Download or read book Numerical Simulation and Modelling of Electronic and Biochemical Systems written by Jaijeet Roychowdhury and published by Now Publishers Inc. This book was released on 2009 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: Numerical simulation and modelling have been growing in importance and seeing steadily increasing practical application. The proliferation of applications and physical domains for which simulation technologies are now needed, compounded by generally increased complexity, has expanded the scope of numerical simulation and modelling within CAD and spurred new research directions. Numerical Simulation and Modelling of Electronic and Biochemical Systems provides an introduction to the fundamentals of numerical simulation, and to the basics of modelling electronic circuits and biochemical reactions. The emphasis is on capturing a minimal set of important concepts succinctly, but concretely enough that the reader will be left with an adequate foundation for further independent exploration. Starting from mathematical models of basic electronic elements, circuits are modelled as nonlinear differential-algebraic equation (DAE) systems. Two basic techniques - quiescent steady state and transient - for solving these differential equations systems are then developed. It is then shown how biochemical reactions can also be modelled deterministically as DAEs. Following this, frequency domain techniques for finding sinusoidal steady states of linear DAEs are developed, as are direct and adjoint techniques for computing parameter sensitivities and the effects of stationary random noise. For readers interested in a glimpse of topics beyond these basics, an introduction to nonlinear periodic steady state methods (harmonic balance and shooting) and the multitime partial differential equation formulation is provided. Also provided is an overview of model order reduction, an important topic of current research that has roots in numerical simulation algorithms. Finally, sample applications of nonlinear oscillator macromodels - in circuits (PLLs), biochemical reaction-diffusion systems and nanoelectronics - are presented.

Download or read book A Guide to Numerical Modelling in Systems Biology written by Peter Deuflhard and published by Springer. This book was released on 2015-07-06 with total page 185 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is intended for students of computational systems biology with only a limited background in mathematics. Typical books on systems biology merely mention algorithmic approaches, but without offering a deeper understanding. On the other hand, mathematical books are typically unreadable for computational biologists. The authors of the present book have worked hard to fill this gap. The result is not a book on systems biology, but on computational methods in systems biology. This book originated from courses taught by the authors at Freie Universität Berlin. The guiding idea of the courses was to convey those mathematical insights that are indispensable for systems biology, teaching the necessary mathematical prerequisites by means of many illustrative examples and without any theorems. The three chapters cover the mathematical modelling of biochemical and physiological processes, numerical simulation of the dynamics of biological networks and identification of model parameters by means of comparisons with real data. Throughout the text, the strengths and weaknesses of numerical algorithms with respect to various systems biological issues are discussed. Web addresses for downloading the corresponding software are also included.

Download or read book Simulation and Verification of Electronic and Biological Systems written by Peng Li and published by Springer Science & Business Media. This book was released on 2011-01-12 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: Simulation and Verification of Electronic and Biological Systems provides a showcase for the Circuit and Multi-Domain Simulation Workshop held in San Jose, California, USA, on November 5, 2009. The nine chapters are contributed by experts in the field and provide a broad discussion of recent developments on simulation, modeling and verification of integrated circuits and biological systems. Specific topics include large scale parallel circuit simulation, industrial practice of fast SPICE simulation, structure-preserving model order reduction of interconnects, advanced simulation techniques for oscillator networks, dynamic stability of static memories and biological systems as well as verification of analog integrated circuits. Simulation and verification are fundamental enablers for understanding, analyzing and designing an extremely broad range of engineering and biological circuits and systems. The design of nanometer integrated electronic systems and emerging biomedical applications have stimulated the development of novel simulation and verification techniques and methodologies. Simulation and Verification of Electronic and Biological Systems provides a broad discussion of recent advances on simulation, modeling and verification of integrated circuits and biological systems and offers a basis for stimulating new innovations.

