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Multiscale Simulation Of Rna Catalysis
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Book Synopsis Multiscale Simulation of RNA Catalysis by : Haoyuan Chen
Download or read book Multiscale Simulation of RNA Catalysis written by Haoyuan Chen and published by . This book was released on 2017 with total page 138 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular simulations have become an essential part in modern chemistry research. Due to the wide variety and complex nature of practical chemistry problems, the multiscale simulation approach, which attempts to solve problems at different scales using different level of theories, has been widely employed. In this dissertation, several practical applications of multiscale simulation methods to the study of RNA catalysis as well as some method development work are presented. In Chapters 3 and 4, detailed investigations using quantum mechanical methods on the transition state structures in native and catalyzed model reactions that mimic RNA self-cleavage are presented, which serve as a baseline for the following mechanistic studies on real catalytic RNAs. Chapter 5 presents an example of a holistic approach on a mechanistic problem in a real catalytic RNA, which is the hammerhead ribozyme. Quantum mechanical methods, classical simulations and hybrid quantum-classical calculations are employed together to resolve the controversial role of residue G12 in hammerhead ribozyme. Finally, in Chapter 6, method developments on an advanced sampling method called the multi-dimensional replica exchange method is presented and applied to two prototypical problems in biochemistry. Taken together, the work presented here provide new insights into the molecular-level mechanism of RNA catalysis, which is of fundamental importance to our understanding of the underlying chemical principles in life.
Book Synopsis Multi-scale Quantum Models for Biocatalysis by : Darrin M. York
Download or read book Multi-scale Quantum Models for Biocatalysis written by Darrin M. York and published by Springer Science & Business Media. This book was released on 2009-05-30 with total page 426 pages. Available in PDF, EPUB and Kindle. Book excerpt: “Multi-scale Quantum Models for Biocatalysis” explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes. This book is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology and for students exposed to these research areas.
Book Synopsis A Multiscale Computational Approach to Study RNase A Catalysis by : Thakshila D. Dissanayake Rallage
Download or read book A Multiscale Computational Approach to Study RNase A Catalysis written by Thakshila D. Dissanayake Rallage and published by . This book was released on 2016 with total page 124 pages. Available in PDF, EPUB and Kindle. Book excerpt: Enzyme catalysis is an extremely important and complex process that is fundamental to biology. Experiments provide a wealth of valuable information about the function of enzymes; however, this information requires the use of computational models to establish a meaningful interpretation that can be used to guide design. Multiscale computational models, which integrate a hierarchy of theoretical methods to address complex biomolecular problems that span large spatial and temporal ranges, afford powerful tools to provide a detailed molecular level interpretation of a wide range of experimental data from which a consensus view of catalytic mechanism may emerge. In this dissertation, I detail my efforts to develop and apply multiscale methods to study the mechanisms of RNA backbone cleavage catalyzed by Ribonuclease A, an important archetype enzyme system, and the factors that regulate its activity. In the first phase of this research, I use molecular dynamics simulations to characterize the structure and dynamics of the active enzyme in solution at different stages along the reaction path. In this work, I demonstrate that the crystallographic structure represents an inactive, catalytically non-relevant state, and make predictions that a conformational change involving the flipping of the side chain of a conserved histidine residue (His12) is required to adopt a catalytically competent conformation. In the second phase of this research, I apply ''constant pH molecular dynamics simulations'' (CpHMD) to characterize the conditional probability of finding key active site residues in a protonation state that supports general acid-base catalysis. This allowed the prediction of pKa shifts for His12, His119 and Lys41, and, for the first time, activity-pH profiles for an enzyme system that can be compared directly with those measured in kinetic experiments. In the third phase of this research, I use combined quantum mechanical/molecular mechanical methods to study the catalytic chemical steps of transphosphorylation. Results of this work predict a free energy landscape for the reaction, from which the minimum free energy pathway that connects reactants and products allows a detailed molecular-level picture of mechanism. In the fourth phase of this research, I extend the CpHMD method to nucleic acid systems, to benchmark the method for the study of ribozymes that catalyze the same reaction as RNase A.
Book Synopsis Ribozymes and RNA Catalysis by : David Malcolm James Lilley
Download or read book Ribozymes and RNA Catalysis written by David Malcolm James Lilley and published by Royal Society of Chemistry. This book was released on 2008 with total page 339 pages. Available in PDF, EPUB and Kindle. Book excerpt: Takes the reader through the origins of catalysis in RNA and necessarily includes significant discussion of structure and folding. The main focus of the book concerns chemical mechanism with extensive comment on how, despite the importance of RNA catalysis in the cell, its origins are still poorly understood and often controversial. The reader is given an outline of the important role of RNA catalysis in many aspects of cell function, including RNA processing and translation.
