DOI

1

Set Voronoi diagrams of 3D assemblies of aspherical particles - Schaller, Fabian M. and Kapfer, Sebastian C. and Evans, Myfanwy E. and Hoffmann, Matthias J. F. and Aste, Tomaso and Saadatfar, Mohammad and Mecke, Klaus and Delaney, Gary W. and Schroeder-Turk, Gerd E.

PHILOSOPHICAL MAGAZINE 93, 3993-4017 (2013)

Abstract : Several approaches to quantitative local structure characterization for particulate assemblies, such as structural glasses or jammed packings, use the partition of space provided by the Voronoi diagram. The conventional construction for spherical mono-disperse particles, by which the Voronoi cell of a particle is that of its centre point, cannot be applied to configurations of aspherical or polydisperse particles. Here, we discuss the construction of a Set Voronoi diagram for configurations of aspherical particles in three-dimensional space. The Set Voronoi cell of a given particle is composed of all points in space that are closer to the surface (as opposed to the centre) of the given particle than to the surface of any other; this definition reduces to the conventional Voronoi diagram for the case of mono-disperse spheres. An algorithm for the computation of the Set Voronoi diagram for convex particles is described, as a special case of a Voronoi-based medial axis algorithm, based on a triangulation of the particles' bounding surfaces. This algorithm is further improved by a pre-processing step based on morphological erosion, which improves the quality of the approximation and circumvents the problems associated with small degrees of particle-particle overlap that may be caused by experimental noise or soft potentials. As an application, preliminary data for the volume distribution of disordered packings of mono-disperse oblate ellipsoids, obtained from tomographic imaging, is computed.

PHILOSOPHICAL MAGAZINE 93, 3993-4017 (2013)

Abstract : Several approaches to quantitative local structure characterization for particulate assemblies, such as structural glasses or jammed packings, use the partition of space provided by the Voronoi diagram. The conventional construction for spherical mono-disperse particles, by which the Voronoi cell of a particle is that of its centre point, cannot be applied to configurations of aspherical or polydisperse particles. Here, we discuss the construction of a Set Voronoi diagram for configurations of aspherical particles in three-dimensional space. The Set Voronoi cell of a given particle is composed of all points in space that are closer to the surface (as opposed to the centre) of the given particle than to the surface of any other; this definition reduces to the conventional Voronoi diagram for the case of mono-disperse spheres. An algorithm for the computation of the Set Voronoi diagram for convex particles is described, as a special case of a Voronoi-based medial axis algorithm, based on a triangulation of the particles' bounding surfaces. This algorithm is further improved by a pre-processing step based on morphological erosion, which improves the quality of the approximation and circumvents the problems associated with small degrees of particle-particle overlap that may be caused by experimental noise or soft potentials. As an application, preliminary data for the volume distribution of disordered packings of mono-disperse oblate ellipsoids, obtained from tomographic imaging, is computed.

DOI

2

How genealogies are affected by the speed of evolution - Brunet, Eric and Derrida, Bernard

PHILOSOPHICAL MAGAZINE 92, 255-271 (2012)

Abstract : In a series of recent works it has been shown that a class of simple models of evolving populations under selection leads to genealogical trees whose statistics are given by the Bolthausen-Sznitman coalescent rather than by the well-known Kingman coalescent in the case of neutral evolution. Here we show that when conditioning the genealogies on the speed of evolution, one finds a one-parameter family of tree statistics which interpolates between the Bolthausen-Sznitman and Kingman coalescents. This interpolation can be calculated explicitly for one specific version of the model, the exponential model. Numerical simulations of another version of the model and a phenomenological theory indicate that this one-parameter family of tree statistics could be universal. We compare this tree structure with those appearing in other contexts, in particular in the mean field theory of spin glasses.

PHILOSOPHICAL MAGAZINE 92, 255-271 (2012)

Abstract : In a series of recent works it has been shown that a class of simple models of evolving populations under selection leads to genealogical trees whose statistics are given by the Bolthausen-Sznitman coalescent rather than by the well-known Kingman coalescent in the case of neutral evolution. Here we show that when conditioning the genealogies on the speed of evolution, one finds a one-parameter family of tree statistics which interpolates between the Bolthausen-Sznitman and Kingman coalescents. This interpolation can be calculated explicitly for one specific version of the model, the exponential model. Numerical simulations of another version of the model and a phenomenological theory indicate that this one-parameter family of tree statistics could be universal. We compare this tree structure with those appearing in other contexts, in particular in the mean field theory of spin glasses.

DOI

3

A model for hierarchical patterns under mechanical stresses - Corson, F. and Henry, H. and Adda-Bedia, M.

PHILOSOPHICAL MAGAZINE 90, 357-373 (2010)

Abstract : We present a model for mechanically-induced pattern formation in growing biological tissues and discuss its application to the development of leaf venation networks. Drawing an analogy with phase transitions in solids, we use a phase field method to describe the transition between two states of the tissue, e.g. the differentiation of leaf veins, and consider a layered system where mechanical stresses are generated by differential growth. We present analytical and numerical results for one-dimensional systems, showing that a combination of growth and irreversibility gives rise to hierarchical patterns. Two-dimensional simulations suggest that such a mechanism could account for the hierarchical, reticulate structure of leaf venation networks, yet point to the need for a more detailed treatment of the coupling between growth and mechanical stresses.

PHILOSOPHICAL MAGAZINE 90, 357-373 (2010)

Abstract : We present a model for mechanically-induced pattern formation in growing biological tissues and discuss its application to the development of leaf venation networks. Drawing an analogy with phase transitions in solids, we use a phase field method to describe the transition between two states of the tissue, e.g. the differentiation of leaf veins, and consider a layered system where mechanical stresses are generated by differential growth. We present analytical and numerical results for one-dimensional systems, showing that a combination of growth and irreversibility gives rise to hierarchical patterns. Two-dimensional simulations suggest that such a mechanism could account for the hierarchical, reticulate structure of leaf venation networks, yet point to the need for a more detailed treatment of the coupling between growth and mechanical stresses.