Related papers: Phyllotaxis, a model
In order to better understand dynamical functions on amounts of natural and man-made complex systems, lots of researchers from a wide range of disciplines, covering statistic physics, mathematics, theoretical computer science, and so on,…
Many microorganisms, with phytoplankton and zooplankton as prominent examples, display phototactic behaviour, that is, the ability to perform directed motion within a light gradient. Here we experimentally demonstrate that sensing of light…
Chemotaxis is typically modeled in the context of cellular motion towards a static, exogenous source of chemoattractant. Here, we propose a time-dependent mechanism of chemotaxis in which a self-propelled particle ({\it e.g.}, a cell)…
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Man-made slender structures are known to be sensitive to high levels of vibration, due to their flexibility, which often cause irreversible damage. In nature, trees repeatedly endure large amplitudes of motion, mostly caused by strong…
Multivariate clustering in astrophysics is a recent development justified by the bigger and bigger surveys of the sky. The phylogenetic approach is probably the most unexpected technique that has appeared for the unsupervised classification…
Mutations of genetic sequences are often accompanied by their recombinations, known as phylogenetic networks. These networks are typically reconstructed from coalescent processes that may arise from optimal merging or fitting together a…
We investigate the distribution of flavonoids, a major category of plant secondary metabolites, across species. Flavonoids are known to show high species specificity, and were once considered as chemical markers for understanding adaptive…
The articulation process of dynamical networks is studied with a functional map, a minimal model for the dynamic change of relationships through iteration. The model is a dynamical system of a function $f$, not of variables, having a…
Sequences of neuronal activation have long been implicated in a variety of brain functions. In particular, these sequences have been tied to memory formation and spatial navigation in the hippocampus, a region of mammalian brains.…
Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…
Our goal is to visualize an additional data dimension of a tree with multifaceted data through superimposition on vertical strips, which we call columns. Specifically, we extend upward drawings of unordered rooted trees where vertices have…
Understanding the pattern formation in communities has been at the center of attention in various fields. Here we introduce a novel model, called an "information-particle model," which is based on the reaction-diffusion model and the…
The Watts-Strogatz algorithm of transferring the square lattice to a small world network is modified by introducing preferential rewiring constrained by connectivity demand. The evolution of the network is two-step: sequential preferential…
Complex systems are usually represented as an intricate set of relations between their components forming a complex graph or network. The understanding of their functioning and emergent properties are strongly related to their structural…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
We study the problem of learning a latent tree graphical model where samples are available only from a subset of variables. We propose two consistent and computationally efficient algorithms for learning minimal latent trees, that is, trees…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the…