Download or read book Foundations of Chemical Reaction Network Theory written by Martin Feinberg and published by Springer. This book was released on 2019-01-31 with total page 475 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an authoritative introduction to the rapidly growing field of chemical reaction network theory. In particular, the book presents deep and surprising theorems that relate the graphical and algebraic structure of a reaction network to qualitative properties of the intricate system of nonlinear differential equations that the network induces. Over the course of three main parts, Feinberg provides a gradual transition from a tutorial on the basics of reaction network theory, to a survey of some of its principal theorems, and, finally, to a discussion of the theory’s more technical aspects. Written with great clarity, this book will be of value to mathematicians and to mathematically-inclined biologists, chemists, physicists, and engineers who want to contribute to chemical reaction network theory or make use of its powerful results.

Download or read book Topics in Chemical Reaction Network Theory written by Matthew Douglas Johnston and published by . This book was released on 2011 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt: Under the assumption of mass-action kinetics, systems of chemical reactions can give rise to a wide variety of dynamical behaviour, including stability of a unique equilibrium concentration, multistability, periodic behaviour, chaotic behaviour, switching behaviour, and many others. In their canonical papers, M. Feinberg, F. Horn and R. Jackson developed so-called Chemical Reaction Network theory which drew a strong connection between the topological structure of the reaction graph and the dynamical behaviour of mass-action systems. A significant amount of work since that time has been conducted expanding upon this connection and fleshing out the theoretical underpinnings of the theory. In this thesis, I focus on three topics within the scope of Chemical Reaction Network theory. 1. Linearization: It is known that complex balanced systems possess within each invariant space of the system a unique positive equilibrium concentration and that that concentration is locally asymptotically stable. F. Horn and R. Jackson determined this through the use of an entropy-like Lyapunov function. ... 2. Persistence: A well-known limitation of the theory is that the stabilities of the positive equilibrium concentrations guaranteed are locally limited. The conjecture that the equilibrium concentrations of complex balanced systems are global attractors of their respective invariant spaces has become known as the Global Attractor Conjecture and has received significant attention recently. This theory has been significantly aided by the realization that trajectories not tending toward the set of positive equilibria must tend toward the boundary of the positive orthant; consequently, persistence is a sufficient condition to affirm the conjecture. ... 3. Linear Conjugacy: It is known that under the mass-action assumption two reaction networks with disparate topological structure may give rise to the same set of differential equations and therefore exhibit the same qualitative dynamical behaviour.

Download or read book Reaction Rate Theory and Rare Events written by Baron Peters and published by Elsevier. This book was released on 2017-03-22 with total page 636 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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

Download or read book Homogeneous Catalysis Concepts and Basics written by Mohammad Reza Rahimpour and published by Elsevier. This book was released on 2024-08-30 with total page 384 pages. Available in PDF, EPUB and Kindle. Book excerpt: Homogeneous Hydrogenation and Metathesis Reactions, a volume in the Advances in Catalysis series, covers hydrogenation and metathesis reactions in two separate sections. The first section is devoted to homogeneous hydrogenation reactions and related processes, including hydrogenation of alkenes, esters, olefins, etc. In the second section, the metathesis reactions of olefins, alkenes, and alkynes are presented. In addition, the industrial application of homogeneous metathesis reactions is investigated. Includes thermodynamic and kinetic studies of homogeneous catalysts Describes transition metal, ligand and solvent role in homogeneous catalysts Explains preparation, characterization, deactivation and regeneration of homogeneous catalysts Presents homogeneous catalysts by clusters, carbenes, fixed metal-complexes, and liquid-liquid multiphase catalysts

Download or read book DNA Computing and Molecular Programming written by Chris Thachuk and published by Springer. This book was released on 2019-07-30 with total page 237 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 25th International Conference on DNA Computing and Molecular Programming, DNA 25, held in Seattle, WA, USA, in August 2019. The 12 full papers presented were carefully selected from 19 submissions. The papers cover a wide range of topics relating to biomolecular computing such as algorithms and models for computation on biomolecular systems; computational processes in vitro and in vivo; molecular switches, gates, devices, and circuits; molecular folding and self-assembly of nanostructures; analysis and theoretical models of laboratory techniques; molecular motors and molecular robotics; information storage; studies of fault-tolerance and error correction; software tools for analysis, simulation, anddesign; synthetic biology and in vitro evolution; and applications in engineering, physics, chemistry, biology, and medicine.

