Overview

Comprising two volumes, RNA: Computational Methods for Structure, Kinetics, and Rational Design is a comprehensive treatment of computational methods concerning the secondary structure, folding kinetics and rational design of RNA. Volume 2 covers secondary structure folding kinetics, starting with an inquiry into whether the ensemble of RNA structures is small-world or scale-free, then proceeding to the identification of local energy minima that create a basin of attraction, leading to a coarse-grained kinetics model. The book describes Markov state models created from secondary structure folding trajectories generated by the kinetic Monte Carlo (Gillespie) algorithm, the first such application. Python code is available at the book’s website, allowing research teams to use the code and extend the approach. Current RNA research concerns the rational design of functional RNA molecules, which The book provides an overview and comparison of various inverse folding algorithms, combinatorial optimization, and the question of whether inverse folding is computationally hard (NP-complete). Another chapter focuses on various types of designed RNA including ribozymes, RNA thermometers, bistable switches, toehold switches, mRNA vaccines, and paper-based COVID-19 tests. The final chapter is a math appendix for the linear algebra and Markov chain results that are essential to folding kinetics. This book provides the nuts, bolts and tools for the next generation of computational work on RNA, especially for the rational design of functional molecules – a topic that not so long ago seemed more like science fiction. Exercises at the end of each chapter introduce new material or related concepts, and solutions are available at the book’s website. It is perfect for advanced undergraduate, graduate and post-graduate readers having analytical interests and skills from areas such as physical chemistry, physics, mathematics, computer science, and statistics. Instructor slides, computer programs and solutions to all exercises from Volumes 1 and 2 can be found at the following website: https://github.com/pgclote/RNA-Computational-methods-for-structure-kinetics-and-rational-design-Solutions-slides-etc.-.

Full Product Details

9781032496665

Table of Contents

Reviews

""This second volume of RNA: Computational Methods for Structure, Kinetics, and Rational Design by Prof. Peter Clote masterfully extends the foundational algorithms from Volume 1 into the critical domains of folding kinetics and inverse folding for RNA design. The rigorous treatment of Monte Carlo methods like Gillespie for trajectory generation, and innovative applications of Markov State Models with Transition Path Theory offers computational biologists unprecedented tools for modeling kinetic barriers and pathways—essential for understanding metastable states in riboswitches and ribozymes. Particularly compelling is the novel adaptation of Markov state models to Gillespie-generated trajectories, enabling precise flux analysis and bottleneck identification in folding ensembles. Clote's persistent use of pseudocode will empower researchers to practically engineer functional RNAs, from thermometers to mRNA vaccines. The book is a vital resource for algorithmic bioinformaticians tackling kinetics in synthetic biology."" --Prof. Dr. Knut Reinert, Algorithmic Bioinformatics Group, Freie Universität Berlin - Reviews for Volume One: ""Prof. Peter Clote is a respected scholar with an unusually rich number of scientific interests: he started his career in mathematical logic, then moved into theoretical computer science and complexity theory. In the 1990’s he moved into the new research field of bioinformatics and developed a group at the University of Munich and then at Boston College. Since that time, he has produced with his students and some colleagues an impressive amount of work mainly relevant to RNA modeling. This book is the result of more than 25 years of research and teaching in Boston, Munich and Paris. What characterizes P. Clote’s work is the extreme care with which he explains the background, then the theoretical concepts coming from biology, chemistry, physics and mathematics that are necessary to model complex RNA molecules, their structure and their behaviour. Finally he describes the algorithms and computer programs that can solve what was considered to be a difficult challenge only a decade ago. The book is written in a very clear manner that makes it accessible to students as a textbook in a first reading, with additional optional material, borrowed from recent research, which will be useful to RNA design engineers and researchers. P. Clote is known as an excellent lecturer and the book inherits of his qualities and competence in the domain. Through the numerous exercises at the end of chapters, this book favors an active reading and opening to current research; the important bibliography will be useful as well. By all standards, this book should become a major reference for an active and comprehensive understanding of RNA, its structure, kinetics and rational design."" --Prof. Jean-Marc Steyaert, Emeritus Professor of the Computer Science Department at Ecole Polytechnique, France ""In RNA: Computational Methods for Structure, Kinetics, and Rational Design, Professor Peter Clote offers a comprehensive and insightful exploration into the intricate world of RNA, combining the realms of biology, mathematics, and computational science with finesse. This book is the beautiful outcome of Clote's profound expertise in the field, presenting a treasure trove of knowledge that will undoubtedly captivate both novices and seasoned researchers alike. What sets this book apart is its seamless integration of theoretical principles with practical applications, making complex concepts accessible to readers from diverse backgrounds. Clote's lucid explanations, coupled with illustrative examples and meticulously curated exercises, empower readers to navigate the intricate landscape of RNA research with confidence. Throughout the book, Clote's passion for his subject matter shines through, infusing each page with enthusiasm and intellectual curiosity. Whether you are a student delving into the fundamentals of RNA or a seasoned researcher seeking to push the boundaries of knowledge, this book is an indispensable companion on your scientific journey. In summary, Professor Peter Clote's ""RNA: Computational Methods for Structure, Kinetics, and Rational Design"" is a tour de force that deserves a place on the bookshelf of every scientist, educator, and enthusiast interested in the fascinating world of RNA. With its unparalleled depth, clarity, and visionary insights, this book not only informs but also inspires, leaving an indelible mark on the landscape of computational biology."" -- Dr. Henri Orland, Institute of Theoretical Physics, Paris-Saclay University, CNRS, CEA, France

Author Information

A Fulbright and Guggenheim fellow, Dr. Clote has held faculty positions in Mathematics, Computer Science and Biology in France, Germany and the United States, including the Gentzen Chair of Computer Science at the University of Munich, and the Digiteo Chair of Excellence at Ecole Polytechnique. This provides a unique background for the current interdisciplinary text on RNA.

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