Stochastic Approach to Chemical Kinetics PDF Download
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Author: Donald Allan McQuarrie
Publisher:
ISBN:
Category : Chemical kinetics
Languages : en
Pages : 82
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Book Description
Author: Donald Allan McQuarrie
Publisher:
ISBN:
Category : Chemical kinetics
Languages : en
Pages : 82
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Book Description
Author: Paola Lecca
Publisher: Elsevier
ISBN: 1908818212
Category : Computers
Languages : en
Pages : 411
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Book Description
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
Author: Péter Érdi
Publisher: Springer
ISBN: 149390387X
Category : Science
Languages : en
Pages : 174
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Book Description
This volume reviews the theory and simulation methods of stochastic kinetics by integrating historical and recent perspectives, presents applications, mostly in the context of systems biology and also in combustion theory. In recent years, due to the development in experimental techniques, such as optical imaging, single cell analysis, and fluorescence spectroscopy, biochemical kinetic data inside single living cells have increasingly been available. The emergence of systems biology brought renaissance in the application of stochastic kinetic methods.
Author: Peter Schuster
Publisher: Springer
ISBN: 3319395025
Category : Science
Languages : en
Pages : 728
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Book Description
This book has developed over the past fifteen years from a modern course on stochastic chemical kinetics for graduate students in physics, chemistry and biology. The first part presents a systematic collection of the mathematical background material needed to understand probability, statistics, and stochastic processes as a prerequisite for the increasingly challenging practical applications in chemistry and the life sciences examined in the second part. Recent advances in the development of new techniques and in the resolution of conventional experiments at nano-scales have been tremendous: today molecular spectroscopy can provide insights into processes down to scales at which current theories at the interface of physics, chemistry and the life sciences cannot be successful without a firm grasp of randomness and its sources. Routinely measured data is now sufficiently accurate to allow the direct recording of fluctuations. As a result, the sampling of data and the modeling of relevant processes are doomed to produce artifacts in interpretation unless the observer has a solid background in the mathematics of limited reproducibility. The material covered is presented in a modular approach, allowing more advanced sections to be skipped if the reader is primarily interested in applications. At the same time, most derivations of analytical solutions for the selected examples are provided in full length to guide more advanced readers in their attempts to derive solutions on their own. The book employs uniform notation throughout, and a glossary has been added to define the most important notions discussed.
Author: Yiannis N. Kaznessis
Publisher: Cambridge University Press
ISBN: 0521765617
Category : Mathematics
Languages : en
Pages : 329
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Book Description
Provides engineers with the knowledge they need to apply thermodynamics and solve engineering challenges at the molecular level.
Author: János Tóth
Publisher:
ISBN: 9781493986422
Category : Chemical kinetics
Languages : en
Pages : 469
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Book Description
Fifty years ago, a new approach to reaction kinetics began to emerge: one based on mathematical models of reaction kinetics, or formal reaction kinetics. Since then, there has been a rapid and accelerated development in both deterministic and stochastic kinetics, primarily because mathematicians studying differential equations and algebraic geometry have taken an interest in the nonlinear differential equations of kinetics, which are relatively simple, yet capable of depicting complex behavior such as oscillation, chaos, and pattern formation. The development of stochastic models was triggered by the fact that novel methods made it possible to measure molecules individually. Now it is high time to make the results of the last half-century available to a larger audience: students of chemistry, chemical engineering and biochemistry, not to mention applied mathematics. Based on recent papers, this book presents the most important concepts and results, together with a wealth of solved exercises. The book is accompanied by the authors' Mathematica package, ReactionKinetics, which helps both students and scholars in their everyday work, and which can be downloaded from http://extras.springer.com/ and also from the authors' websites. Further, the large set of unsolved problems provided may serve as a springboard for individual research.