Download or read book Dynamic Systems Biology Modeling and Simulation written by Joseph DiStefano III and published by Academic Press. This book was released on 2015-01-10 with total page 886 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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]

Download or read book Mathematical Modelling and Computer Simulation of Activated Sludge Systems written by Jacek Makinia and published by IWA Publishing. This book was released on 2020-03-02 with total page 682 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mathematical Modelling and Computer Simulation of Activated Sludge Systems – Second Edition provides, from the process engineering perspective, a comprehensive and up-to-date overview regarding various aspects of the mechanistic (“white box”) modelling and simulation of advanced activated sludge systems performing biological nutrient removal. In the new edition of the book, a special focus is given to nitrogen removal and the latest developments in modelling the innovative nitrogen removal processes. Furthermore, a new section on micropollutant removal has been added. The focus of modelling has been shifting in the last years to models that can describe the performance of a whole plant (plant-wide modelling). The expanded part of this new edition introduces models describing the most important processes interrelated with the mainstream activated sludge systems as well as models describing the energy balance, operating costs and environmental impact. The complex process evaluation, including minimization of energy consumption and carbon footprint, is in line with the present and future wastewater treatment goals. By combining a general introduction and a textbook, this book serves both intermediate and more experienced model users, both researchers and practitioners, as a comprehensive guide to modelling and simulation studies. The book can be used as a supplemental material at graduate and post-graduate levels of wastewater engineering/modelling courses.

Download or read book Mathematical Modeling of Complex Biological Systems written by Abdelghani Bellouquid and published by Springer Science & Business Media. This book was released on 2006-08-17 with total page 194 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the evolution of several socio-biological systems using mathematical kinetic theory. Specifically, it deals with modeling and simulations of biological systems whose dynamics follow the rules of mechanics as well as rules governed by their own ability to organize movement and biological functions. It proposes a new biological model focused on the analysis of competition between cells of an aggressive host and cells of a corresponding immune system. Proposed models are related to the generalized Boltzmann equation. The book may be used for advanced graduate courses and seminars in biological systems modeling.

Download or read book Final Technical Report Multiscale Simulation Algorithms for Biochemical Systems written by and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Biochemical systems are inherently multiscale and stochastic. In microscopic systems formed by living cells, the small numbers of reactant molecules can result in dynamical behavior that is discrete and stochastic rather than continuous and deterministic. An analysis tool that respects these dynamical characteristics is the stochastic simulation algorithm (SSA, Gillespie, 1976), a numerical simulation procedure that is essentially exact for chemical systems that are spatially homogeneous or well stirred. Despite recent improvements, as a procedure that simulates every reaction event, the SSA is necessarily inefficient for most realistic problems. There are two main reasons for this, both arising from the multiscale nature of the underlying problem: (1) stiffness, i.e. the presence of multiple timescales, the fastest of which are stable; and (2) the need to include in the simulation both species that are present in relatively small quantities and should be modeled by a discrete stochastic process, and species that are present in larger quantities and are more efficiently modeled by a deterministic differential equation (or at some scale in between). This project has focused on the development of fast and adaptive algorithms, and the fun- damental theory upon which they must be based, for the multiscale simulation of biochemical systems. Areas addressed by this project include: (1) Theoretical and practical foundations for ac- celerated discrete stochastic simulation (tau-leaping); (2) Dealing with stiffness (fast reactions) in an efficient and well-justified manner in discrete stochastic simulation; (3) Development of adaptive multiscale algorithms for spatially homogeneous discrete stochastic simulation; (4) Development of high-performance SSA algorithms.

Download or read book Computational Modeling of Biological Systems written by Nikolay V Dokholyan and published by Springer Science & Business Media. This book was released on 2012-02-12 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computational modeling is emerging as a powerful new approach to study and manipulate biological systems. Multiple methods have been developed to model, visualize, and rationally alter systems at various length scales, starting from molecular modeling and design at atomic resolution to cellular pathways modeling and analysis. Higher time and length scale processes, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. This book provides an overview of the established computational methods used for modeling biologically and medically relevant systems.