Download or read book Out of Equilibrium Supra molecular Systems and Materials written by Nicolas Giuseppone and published by John Wiley & Sons. This book was released on 2021-07-19 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt: Out-of-Equilibrium (Supra)molecular Systems and Materials A must-have resource that covers everything from out-of-equilibrium chemical systems to active materials Out-of-Equilibrium (Supra)molecular Systems and Materials presents a comprehensive overview of the synthetic approaches that use molecular and supramolecular bonds in various out-of-equilibrium situations. With contributions from noted experts on the topic, the text contains information on the design of dissipative chemical systems that adapt their structures in space and time when fueled by an external source of energy. The contributors also examine molecules, nanoscale objects and materials that can produce mechanical work based on molecular machines. Additionally, the book explores living supramolecular polymers that can be trapped in kinetically stable states, as well as out-of-equilibrium chemical networks and oscillators that are important to understand the emergence of complex behaviors and, in particular, the origin of life. This important book: Offers comprehensive coverage of fields from design of out-of-equilibrium self-assemblies to molecular machines and active materials Presents information on a highly emerging and interdisciplinary topic Includes contributions from internationally renowned scientists Written for chemists, physical chemists, biochemists, material scientists, Out-of-Equilibrium (Supra)molecular Systems and Materials is an indispensable resource written by top scientists in the field.

Download or read book Computer Algebra in Scientific Computing written by François Boulier and published by Springer Nature. This book was released on 2020-10-17 with total page 644 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book constitutes the refereed proceedings of the 22nd International Workshop on Computer Algebra in Scientific Computing, CASC 2020, held in Linz, Austria, in September 2020. The conference was held virtually due to the COVID-19 pandemic. The 34 full papers presented together with 2 invited talks were carefully reviewed and selected from 41 submissions. They deal with cutting-edge research in all major disciplines of computer algebra. The papers cover topics such as polynomial algebra, symbolic and symbolic-numerical computation, applications of symbolic computation for investigating and solving ordinary differential equations, applications of CAS in the investigation and solution of celestial mechanics problems, and in mechanics, physics, and robotics.

Download or read book Foundations of Chemistry written by Philippa B. Cranwell and published by John Wiley & Sons. This book was released on 2021-08-02 with total page 595 pages. Available in PDF, EPUB and Kindle. Book excerpt: FOUNDATIONS OF CHEMISTRY A foundation-level guide to chemistry for physical, life sciences and engineering students Foundations of Chemistry: An Introductory Course for Science Students fills a gap in the literature to provide a basic chemistry text aimed at physical sciences, life sciences and engineering students. The authors, noted experts on the topic, offer concise explanations of chemistry theory and the principles that are typically reviewed in most one year foundation chemistry courses and first year degree-level chemistry courses for non-chemists. The authors also include illustrative examples and information on the most recent applications in the field. Foundations of Chemistry is an important text that outlines the basic principles in each area of chemistry - physical, inorganic and organic - building on prior knowledge to quickly expand and develop a student's knowledge and understanding. Key features include: Worked examples showcase core concepts and practice questions. Margin comments signpost students to knowledge covered elsewhere and are used to highlight key learning objectives. Chapter summaries list the main concepts and learning points.

Download or read book The Statistical Mechanics of Irreversible Phenomena written by Pierre Gaspard and published by Cambridge University Press. This book was released on 2022-07-28 with total page 689 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides a comprehensive and self-contained overview of recent progress in nonequilibrium statistical mechanics, in particular, the discovery of fluctuation relations and other time-reversal symmetry relations. The significance of these advances is that nonequilibrium statistical physics is no longer restricted to the linear regimes close to equilibrium, but extends to fully nonlinear regimes. These important new results have inspired the development of a unifying framework for describing both the microscopic dynamics of collections of particles, and the macroscopic hydrodynamics and thermodynamics of matter itself. The book discusses the significance of this theoretical framework in relation to a broad range of nonequilibrium processes, from the nanoscale to the macroscale, and is essential reading for researchers and graduate students in statistical physics, theoretical chemistry and biological physics.