Author: Péter Érdi
Publisher: Manchester University Press
ISBN: 9780719022081
Category : Science
Languages : en
Pages : 296
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Book Description
Author: Jean-Bernard Lasserre
Publisher: World Scientific
ISBN: 1848164467
Category : Mathematics
Languages : en
Pages : 384
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Book Description
1. The generalized moment problem. 1.1. Formulations. 1.2. Duality theory. 1.3. Computational complexity. 1.4. Summary. 1.5. Exercises. 1.6. Notes and sources -- 2. Positive polynomials. 2.1. Sum of squares representations and semi-definite optimization. 2.2. Nonnegative versus s.o.s. polynomials. 2.3. Representation theorems : univariate case. 2.4. Representation theorems : mutivariate case. 2.5. Polynomials positive on a compact basic semi-algebraic set. 2.6. Polynomials nonnegative on real varieties. 2.7. Representations with sparsity properties. 2.8. Representation of convex polynomials. 2.9. Summary. 2.10. Exercises. 2.11. Notes and sources -- 3. Moments. 3.1. The one-dimensional moment problem. 3.2. The multi-dimensional moment problem. 3.3. The K-moment problem. 3.4. Moment conditions for bounded density. 3.5. Summary. 3.6. Exercises. 3.7. Notes and sources -- 4. Algorithms for moment problems. 4.1. The overall approach. 4.2. Semidefinite relaxations. 4.3. Extraction of solutions. 4.4. Linear relaxations. 4.5. Extensions. 4.6. Exploiting sparsity. 4.7. Summary. 4.8. Exercises. 4.9. Notes and sources. 4.10. Proofs -- 5. Global optimization over polynomials. 5.1. The primal and dual perspectives. 5.2. Unconstrained polynomial optimization. 5.3. Constrained polynomial optimization : semidefinite relaxations. 5.4. Linear programming relaxations. 5.5. Global optimality conditions. 5.6. Convex polynomial programs. 5.7. Discrete optimization. 5.8. Global minimization of a rational function. 5.9. Exploiting symmetry. 5.10. Summary. 5.11. Exercises. 5.12. Notes and sources -- 6. Systems of polynomial equations. 6.1. Introduction. 6.2. Finding a real solution to systems of polynomial equations. 6.3. Finding all complex and/or all real solutions : a unified treatment. 6.4. Summary. 6.5. Exercises. 6.6. Notes and sources -- 7. Applications in probability. 7.1. Upper bounds on measures with moment conditions. 7.2. Measuring basic semi-algebraic sets. 7.3. Measures with given marginals. 7.4. Summary. 7.5. Exercises. 7.6. Notes and sources -- 8. Markov chains applications. 8.1. Bounds on invariant measures. 8.2. Evaluation of ergodic criteria. 8.3. Summary. 8.4. Exercises. 8.5. Notes and sources -- 9. Application in mathematical finance. 9.1. Option pricing with moment information. 9.2. Option pricing with a dynamic model. 9.3. Summary. 9.4. Notes and sources -- 10. Application in control. 10.1. Introduction. 10.2. Weak formulation of optimal control problems. 10.3. Semidefinite relaxations for the OCP. 10.4. Summary. 10.5. Notes and sources -- 11. Convex envelope and representation of convex sets. 11.1. The convex envelope of a rational function. 11.2. Semidefinite representation of convex sets. 11.3. Algebraic certificates of convexity. 11.4. Summary. 11.5. Exercises. 11.6. Notes and sources -- 12. Multivariate integration 12.1. Integration of a rational function. 12.2. Integration of exponentials of polynomials. 12.3. Maximum entropy estimation. 12.4. Summary. 12.5. Exercises. 12.6. Notes and sources -- 13. Min-max problems and Nash equilibria. 13.1. Robust polynomial optimization. 13.2. Minimizing the sup of finitely many rational cunctions. 13.3. Application to Nash equilibria. 13.4. Exercises. 13.5. Notes and sources -- 14. Bounds on linear PDE. 14.1. Linear partial differential equations. 14.2. Notes and sources
Author: Baron Peters
Publisher: Elsevier
ISBN: 0444594701
Category : Technology & Engineering
Languages : en
Pages : 636
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Book Description
Reaction Rate Theory and Rare Events bridges the historical gap between these subjects because the increasingly multidisciplinary nature of scientific research often requires an understanding of both reaction rate theory and the theory of other rare events. The book discusses collision theory, transition state theory, RRKM theory, catalysis, diffusion limited kinetics, mean first passage times, Kramers theory, Grote-Hynes theory, transition path theory, non-adiabatic reactions, electron transfer, and topics from reaction network analysis. It is an essential reference for students, professors and scientists who use reaction rate theory or the theory of rare events. In addition, the book discusses transition state search algorithms, tunneling corrections, transmission coefficients, microkinetic models, kinetic Monte Carlo, transition path sampling, and importance sampling methods. The unified treatment in this book explains why chemical reactions and other rare events, while having many common theoretical foundations, often require very different computational modeling strategies. - Offers an integrated approach to all simulation theories and reaction network analysis, a unique approach not found elsewhere - Gives algorithms in pseudocode for using molecular simulation and computational chemistry methods in studies of rare events - Uses graphics and explicit examples to explain concepts - Includes problem sets developed and tested in a course range from pen-and-paper theoretical problems, to computational exercises
Author: Radek Erban
Publisher: Cambridge University Press
ISBN: 1108572995
Category : Mathematics
Languages : en
Pages : 322
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Book Description
This practical introduction to stochastic reaction-diffusion modelling is based on courses taught at the University of Oxford. The authors discuss the essence of mathematical methods which appear (under different names) in a number of interdisciplinary scientific fields bridging mathematics and computations with biology and chemistry. The book can be used both for self-study and as a supporting text for advanced undergraduate or beginning graduate-level courses in applied mathematics. New mathematical approaches are explained using simple examples of biological models, which range in size from simulations of small biomolecules to groups of animals. The book starts with stochastic modelling of chemical reactions, introducing stochastic simulation algorithms and mathematical methods for analysis of stochastic models. Different stochastic spatio-temporal models are then studied, including models of diffusion and stochastic reaction-diffusion modelling. The methods covered include molecular dynamics, Brownian dynamics, velocity jump processes and compartment-based (lattice-based) models.
