This is a short and self-contained introduction to the field of mathematical modeling of gene-networks in bacteria. As an entry point to the field, we focus on the analysis of simple gene-network dynamics. The notes commence with an introduction to the deterministic modeling of gene-networks, with extensive reference to applicable results coming from dynamical systems theory. The second part of the notes treats extensively several approaches to the study of gene-network dynamics in the pre...

Written by a well-known professor of physiology at McGill University, this text presents an informative exploration of the basis of the Second Law of Thermodynamics, detailing the fundamental dynamic properties behind the construction of statistical mechanics.Topics include maximal entropy principles; invertible and noninvertible systems; ergodicity and unique equilibria; asymptotic periodicity and entropy evolution; and open discrete and continuous time systems. The author demonstr...

This book analyzes the impact of quiescent phases on biological models. Quiescence arises, for example, when moving individuals stop moving, hunting predators take a rest, infected individuals are isolated, or cells enter the quiescent compartment of the cell cycle. In the first chapter of Topics in Mathematical Biology general principles about coupled and quiescent systems are derived, including results on shrinking periodic orbits and stabilization of oscillations via quiescence. In subs...

This monograph has arisen out of a number of attempts spanning almost five decades to understand how one might examine the evolution of densities in systems whose dynamics are described by differential delay equations. Though the authors have no definitive solution to the problem, they offer this contribution in an attempt to define the problem as they see it, and to sketch out several obvious attempts that have been suggested to solve the problem and which seem to have failed. They hope t...

There is a widespread assumption that the universe in general, and life in particular, is 'getting more complex with time'. This book brings together a wide range of experts in science, philosophy and theology and unveils their joint effort in exploring this idea. They confront essential problems behind the theory of complexity and the role of life within it: what is complexity? When does it increase, and why? Is the universe evolving towards states of ever greater complexity and diversity...

The Logic of Chance offers a reappraisal and a new synthesis of theories, concepts, and hypotheses on the key aspects of the evolution of life on earth in light of comparative genomics and systems biology. The author presents many specific examples from systems and comparative genomic analysis to begin to build a new, much more detailed, complex, and realistic picture of evolution. The book examines a broad range of topics in evolutionary biology including  the inadequacy of natur...

This highly unusual book began as a serious inquiry into Schrödinger's question, “What is life?”, and as a celebration of life itself. It takes the reader on a voyage of discovery through many areas of contemporary physics, from non-equilibrium thermodynamics and quantum optics to liquid crystals and fractals, all necessary for illuminating the problem of life. In the process, the reader is treated to a rare and exquisite view of the organism, gaining novel insights not only into the physi...

In the hard sciences, which can often feel out of grasp for many lay readers, there are "great thinkers" who go far beyond the equations, formulas, and research. Minds such as Stephen Hawking philosophize about the functions and nature of the universe, the implications of our existence, and other impossibly fascinating, yet difficult questions. Stuart A. Kauffman is one of those great thinkers. He has dedicated his lifetime to researching "complex systems" at prestigious institutions and n...

Thirty years ago, biologists could get by with a rudimentary grasp of mathematics and modeling. Not so today. In seeking to answer fundamental questions about how biological systems function and change over time, the modern biologist is as likely to rely on sophisticated mathematical and computer-based models as traditional fieldwork. In this book, Sarah Otto and Troy Day provide biology students with the tools necessary to both interpret models and to build their own.The book star...

This exceptional book is concerned with the application of fractals and chaos, as well as other concepts from nonlinear dynamics to biomedical phenomena. Herein we seek to communicate the excitement being experienced by scientists upon making application of these concepts within the life sciences. Mathematical concepts are introduced using biomedical data sets and the phenomena being explained take precedence over the mathematics.In this new edition what has withstood the test of time has ...

Addressing the emergence of life from a systems biology perspective, this new edition has undergone extensive revision, reflecting changes in scientific understanding and evolution of thought on the question 'what is life?'. With an emphasis on the philosophical aspects of science, including the epistemic features of modern synthetic biology, and also providing an updated view of the autopoiesis/cognition theory, the book gives an exhaustive treatment of the biophysical properties of vesic...

This book evolved from an interdisciplinary graduate course entitled 'Molecular Modeling' developed at New York University. Its primary goal is to stimulate excitement for molecular modeling research while providing grounding in the discipline. Scientists who wish to enter, or become familiar with, the field of biomolecular modeling and simulation may benefit from the broad coverage of problems and approaches.