Download or read book Design and Analysis of Biomolecular Circuits written by Heinz Koeppl and published by Springer Science & Business Media. This book was released on 2011-05-21 with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt: The book deals with engineering aspects of the two emerging and intertwined fields of synthetic and systems biology. Both fields hold promise to revolutionize the way molecular biology research is done, the way today’s drug discovery works and the way bio-engineering is done. Both fields stress the importance of building and characterizing small bio-molecular networks in order to synthesize incrementally and understand large complex networks inside living cells. Reminiscent of computer-aided design (CAD) of electronic circuits, abstraction is believed to be the key concept to achieve this goal. It allows hiding the overwhelming complexity of cellular processes by encapsulating network parts into abstract modules. This book provides a unique perspective on how concepts and methods from CAD of electronic circuits can be leveraged to overcome complexity barrier perceived in synthetic and systems biology.

Download or read book Advanced Mathematical Techniques in Computational and Intelligent Systems written by Sandeep Singh and published by CRC Press. This book was released on 2023-11-20 with total page 285 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book comprehensively discusses the modeling of real-world industrial problems and innovative optimization techniques such as heuristics, finite methods, operation research techniques, intelligent algorithms, and agent- based methods. Discusses advanced techniques such as key cell, Mobius inversion, and zero suffix techniques to find initial feasible solutions to optimization problems. Provides a useful guide toward the development of a sustainable model for disaster management. Presents optimized hybrid block method techniques to solve mathematical problems existing in the industries. Covers mathematical techniques such as Laplace transformation, stochastic process, and differential techniques related to reliability theory. Highlights application on smart agriculture, smart healthcare, techniques for disaster management, and smart manufacturing. Advanced Mathematical Techniques in Computational and Intelligent Systems is primarily written for graduate and senior undergraduate students, as well as academic researchers in electrical engineering, electronics and communications engineering, computer engineering, and mathematics.

Download or read book Foundations of Computational Mathematics Hong Kong 2008 written by Felipe Cucker and published by Cambridge University Press. This book was released on 2009-07-02 with total page 287 pages. Available in PDF, EPUB and Kindle. Book excerpt: Surveys and summaries of the latest research in numerical analysis, optimization, computer algebra and scientific computing.

Download or read book Uniqueness of Equilibria for Complex Chemical Reaction Networks written by Haixia Ji and published by . This book was released on 2011 with total page 214 pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Each chemical reaction network taken with mass action kinetics gives rise to a system of polynomial differential equations that govern the species concentrations, and in those equations many parameters (rate constants) appear. Even for a moderately sized network with several species and several reactions the resulting equations can be highly intricate. This thesis addresses the problem of determining whether a given chemical reaction network, taken with mass action kinetics, has the capacity to admit multiple positive steady states - that is, whether for the network there are rate constant values such that the resulting polynomial differential equations admit two distinct stoichiometrically-compatible steady states in which all species concentrations are positive. The theory developed extends earlier work by Ellison and Feinberg and is implemented in a Windows-based computer program that has been made internet-available.

Download or read book DNA and RNA Based Computing Systems written by Evgeny Katz and published by John Wiley & Sons. This book was released on 2021-04-12 with total page 408 pages. Available in PDF, EPUB and Kindle. Book excerpt: Discover the science of biocomputing with this comprehensive and forward-looking new resource DNA- and RNA-Based Computing Systems delivers an authoritative overview of DNA- and RNA-based biocomputing systems that touches on cutting-edge advancements in computer science, biotechnology, nanotechnology, and materials science. Accomplished researcher, academic, and author Evgeny Katz offers readers an examination of the intersection of computational, chemical, materials, and engineering aspects of biomolecular information processing. A perfect companion to the recently published Enzyme-Based Computing by the same editor, the book is an authoritative reference for those who hope to better understand DNA- and RNA-based logic gates, multi-component logic networks, combinatorial calculators, and related computational systems that have recently been developed for use in biocomputing devices. DNA- and RNA-Based Computing Systems summarizes the latest research efforts in this rapidly evolving field and points to possible future research foci. Along with an examination of potential applications in biosensing and bioactuation, particularly in the field of biomedicine, the book also includes topics like: A thorough introduction to the fields of DNA and RNA computing, including DNA/enzyme circuits A description of DNA logic gates, switches and circuits, and how to program them An introduction to photonic logic using DNA and RNA The development and applications of DNA computing for use in databases and robotics Perfect for biochemists, biotechnologists, materials scientists, and bioengineers, DNA- and RNA-Based Computing Systems also belongs on the bookshelves of computer technologists and electrical engineers who seek to improve their understanding of biomolecular information processing. Senior undergraduate students and graduate students in biochemistry, materials science, and computer science will also benefit from this book.

