Model integration - the process by which different modelling efforts can be brought together to simulate the target system - is a core technology in the field of Systems Biology. In the work presented here model integration was addressed directly taking cancer systems as an example. An in-depth literature review was carried out to survey the model forms and types currently being utilised. This was used to formalise the main challenges that model integration poses, namely that of paradigm (the formalism on which a model is based), focus (the real-world system the model represents) and scale. A two-tier model integration strategy, including a knowledge-driven approach to address model semantics, was developed to tackle these challenges. In the first step a novel description of models at the level of behaviour, rather than the precise mathematical or computational basis of the model, is developed by distilling a set of abstract classes and properties. These can accurately describe model behaviour and hence describe focus in a way that can be integrated with behavioural descriptions of other models. In the second step this behaviour is decomposed into an agent-based system by translating the models into local interaction rules. The book provides a detailed and highly integrated presentation of the method, encompassing both its novel theoretical and practical aspects, which will enable the reader to practically apply it to their model integration needs in academic research and professional settings. The text is self-supporting. It also includes an in-depth current bibliography to relevant research papers and literature. The review of the current state of the art in tumour modelling provides added value.

Holistic Engineering Education: Beyond Technology is a compilation of coordinated and focused essays from world leaders in the engineering profession who are dedicated to a transformation of engineering education and practice. The contributors define a new and holistic approach to education and practice that captures the creativity, interdisciplinarity, complexity, and adaptability required for the profession to grow and truly serve global needs. With few exceptions today, engineering students and professionals continue to receive a traditional, technically-based education and training using curriculum models developed for early 20th century manufacturing and machining. While this educational paradigm has served engineering well, helping engineers create awe-inspiring machines and technologies for society, the coursework and expectations of most engineering programs eschew breadth and intellectual exploration to focus on consistent technological precision and study. Why this dichotomy? While engineering will always need precise technological skill, the 21st century innovation economy demands a new professional perspective that recognizes the value of complex systems thinking, cross-disciplinary collaborations, economic and environmental impacts (sustainability), and effective communication to global and community leaders, thus enabling engineers to consider "the whole patient" of society's needs. The goal of this book is to inspire, lead, and guide this critically needed transformation of engineering education. "Holistic Engineering Education: Beyond Technology points the way to a transformation of engineering education and practice that will be sufficiently robust, flexible, and systems-oriented to meet the grand challenges of the 21st century with their ever-increasing scale, complexity, and transdisciplinary nature." -- Charles Vest, President, National Academy of Engineering; President Emeritus, MIT "This collection of essays provides compelling arguments for the need of an engineering education that prepares engineers for the problems of the 21st century. Following the National Academy's report on the Engineer of 2020, this book brings together experts who make the case for an engineering profession that looks beyond developing just cool technologies and more into creating solutions that can address important problems to benefit real people." -- Linda Katehi, Chancellor, University of California at Davis "This superb volume offers a provocative portrait of the exciting future of engineering education...A dramatically new form of engineering education is needed that recognizes this field as a liberal art, as a profession that combines equal parts technical rigor and creative design...The authors challenge the next generation to engineering educators to imagine, think and act in new ways. " -- Lee S. Shulman, President Emeritus, The Carnegie Foundation for the Advancement of Teaching and Charles E. Ducommun Professor of Education Emeritus, Stanford University

Oligopoly theory is one of the most intensively studied areas of mathematical economics. On the basis of the pioneering works of Cournot (1838), many res- rchers have developed and extensively examined the different variants of oligopoly models. Initially, the existence and uniqueness of the equilibrium of the different types of oligopolies was the main concern, and later the dynamic extensions of these models became the focus. The classical result of Theocharis (1960) asserts that under discrete time scales and static expectations, the equilibrium of a sing- product oligopoly without product differentiation and with linear price and cost functions is asymptotically stable if and only if it is a duopoly. In the continuous time case, asymptotic stability is guaranteed for any number of ?rms. In these cases the resulting dynamical systems are also linear, where local and global asymptotic stability are equivalent to each other. The classical book of Okuguchi (1976) gives a comprehensive summary of the earlier results and developments. The multipr- uct extensionshave been discussed in Okuguchiand Szidarovszky(1999);however, nonlinear features were barely touched upon in these contributions. WiththedevelopmentofthecriticalcurvemethodbyGumowskiandMira(1980) (see also Mira et al. (1996))fordiscrete time systemsand the introductionof cont- uously distributed information lags by Invernizzi and Medio (1991) in continuous time systems, increasing attention has been given to the global dynamics of n- linear oligopolies. The authors of this book have devoted a great deal of research effort to this area.

