Related papers: Phyllotaxis, a model
We characterize the compatibility of a collection of unrooted phylogenetic trees as a question of determining whether a graph derived from these trees --- the display graph --- has a specific kind of triangulation, which we call legal. Our…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Many organisms exhibit branching morphologies that twist around each other and become entangled. Entanglement occurs when different objects interlock, creating complex and often irreversible configurations. This physical phenomenon is…
Many biological processes have been the source of inspiration for heuristic methods that generate high-quality solutions to solve optimization and search problems. This thesis presents an epigenetic technique for Evolutionary Algorithms,…
We explore a simplified class of models we call swarms, which are inspired by the collective behavior of social insects. We perform a mean-field stability analysis and perform numerical simulations of the model. Several interesting types of…
This paper considers a process for the creation and subsequent firing of sequences of neuronal patterns, as might be found in the human brain. The scale is one of larger patterns emerging from an ensemble mass, possibly through some type of…
Based on symmetry consideration of migration and shape deformations, we formulate phenomenologically the dynamics of cell crawling in two dimensions. Forces are introduced to change the cell shape. The shape deformations induce migration of…
Nature features a plethora of extraordinary photonic architectures that have been optimized through natural evolution. While numerical optimization is increasingly and successfully used in photonics, it has yet to replicate any of these…
The evolution of multicellular organisms from monocellular ancestors represents one of the greatest advances of the history of life. The assembly of such multicellular organisms requires signalling and response between cells: over millions…
The pathway is a biological term that refers to a series of interactions between molecules in a cell that causes a certain product or a change in the cell. Pathway analysis is a powerful method for gene expression analysis. Through pathway…
Patterns are fundamental to human cognition, enabling the recognition of structure and regularity across diverse domains. In this work, we focus on structural repeats, patterns that arise from the repetition of hierarchical relations within…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Signal processing in biological systems is delicately executed by specialised networks, which are modular assemblies of network motifs. The motifs are independently functional circuits found in enormous numbers in any living cell. A very…
It is widely accepted that the hippocampal place cells' spiking activity produces a cognitive map of space. However, many details of this representation's physiological mechanism remain unknown. For example, it is believed that the place…
A set of general allometric scaling laws is derived for different systems represented by tree networks. The formulation postulates self-similar networks with an arbitrary number of branches developed in each generation, and with an…
The use of complex networks as a modern approach to understanding the world and its dynamics is well-established in literature. The adjacency matrix, which provides a one-to-one representation of a complex network, can also yield several…
Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a…
Habituation - a phenomenon in which a dynamical system exhibits a diminishing response to repeated stimulations that eventually recovers when the stimulus is withheld - is universally observed in living systems from animals to unicellular…
Plant phenotyping (Guo et al. 2021; Pieruschka et al. 2019) focuses on studying the diverse traits of plants related to the plants' growth. To be more specific, by accurately measuring the plant's anatomical, ontogenetical, physiological…