Modeling Macro-Molecular Interfaces with Intervor

International audienceIntervor is a software computing a parameter-free representation of macro-molecular interfaces, based on the a-complex of the atoms. Given two interacting partners, possibly with water molecules squeezed in-between them, Intervor computes an interface model which has the following characteristics: (i) it identifies the atoms of the partners which are in direct contact and those whose interaction is water mediated, (ii) it defines a geometric complex separating the partners, the Voronoi interface, whose geometric and topological descriptions are straightforward (surface area, number of patches, curvature), (iii) it allows the definition of the depth of atoms at the interface, thus going beyond the traditional dissection of an interface into a core and a rim. These features can be used to investigate correlations between structural parameters and key properties such as the conservation of residues, their polarity, the water dynamics at the interface, mutagenesis data, etc

Robust and Efficient Delaunay Triangulations of Points on Or Close to a Sphere

International audienceWe propose two ways to compute the Delaunay triangulation of points on a sphere, or of rounded points close to a sphere, both based on the classic incremental algorithm initially designed for the plane. We use the so-called space of circles as mathematical background for this work. We present a fully robust implementation built upon existing generic algorithms provided by the Cgal library. The efficiency of the implementation is established by benchmarks

Relationship Between Crystallization, Mechanical and Gas Barrier Properties of Poly(ethylene furanoate) (PEF) in Multinanolayered PLA-PEF and PET-PEF Films

onlineFood packaging films must be reinvented in order to answer the new demanding ecological requirements. Biobased and/or biodegradable polymers appear as an interesting alternative to reduce petroleum dependence and carbon dioxide emissions. Poly(ethylene furanoate) (PEF) appears today as a new promising biopolymer thanks to its good gas barrier and mechanical properties, despite its high price that could limit its industrial applications. Its combination with other polymers is thus of great interest and for the first time, film coextrusion process is used to create PLA-PEF and PET-PEF multi-micro/nano layered films. A new PEF grade developed by AVA Biochem in the H2020 Mypack program, has been used and firstly analysed in terms of melt processability, mechanical, thermal and gas barrier properties. Our major results confirmed the good gas barrier as well as mechanical properties of amorphous PEF. Post-extrusion PEF bulk thermal crystallization led to very brittle material making gas barrier measurements impossible. Micro/nanolayered PLA-PEF and PET-PEF films with different PEF layer thicknesses have been processed and post-extrusion annealing treatment was carried out. The relationship between crystallinity, mechanical and gas barrier properties will be investigated.Projet européen Mypac

Computing the Arrangement of Circles on a Sphere, with Applications in Structural Biology

Balls and spheres are the simplest modeling primitives after affine ones, which accounts for their ubiquitousness in Computer Science and Applied Mathematics. Amongst the many applications, we may cite their prevalence when it comes to modeling our ambient 3D space, or to handle molecular shapes using Van der Waals models. If most of the applications developed so far are based upon simple geometric tests between balls, in particular the intersection test, a number of applications would obviously benefit from finer pieces of information. Consider a sphere S0 and a list of circles on it, each such circle stemming from the intersection between S0 and another sphere, say Si. Also assume that Si has an accompanying ball Bi. This paper develops an integrated framework, based on the generalization of the Bentley-Ottmann algorithm to the spherical setting, to (i)compute the exact arrangement of circles on S0 (ii)construct in a single pass the half-edge data structure encoding the arrangement induced by the circles (iii)report the covering list of each face of this arrangement, i.e. the list of balls containing it. As an illustration, the covering lists are used as the building block of a geometric optimization algorithm aiming at selecting diverse conformational ensembles for flexible protein-protein docking

Note - Des applications informatiques pour faciliter l’acquisition des données « Macrophytes » dans les réseaux de surveillance des masses d’eau continentales

Les macrophytes ont été reconnus élément de qualité biologique mais, pour exploiter au mieux les informations qu’ils fournissent, il convient de mettre en place des outils performants. Quels choix techniques ont été retenus pour rendre ces données les plus pertinentes possibles

Arrangements de cercles sur une sphère (algorithmes et applications aux modèles moléculaires représentés par une union de boules)