Download or read book Catalytic RNA written by and published by Academic Press. This book was released on 2013-10-21 with total page 255 pages. Available in PDF, EPUB and Kindle. Book excerpt: This special volume of Progress in Molecular Biology and Translational Science focuses on catalytic RNA. Written by experts in the field, the reviews cover a range of topics, from hammerhead ribozymes to spliceosome catalysis to Varkud satellite and hairpin ribozymes. Contributions from leading authorities Informs and updates on all the latest developments in the field
Book Synopsis Modeling of RNA Catalysis by : Tomasz Bereźniak
Download or read book Modeling of RNA Catalysis written by Tomasz Bereźniak and published by . This book was released on 2012 with total page 118 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Multiscale Simulation Methods for Nanomaterials by : Richard B. Ross
Download or read book Multiscale Simulation Methods for Nanomaterials written by Richard B. Ross and published by John Wiley & Sons. This book was released on 2008-02-04 with total page 300 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book stems from the American Chemical Society symposium, Large Scale Molecular Dynamics, Nanoscale, and Mesoscale Modeling and Simulation: Bridging the Gap, that delved into the latest methodologies and applications for largescale, multiscale, and mesoscale modeling and simulation. It presents real-world applications of simulated and synthesized materials, including organic-, inorganic-, bio-, and nanomaterials, and helps readers determine the best method for their simulation. It gets novices up to speed quickly and helps experienced practitioners discover novel approaches and alternatives.
Book Synopsis Computational Methods for Understanding Riboswitches by :
Download or read book Computational Methods for Understanding Riboswitches written by and published by Academic Press. This book was released on 2015-02-24 with total page 449 pages. Available in PDF, EPUB and Kindle. Book excerpt: This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers computational prediction RNA structure and dynamics, including such topics as computational modeling of RNA secondary and tertiary structures, riboswitch dynamics, and ion-RNA, ligand-RNA and DNA-RNA interactions. Continues the legacy of this premier serial with quality chapters authored by leaders in the field Covers computational methods and applications in RNA structure and dynamics Contains chapters with emerging topics such as RNA structure prediction, riboswitch dynamics and thermodynamics, and effects of ions and ligands.
Download or read book RNA written by Marlene Belfort and published by Elsevier Publishing Company. This book was released on 1989 with total page 252 pages. Available in PDF, EPUB and Kindle. Book excerpt: The conference on RNA: Catalysis, Splicing, Evolution brought together a unique assembly of scientific leaders in this currently very important field. Two participants of this Conference, Drs. T.R. Cech and S. Altman, were just awarded the 1989 Nobel prize in chemistry, which attests to the timeliness of this volume. The critical reviews authored by these two prominent scientists are included. For those scientists with roots in this field, who do not subscribe to GENE, this is an excellent opportunity to obtain a masterly collection of papers. All the original papers and reviews have undergone the rigorous peer review of the journal Gene.
Book Synopsis Modeling the Mechanisms of RNA Catalysis by : Evelyn A. Mayaan
Download or read book Modeling the Mechanisms of RNA Catalysis written by Evelyn A. Mayaan and published by . This book was released on 2005 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Catalytic RNA written by Fritz Eckstein and published by Springer. This book was released on 1997-04-09 with total page 418 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, unprecedented advances in many aspects of the molecular biology of nucleic acids have been witnessed. The area of RNA chemistry has undergone a kind of explosion, with a huge interest in RNA-mediated catalysis. At the same time, our structural understanding of DNA-protein interactions has increased enormously, and the related area of RNA-protein interactions is beginning to gather pace. This softcover edition from the successful series Nucleic Acids and Molecular Biology is devoted to the structure and mechanism of ribozymes, and their potential exploitation. The subject has both important evolutionary implications and potential practical application in the development of therapeutic agents for diseases such as AIDS.
