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.

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.

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

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

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.

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.

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.

One critical barrier leading to successful implementation of flexible manufacturing and related automated systems is the ever-increasing complexity of their modeling, analysis, simulation, and control. Research and development over the last three decades has provided new theory and graphical tools based on Petri nets and related concepts for the design of such systems. The purpose of this book is to introduce a set of Petri-net-based tools and methods to address a variety of problems associated with the design and implementation of flexible manufacturing systems (FMSs), with several implementation examples.There are three ways this book will directly benefit readers. First, the book will allow engineers and managers who are responsible for the design and implementation of modern manufacturing systems to evaluate Petri nets for applications in their work. Second, it will provide sufficient breadth and depth to allow development of Petri-net-based industrial applications. Third, it will allow the basic Petri net material to be taught to industrial practitioners, students, and academic researchers much more efficiently. This will foster further research and applications of Petri nets in aiding the successful implementation of advanced manufacturing systems.

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.

This edited volume provides insights into and tools for the modeling, analysis, optimization, and control of large-scale networks in the life sciences and in engineering. Large-scale systems are often the result of networked interactions between a large number of subsystems, and their analysis and control are becoming increasingly important. The chapters of this book present the basic concepts and theoretical foundations of network theory and discuss its applications in different scientific areas such as biochemical reactions, chemical production processes, systems biology, electrical circuits, and mobile agents. The aim is to identify common concepts, to understand the underlying mathematical ideas, and to inspire discussions across the borders of the various disciplines. The book originates from the interdisciplinary summer school “Large Scale Networks in Engineering and Life Sciences” hosted by the International Max Planck Research School Magdeburg, September 26-30, 2011, and will therefore be of interest to mathematicians, engineers, physicists, biologists, chemists, and anyone involved in the network sciences. In particular, due to their introductory nature the chapters can serve individually or as a whole as the basis of graduate courses and seminars, future summer schools, or as reference material for practitioners in the network sciences.