Non-linear stochastic systems are at the center of many engineering disciplines and progress in theoretical research had led to a better understanding of non-linear phenomena. This book provides information on new fundamental results and their applications which are beginning to appear across the entire spectrum of mechanics. The outstanding points of these proceedings are Coherent compendium of the current state of modelling and analysis of non-linear stochastic systems from engineering, applied mathematics and physics point of view. Subject areas include: Multiscale phenomena, stability and bifurcations, control and estimation, computational methods and modelling. For the Engineering and Physics communities, this book will provide first-hand information on recent mathematical developments. The applied mathematics community will benefit from the modelling and information on various possible applications.

For the present edition four chapters have been added which form the fourth 1 part at the end of the book . Entitled The triumph of neoliberalism , the new partexplains how theimplementation worldwide oftheneoliberal agenda paved the way for the present crisis. As a matter of fact, the evidence provided in chapter 9 suggests that the present crisis already began to build up in the mid-1970s. It is around 1975 that (real) US wages reached a peak-level they would never regain in f- lowing decades. It was also around 1975 that the number of strikes began to fall sharply. The mid-1970s also marked the beginning of a huge in ow of immigrants (in large part of Hispanic origin) into the United States. The in ated supply of labor depressed wages and this had the consequence that consumption could be increased only by an unprecedented development of credit. Perhaps the reader may think that to blame the prevailing economic system for the unfolding depression is a fairly common and all too easy temptation.

The spectacular success of the scientific enterprise over the last four hundred years has led to the promise of an all encompassing vision of the natural world. In this elegant picture, everything we observe is based upon just a few fundamental processes and entities. The almost infinite variety and complexity of the world is thus the product of emergence. But the concept of emergence is fraught with controversy and confusion. This book ponders the question of how emergence should be understood within the scientific picture, and whether a complete vision of the world can be attained that includes consciousness.

This book explores non-extensive statistical mechanics in non-equilibrium thermodynamics, and presents an overview of the strong nonlinearity of chaos and complexity in natural systems, drawing on relevant mathematics from topology, measure-theory, inverse and ill-posed problems, set-valued analysis, and nonlinear functional analysis. It offers a self-contained theory of complexity and complex systems as the steady state of non-equilibrium systems, denoting a homeostatic dynamic equilibrium between stabilizing order and destabilizing disorder.

The primary goal of the book is to present the ideas and research findings of active researchers such as physicists, economists, mathematicians and financial engineers working in the field of "Econophysics," who have undertaken the task of modeling and analyzing systemic risk, network dynamics and other topics. Of primary interest in these studies is the aspect of systemic risk, which has long been identified as a potential scenario in which financial institutions trigger a dangerous contagion mechanism, spreading from the financial economy to the real economy. This type of risk, long confined to the monetary market, has spread considerably in the recent past, culminating in the subprime crisis of 2008. As such, understanding and controlling systemic risk has become an extremely important societal and economic challenge. The Econophys-Kolkata VI conference proceedings are dedicated to addressing a number of key issues involved. Several leading researchers in these fields report on their recent work and also review contemporary literature on the subject.

Materials sciences relate the macroscopic properties of materials to their microscopic structure and postulate the need for holistic multiscale research. The investigation of shape memory alloys is a prime example in this regard. This particular class of materials exhibits strong coupling of temperature, strain and stress, determined by solid state phase transformations of their metallic lattices. The present book presents a collection of simulation studies of this behaviour. Employing conceptually simple but comprehensive models, the fundamental material properties of shape memory alloys are qualitatively explained from first principles. Using contemporary methods of molecular dynamics simulation experiments, it is shown how microscale dynamics may produce characteristic macroscopic material properties. The work is rooted in the materials sciences of shape memory alloys and covers thermodynamical, micro-mechanical and crystallographical aspects. It addresses scientists in these research fields and their students.

The "Turbulence and Interactions 2009" (TI2009) conference was held in Saint- Luce on the island of La Martinique, France, on May 31-June 5, 2009. The sci- tific sponsors of the conference were * DGA * Ecole Polytechnique Federale de Lausanne (EPFL), * ERCOFTAC : European Research Community on Flow, Turbulence and Combustion, * Institut Jean Le Rond d'Alembert, Paris, * ONERA. This second TI conference was very successful as it attracted 65 researchers from 17 countries. The magnificent venue and the beautiful weather helped the participants to discuss freely and casually, share ideas and projects, and spend very good times all together. The organisers were fortunate in obtaining the presence of the following - vited speakers: L. Fuchs (KTH, Stockholm and Lund University), J. Jimenez (Univ. Politecnica Madrid), C.-H. Moeng (NCAR), A. Scotti (University of North Carolina), L. Shen (Johns Hopkins University) and A.J. Smits (Princeton Univ- sity). The topics covered by the 62 contributed papers ranged from experimental results through theory to computations. They represent a snapshot of the state-- the-art in turbulence research. The papers of the conference went through the usual reviewing process and the result is given in this book of Proceedings. In the present volume, the reader will find the keynote lectures followed by the contributed talks given in alphabetical order of the first author.

