The 1997 Les Houches workshop on "Dynamical Network in Physics and Biology" was the third in a series of meetings "At the Frontier between Physics and Biology". Our objective with these workshops is to create a truly interdisciplinary forum for researchers working on outstanding problems in biology, but using different approaches (physical, chemical or biological). Generally speaking, the biologists are trained in the particular and motivated by the specifics, while, in contrast, the physicists deal with generic and "universal" models. All agree about the necessity of developing "robust" models. The specific aim of the workshop was to bridge the gap between physics and biology in the particular field of interconnected dynamical networks. The proper functioning of a living organism of any complexity requires the coordinated activity of a great number of "units". Units, or, in physical terms, degrees of freedom that couple to one another, typically form networks. The physical or biological properties of interconnected networks may drastically differ from those of the individual units: the whole is not simply an assembly of its parts, as can be demonstrated by the following examples. Above a certain (critical) concentration the metallic islands, randomly distributed in an insulating matrix, form an interconnected network. At this point the macroscopic conductivity of the system becomes finite and the amorphous metal is capable of carrying current. The value of the macroscopic conductivity typically is very different from the conductivity of the individual metallic islands.

The availability of large data sets have allowed researchers to uncover complex properties such as large scale fluctuations and heterogeneities in many networks which have lead to the breakdown of standard theoretical frameworks and models. Until recently these systems were considered as haphazard sets of points and connections. Recent advances have generated a vigorous research effort in understanding the effect of complex connectivity patterns on dynamical phenomena. For example, a vast number of everyday systems, from the brain to ecosystems, power grids and the Internet, can be represented as large complex networks. This new and recent account presents a comprehensive explanation of these effects.

This book brings together two emerging research areas: synchronization in coupled nonlinear systems and complex networks, and study conditions under which a complex network of dynamical systems synchronizes. While there are many texts that study synchronization in chaotic systems or properties of complex networks, there are few texts that consider the intersection of these two very active and interdisciplinary research areas. The main theme of this book is that synchronization conditions can be related to graph theoretical properties of the underlying coupling topology. The book introduces ideas from systems theory, linear algebra and graph theory and the synergy between them that are necessary to derive synchronization conditions. Many of the results, which have been obtained fairly recently and have until now not appeared in textbook form, are presented with complete proofs. This text is suitable for graduate-level study or for researchers who would like to be better acquainted with the latest research in this area. Sample Chapter(s). Chapter 1: Introduction (76 KB). Contents: Graphs, Networks, Laplacian Matrices and Algebraic Connectivity; Graph Models; Synchronization in Networks of Nonlinear Continuous-Time Dynamical Systems; Synchronization in Networks of Coupled Discrete-Time Systems; Synchronization in Network of Systems with Linear Dynamics; Agreement and Consensus Problems in Groups of Interacting Agents. Readership: Graduate students and researchers in physics, applied mathematics and engineering.

This volume is a tutorial for the study of dynamical systems on networks. It discusses both methodology and models, including spreading models for social and biological contagions. The authors focus especially on “simple” situations that are analytically tractable, because they are insightful and provide useful springboards for the study of more complicated scenarios. This tutorial, which also includes key pointers to the literature, should be helpful for junior and senior undergraduate students, graduate students, and researchers from mathematics, physics, and engineering who seek to study dynamical systems on networks but who may not have prior experience with graph theory or networks. Mason A. Porter is Professor of Nonlinear and Complex Systems at the Oxford Centre for Industrial and Applied Mathematics, Mathematical Institute, University of Oxford, UK. He is also a member of the CABDyN Complexity Centre and a Tutorial Fellow of Somerville College. James P. Gleeson is Professor of Industrial and Applied Mathematics, and co-Director of MACSI, at the University of Limerick, Ireland.

This book is the culmination of three years of research effort on a multidisciplinary project in which physicists, mathematicians, computer scientists and social scientists worked together to arrive at a unifying picture of complex networks. The contributed chapters form a reference for the various problems in data analysis visualization and modeling of complex networks.

This book provides a complete study on neural structures exhibiting nonlinear and stochastic dynamics, elaborating on neural dynamics by introducing advanced models of neural networks. It overviews the main findings in the modelling of neural dynamics in terms of electrical circuits and examines their stability properties with the use of dynamical systems theory. It is suitable for researchers and postgraduate students engaged with neural networks and dynamical systems theory.

This volume presents a timely and comprehensive overview of biological networks at all organization levels in the spirit of the complex system approach. It discusses the transversal issues and fundamental principles as well as the overall structure, dynamics, and modeling of a wide array of biological networks at the molecular, cellular, and population levels. Anchored in both empirical data and a strong theoretical background, the book therefore lends valuable credence to the complex systems approach.

The book presents nine mini-courses from a summer school, Dynamics of Biological Systems, held at the University of Alberta in 2016, as part of the prestigious seminar series: Séminaire de Mathématiques Supérieures (SMS). It includes new and significant contributions in the field of Dynamical Systems and their applications in Biology, Ecology, and Medicine. The chapters of this book cover a wide range of mathematical methods and biological applications. They - explain the process of mathematical modelling of biological systems with many examples, - introduce advanced methods from dynamical systems theory, - present many examples of the use of mathematical modelling to gain biological insight - discuss innovative methods for the analysis of biological processes, - contain extensive lists of references, which allow interested readers to continue the research on their own. Integrating the theory of dynamical systems with biological modelling, the book will appeal to researchers and graduate students in Applied Mathematics and Life Sciences.

An overview of current models of biological systems, reflecting the major advances that have been made over the past decade.

Biophysical models have been used in biology for decades, but they have been limited in scope and size. In this book, Bernhard Ø. Palsson shows how network reconstructions that are based on genomic and bibliomic data, and take the form of established stoichiometric matrices, can be converted into dynamic models using metabolomic and fluxomic data. The Mass Action Stoichiometric Simulation (MASS) procedure can be used for any cellular process for which data is available and allows a scalable step-by-step approach to the practical construction of network models. Specifically, it can treat integrated processes that need explicit accounting of small molecules and protein, which allows simulation at the molecular level. The material has been class-tested by the author at both the undergraduate and graduate level. All computations in the text are available online in MATLAB® and Mathematica® workbooks, allowing hands-on practice with the material.