Related papers: Function Constrains Network Architecture and Dynam…
Canalization is a key organizing principle in complex systems, particularly in gene regulatory networks. It describes how certain input variables exert dominant control over a function's output, thereby imposing hierarchical structure and…
Dynamical systems theory and complexity science provide powerful tools for analysing artificial agents and robots. Furthermore, they have been recently proposed also as a source of design principles and guidelines. Boolean networks are a…
Random Boolean networks are models of disordered causal systems that can occur in cells and the biosphere. These are open thermodynamic systems exhibiting a flow of energy that is dissipated at a finite rate. Life does work to acquire more…
Experimental results often do not assess network structure; rather, the network structure is inferred by the dynamics of the nodes. From the dynamics of the nodes one then constructs a network of functional relations, termed the functional…
We present and discuss the results of an experimental analysis in the design of Boolean networks by means of genetic algorithms. A population of networks is evolved with the aim of finding a network such that the attractor it reaches is of…
The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…
A logical function can be used to characterizing a property of a state of Boolean network (BN), which is considered as an aggregation of states. To illustrate the dynamics of a set of logical functions, which characterize our concerned…
Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…
Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Boolean networks are popular tools for the exploration of qualitative dynamical properties of biological systems. Several dynamical interpretations have been proposed based on the same logical structure that captures the interactions…
Nature is rife with networks that are functionally optimized to propagate inputs in order to perform specific tasks. Whether via genetic evolution or dynamic adaptation, many networks create functionality by locally tuning interactions…
Boolean networks have been widely used in many areas of science and engineering to represent various dynamical behaviour. In systems biology, they became useful tools to study the dynamical characteristics of large-scale biomolecular…
Cells integrate signals and make decisions about their future state in short amounts of time. A lot of theoretical effort has gone into asking how to best design gene regulatory circuits that fulfill a given function, yet little is known…
A Boolean network model of the cell-cycle regulatory network of fission yeast (Schizosaccharomyces Pombe) is constructed solely on the basis of the known biochemical interaction topology. Simulating the model in the computer, faithfully…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
Neural networks can emulate nonlinear physical systems with high accuracy, yet they may produce physically-inconsistent results when violating fundamental constraints. Here, we introduce a systematic way of enforcing nonlinear analytic…
Prestrained elastic networks arise in a number of biological and technological systems ranging from the cytoskeleton of cells to tensegrity structures. To understand the response of such a network as a function of the prestrain, we consider…
Functional networks of complex systems are obtained from the analysis of the temporal activity of their components, and are often used to infer their unknown underlying connectivity. We obtain the equations relating topology and function in…
Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of…