Related papers: Modeling network dynamics: the lac operon, a case …
We review theoretical approaches to the understanding of food webs. After an overview of the available food web data, we discuss three different classes of models. The first class comprise static models, which assign links between species…
The recently introduced complex active optical network (LANER) generalizes the concept of laser system to a collection of links, building a bridge with random-laser physics and quantum-graphs theory. So far, LANERs have been studied with a…
Self-organisation of individuals within large collectives occurs throughout biology. Mathematical models can help elucidate the individual-level mechanisms behind these dynamics, but analytical tractability often comes at the cost of…
Modeling and optimization of metabolic networks has been one of the hottest topics in computational systems biology within recent years. However, the complexity and uncertainty of these networks in addition to the lack of necessary data has…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
Complex network theory provides a unifying framework for the study of structured dynamic systems. The current literature emphasizes a widely reported phenomenon of intermittent interaction among network vertices. In this paper, we introduce…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
This paper is an introduction to the membrane potential equation for neurons. Its properties are described, as well as sample applications. Networks of these equations can be used for modeling neuronal systems, which also process images and…
Transcription regulation typically involves the binding of proteins over long distances on multiple DNA sites that are brought close to each other by the formation of DNA loops. The inherent complexity of the assembly of regulatory…
In this article we highlight chemotaxis (cellular movement) as a rich source of potential engineering applications and computational models, highlighting current research and possible future work. We first give a brief description of the…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
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…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
We introduce a new phenomenological one-scale model for the evolution of domain wall networks, and test it against high-resolution field theory numerical simulations. We argue that previous numerical estimates of wall velocities are…
Living neuronal networks in dissociated neuronal cultures are widely known for their ability to generate highly robust spatiotemporal activity patterns in various experimental conditions. These include neuronal avalanches satisfying the…
Recent experimental and theoretical studies suggest that crystallization and glass-like solidification are useful analogies for understanding cell ordering in confluent biological tissues. It remains unexplored how cellular ordering…
We propose a physical model for developmental process at cellular level to discuss the mechanism of epigenetic landscape. In our simplified model, a minimal model, the network of the interaction among cells generates the landscape…
Multi-valued logical models can be used to describe biological networks on a high level of abstraction based on the network structure and logical parameters capturing regulatory effects. Interestingly, the dynamics of two distinct models…
The immune system can be thought as a complex network of different interacting elements. A cellular automaton, defined in shape-space, was recently shown to exhibit self-regulation and complex behavior and is, therefore, a good candidate to…
Based on a detailed microscopic test scenario motivated by recent empirical studies of single-vehicle data, several cellular automaton models for traffic flow are compared. We find three levels of agreement with the empirical data: 1)…