Depuis les travaux précurseurs de Richard et al., les constructions géométriques occupent une place importante dans la description des macro-molécules et leurs assemblages. En particulier, certains complexes cellulaires liés au diagramme de Voronoï ont été utilisés pour décrire les propriétés de compacité des empilement atomiques, calculer des surfaces moléculaires, ou encore détecter des cavités à la surface des molécules. Cette thèse se positionne dans ce contexte, et après une brève introduction à la structure des protéines, détaille quatre contributions. Premièrement, en utilisant le principe de balayage introduit par Bentley et Ottmann, cette thèse présente le premier algorithme effectif pour construire l'arrangement exact de cercles sur une sphère. De plus, en supposant que les cercles proviennent de l'intersection entre sphères, une stratégie pour calculer les listes couvrantes d'une face de l'arrangement (i.e. la liste des boules qui la recouvrent) est proposée. L'exactitude n'étant pas une fin en soi, mais plutôt une façon de rendre l'algorithmique robuste, nous montrons expérimentalement que le surcoût induit est modeste. Deuxièmement, cette thèse développe les primitives algébriques et géométriques requises par l'algorithme de balayage afin de le rendre générique et robuste. Ces primitives sont intégrées dans une contexte plus général, à savoir le noyau CGAL pour les objets sphériques. Troisièmement, la machinerie introduite est utilisée pour traiter un problème de biologie structurale computationelle : la sélection d'un sous-ensemble varié à partir d'un ensemble redondant de conformations de boucles. Nous proposons de résoudre ce problème de sélection en retenant les représentants qui maximisent l'aire ou le volume de la sélection. Ces questions peuvent être traitées géométriquement à l'aide d'arrangements de cercles sur une sphère. La validation est faîte sur deux fronts. D'un point de vue géométrique, nous montrons que notre approche génère des sélections dont l'aire de la surface moléculaire équivaut à celle de sélections obtenues par des stratégies classiques, mais qui sont de taille nettement inférieure. Du point de vue amarrage de protéines, nous montrons que nos sélections améliorent de manière significative les résultats obtenus à l'aide d'un algorithme manipulant des parties flexibles. Pour finir, nous discutons les problèmes et choix d'implémentation, en les replaçant dans le contexte de la librairie CGAL.Since the early work of Richard et al., geometric constructions have been paramount for the description of macromolecules and macro-molecular assemblies. In particular, Voronoï and related constructions have been used to describe the packing properties of atoms, to compute molecular surfaces, to find cavities. This thesis falls in this realm, and after a brief introduction to protein structure, makes four contributions. First, using the sweep line paradigm of Bentley and Ottmann, we present the first effective algorithm able to construct the exact arrangement of circles on a sphere. Moreover, assuming the circles stem from the intersection between spheres, we present a strategy to report the covering list of a face of the arrangement-that is the list of spheres covering it. Along the way, we ascertain the fact that exactness of the arrangement can be achieved with a small computational overhead. Second, we develop the algebraic and geometric primitives required by the sweep algorithm, so as to make it generic and robust. These primitives are integrated in a broader context, namely the CGAL 3D Spherical Kernel. Third, we use the aforementioned machinery to tackle a computational structural biology problem, namely the selection of diverse conformations from a large redundant set. We propose to solve this selection problem by computing representatives maximizing the surface area or the volume of the selection. From a geometric standpoint, these questions can be handled resorting to arrangements of circles and spheres. The validation is carried out along two lines. On the geometric side, we show that our elections match the molecular surface area of selections output by standard strategies but using a smaller number of onformers by one and two orders of magnitude. On the docking side, we show that our selections can significantly improve the results obtained for a flexible-loop docking algorithm. Finally, we discuss the implementation issues and the design choices, in the context of the best practices underlying the development of CGAL.DIJON-BU Sciences Economie (212312102) / SudocSudocFranceF

Computing the Volume of Union of Balls: a Certified Algorithm

International audienceBalls and spheres are amongst the simplest 3D modeling primitives, and computing the volume of a union of balls is elementary problem. Although a number of strategies addressing this problem have been investigated in several communities, we are not aware of any robust algorithm, and present the first such algorithm. Our calculation relies on the decomposition of the volume of the union into convex regions, namely the restrictions of the balls to their regions in the power diagram. Theoretically, we establish a formula for the volume of a restriction, based on Gauss' divergence theorem. The proof being constructive, we develop the associated algorithm. On the implementation side, we carefully analyse the predicates and constructions involved in the volume calculation, and present a certified implementation relying on interval arithmetic. The result is certified in the sense that the exact volume belongs to the interval computed. Experimental results are presented on hand-crafted models illustrating various difficulties, as well as on the 58,898 models found in the tenth of July 2009 release of the Protein Data Bank

ESBTL: efficient PDB parser and data structure for the structural and geometric analysis of biological macromolecules.

International audienceThe ever increasing number of structural biological data calls for robust and efficient software for analysis. Easy Structural Biology Template Library (ESBTL) is a lightweight C++ library that allows the handling of PDB data and provides a data structure suitable for geometric constructions and analyses. The parser and data model provided by this ready-to-use include-only library allows adequate treatment of usually discarded information (insertion code, atom occupancy, etc.) while still being able to detect badly formatted files. The template-based structure allows rapid design of new computational structural biology applications and is fully compatible with the new remediated PDB archive format. It also allows the code to be easy-to-use while being versatile enough to allow advanced user developments. AVAILABILITY: ESBTL is freely available under the GNU General Public License from http://esbtl.sf.net. The web site provides the source code, examples, code snippets and documentation

Des méthodes basées sur les peuplements de macrophytes pour évaluer l’état écologique des milieux aquatiques

En tant que base principale de la production primaire dans la plupart des hydrosystèmes, les macrophytes peuvent apporter des informations précieuses sur l’état de santé des milieux aquatiques. Comment traduire ces informations pour évaluer l’état de santé et gérer ces milieux