There is no doubt that nowadays, biology benefits greatly from mathematics. In particular, cellular biology is, besides population dynamics, a field where tech niques of mathematical modeling are widely used. This is reflected by the large number of journal articles and congress proceedings published every year on the dynamics of complex cellular processes. This applies, among others, to metabolic control analysis, where the number of articles on theoretical fundamentals and experimental applications has increased for about 15 years. Surprisingly, mono graphs and textbooks dealing with the modeling of metabolic systems are still exceptionally rare. We think that now time is ripe to fill this gap. This monograph covers various aspects of the mathematical description of enzymatic systems, such as stoichiometric analysis, enzyme kinetics, dynamical simulation, metabolic control analysis, and evolutionary optimization. We believe that, at present, these are the main approaches by which metabolic systems can be analyzed in mathematical terms. Although stoichiometric analysis and enzyme kinetics are classical fields tracing back to the beginning of our century, there are intriguing recent developments such as detection of elementary biochemical syn thesis routes and rate laws for the situation of metabolic channeling, which we have considered worth being included. Evolutionary optimization of metabolic systems is a rather new field with promising prospects. Its goal is to elucidate the structure and functions of these systems from an evolutionary viewpoint.

Current biological research demands the extensive use of sophisticated mathematical methods and computer-aided analysis of experiments and data. This highly interdisciplinary volume focuses on structural, dynamical and functional aspects of cellular systems and presents corresponding experiments and mathematical models. The book may serve as an introduction for biologists, mathematicians and physicists to key questions in cellular systems which can be studied with mathematical models. Recent model approaches are presented with applications in cellular metabolism, intra- and intercellular signaling, cellular mechanics, network dynamics and pattern formation. In addition, applied issues such as tumor cell growth, dynamics of the immune system and biotechnology are included.

The complexity of biological systems has intrigued scientists from many disciplines and has given birth to the highly influential field of systems biology wherein a wide array of mathematical techniques, such as flux balance analysis, and technology platforms, such as next generation sequencing, is used to understand, elucidate, and predict the functions of complex biological systems. More recently, the field of synthetic biology, i.e., de novo engineering of biological systems, has emerged. Scientists from various fields are focusing on how to render this engineering process more predictable, reliable, scalable, affordable, and easy. Systems and control theory is a branch of engineering and applied sciences that rigorously deals with the complexities and uncertainties of interconnected systems with the objective of characterising fundamental systemic properties such as stability, robustness, communication capacity, and other performance metrics. Systems and control theory also strives to offer concepts and methods that facilitate the design of systems with rigorous guarantees on these properties. Over the last 100 years, it has made stellar theoretical and technological contributions in diverse fields such as aerospace, telecommunication, storage, automotive, power systems, and others. Can it have, or evolve to have, a similar impact in biology? The chapters in this book demonstrate that, indeed, systems and control theoretic concepts and techniques can have a significant impact in systems and synthetic biology. Volume II contains chapters contributed by leading researchers in the field of systems and synthetic biology that concern modeling physiological processes and bottom-up constructions of scalable biological systems. The modeling problems include characterisation and synthesis of memory, understanding how homoeostasis is maintained in the face of shocks and relatively gradual perturbations, understanding the functioning and robustness of biological clocks such as those at the core of circadian rhythms, and understanding how the cell cycles can be regulated, among others. Some of the bottom-up construction problems investigated in Volume II are as follows: How should biomacromolecules, platforms, and scalable architectures be chosen and synthesised in order to build programmable de novo biological systems? What are the types of constrained optimisation problems encountered in this process and how can these be solved efficiently? As the eminent computer scientist Donald Knuth put it, "biology easily has 500 years of exciting problems to work on". This edited book presents but a small fraction of those for the benefit of (1) systems and control theorists interested in molecular and cellular biology and (2) biologists interested in rigorous modelling, analysis and control of biological systems.

Dynamic Biological Organization is a fascinating account of the living organisms as dynamic systems, based on the concept that the spatio-temporal coherence of events within a living system result from the intrinsic dynamics of the processes taking place within that sysem. The authors of this important work, Miguel Aon and Sonia Cortassa have travelled widely to work in some of the leading research laboratories to accumulate a large information base on which to assemble this book. Taking a transdisciplinary approach, the authors draw on work at the interface of biochemistry, genetics, physiology, thermodynamics, kinetics and biomathematics, using mathematical models throughout to corroborate and analyze the biological complexity presented. Emphasizing biological processes occuring at the cellular level. Dynamic Biological Organization gives exciting insights into the experimental and theoretical applications of modern scientific paradigms to fundamental biological processes.

This book provides an entry point into Systems Biology for researchers in genetics, molecular biology, cell biology, microbiology and biomedical science to understand the key concepts to expanding their work. Chapters organized around broader themes of Organelles and Organisms, Systems Properties of Biological Processes, Cellular Networks, and Systems Biology and Disease discuss the development of concepts, the current applications, and the future prospects. Emphasis is placed on concepts and insights into the multi-disciplinary nature of the field as well as the importance of systems biology in human biological research. Technology, being an extremely important aspect of scientific progress overall, and in the creation of new fields in particular, is discussed in 'boxes' within each chapter to relate to appropriate topics. - 2013 Honorable Mention for Single Volume Reference in Science from the Association of American Publishers' PROSE Awards - Emphasizes the interdisciplinary nature of systems biology with contributions from leaders in a variety of disciplines - Includes the latest research developments in human and animal models to assist with translational research - Presents biological and computational aspects of the science side-by-side to facilitate collaboration between computational and biological researchers

The metabolic regulation of a cell system is of critical importance in systems biology, and a robust model of these mechanisms is essential in predicting the effects on the metabolism of both the culture environment and the knockout of specific genes. Bacterial cellular metabolic systems focuses on this highly topical subject in relation to culture environment and provides a detailed analysis from gene level to metabolic level regulation, as well as offering a discussion of the most recent modelling approaches. The book begins with an introduction to metabolic mechanisms and to the metabolic regulation of a cell, before moving on to discussing the action of global regulators in response to a specific culture environment. The second half of the book examines conventional flux balance analysis and its applications, 13C-metabolic flux analysis, and the effect of a specific gene knockout on the metabolism. - Comprehensive account of metabolic regulation via global regulators in response to changes in the culture environment - Basic formulation of 13C-metabolic flux analysis based on 13C-labelling experiments - Systems biology approach for the modelling and computer simulation of the main metabolic pathways of a cell system