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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.
List of contents
1. RNA world hypothesis (Gilbert) and diverse roles of RNA in cell biology 2. Review of thermodynamics for ab initio secondary structure modeling 3. Energy parameters via optical melting 4. Dynamic programming thermodynamics-based algorithms for structure prediction a) Minimum free energy structure, and variants thereof b) Partition function, sampling low energy structures for biological applications c) Saturated and locally optimal structures, expected 5'-3' distance 5. Coarse-grained kinetics via basins of attraction a) Gillespie's algorithm b) Kinfold, KFOLD, and related algorithms 6. Markov state models for secondary structure kinetics 7. Rational design of RNA structures a) Inverse folding problem b) Ribozyme and riboswitch design Appendix: Review of linear algebra and Markov processes for applications in kinetics
About the author
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.
