Dynamic Biological Networks


Book Description

This introduction to the crustacean stomatogastric nervous system (STNS) describes some of the best-understood neural networks in the animal kingdom at cellular, network, behavioural, comparative and evolutionary levels of analysis.




The Dynamics of Biological Systems


Book Description

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.




Handbook on Biological Networks


Book Description

Networked systems are all around us. The accumulated evidence of systems as complex as a cell cannot be fully understood by studying only their isolated constituents, giving rise to a new area of interest in research ? the study of complex networks. In a broad sense, biological networks have been one of the most studied networks, and the field has benefited from many important contributions. By understanding and modeling the structure of a biological network, a better perception of its dynamical and functional behavior is to be expected. This unique book compiles the most relevant results and novel insights provided by network theory in the biological sciences, ranging from the structure and dynamics of the brain to cellular and protein networks and to population-level biology.




Systems Biology: Simulation of Dynamic Network States


Book Description

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.




Biological Networks


Book Description

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.




Dynamics of Biological Systems


Book Description

From the spontaneous rapid firing of cortical neurons to the spatial diffusion of disease epidemics, biological systems exhibit rich dynamic behaviour over a vast range of time and space scales. Unifying many of these diverse phenomena, Dynamics of Biological Systems provides the computational and mathematical platform from which to understand the underlying processes of the phenomena. Through an extensive tour of various biological systems, the text introduces computational methods for simulating spatial diffusion processes in excitable media, such as the human heart, as well as mathematical tools for dealing with systems of nonlinear ordinary and partial differential equations, such as neuronal activation and disease diffusion. The mathematical models and computer simulations offer insight into the dynamics of temporal and spatial biological systems, including cardiac pacemakers, artificial electrical defibrillation, pandemics, pattern formation, flocking behaviour, the interaction of autonomous agents, and hierarchical and structured network topologies. Tools from complex systems and complex networks are also presented for dealing with real phenomenological systems. With exercises and projects in each chapter, this classroom-tested text shows students how to apply a variety of mathematical and computational techniques to model and analyze the temporal and spatial phenomena of biological systems. MATLAB® implementations of algorithms and case studies are available on the author’s website.




Models of Life


Book Description

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




Dynamical Systems on Networks


Book Description

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.




Self-Organized Biological Dynamics and Nonlinear Control


Book Description

The growing impact of nonlinear science on biology and medicine is fundamentally changing our view of living organisms and disease processes. This book introduces the application to biomedicine of a broad range of interdisciplinary concepts from nonlinear dynamics, such as self-organization, complexity, coherence, stochastic resonance, fractals and chaos. It comprises 18 chapters written by leading figures in the field and covers experimental and theoretical research, as well as the emerging technological possibilities such as nonlinear control techniques for treating pathological biodynamics, including heart arrhythmias and epilepsy. This book will attract the interest of professionals and students from a wide range of disciplines, including physicists, chemists, biologists, sensory physiologists and medical researchers such as cardiologists, neurologists and biomedical engineers.




Applications of Dynamical Systems in Biology and Medicine


Book Description

This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control. Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction. Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation.