Chemical Theory and Multiscale Simulation in Biomolecules
From Principles to Case Studies
- 1st Edition - March 28, 2024
- Imprint: Elsevier
- Author: Guohui Li
- Language: English
- Paperback ISBN:9 7 8 - 0 - 3 2 3 - 9 5 9 1 7 - 9
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 5 9 1 8 - 6
Chemical Theory and Multiscale Simulation in Biomolecules: From Principles to Case Studies helps readers understand what simulation is, what information modeling of biomolecu… Read more
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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
Anyone who wants to engage in theoretical calculation and molecular simulation of biological macromolecules, including students and researchers across chemistry, biology, medicine, and physics
1 Introduction
Part I Basic knowledge2 Molecular Mechanics and force field2.1 all-atom model2.2 polarizable model2.3 coarse-grained model3 Quantum Chemistry Theory3.1 Hartree-Fock and post HF method3.2 Density-Functional Theory3.3 Semi-empirical method4 Machine Learning4.1 Artificial neural network4.1.1 Neural Network4.1.2 Deep Learing4.2 Cluster Analysis4.3 Classification and Regressions Trees4.4 Dimensionality Reduction
Part II Methods and Approaches5 Monte Carlo and Molecular Dynamics5.1 Monte Carlo5.2 Molecular Dynamics6 Control and adjustment of simulation conditions6.1 Solvent6.2 Boundary Conditions6.3 Restraint and Constraint6.4 Temperature and Pressure6.5 Advanced method of saving time-cost7 Multiscale Model7.1 QM/MM7.2 MM-Corse Grained8 Enhanced sampling8.1 Umbrella Sampling8.2 Steered Molecular Dynamics8.3 Metadynamics8.4 Targeted Molecular Dynamics8.5 Markov State Models8.6 reweighting method9 Software and Hardware9.1 QM software9.2 MD software9.3 CPU, GPU, FPGA and ASIC
Part III Applications and case studies10 Protein folding and structure prediction11 RNA folding and structure prediction12 Enzyme catalysis13 Post-translational modification of proteins14 Regulation of small molecule on proteins15 Recognition of protein with nucleic acid16 Dynamics and functions of membrane proteins17 Assembly and functions of multiple components complex18 Protein and small molecule design
Part IV Future directions and perspectives
- Edition: 1
- Published: March 28, 2024
- Imprint: Elsevier
- Language: English
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Guohui Li
Since obtaining a Ph.D. from the Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Guohui Li has worked in the Department of chemistry, University of Mexico, University of Wisconsin Madison, Harvard Medical School and Biogen idea Inc., returning to China in 2009. At present, he has published more than 120 papers in the world's top academic journals, participated in the compilation of two books, and has been invited to give reports at international conferences and served as co chairman for many. His research is devoted to the theory and calculation of biological macromolecular systems.
Affiliations and expertise
Dalian Institute of Chemical Physics, Dalian, ChinaRead Chemical Theory and Multiscale Simulation in Biomolecules on ScienceDirect