Deterministic Versus Stochastic Modelling In Biochemistry And Systems Biology
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Deterministic Versus Stochastic Modelling in Biochemistry and Systems Biology
Stochastic kinetic methods are currently considered to be the most realistic and elegant means of representing and simulating the dynamics of biochemical and biological networks. Deterministic versus stochastic modelling in biochemistry and systems biology introduces and critically reviews the deterministic and stochastic foundations of biochemical kinetics, covering applied stochastic process theory for application in the field of modelling and simulation of biological processes at the molecular scale. Following an overview of deterministic chemical kinetics and the stochastic approach to biochemical kinetics, the book goes onto discuss the specifics of stochastic simulation algorithms, modelling in systems biology and the structure of biochemical models. Later chapters cover reaction-diffusion systems, and provide an analysis of the Kinfer and BlenX software systems. The final chapter looks at simulation of ecodynamics and food web dynamics. - Introduces mathematical concepts and formalisms of deterministic and stochastic modelling through clear and simple examples - Presents recently developed discrete stochastic formalisms for modelling biological systems and processes - Describes and applies stochastic simulation algorithms to implement a stochastic formulation of biochemical and biological kinetics
Identifiability and Regression Analysis of Biological Systems Models
This richly illustrated book presents the latest techniques for the identifiability analysis and standard and robust regression analysis of complex dynamical models, and looks at their objectives. It begins by providing a definition of complexity in dynamic systems, introducing the concepts of system size, density of interactions, stiff dynamics, and the hybrid nature of determination. The discussion then turns to the mathematical foundations of model structural and practical identifiability analysis, multilinear and non-linear regression analysis, and best predictor selection, and their algorithmic procedures. Although the featured examples mainly focus on applications to biochemistry and systems biology, the methodologies described can also be employed in other disciplines such as physics and the environmental sciences. Readers will learn how to determine identifiability conditions, how to search for an identifiable model, and how to conduct their own regression analysis and diagnostics without supervision. This new edition includes a concise, yet comprehensive treatment of the main artificial intelligence methods which can be used for parameter inference in models of complex dynamic biological systems. It emphasizes the most efficient solutions for generating synthetic data that augment the training data and which are indispensable for machine learning procedures. Featuring a wealth of real-world examples, exercises, and R codes, the book addresses the needs of doctoral students and researchers in bioinformatics, bioengineering, systems biology, biophysics, biochemistry, the environmental sciences and experimental physics. Familiarity with the fundamentals of probability and statistics (as provided in first-year university courses) and a basic grasp of R are assumed.
Theoretical Physics for Biological Systems
Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.