Quantum Mechanical Simulation Methods For Studying Biological Systems
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Quantum Mechanical Simulation Methods For Studying Biological Systems
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Author : Dominique Bicout
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-03-09
Quantum Mechanical Simulation Methods For Studying Biological Systems written by Dominique Bicout and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-03-09 with Science categories.
It is now generally agreed that a deeper understanding of biological processes requires a multi-disciplinary approach employing the tools of biology, chemistry, and physics. Such understanding involves study of biomacromolecules and their functions, which includes how they interact, their reactions, and how information is transmitted between them. This volume is devoted to quantum mechanical simulation techniques, which have developed rapidly in recent years. It covers quantum mechanical calculations of large systems, molecular dynamics combining quantum and classical algorithms, quantum dynamical simulations, and electron and proton transfer processes in proteins and in solutions.
Quantum Mechanical Simulation Methods
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Author : Collectif
language : en
Publisher:
Release Date : 1996-02
Quantum Mechanical Simulation Methods written by Collectif and has been published by this book supported file pdf, txt, epub, kindle and other format this book has been release on 1996-02 with categories.
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes
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Author : Adam Liwo
language : en
Publisher: Springer Science & Business Media
Release Date : 2013-07-17
Computational Methods To Study The Structure And Dynamics Of Biomolecules And Biomolecular Processes written by Adam Liwo and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2013-07-17 with Technology & Engineering categories.
Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.
Computer Simulation Of Biomolecular Systems
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Author : W.F. van Gunsteren
language : en
Publisher: Springer Science & Business Media
Release Date : 1997-11-30
Computer Simulation Of Biomolecular Systems written by W.F. van Gunsteren and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 1997-11-30 with Science categories.
This book is the third volume in this highly successful series. Since the first volume in 1989 and the second in 1993, many exciting developments have occurred in the development of simulation techniques and their application to key biological problems such as protein folding, protein structure prediction and structure-based design, and in how, by combining experimental and theoretical approaches, very large biological systems can be studied at the molecular level. This series attempts to capture that progress. Volume 3 includes contributions that highlight developments in methodology which enable longer and more realistic simulations (e.g. multiple time steps and variable reduction techniques), a study of force fields for proteins and new force field development, a novel approach to the description of molecular shape and the use of molecular shape descriptors, the study of condensed phase chemical reactions, the use of electrostatic techniques in the study of protonation, equilibria and flexible docking studies, structure refinement using experimental data (X-ray, NMR, neutron, infrared) and theoretical methods (solvation models, normal mode analysis, MD simulations, MC lattice dynamics, and knowledge-based potentials). There are several chapters that show progress in the development of methodologies for the study of folding processes, binding affinities, and the prediction of ligand-protein complexes. The chapters, contributed by experienced researchers, many of whom are leaders in their field of study, are organised to cover developments in: simulation methodology the treatment of electrostatics protein structure refinement the combined experimental and theoretical approaches to the study of very large biological systems applications and methodology involved in the study of protein folding applications and methodology associated with structure-based design.
Biomolecular Simulations
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Author : Luca Monticelli
language : en
Publisher: Humana Press
Release Date : 2012-10-04
Biomolecular Simulations written by Luca Monticelli and has been published by Humana Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-10-04 with Science categories.
Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced. Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems.
Theoretical Physics For Biological Systems
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Author : Paola Lecca
language : en
Publisher: CRC Press
Release Date : 2019-01-30
Theoretical Physics For Biological Systems written by Paola Lecca and has been published by CRC Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2019-01-30 with Medical categories.
Quantum physics provides the concepts and their mathematical formalization that lend themselves to describe important properties of biological networks topology, such as vulnerability to external stress and their dynamic response to changing physiological conditions. A theory of networks enhanced with mathematical concepts and tools of quantum physics opens a new area of biological physics, the one of systems biological physics.
Computer Simulations In Molecular Biology
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Author : Hiqmet Kamberaj
language : en
Publisher: Springer Nature
Release Date : 2023-07-31
Computer Simulations In Molecular Biology written by Hiqmet Kamberaj and has been published by Springer Nature this book supported file pdf, txt, epub, kindle and other format this book has been release on 2023-07-31 with Science categories.
This book covers a range of topics in quantum mechanics and molecular dynamics simulation, including computational modeling and machine learning approaches. The book also provides a Python GUI and tutorials for simulating molecular biological systems and presents case studies of quantum mechanics simulations for predicting electronic properties. Its pedagogical formatting makes it easy for students to understand and follow and has been praised for providing clear and detailed explanations of complex topics. This book is ideal for graduate students and researchers in theoretical and computational biophysics, physics, chemistry, and materials science, as well as postgraduates in applied mathematics, computer science, and bioinformatics.
Quantum Simulations Of Materials And Biological Systems
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Author : Jun Zeng
language : en
Publisher: Springer Science & Business Media
Release Date : 2012-07-26
Quantum Simulations Of Materials And Biological Systems written by Jun Zeng and has been published by Springer Science & Business Media this book supported file pdf, txt, epub, kindle and other format this book has been release on 2012-07-26 with Science categories.
Quantum Simulations of Materials and Biological Systems features contributions from leading world experts in the fields of density functional theory (DFT) and its applications to material and biological systems. The recent developments of correlation functionals, implementations of Time-dependent algorithm into DFTB+ method are presented. The applications of DFT method to large materials and biological systems such as understanding of optical and electronic properties of nanoparticles, X-ray structure refinement of proteins, the catalytic process of enzymes and photochemistry of phytochromes are detailed. In addition, the book reviews the recent developments of methods for protein design and engineering, as well as ligand-based drug design. Some insightful information about the 2011 International Symposium on Computational Sciences is also provided. Quantum Simulations of Materials and Biological Systems is aimed at faculties and researchers in the fields of computational physics, chemistry and biology, as well as at the biotech and pharmaceutical industries.
Multi Scale Quantum Models For Biocatalysis
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Author : Darrin M. York
language : en
Publisher: Springer
Release Date : 2009-08-29
Multi Scale Quantum Models For Biocatalysis written by Darrin M. York and has been published by Springer this book supported file pdf, txt, epub, kindle and other format this book has been release on 2009-08-29 with Science categories.
“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.
A Practical Introduction To The Simulation Of Molecular Systems
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Author : Martin J. Field
language : en
Publisher: Cambridge University Press
Release Date : 2007-07-19
A Practical Introduction To The Simulation Of Molecular Systems written by Martin J. Field and has been published by Cambridge University Press this book supported file pdf, txt, epub, kindle and other format this book has been release on 2007-07-19 with Science categories.
Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.