Related papers: Phyllotaxis, a model
Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with…
In complex systems, groups of interacting objects may form prevalent and persistent spatiotemporal patterns, which we refer to as motifs. These motifs can exhibit features that reveal how individual objects interact with one another.…
A determinant property of the structure of a biological network is the distribution of local connectivity patterns, i.e., network motifs. In this work, a method for creating directed, unweighted networks while promoting a certain…
The advances in understanding complex networks have generated increasing interest in dynamical processes occurring on them. Pattern formation in activator-inhibitor systems has been studied in networks, revealing differences from the…
Epithelial cell clusters often move collectively on a substrate. Mechanical signals play a major role in organizing this behavior. There are a number of experimental observations in these systems which await a comprehensive explanation.…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…
We study a cross-diffusion model for tissue regeneration which involves the dynamics of human mesenchymal stem cells interacting with chondrocytes in a medium containing a differentiation factor. The latter acts as a chemoattractant for the…
In this work we approach cell migration under a large-scale assumption, so that the system reduces to a particle in motion. Unlike classical particle models, the cell displacement results from its internal activity: the cell velocity is a…
We study fluctuations of particle absorption by a three-dimensional domain with multiple absorbing patches. The domain is in contact with a gas of interacting diffusing particles. This problem is motivated by living cell sensing via…
Active particles with a (magnetic) dipole moment are of interest for steering self-propelled motion, but also result in novel collective effects due to their dipole-dipole interaction. Here systems of active dipolar particles are studied…
A tanglegram consists of two rooted binary trees and a perfect matching between their leaves, and a planar tanglegram is one that admits a layout with no crossings. We show that the problem of generating planar tanglegrams uniformly at…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
A novel, protean, topological soliton has recently been shown to emerge in systems of repulsive particles in cylindrical geometries, whose statics is described by the number-theoretical objects of phyllotaxis. Here we present a minimal and…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Linear model trees are regression trees that incorporate linear models in the leaf nodes. This preserves the intuitive interpretation of decision trees and at the same time enables them to better capture linear relationships, which is hard…
We investigate the behavior of self-propelled particles under cyclic stretching, inspired by the characteristic pattern dynamics observed in microtubule (MT) motility assays subjected to uniaxial cyclic substrate stretching. We develop a…
Particles that are catalytically-active and chemotactic can interact through the concentration fields upon which they act, which in turn may lead to wide-scale spatial self-organization. When these active particles interact through several…
Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to…
Phylogenetic networks are rooted acyclic directed graphs in which the leaves are identified with members of a set X of species. The cluster of a vertex is the set of leaves that are descendants of the vertex. A network is "distinct-cluster"…