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Author: Bruce Hannon Publisher: Springer Science & Business Media ISBN: 1461206510 Category : Science Languages : en Pages : 399
Book Description
Models help us understand the dynamics of real-world processes by using the computer to mimic the actual forces that are known or assumed to result in a system's behavior. This book does not require a substantial background in mathematics or computer science.
Author: Bruce Hannon Publisher: Springer Science & Business Media ISBN: 1461206510 Category : Science Languages : en Pages : 399
Book Description
Models help us understand the dynamics of real-world processes by using the computer to mimic the actual forces that are known or assumed to result in a system's behavior. This book does not require a substantial background in mathematics or computer science.
Author: Arianna Bianchi Publisher: Springer Nature ISBN: 3030225836 Category : Mathematics Languages : en Pages : 278
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.
Author: Michael Small Publisher: CRC Press ISBN: 1439853363 Category : Mathematics Languages : en Pages : 286
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.
Author: Joseph DiStefano III Publisher: Academic Press ISBN: 0124104932 Category : Science Languages : en Pages : 886
Book Description
Dynamic Systems Biology Modeling and Simuation consolidates and unifies classical and contemporary multiscale methodologies for mathematical modeling and computer simulation of dynamic biological systems – from molecular/cellular, organ-system, on up to population levels. The book pedagogy is developed as a well-annotated, systematic tutorial – with clearly spelled-out and unified nomenclature – derived from the author's own modeling efforts, publications and teaching over half a century. Ambiguities in some concepts and tools are clarified and others are rendered more accessible and practical. The latter include novel qualitative theory and methodologies for recognizing dynamical signatures in data using structural (multicompartmental and network) models and graph theory; and analyzing structural and measurement (data) models for quantification feasibility. The level is basic-to-intermediate, with much emphasis on biomodeling from real biodata, for use in real applications. - Introductory coverage of core mathematical concepts such as linear and nonlinear differential and difference equations, Laplace transforms, linear algebra, probability, statistics and stochastics topics - The pertinent biology, biochemistry, biophysics or pharmacology for modeling are provided, to support understanding the amalgam of "math modeling with life sciences - Strong emphasis on quantifying as well as building and analyzing biomodels: includes methodology and computational tools for parameter identifiability and sensitivity analysis; parameter estimation from real data; model distinguishability and simplification; and practical bioexperiment design and optimization - Companion website provides solutions and program code for examples and exercises using Matlab, Simulink, VisSim, SimBiology, SAAMII, AMIGO, Copasi and SBML-coded models - A full set of PowerPoint slides are available from the author for teaching from his textbook. He uses them to teach a 10 week quarter upper division course at UCLA, which meets twice a week, so there are 20 lectures. They can easily be augmented or stretched for a 15 week semester course - Importantly, the slides are editable, so they can be readily adapted to a lecturer's personal style and course content needs. The lectures are based on excerpts from 12 of the first 13 chapters of DSBMS. They are designed to highlight the key course material, as a study guide and structure for students following the full text content - The complete PowerPoint slide package (~25 MB) can be obtained by instructors (or prospective instructors) by emailing the author directly, at: [email protected]
Author: Jorge Carballido-Landeira Publisher: Springer ISBN: 303016585X Category : Mathematics Languages : en Pages : 111
Book Description
This book collects recent advances in the field of nonlinear dynamics in biological systems. Focusing on medical applications as well as more fundamental questions in biochemistry, it presents recent findings in areas such as control in chemically driven reaction-diffusion systems, electrical wave propagation through heart tissue, neural network growth, chiral symmetry breaking in polymers and mechanochemical pattern formation in the cytoplasm, particularly in the context of cardiac cells. It is a compilation of works, including contributions from international scientists who attended the “2nd BCAM Workshop on Nonlinear Dynamics in Biological Systems,” held at the Basque Center for Applied Mathematics, Bilbao in September 2016. Embracing diverse disciplines and using multidisciplinary approaches – including theoretical concepts, simulations and experiments – these contributions highlight the nonlinear nature of biological systems in order to be able to reproduce their complex behavior. Edited by the conference organizers and featuring results that represent recent findings and not necessarily those presented at the conference, the book appeals to applied mathematicians, biophysicists and computational biologists.
Author: Russell Schwartz Publisher: MIT Press ISBN: 0262195844 Category : Science Languages : en Pages : 403
Book Description
A practice-oriented survey of techniques for computational modeling and simulation suitable for a broad range of biological problems. There are many excellent computational biology resources now available for learning about methods that have been developed to address specific biological systems, but comparatively little attention has been paid to training aspiring computational biologists to handle new and unanticipated problems. This text is intended to fill that gap by teaching students how to reason about developing formal mathematical models of biological systems that are amenable to computational analysis. It collects in one place a selection of broadly useful models, algorithms, and theoretical analysis tools normally found scattered among many other disciplines. It thereby gives the aspiring student a bag of tricks that will serve him or her well in modeling problems drawn from numerous subfields of biology. These techniques are taught from the perspective of what the practitioner needs to know to use them effectively, supplemented with references for further reading on more advanced use of each method covered. The text, which grew out of a class taught at Carnegie Mellon University, covers models for optimization, simulation and sampling, and parameter tuning. These topics provide a general framework for learning how to formulate mathematical models of biological systems, what techniques are available to work with these models, and how to fit the models to particular systems. Their application is illustrated by many examples drawn from a variety of biological disciplines and several extended case studies that show how the methods described have been applied to real problems in biology.
