Related papers: Minimal branching and fusion morphogenesis approac…

Most real systems are growing. In order to model the evolution of real systems, many growing network models have been proposed to reproduce some specific topology properties. As the structure strongly influences the network function,…

It was hypothesized that the structures of biological transport networks are the result of either energy consumption or adaptation dynamics. Although approaches based on these hypotheses can produce optimal network and form loop structures,…

Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…

Physical Flow Networks are different infrastructure networks that allow the flow of physical commodities through edges between its constituent nodes. These include power grid, natural gas transmission network, water pipelines etc. In such…

We present an analysis of the topologies of a class of networks which are optimal in terms of the requirements of having as short a route as possible between any two nodes while yet keeping the congestion in the network as low as possible.…

We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications…

While biological neural networks develop from compact genomes using relatively simple rules, modern artificial neural architecture search methods mostly involve explicit and routine manual work. In this paper, we introduce MorphoNAS…

One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…

The true slime mould Physarum polycephalum is a recent well studied example of how complex transport networks emerge from simple auto-catalytic and self- organising local interactions, adapting structure and function against changing…

We investigate morphologies of proliferating cellular tissue using a newly developed numerical simulation model for mechanical cell division. The model reproduces structures of simple multi-cellular organisms via simple rules for selective…

A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…

In eukaryotic cells, mitochondria form networks that range from highly fused interconnected structures to fragmented populations of individual organelles that undergo transient interactions. These structures can be described as temporal…

Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…

Intracellular transport is essential for maintaining proper cellular function in most eukaryotic cells, with perturbations in active transport resulting in several types of disease. Efficient delivery of critical cargos to specific…

Understanding how different networks relate to each other is key for obtaining a greater insight into complex systems. Here, we introduce an intuitive yet powerful framework to characterise the relationship between two networks comprising…

Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…

We present a minimal driven lattice gas model which generates the morphological characteristics associated with single colony mycelium arising from the growth and branching process of fungal hyphae, which is fed by a single source of…

An important feature of many complex systems, both natural and artificial, is the structure and organization of their interaction networks with interesting properties. Here we present a theory of self-organization by evolutionary adaptation…

We introduce a methodology to study the possible matter flows of an ecosystem defined by observational biomass data and realistic biological constraints. The flows belong to a polyhedron in a multi dimensional space making statistical…

Branching in vascular networks and in overall organismic form is one of the most common and ancient features of multicellular plants, fungi, and animals. By combining machine-learning techniques with new theory that relates vascular form to…