Download or read book Biological Reaction Engineering written by Elmar Heinzle and published by John Wiley & Sons. This book was released on 2021-04-06 with total page 560 pages. Available in PDF, EPUB and Kindle. Book excerpt: Die Dynamik biotechnologischer Produktionsprozesse ist äußerst komplex. Ziel des Buches ist es, diese Vorgänge durch systematische Modellbildung und Computersimulation verständlich und durchschaubar zu machen. Es werden ohne viel mathematisches Rüstzeug Grundprinzipien erklärt und anhand von zahlreichen praxisrelevanten Beispielen alle wichtigen Aspekte der Bioverfahrenstechnik ausführlich beschrieben. Modellierte biologische Systeme reichen vom einzelnen Enzym bis zu ganzen metabolischen Netzwerken und Multi-Organismen Systemen. Die kinetischen Modelle werden mit Reaktormodellen kombiniert, was oft mit verschiedenen Konfigurationen von Zu- und Abläufen und Stofftransportprozessen kombiniert ist. In vielen Beispielen werden Regelung und Optimierung der Prozesse behandelt. Die Simulationsbeispiele reichen von theoretischen Schulbeispielen bis zu aktuellen Forschungsarbeiten. Die verwendete Simulationssprache Berkeley Madonna erlaubt nach einer sehr kurzen Einarbeitung ein schnelles interaktives Üben. Der Leser kann die vorgegebenen Beispiele beliebig verändern, um sie seinem Problemfall anzupassen. Die langjährige Lehrerfahrung der Autoren an Hochschulen und Weiterbildungskursen spiegelt sich in dem Buch wider und macht es geeignet für alle Biochemiker, Biotechnologen, Bioingenieure und Verfahrenstechniker, die an Modellierung und Simulation interessiert sind. Die eingesetzte Software Berkeley Madonna für Mac und PC kann direkt von der Berkeley Madonna Webseite bezogen werden: www.berkeleymadonna.com Zusätzliches Online Material, d.h. Programme für alle Simulationsbeispiele, eine kurze Beschreibung der Verwendung der eingesetzten Simulationssoftware Berkeley Madonna und Lösungen von Übungsaufgaben kann als Zusatzmaterial (Zip-Datei) direkt von dieser Webseite heruntergeladen werden. Alle Beispiele können auch mit der kostenlosen Demo-Version von Berkeley Madonna benützt werden. Für Käufer des Buches ist Berkeley Madonna zu einem reduzierten Preis erhältlich. Hinweise dazu gibt es im Anhang des Buches.

Download or read book Stochastic Dynamics in Computational Biology written by Stefanie Winkelmann and published by Springer Nature. This book was released on 2021-01-04 with total page 284 pages. Available in PDF, EPUB and Kindle. Book excerpt: The aim of this book is to provide a well-structured and coherent overview of existing mathematical modeling approaches for biochemical reaction systems, investigating relations between both the conventional models and several types of deterministic-stochastic hybrid model recombinations. Another main objective is to illustrate and compare diverse numerical simulation schemes and their computational effort. Unlike related works, this book presents a broad scope in its applications, from offering a detailed introduction to hybrid approaches for the case of multiple population scales to discussing the setting of time-scale separation resulting from widely varying firing rates of reaction channels. Additionally, it also addresses modeling approaches for non well-mixed reaction-diffusion dynamics, including deterministic and stochastic PDEs and spatiotemporal master equations. Finally, by translating and incorporating complex theory to a level accessible to non-mathematicians, this book effectively bridges the gap between mathematical research in computational biology and its practical use in biological, biochemical, and biomedical systems.

Download or read book Simulation and Verification of Electronic and Biological Systems written by Peng Li and published by Springer. This book was released on 2011-01-16 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: Simulation and Verification of Electronic and Biological Systems provides a showcase for the Circuit and Multi-Domain Simulation Workshop held in San Jose, California, USA, on November 5, 2009. The nine chapters are contributed by experts in the field and provide a broad discussion of recent developments on simulation, modeling and verification of integrated circuits and biological systems. Specific topics include large scale parallel circuit simulation, industrial practice of fast SPICE simulation, structure-preserving model order reduction of interconnects, advanced simulation techniques for oscillator networks, dynamic stability of static memories and biological systems as well as verification of analog integrated circuits. Simulation and verification are fundamental enablers for understanding, analyzing and designing an extremely broad range of engineering and biological circuits and systems. The design of nanometer integrated electronic systems and emerging biomedical applications have stimulated the development of novel simulation and verification techniques and methodologies. Simulation and Verification of Electronic and Biological Systems provides a broad discussion of recent advances on simulation, modeling and verification of integrated circuits and biological systems and offers a basis for stimulating new innovations.