Download or read book Foundations of Bioenergetics written by Harold Morowitz and published by Elsevier. This book was released on 2012-12-02 with total page 365 pages. Available in PDF, EPUB and Kindle. Book excerpt: Foundations of Bioenergetics provides an introduction to the physical foundations of bioenergetics and the methods of applying these constructs to biological problems. It combines parts of thermal physics, biochemistry, ecology, and cellular and organismic biology into a single coherent work. Much of the material in this volume comes from ""Entropy for Biologists,"" an introductory thermodynamics book aimed particularly at life scientists. Some of the topics originally appeared in the monograph ""Energy Flow in Biology."" The current volume expands on that material with respect to biological applications and attempts to bridge the gap between physics and biology. The book explains basic concepts such as energy, temperature, the second law of thermodynamics, entropy, information theory, and statistical mechanics. It discusses the relations between thermodynamics and statistical mechanics, free-energy functions, radiant energy, the free energy of cells and tissue, chemical kinetics, and cyclic flows. It examines the relationships between energy flows and biological processes; applications of the concepts of Gibbs free energy, chemical potential, and activity; and measurements of temperature, energy, and thermochemical quantities. The book also includes chapters that deal with irreversible dynamics, irreversible theory, and osmotic flow.

Download or read book An Introduction to Undergraduate Research in Computational and Mathematical Biology written by Hannah Callender Highlander and published by Springer Nature. This book was released on 2020-02-17 with total page 479 pages. Available in PDF, EPUB and Kindle. Book excerpt: Speaking directly to the growing importance of research experience in undergraduate mathematics programs, this volume offers suggestions for undergraduate-appropriate research projects in mathematical and computational biology for students and their faculty mentors. The aim of each chapter is twofold: for faculty, to alleviate the challenges of identifying accessible topics and advising students through the research process; for students, to provide sufficient background, additional references, and context to excite students in these areas and to enable them to successfully undertake these problems in their research. Some of the topics discussed include: • Oscillatory behaviors present in real-world applications, from seasonal outbreaks of childhood diseases to action potentials in neurons • Simulating bacterial growth, competition, and resistance with agent-based models and laboratory experiments • Network structure and the dynamics of biological systems • Using neural networks to identify bird species from birdsong samples • Modeling fluid flow induced by the motion of pulmonary cilia Aimed at undergraduate mathematics faculty and advanced undergraduate students, this unique guide will be a valuable resource for generating fruitful research collaborations between students and faculty.

Download or read book Biology and Control Theory Current Challenges written by Isabelle Queinnec and published by Springer. This book was released on 2007-08-07 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Creating some links between control feedback and biology modeling communities based on similarities in modeling, observing and perceiving alive structures, and analyzing interconnections between biological structures and subsystems was the main objective of this volume. In this context, biology systems need appropriate analysis tools due to their structure and hierarchy, complexity and environment interference, and we believe that these aspects may generate interesting research topics in control area. Indeed, several works, raising the potential impact of control developments to bring some beginning of answers in the context of biological systems, have been published in the recent years. The idea of this book was conceived in the context mentioned above with the objective to help in claiming many of the problems for control researchers, starting discussions and opening interactive debates between the control and biology communities, and, finally, to alert graduate students to the many interesting ideas at the frontier between control feedback theory and biology.