Related papers: Geometrical constraints in a gene network model an…
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…
Motivated by the empirical analysis of the air transportation system, we define a network model that includes geographical attributes along with topological and weight (traffic) properties. The introduction of geographical attributes is…
Cell fate decisions emerge as a consequence of a complex set of gene regulatory networks. Models of these networks are known to have more parameters than data can determine. Recent work, inspired by Waddington's metaphor of a landscape, has…
We consider here the morphogenesis (pattern formation) problem for some genetic network models. First, we show that any given spatio-temporal pattern can be generated by a genetic network involving a sufficiently large number of genes.…
Morphological development into evolutionary patterns under structural instability is ubiquitous in living systems and often of vital importance for engineering structures. Here we propose a data-driven approach to understand and predict…
Geometric constraints impact the formation of a broad range of spatial networks, from amino acid chains folding to proteins structures to rearranging particle aggregates. How the network of interactions dynamically self-organizes in such…
Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and…
A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…
Inspired by the structure of technological networks, we discuss network evolution mechanisms which give rise to topological properties found in real spatial networks. Thus, the peculiar structure of transport and distribution networks is…
In biological systems, the growth of cells, tissues, and organs is influenced by mechanical cues. Locally, cell growth leads to a mechanically heterogeneous environment as cells pull and push their neighbors in a cell network. Despite this…
The formation of neuron networks is a process of fundamental importance for understanding the development of the nervous system and for creating biomimetic devices for tissue engineering and neural repair. The basic process that controls…
Morphogenetic patterns are highly sophisticated dissipative structures. Are they governed by the same general mechanisms as chemical and hydrodynamic patterns? Turing's symmetry breaking and Wolpert's signalling provide alternative…
A fundamental understanding of the network architecture of the brain is necessary for the further development of theories explicating circuit function. Perhaps as a derivative of its initial application to abstract informational systems,…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
A graphical model is a statistical model that is associated to a graph whose nodes correspond to variables of interest. The edges of the graph reflect allowed conditional dependencies among the variables. Graphical models admit…
The human connectome represents a network map of the brain's wiring diagram and the pattern into which its connections are organized is thought to play an important role in cognitive function. The generative rules that shape the topology of…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Network generators that capture the Internet's large-scale topology are crucial for the development of efficient routing protocols and modeling Internet traffic. Our ability to design realistic generators is limited by the incomplete…
Mathematical models play an increasingly important role in the interpretation of biological experiments. Studies often present a model that generates the observations, connecting hypothesized process to an observed pattern. Such generative…
Turing patterns, arising from the interplay between competing species of diffusive particles, has long been an important concept for describing non-equilibrium self-organization in nature, and has been extensively investigated in many…