Rna: Computational Methods for Structure, Kinetics, and Rational Design: Volume Two
暫譯: RNA：結構、動力學與理性設計的計算方法：第二卷
Clote, Peter G.
商品描述
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.-.
商品描述(中文翻譯)
本書由兩卷組成，RNA: Computational Methods for Structure, Kinetics, and Rational Design 是一本全面探討有關 RNA 的計算方法，包括其二級結構、摺疊動力學和理性設計。第二卷涵蓋了二級結構的摺疊動力學，首先探討 RNA 結構的集合是否為小世界或無尺度，然後進一步識別創造吸引盆地的局部能量最小值，最終導出一個粗粒度的動力學模型。
本書描述了從由動力學蒙地卡羅（Gillespie）算法生成的二級結構摺疊軌跡中創建的馬可夫狀態模型，這是首次此類應用。書中提供的 Python 代碼可在書籍網站上獲得，允許研究團隊使用該代碼並擴展該方法。目前的 RNA 研究涉及功能性 RNA 分子的理性設計，本書提供了各種逆摺疊算法、組合優化的概述和比較，以及逆摺疊是否計算上困難（NP 完全）這一問題。另一章專注於各類設計的 RNA，包括核酶、RNA 溫度計、雙穩態開關、腳踏開關、mRNA 疫苗和基於紙張的 COVID-19 測試。最後一章是數學附錄，涵蓋了對於摺疊動力學至關重要的線性代數和馬可夫鏈結果。
本書提供了下一代 RNA 計算工作所需的基本工具，特別是針對功能性分子的理性設計——這一主題不久前還似乎更像是科幻小說。每章結尾的練習題引入新材料或相關概念，解答可在書籍網站上獲得。非常適合具有分析興趣和技能的高年級本科生、研究生及博士後讀者，這些技能來自物理化學、物理學、數學、計算機科學和統計學等領域。
第一卷和第二卷的教學幻燈片、計算機程序及所有練習的解答可在以下網站找到：https://github.com/pgclote/RNA-Computational-methods-for-structure-kinetics-and-rational-design-Solutions-slides-etc.-。
作者簡介
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.
作者簡介(中文翻譯)
一位富布賴特獎學金和古根海姆獎學金得主，Clote 博士曾在法國、德國和美國的數學、計算機科學和生物學領域擔任教職，包括慕尼黑大學的 Gentzen 計算機科學講座和法國高等工藝學院的 Digiteo 卓越講座。這為目前關於 RNA 的跨學科文本提供了獨特的背景。