This is the second of two volumes offering the very first comprehensive treatise of self-organization and non-linear dynamics in electrochemical systems. The first volume covers general principles of self-organization as well as temporal instabilities. The content of both volumes is organized so that each description of a particular electrochemical system is preceded by an introduction to basic concepts of nonlinear dynamics, in order to help the reader unfamiliar with this discipline to understand at least fundamental concepts and the methods of stability analysis. The presentation of the systems is not limited to laboratory models but stretches out to real-life objects and processes, including systems of biological importance, such as neurons in living matter. Marek Orlik presents a comprehensive and consistent survey of the field.

This new edition strives yet again to provide readers with a working knowledge of chaos theory and dynamical systems. It does so through parallel introductory explanations in the book and interaction with carefully-selected programs supplied on the accompanying disk. The programs enable readers, especially advanced-undergraduate students in physics, engineering, and math, to tackle relevant physical systems quickly on their PCs, without distraction from algorithmic details. For the third edition of Chaos: A Program Collection for the PC, each of the previous twelve programs is polished and rewritten in C++ (both Windows and Linux versions are included). A new program treats kicked systems, an important class of two-dimensional problems.

The contributions to this volume review the mathematical description of complex phenomena from both a deterministic and stochastic point of view. The interface between theoretical models and the understanding of complexity in engineering, physics and chemistry is explored. The reader will find information on neural networks, chemical dissipation, fractal diffusion, problems in accelerator and fusion physics, pattern formation and self-organisation, control problems in regions of insta- bility, and mathematical modeling in biology.

Until now the important concept of quantum chaos has remained somewhat ill defined. This volume tackles the ubiquitous borderline between classical andquantum mechanics, studying in particular the semiclassical limit of chaotic systems. The effects of disorder from dynamics and their relation to stochastic systems, quantum coherence effects in mesoscopic systems, and the relevant theoretical approaches are fruitfully combined in this volume. The major paradigms of what is called quantum chaos, random matrix theory and applications to condensed matter and nuclear physics are presented. Detailed discussions of experimental work with particular emphasis on atomic physics are included. The book is highly recommended for graduate-student seminars.

Combined for researchers and graduate students the articles from the Sitges Summer School together form an excellent survey of the applications of neural-network theory to statistical mechanics and computer-science biophysics. Various mathematical models are presented together with their interpretation, especially those to do with collective behaviour, learning and storage capacity, and dynamical stability.

Although the study of dynamical systems is mainly concerned with single trans formations and one-parameter flows (i. e. with actions of Z, N, JR, or JR+), er godic theory inherits from statistical mechanics not only its name, but also an obligation to analyze spatially extended systems with multi-dimensional sym metry groups. However, the wealth of concrete and natural examples, which has contributed so much to the appeal and development of classical dynamics, is noticeably absent in this more general theory. A remarkable exception is provided by a class of geometric actions of (discrete subgroups of) semi-simple Lie groups, which have led to the discovery of one of the most striking new phenomena in multi-dimensional ergodic theory: under suitable circumstances orbit equivalence of such actions implies not only measurable conjugacy, but the conjugating map itself has to be extremely well behaved. Some of these rigidity properties are inherited by certain abelian subgroups of these groups, but the very special nature of the actions involved does not allow any general conjectures about actions of multi-dimensional abelian groups. Beyond commuting group rotations, commuting toral automorphisms and certain other algebraic examples (cf. [39]) it is quite difficult to find non-trivial smooth Zd-actions on finite-dimensional manifolds. In addition to scarcity, these examples give rise to actions with zero entropy, since smooth Zd-actions with positive entropy cannot exist on finite-dimensional, connected manifolds. Cellular automata (i. e.

This book is devoted to the applications of the mathematical theory of solitons to physics, statistical mechanics, and molecular biology. It contains contributions on the signature and spectrum of solitons, nonlinear excitations in prebiological systems, experimental and theoretical studies on chains of hydrogen-bonded molecules, nonlinear phenomena in solid-state physics, including charge density waves, nonlinear wave propagation, defects, gap solitons, and Josephson junctions. The content is interdisciplinary in nature and displays the new trends in nonlinear physics.

