Computational Methods For Transition States And Pathways In Rare Events
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Computational Methods for Transition States and Pathways in Rare Events
Based on the calculation of transition states and the identification of transition paths, this book aims to provide a comprehensive guide to understanding and simulating rare events. The author introduces both fundamental concepts of transition states and pathways and advanced computational techniques, focusing on Gentlest Ascent Dynamics (GAD) and its variants. In particular, she explores enhanced numerical methods such as the convex splitting method and the Scalar Auxiliary Variable (SAV) approach within the Iterative Minimization Formulation (IMF). In addition, the book applies these methods to real-world problems, highlighting the string method and the geometric Minimum Action Method (gMAM) for computing transition paths. The book is written for researchers and practitioners in fields such as applied mathematics, physics, chemistry, and computational science who are interested in the underlying mechanisms of rare events and their transition processes. Chapters 3 and 4 of this book are each freely available as a downloadable Open Access PDF at http://www.taylorfrancis.com under a Creative Commons Attribution-Non Commercial-No Derivatives (CC-BY-NC-ND) 4.0 license.
Computational Methods for Transition States and Pathways in Rare Events
Based on the calculation of transition states and the identification of transition paths, this book aims to provide a comprehensive guide to understanding and simulating rare events. The author introduces both fundamental concepts of transition states and pathways and advanced computational techniques, focusing on Gentlest Ascent Dynamics (GAD) and its variants. In particular, she explores enhanced numerical methods such as the convex splitting method and the Scalar Auxiliary Variable (SAV) approach within the Iterative Minimization Formulation (IMF). In addition, the book applies these methods to real-world problems, highlighting the string method and the geometric Minimum Action Method (gMAM) for computing transition paths. The book is written for researchers and practitioners in fields such as applied mathematics, physics, chemistry, and computational science who are interested in the underlying mechanisms of rare events and their transition processes. Chapters 3 and 4 of this book are each freely available as a downloadable Open Access PDF at http: //www.taylorfrancis.com under a Creative Commons Attribution-Non Commercial-No Derivatives (CC-BY-NC-ND) 4.0 license.
Reaction Rate Theory and Rare Events
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