Download or read book Chemical Engineering Dynamics Includes CD ROM written by John Ingham and published by Wiley-VCH. This book was released on 2007 with total page 660 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book, the modelling of dynamic chemical engineering processes is presented in a highly understandable way using the unique combination of simplified fundamental theory and direct hands-on computer simulation. The mathematics is kept to a minimum, and yet the nearly 100 examples supplied on www.wiley-vch.de illustrate almost every aspect of chemical engineering science. Each example is described in detail, including the model equations. They are written in the modern user-friendly simulation language Berkeley Madonna, which can be run on both Windows PC and Power-Macintosh computers. Madonna solves models comprising many ordinary differential equations using very simple programming, including arrays. It is so powerful that the model parameters may be defined as "sliders", which allow the effect of their change on the model behavior to be seen almost immediately. Data may be included for curve fitting, and sensitivity or multiple runs may be performed. The results can be seen simultaneously on multiple-graph windows or by using overlays. The resultant learning effect of this is tremendous. The examples can be varied to fit any real situation, and the suggested exercises provide practical guidance. The extensive experience of the authors, both in university teaching and international courses, is reflected in this well-balanced presentation, which is suitable for the teacher, the student, the chemist or the engineer. This book provides a greater understanding of the formulation and use of mass and energy balances for chemical engineering, in a most stimulating manner. This book is a third edition, which also includes biological, environmental and food process examples.

Download or read book An Introduction to the Computer Simulation of Biochemical Systems written by I. F. Vujicic and published by . This book was released on 1971 with total page 47 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Conservation Equations And Modeling Of Chemical And Biochemical Processes written by Said S.E.H. Elnashaie and published by CRC Press. This book was released on 2003-03-26 with total page 672 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presenting strategies in control policies, this text uses a systems theory approach to predict, simulate and streamline plant operation, conserve fuel and resources, and increase workplace safety in the manufacturing, chemical, petrochemical, petroleum, biochemical and energy industries. Topics of discussion include system theory and chemical/biochemical engineering systems, steady state, unsteady state, and thermodynamic equilibrium, modeling of systems, fundamental laws governing the processes in terms of the state variables, different classifications of physical models, the story of chemical engineering in relation to system theory and mathematical modeling, overall heat balance with single and multiple chemical reactions and single and multiple reactions.

Download or read book Introduction to Modeling Biological Cellular Control Systems written by Weijiu Liu and published by Springer Science & Business Media. This book was released on 2012-04-26 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: This textbook contains the essential knowledge in modeling, simulation, analysis, and applications in dealing with biological cellular control systems. In particular, the book shows how to use the law of mass balance and the law of mass action to derive an enzyme kinetic model - the Michaelis-Menten function or the Hill function, how to use a current-voltage relation, Nernst potential equilibrium equation, and Hodgkin and Huxley's models to model an ionic channel or pump, and how to use the law of mass balance to integrate these enzyme or channel models into a complete feedback control system. The book also illustrates how to use data to estimate parameters in a model, how to use MATLAB to solve a model numerically, how to do computer simulations, and how to provide model predictions. Furthermore, the book demonstrates how to conduct a stability and sensitivity analysis on a model.

Download or read book Computational Chemistry Computer Simulation Techniques written by Edward Timoshenko and published by Edward Timoshenko. This book was released on 2021-05-06 with total page 32 pages. Available in PDF, EPUB and Kindle. Book excerpt: We describe the important role of the in-silico methods in modern Chemistry and Physics of complex systems and overview the major techniques. The Born-Oppenheimer approximation for electronic configurations is introduced. Classical treatment of the motion of nuclei is then considered. Potential energy surfaces, force fields, geometry optimization and energy minimisation methods are discussed. The Newton’s equations of motion and their numerical integration methods are presented with the Euler and Verlet algorithms. Calculation of various observable averages is considered in Molecular Dynamics techniques in the NVE, NVT and NPT ensembles. Brownian stochastic Dynamics and the use of random numbers generators are introduced. Equilibrium simulations based on the Monte Carlo importance sampling methods and the Metropolis algorithm are discussed. The variational approach for the Schrödinger equation and various modern Quantum Chemistry methods for the electronic configurations of atomic and molecular systems are reviewed.

Download or read book Example of a Large model Simulation of the Blood Biochemical System written by James V Maloney (Jr) and published by . This book was released on 1965 with total page 33 pages. Available in PDF, EPUB and Kindle. Book excerpt: The paper outlines a formal procedure for simulating certain aspects of the biochemistry of a viable system. The procedure is based on a mathematical model and a computer program. The plausibility of constructing detailed models of large biochemical systems is demonstrated. The object of the paper is to demonstrate that a mathematical program can simulate the functions of a selected viable system. For this purpose, a mathematical model of viable blood known as the 'SF Blood' model was chosen. The 'SF Blood' model is a reasonable representation of the respiratory function of the adult-restingmale blood.