The emphasis of this book is on engineering aspects of fluid turbulence. The book explains for example how to tackle turbulence in industrial applications. It is useful to several disciplines, such as, mechanical, civil, chemical, aerospace engineers and also to professors, researchers, beginners, under graduates and post graduates. The following issues are emphasized in the book: - Modeling and computations of engineering flows: The author discusses in detail the quantities of interest for engineering turbulent flows and how to select an appropriate turbulence model; Also, a treatment of the selection of appropriate boundary conditions for the CFD simulations is given. - Modeling of turbulent convective heat transfer: This is encountered in several practical situations. It basically needs discussion on issues of treatment of walls and turbulent heat fluxes. - Modeling of buoyancy driven flows, for example, smoke issuing from chimney, pollutant discharge into water bodies, etc

The pedagogically presented lectures deal with viscoelastic behaviour of fluids, the compatibility of rheological theories with nonequilibrium thermodynamics, fluids under shear, and polymer behaviour in solution and in biological systems. The main aims of the book are to stress the importance of the study of rheological systems for statistical physics and nonequilibrium thermodynamics and to present recent results in rheological modelling. The book will be a valuable source for both students and researchers.

Nature provides many examples of coherent nonlinear structures and waves, and these have been observed and studied in various fields ranging from fluids and plasmas through solid-state physics to chemistry and biology. These proceedings reflect the remarkable process in understanding and modeling nonlinear phenomena in various systems that has recently been made.Experimental, numerical, and theoretical activities interact in various studies that are presented according to the following classification: magnetic and optical systems, biosystems and molecular systems, lattice excitations and localized modes, two-dimensional structures, theoretical physics, and mathematical methods. The book addresses researchers and graduate students from biology, engineering, mathematics, and physics.

Beginning with Nobel laureate I. Prigogine's lecture "Entropy Revisited", this book gives a well-balanced survey on capillarity properties at liquid and solid interfaces. It approaches the subject from both the microscopic (statistical mechanics) and the macroscopic (mechanics and thermodynamics) points of view. Experimental aspects and technological applications are also presented. The book addresses researchers and graduate students of physics and physical chemistry.

This book explains the minimum error entropy (MEE) concept applied to data classification machines. Theoretical results on the inner workings of the MEE concept, in its application to solving a variety of classification problems, are presented in the wider realm of risk functionals. Researchers and practitioners also find in the book a detailed presentation of practical data classifiers using MEE. These include multi-layer perceptrons, recurrent neural networks, complexvalued neural networks, modular neural networks, and decision trees. A clustering algorithm using a MEE-like concept is also presented. Examples, tests, evaluation experiments and comparison with similar machines using classic approaches, complement the descriptions.

Stability conditions for functional differential equations can be obtained using Lyapunov functionals. Lyapunov Functionals and Stability of Stochastic Functional Differential Equations describes the general method of construction of Lyapunov functionals to investigate the stability of differential equations with delays. This work continues and complements the author's previous book Lyapunov Functionals and Stability of Stochastic Difference Equations, where this method is described for difference equations with discrete and continuous time. The text begins with both a description and a delineation of the peculiarities of deterministic and stochastic functional differential equations. There follows basic definitions for stability theory of stochastic hereditary systems, and the formal procedure of Lyapunov functionals construction is presented. Stability investigation is conducted for stochastic linear and nonlinear differential equations with constant and distributed delays. The proposed method is used for stability investigation of different mathematical models such as: * inverted controlled pendulum; * Nicholson's blowflies equation; * predator-prey relationships; * epidemic development; and * mathematical models that describe human behaviours related to addictions and obesity. Lyapunov Functionals and Stability of Stochastic Functional Differential Equations is primarily addressed to experts in stability theory but will also be of interest to professionals and students in pure and computational mathematics, physics, engineering, medicine, and biology.

This thesis presents a novel coarse-grained model of DNA, in which bases are represented as rigid nucleotides. The model is shown to quantitatively reproduce many phenomena, including elastic properties of the double-stranded state, hairpin formation in single strands and hybridization of pairs of strands to form duplexes, the first time such a wide range of properties has been captured by a coarse-grained model. The scope and potential of the model is demonstrated by simulating DNA tweezers, an iconic nanodevice, and a two-footed DNA walker - the first time that coarse-grained modelling has been applied to dynamic DNA nanotechnology.

The domain of non-extensive thermostatistics has been subject to intensive research over the past twenty years and has matured significantly. Generalised Thermostatistics cuts through the traditionalism of many statistical physics texts by offering a fresh perspective and seeking to remove elements of doubt and confusion surrounding the area. The book is divided into two parts - the first covering topics from conventional statistical physics, whilst adopting the perspective that statistical physics is statistics applied to physics. The second developing the formalism of non-extensive thermostatistics, of which the central role is played by the notion of a deformed exponential family of probability distributions. Presented in a clear, consistent, and deductive manner, the book focuses on theory, part of which is developed by the author himself, but also provides a number of references towards application-based texts. Written by a leading contributor in the field, this book will provide a useful tool for learning about recent developments in generalized versions of statistical mechanics and thermodynamics, especially with respect to self-study. Written for researchers in theoretical physics, mathematics and statistical mechanics, as well as graduates of physics, mathematics or engineering. A prerequisite knowledge of elementary notions of statistical physics and a substantial mathematical background are required.