Author: Ina Koch Publisher: Springer Science & Business Media ISBN: 1849964742 Category : Computers Languages : en Pages : 378
Book Description
The emerging, multi-disciplinary field of systems biology is devoted to the study of the relationships between various parts of a biological system, and computer modeling plays a vital role in the drive to understand the processes of life from an holistic viewpoint. Advancements in experimental technologies in biology and medicine have generated an enormous amount of biological data on the dependencies and interactions of many different molecular cell processes, fueling the development of numerous computational methods for exploring this data. The mathematical formalism of Petri net theory is able to encompass many of these techniques. This essential text/reference presents a comprehensive overview of cutting-edge research in applications of Petri nets in systems biology, with contributions from an international selection of experts. Those unfamiliar with the field are also provided with a general introduction to systems biology, the foundations of biochemistry, and the basics of Petri net theory. Further chapters address Petri net modeling techniques for building and analyzing biological models, as well as network prediction approaches, before reviewing the applications to networks of different biological classification. Topics and features: investigates the modular, qualitative modeling of regulatory networks using Petri nets, and examines an Hybrid Functional Petri net simulation case study; contains a glossary of the concepts and notation used in the book, in addition to exercises at the end of each chapter; covers the topological analysis of metabolic and regulatory networks, the analysis of models of signaling networks, and the prediction of network structure; provides a biological case study on the conversion of logical networks into Petri nets; discusses discrete modeling, stochastic modeling, fuzzy modeling, dynamic pathway modeling, genetic regulatory network modeling, and quantitative analysis techniques; includes a Foreword by Professor Jens Reich, Professor of Bioinformatics at Humboldt University and Max Delbrück Center for Molecular Medicine in Berlin. This unique guide to the modeling of biochemical systems using Petri net concepts will be of real utility to researchers and students of computational biology, systems biology, bioinformatics, computer science, and biochemistry.
Author: Joseph Distefano, 3rd Publisher: ISBN: 9781733495004 Category : Languages : en Pages : 354
Book Description
This textbook is uniquely crafted for use in teaching undergraduate students in the life, math, computer and other sciences and engineering. It is INTRODUCTORY LEVEL, for students who have taken or are currently completing their undergraduate math requirements, and are acquiring analytical-thinking and doing skills, along with introductory biology, chemistry and physics subject matter. It's about learning HOW to model and simulate dynamic biological systems, which also makes it useful for graduate students and professional researchers who want a more rigorous treatment of introductory life science math modeling, integrated with the biology. It brings together the multidisciplinary pedagogy of these subjects into a SINGLE INTRODUCTORY MODELING METHODOLOGY COURSE, crystalizing the experience of an author who has been teaching dynamic biosystems modeling and simulation methodology for the life sciences for more than 50 years. DiStefano maximizes accessibility and "systems-math-biology" integration - without diminishing conceptual rigor. Minimally essential applied math and SYSTEMS ENGINEERING METHODS are included, along with a synopsis of the biology and physiology underlying dynamic biosystem modeling, all in a modeling pedagogy context. This textbook fills a major need in the training of contemporary biology students.Dynamic biosystems modeling methodology is presented over 12 distinctive chapters, primarily with systems diagrams and simple differential equations and algebra for expressing them quantitatively, integrated with the biology. Solving and analyzing (quantifying) the biomodels are then accomplished by simulation, using a facile control system simulation language Simulink, a GUI/Matlab toolbox that emulates control systems diagramming, rather than by "coding" the model in a standard computer programming language. Students see and work with the system model - not the code - a big plus. Higher math and complex analytical solutions are avoided.Each chapter begins with a list of LEARNING GOALS, to help with both perspective for the chapter material, and retrospective, to measure learning. EXERCISES for the student at the end of each chapter are designed to test and reinforce learning. A SOLUTIONS MANUAL for chapter exercises is available to qualified instructors from the author, as are LECTURE SLIDES and LAB ASSIGNMENTS AND SOLUTIONS, for courses that adopt the textbook for student use.
Author: Bruce Hannon
Author: Bruce Hannon
Author: Kim Sneppen
Author: B. Hannon
Author: Arianna Bianchi
Author: Michael Small
Author: Joseph DiStefano III
Author: Jorge Carballido-Landeira
Author: Russell Schwartz
Author: Ina Koch
Author: Joseph Distefano, 3rd