Book Synopsis Catalysis In Chemistry And Biology - Proceedings Of The 24th International Solvay Conference On Chemistry by : Kurt Wuthrich
Download or read book Catalysis In Chemistry And Biology - Proceedings Of The 24th International Solvay Conference On Chemistry written by Kurt Wuthrich and published by World Scientific. This book was released on 2018-06-27 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Proceedings of the 24th International Solvay Conference on Chemistry comprise contributed short personal statements and transcripts of in-depth discussions on 'Catalysis in Chemistry and Biology' from a by-invitation-only select group of 48 eminent scientists, including four Nobel Laureates, from all parts of the world. The theme of the conference was presented in six sessions, along which the Proceedings are organized. The first session on 'Homogeneous Catalysis,' chaired by Professor Robert Grubbs, is devoted to basic research on catalysis in homogeneous solutions and applications thereof. 'Heterogeneous Catalysis and Characterization of Catalyst Surfaces,' chaired by Professor Gerhard Ertl, includes extensive references to industrial applications of catalysis on solid supports, and discussions on the experimental techniques used in this field. 'Catalysis by Microporous Materials,' chaired by Professor Mark E. Davis, is devoted to a detailed characterization of this particular class of solid support catalysts, with special emphasis on model analysis of the processes catalyzed by these materials. 'Catalysis under Extreme Conditions: Studies at High Pressure and High Temperatures — Relations with Processes in Nature,' chaired by Professor Henk N W Lekkerkerker, broadens the scope of the two preceding sessions with exciting illustrations. The sessions on 'Catalysis by Protein Enzymes,' chaired by Prof. JoAnne Stubbe, and 'Catalysis by Ribozymes in Molecular Machines,' chaired by Prof. David Lilley, present at the same time an exciting extension of and a contrast to the initial four sessions. The combination of the six sessions provides an impressive overview, giving innovative insights into relationships between catalysis in chemical processes and in biological systems, and a unique outlook to anticipated developments in the coming years and the more distant future.
Book Synopsis Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations by : Valentina Tozzini
Download or read book Multiscale Modeling From Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations written by Valentina Tozzini and published by Frontiers Media SA. This book was released on 2020-10-27 with total page 235 pages. Available in PDF, EPUB and Kindle. Book excerpt: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact.
Book Synopsis Annual Reports in Computational Chemistry by : Ralph A. Wheeler
Download or read book Annual Reports in Computational Chemistry written by Ralph A. Wheeler and published by Elsevier. This book was released on 2010-09-06 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: Annual Reports in Computational Chemistry is a new periodical providing timely and critical reviews of important topics in computational chemistry as applied to all chemical disciplines. Topics covered include quantum chemistry, molecular mechanics, force fields, chemical education, and applications in academic and industrial settings. Each volume is organized into (thematic) sections with contributions written by experts. Focusing on the most recent literature and advances in the field, each article covers a specific topic of importance to computational chemists. Annual Reports in Computational Chemistry is a "must" for researchers and students wishing to stay up-to-date on current developments in computational chemistry. Broad coverage of computational chemistry and up-to-date information Topics covered include bioinformatics, drug discovery, protein NMR, simulation methodologies, and applications in academic and industrial settings Each chapter reviews the most recent literature on a specific topic of interest to computational chemists
Book Synopsis Ab Initio Molecular Dynamics by : Dominik Marx
Download or read book Ab Initio Molecular Dynamics written by Dominik Marx and published by Cambridge University Press. This book was released on 2009-04-30 with total page 503 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.
Download or read book RNA Folding written by Ronny Lorenz and published by Springer Nature. This book was released on with total page 407 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Chemical Theory and Multiscale Simulation in Biomolecules by : Guohui Li
Download or read book Chemical Theory and Multiscale Simulation in Biomolecules written by Guohui Li and published by Elsevier. This book was released on 2024-03-28 with total page 399 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Theory and Multiscale Simulation in Biomolecules: From Principles to Case Studies helps readers understand what simulation is, what information modeling of biomolecules can provide, and how to compare this information with experiments. Beginning with an introduction to computational theory for modeling, the book goes on to describe how to control the conditions of modeling systems and possible strategies for time-cost savings in computation. Part Two further outlines key methods, with step-by-step guidance supporting readers in studying and practicing simulation processes. Part Three then shows how these theories are controlled and applied in practice, through examples and case studies on varied applications. This book is a practical guide for new learners, supporting them in learning and applying molecular modeling in practice, whilst also providing more experienced readers with the knowledge needed to gain a deep understanding of the theoretical background behind key methods. Presents computational theory alongside case studies to help readers understand the use of simulation in practice Includes extensive examples of different types of simulation methods and approaches to result analysis Provides an overview of the current academic frontier and research challenges, encouraging creativity and directing attention to current problems
