Related papers: Model of Morphogenesis
Feedback loops are major components of biochemical systems. Many systems show multiple such (positive or negative) feedback loops. Nevertheless, very few quantitative analyses address the question how such multiple feedback loops evolved.…
A two-dimensional mathematical model for dynamics of endothelial cells in angiogenesis is investigated. Angiogenesis is a morphogenic process in which new blood vessels emerge from an existing vascular network. Recently a one-dimensional…
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semi-atomistic protein models. Our study investigated both the biophysics of conformational transitions as well as the possibility of increasing…
Developmental trajectories are known to be canalized, or robust to both environmental and genetic perturbations. However, even when these trajectories are decanalized by an environmental perturbation outside of the range of conditions to…
Motion prediction is essential and challenging for autonomous vehicles and social robots. One challenge of motion prediction is to model the interaction among traffic actors, which could cooperate with each other to avoid collisions or form…
"Oscillations" occur in quite different kinds of many-particle-systems when two groups of particles with different directions of motion meet or intersect at a certain spot. We present a model of pedestrian motion that is able to reproduce…
Mitochondrial networks exhibit a variety of complex behaviors, including coordinated cell-wide oscillations of energy states as well as a phase transition (depolarization) in response to oxidative stress. Since functional and structural…
The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a great variety of complex systems has been successfully described as networks whose…
Many human social phenomena, such as cooperation, the growth of settlements, traffic dynamics and pedestrian movement, appear to be accessible to mathematical descriptions that invoke self-organization. Here we develop a model of pedestrian…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
Two recent streams of work suggest that pairwise interactions may be sufficient to capture the complexity of biological systems ranging from protein structure to networks of neurons. In one approach, possible amino acid sequences in a…
Pathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation of one pathway from another. Conversely,…
Diagonal or chevron patterns are known to spontaneously emerge at the intersection of two perpendicular flows of self-propelled particles, e.g. pedestrians. The instability responsible for this pattern formation has been studied in previous…
We study the spatial patterns formed by a system of interacting particles where the mobility of any individual is determined by the population crowding at two different spatial scales. In this way we model the behavior of some biological…
We develop a theory of percolation with plasticity systems (PWPs) rendering properties of interest for neuromorphic computing. Unlike the standard percolation between two large electrodes, they have multiple ($N\gg 1$) interfaces and…
Systems composed of distinct complex networks are present in many real-world environments, from society to ecological systems. In the present paper, we propose a network model obtained as a consequence of interactions between two species…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
Mechanisms of pattern formation---of which the Turing instability is an archetype---constitute an important class of dynamical processes occurring in biological, ecological and chemical systems. Recently, it has been shown that the Turing…
We describe pattern formation in ecological systems using a version of the classical Lotka-Volterra model characterized by a spatial scale which controls the predator-prey interaction range. Analytical and simulational results show that…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…