphanou & Nicolas Glade (2015). A Conceptual Model of Morphogenesis and Regeneration. Acta Biotheoretica 63 (3):283-294.
    This paper is devoted to computer modelling of the development and regeneration of multicellular biological structures. Some species are able to regenerate parts of their body after amputation damage, but the global rules governing cooperative cell behaviour during morphogenesis are not known. Here, we consider a simplified model organism, which consists of tissues formed around special cells that can be interpreted as stem cells. We assume that stem cells communicate with each other by a set of signals, and that the (...)
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  3.  7
    Angélique Stéphanou & Nicolas Glade (2015). Modeling the Enzyme Kinetic Reaction. Acta Biotheoretica 63 (3):239-256.
    The Enzymatic control reactions model was presented within the scope of fractional calculus. In order to accommodate the usual initial conditions, the fractional derivative used is in Caputo sense. The methodologies of the three analytical methods were used to derive approximate solution of the fractional nonlinear system of differential equations. Two methods use integral operator and the other one uses just an integral. Numerical results obtained exhibit biological behavior of real world problem.
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  4.  11
    Jacques Demongeot, Nicolas Glade & Andrés Moreira (2008). Evolution and RNA Relics. A Systems Biology View. Acta Biotheoretica 56 (1-2):5-25.
    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 ring structures that present, overlap included, one and only one codon by synonymy class as solutions of a combinatory variational (...)
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  5.  6
    Angélique Stéphanou & Nicolas Glade (2015). Computing with Synthetic Protocells. Acta Biotheoretica 63 (3):309-323.
    In this article we present a new kind of computing device that uses biochemical reactions networks as building blocks to implement logic gates. The architecture of a computing machine relies on these generic and composable building blocks, computation units, that can be used in multiple instances to perform complex boolean functions. Standard logical operations are implemented by biochemical networks, encapsulated and insulated within synthetic vesicles called protocells. These protocells are capable of exchanging energy and information with each other through transmembrane (...)
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  6.  6
    Angélique Stéphanou & Nicolas Glade (2015). Towards a Behavioral-Matching Based Compilation of Synthetic Biology Functions. Acta Biotheoretica 63 (3):325-339.
    The field of synthetic biology is looking forward engineering framework for safely designing reliable de-novo biological functions. In this undertaking, Computer-Aided-Design environments should play a central role for facilitating the design. Although, CAD environment is widely used to engineer artificial systems the application in synthetic biology is still in its infancy. In this article we address the problem of the design of a high level language which at the core of CAD environment. More specifically the Gubs language is a specification (...)
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  7.  17
    Nicolas Glade (2012). On the Nature and Shape of Tubulin Trails: Implications on Microtubule Self-Organization. Acta Biotheoretica 60 (1-2):55-82.
    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 to (...)
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  8.  13
    Nicolas Glade, Jacques Demongeot & James Tabony (2002). Numerical Simulations of Microtubule Self-Organisation by Reaction and Diffusion. Acta Biotheoretica 50 (4):239-268.
    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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  9.  15
    Abdessalem Chekhchoukh & Nicolas Glade (2012). Influence of Sparkle and Saccades on Tongue Electro-Stimulation-Based Vision Substitution of 2D Vectors. Acta Biotheoretica 60 (1-2):41-53.
    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 moving (...)
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  10.  2
    Angélique Stéphanou & Nicolas Glade (2015). XXXIVth Seminar of the French-Speaking Society for Theoretical Biology: Saint-Flour , France, 26–28 May, 2014. Acta Biotheoretica 63 (3):237-238.
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  11.  1
    Angélique Stéphanou & Nicolas Glade (2015). Implementation of a Model of Bodily Fluids Regulation. Acta Biotheoretica 63 (3):269-282.
    The classic model of blood pressure regulation by Guyton et al. set a new standard for quantitative exploration of physiological function and led to important new insights, some of which still remain the focus of debate, such as whether the kidney plays the primary role in the genesis of hypertension. Key to the success of this model was the fact that the authors made the computer code freely available and eventually provided a convivial user interface for exploration of model behavior (...)
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  12. Angélique Stéphanou & Nicolas Glade (2015). Programming the Emergence in Morphogenetically Architected Complex Systems. Acta Biotheoretica 63 (3):295-308.
    Large sets of elements interacting locally and producing specific architectures reliably form a category that transcends the usual dividing line between biological and engineered systems. We propose to call them morphogenetically architected complex systems. While taking the emergence of properties seriously, the notion of MACS enables at the same time the design of operational means that allow controlling and even, paradoxically, programming this emergence. To demonstrate our claim, we first show that among all the self-organized systems studied in the field (...)
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