An elasto-hydrodynamical model of friction for the locomotion of Caenorhabditis elegans

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Modélisation des structures chimiques des macromolécules sédimentaires : le logiciel XMOL Software Modeling the Chemical Structures of Sedimentary Macromolecules: the Xmol Software

Cet article présente le logiciel XMOL qui prédit et construit, dans un espace tridimensionnel, des structures de macromolécules sédimentaires. La prédiction a pour base une bibliothèque de molécules et un système d'équations. La bibliothèque contient les groupes moléculaires (domaines aromatiques, naphténoaromatiques, naphténiques et chaînes aliphatiques) présents dans la matière organique. Elle est générée par l'utilisateur à l'aide d'un éditeur de molécules. La liste des éléments choisis n'est pas exhaustive, toute nouvelle molécule analysée peut et doit être insérée dans la bibliothèque. Le système d'équations linéairement indépendantes traduit les résultats des analyses physico-chimiques ainsi qu'un certain nombre d'hypothèses. Les hypothèses révèlent l'insuffisance des données analytiques; elles devraient à terme disparaître. Les structures macromoléculaires prédites sont des combinaisons linéaires des éléments de la bibliothèque solutions du système d'équations. Elles sont cohérentes d'un point de vue statistique avec les résultats d'analyse. La construction des structures utilise des techniques d'algorithmique graphique et géométrique. Les macromolécules modélisées ont une conformation réaliste. <br> This article describes the XMOL software used for predicting and constructing the structures of sedimentary macromolecules in a 3-D space. Prediction is based on a molecule library and a system of linear equations. The library contains the molecular groups (aromatic, naphtheno-aromatic and naphthenic domains and aliphatic chains) present in organic matter. It is generated by the user by means of a molecule editor. The list of elements chosen is not exhaustive. Any new molecule identified by analyses can and must be inserted into the library. The system of linearly independant equations reflects the results of physicochemical analyses as well as a number of hypotheses. The hypotheses compensate for the lack of analytical data. They should disappear with the availability of new analyses. The macromolecular structures predicted by solving the system of equations are linear combinations of the elements of the library. They are coherent with the analyses according to the statistical standpoint. Construction of these structures makes use of graphic and geometric algorithmic techniques. The macromolecules modeled have a realistic conformation and are in agreement with energy minimization

An elasto-hydrodynamical model of friction for the locomotion of Caenorhabditis elegans

Caenorhabditis elegans (C. elegans) is one of the most studied organisms by biologists. Composed of around one thousand cells, easy to culture and to modify genetically, it is a good model system to address fundamental physiological questions and in particular to investigate neuromuscular processes. Many C. elegans mutants can be distinguished by their locomotion phenotype and it then important to understand the biomechanics of their locomotion and in particular the mechanics of their undulating crawling motion on agar aqueous gels where they are commonly grown and observed. In this article, we present a mechanical model of the friction of the worms on their substrate where we have included capillarity (which pins the worm of the gel), the hydrodynamics of the lubrication film (between worm and gel) and the substrate/body elasticity. We determine the ratio of the transverse to longitudinal friction coefficients of the worm body on the culture gel as a function of a control parameter which describes the relative role of the deformation of the gel and the viscous dissipation in the lubrication film. Experimentally this ratio is - for soft gels - larger than the maximal value predicted by our model (this maximum is equal to 2, the value for an infinite cylinder in bulk liquid) and we propose to include the plasticity of the gel (i.e. the dissipation of the deformation of the gel) for a better description of the worm/gel interaction