Bøger af Jiapu Zhang

COVID-19 has brought us extensive research databases in the fields of biophysics, biology, and bioinformatics. To extract valuable structural bioinformatic information of SARS-CoV-2 structural and nonstructural proteins, it is necessary to work with large-scale datasets of molecular dynamics (MD) trajectories that need to be optimized. This monograph serves as a comprehensive guide to optimization-based MD studies of the molecular structures of SARS-CoV-2 proteins and RNA. The book begins by performing local optimization, taking into account the three-body movement and optimizing the noncovalent bonds of each molecular structure. The optimized structures reach a transition state that offers the best stability and lowest energy. The optimization process utilizes a hybrid strategy that combines mathematical optimization with various local search algorithms. This approach significantly reduces data volume while eliminating irrelevant bioinformatics data. To gain a thoroughunderstanding of molecular stability and the mechanism of action, it is essential to consider not only static NMR, X-ray, or cryo-EM structures but also dynamic information obtained through MD or Quantum Mechanics/Molecular Mechanics (QM/MM) simulations. These simulations capture the internal motions and dynamic processes of molecules. Furthermore, for each protein, the structural bioinformatics obtained from the optimized structure is validated by analyzing large-scale MD trajectory databases, which are openly and freely available online. The analysis includes key structural bioinformatics aspects such as salt bridge electrostatic interactions, hydrogen bonds, van der Waals interactions, and hydrophobic interactions specific to each SARS-CoV-2 molecular structure. The book also delves into discussions on drugs, vaccines, and the origins of the virus. Additionally, pandemic mathematical models, including those incorporating time delays, are explored. This book is particularly valuable for professionals working in practical computing roles within computational biochemistry, computational biophysics, optimization and molecular dynamics, structural bioinformatics, biological mathematics, and related fields. It serves as an accessible introduction to these disciplines and is also an excellent teaching resource for students.

This documentary of father's diaries of work, life, family and country written during the period from 1966 to 1971, is on the study of literature, art, history, politics, economy, social policy, education, health, justice, and ideological trends of that period of history; it is obviously helpful. We hope that these diaries can make people remember the revolutionary era of revolution and construction, and learn for today. The publication of this document also can let my father's diaries see the light of time.

In chemistry, physics, biophysics, biochemistry, biomedicine, bioinformatics, applied mathematics and theoretical physics, Molecular dynamics (MD) simulating physical movements of atoms and molecules is widely applied. Amber and Gromacs etc are very popular and practical MD packages. This book applies these packages to biomolecules and materials. It provides comprehensive MD materials and methods to put MD into actions. This book clearly has a value to MD simulation staff (in research or teaching) in the fields of chemistry, physics, biophysics, biochemistry, biomedicine, bioinformatics, applied mathematics and theoretical physics. This book fully illuminates MD application to prion proteins from many points of view. The author was awarded numerous world-wide impacts and fame for the successful MD application. Prion diseases can be caused by the body¿s own proteins not requiring either DNA, RNA, or both; they are "structural conformational" diseases so very proper to be studied by MD technologies. Rabbits, dogs and horses are reported to be immune to prion diseases. The author using MD technologies preliminarily revealed some surprising secrets from rabbits against prion diseases

Other PrP models and doppel models are also MD studied in this book. Secondly, all the mutants of mouse PrP and human PrP are well studied by this book.

This monograph is the first easy-to-read-and-understand book on prion proteins' molecular dynamics (MD) simulations and on prions' molecular modelling (MM) constructions.