Related papers: Evolving Gene Regulatory Networks with Mobile DNA …
Regulatory networks consist of interacting molecules with a high degree of mutual chemical specificity. How can these molecules evolve when their function depends on maintenance of interactions with cognate partners and simultaneous…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
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 present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…
Artificial neurons built on synthetic gene networks have potential applications ranging from complex cellular decision-making to bioreactor regulation. Furthermore, due to the high information throughput of natural systems, it provides an…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
Boolean networks may be viewed as idealizations of biological genetic networks, where each node is represented by an on-off switch which is a function of the binary output from some other nodes. We evolve connectivity in a single Boolean…
DNA and other biopolymers are being investigated as new computing substrates and alternative to silicon-based digital computers. However, the established top-down design of biomolecular interaction networks remains challenging and does not…
The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…
DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene…
Life evolved organisms to adapt dynamically to their environment and autonomously exhibit behaviours. While complex behaviours in organisms are typically associated with the capability of neurons to process information, the unicellular…
The study of network structural controllability focuses on the minimum number of driver nodes needed to control a whole network. Despite intensive studies on this topic, most of them consider static networks only. It is well-known, however,…
Molecular chaperones play a prominent role in signaling and transcriptional regulatory networks of the cell. Recent advances uncovered that chaperones act as genetic buffers stabilizing the phenotype of various cells and organisms and may…
Random Boolean networks (RBNs) are models of genetic regulatory networks. It is useful to describe RBNs as self-organizing systems to study how changes in the nodes and connections affect the global network dynamics. This article reviews…
We successfully evolved a neural network controller that produces dynamic walking in a simulated bipedal robot with compliant actuators, a difficult control problem. The evolutionary evaluation uses a detailed software simulation of a…
Random Boolean networks (RBNs) have been a popular model of genetic regulatory networks for more than four decades. However, most RBN studies have been made with random topologies, while real regulatory networks have been found to be…
Plasmodium of true slime mold, Physarum polycephalum, is an amoeboid organism, which spreads with developing tubular network structure and crawls on two-dimensional plane with oscillating the cell thickness. The plasmodium transforms its…