Hybrid Methods of Molecular Modeling PDF Download
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Author: Andrei L. Tchougréeff
Publisher: Springer Science & Business Media
ISBN: 1402081898
Category : Science
Languages : en
Pages : 360
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Book Description
This is a self-contained advanced review offering step by step derivation of the consistent theoretical picture of hybrid modeling methods and the thorough analysis of the concepts and current practical methods of hybrid modeling based on this theory. The book presents its material in a sequential way paying attention both to the physical soundness of the approximations used and to the mathematical rigor necessary for practical developing of the robust modeling code.
Author: Andrei L. Tchougréeff
Publisher: Springer Science & Business Media
ISBN: 1402081898
Category : Science
Languages : en
Pages : 360
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Book Description
This is a self-contained advanced review offering step by step derivation of the consistent theoretical picture of hybrid modeling methods and the thorough analysis of the concepts and current practical methods of hybrid modeling based on this theory. The book presents its material in a sequential way paying attention both to the physical soundness of the approximations used and to the mathematical rigor necessary for practical developing of the robust modeling code.
Author: Haruki Nakamura
Publisher: Springer
ISBN: 9811322007
Category : Science
Languages : en
Pages : 270
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Book Description
This book presents a new emerging concept of "Integrative Structural Biology". It covers current trends of the molecular and cellular structural biology, providing new methods to observe, validate, and keep the structural models of the large cellular machines with recent scientific results. Structures of very large macromolecular machines in cells are being determined by combining observations from complementary experimental methods. Thus, this volume presents the each methods such as X-ray crystallography, NMR spectroscopy, 3DEM, small-angle scattering (SAS), FRET, crosslinking, and enables the readers to understand the hybrid methods. This book discusses how those integrative models should be represented, validated and archived. A unique highlight of this book is discussion of the data validation and archive, which are big problems in this filed along with the progress of this field. The researchers in biology will be interested in this book as a guide book for learning the current structure biology, but also those in structure biology may use this book as a comprehensive reference to cover broad topics.
Author: Martin J. Field
Publisher: Cambridge University Press
ISBN: 1139465813
Category : Science
Languages : en
Pages : 294
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Book Description
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.
Author: Jianzhong Wu
Publisher: Springer
ISBN: 9811025029
Category : Science
Languages : en
Pages : 331
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Book Description
This book presents tutorial overviews for many applications of variational methods to molecular modeling. Topics discussed include the Gibbs-Bogoliubov-Feynman variational principle, square-gradient models, classical density functional theories, self-consistent-field theories, phase-field methods, Ginzburg-Landau and Helfrich-type phenomenological models, dynamical density functional theory, and variational Monte Carlo methods. Illustrative examples are given to facilitate understanding of the basic concepts and quantitative prediction of the properties and rich behavior of diverse many-body systems ranging from inhomogeneous fluids, electrolytes and ionic liquids in micropores, colloidal dispersions, liquid crystals, polymer blends, lipid membranes, microemulsions, magnetic materials and high-temperature superconductors. All chapters are written by leading experts in the field and illustrated with tutorial examples for their practical applications to specific subjects. With emphasis placed on physical understanding rather than on rigorous mathematical derivations, the content is accessible to graduate students and researchers in the broad areas of materials science and engineering, chemistry, chemical and biomolecular engineering, applied mathematics, condensed-matter physics, without specific training in theoretical physics or calculus of variations.
Author: Daan Frenkel
Publisher: Elsevier
ISBN: 0080519989
Category : Science
Languages : en
Pages : 661
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Book Description
Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text. Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on: - Transition path sampling and diffusive barrier crossing to simulaterare events - Dissipative particle dynamic as a course-grained simulation technique - Novel schemes to compute the long-ranged forces - Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations - Multiple-time step algorithms as an alternative for constraints - Defects in solids - The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules - Parallel tempering for glassy Hamiltonians Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.
Author: Andreas Kukol
Publisher: Humana Press
ISBN: 9781493954919
Category : Science
Languages : en
Pages : 474
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Book Description
Molecular Modeling of Proteins, Second Edition provides a theoretical background of various methods available and enables non-specialists to apply methods to their problems by including updated chapters and new material not covered in the first edition. This detailed volume opens by featuring classical and advanced simulation methods as well as methods to set-up complex systems such as lipid membranes and membrane proteins and continues with chapters devoted to the simulation and analysis of conformational changes of proteins, computational methods for protein structure prediction, usage of experimental data in combination with computational techniques, as well as protein-ligand interactions, which are relevant in the drug design process. Written for the highly successful Methods in Molecular Biology series, chapters include thorough introductions, step-by-step instructions and notes on troubleshooting and avoiding common pitfalls. Update-to-date and authoritative, Molecular Modeling of Proteins, Second Edition aims to aid researchers in the physical, chemical and biosciences interested in utilizing this powerful technology.
Author: J. Leszczynski
Publisher: Elsevier
ISBN: 008052964X
Category : Science
Languages : en
Pages : 663
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Book Description
This book covers applications of computational techniques to biological problems. These techniques are based by an ever-growing number of researchers with different scientific backgrounds - biologists, chemists, and physicists.The rapid development of molecular biology in recent years has been mirrored by the rapid development of computer hardware and software. This has resulted in the development of sophisticated computational techniques and a wide range of computer simulations involving such methods. Among the areas where progress has been profound is in the modeling of DNA structure and function, the understanding at a molecular level of the role of solvents in biological phenomena, the calculation of the properties of molecular associations in aqueous solutions, computationally assisted drug design, the prediction of protein structure, and protein - DNA recognition, to mention just a few examples. This volume comprises a balanced blend of contributions covering such topics. They reveal the details of computational approaches designed for biomoleucles and provide extensive illustrations of current applications of modern techniques.A broad group of readers ranging from beginning graduate students to molecular biology professions should be able to find useful contributions in this selection of reviews.
Author: Alan Hinchliffe
Publisher: John Wiley & Sons
ISBN: 0470030054
Category : Science
Languages : en
Pages : 428
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Book Description
Presenting a concise, basic introduction to modelling and computational chemistry this text includes relevant introductory material to ensure greater accessibility to the subject. Provides a comprehensive introduction to this evolving and developing field Focuses on MM, MC, and MD with an entire chapter devoted to QSAR and Discovery Chemistry. Includes many real chemical applications combined with worked problems and solutions provided in each chapter Ensures that up-to-date treatment of a variety of chemical modeling techniques are introduced.
Author: Tamar Schlick
Publisher: Springer Science & Business Media
ISBN: 0387224645
Category : Science
Languages : en
Pages : 669
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Book Description
Very broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text
Author: Beena Rai
Publisher: CRC Press
ISBN: 1439840784
Category : Science
Languages : en
Pages : 400
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Book Description
Molecular modeling (MM) tools offer significant benefits in the design of industrial chemical plants and material processing operations. While the role of MM in biological fields is well established, in most cases MM works as an accessory in novel products/materials development rather than a tool for direct innovation. As a result, MM engineers and practitioners are often seized with the question: "How do I leverage these tools to develop novel materials or chemicals in my industry?" Molecular Modeling for the Design of Novel Performance Chemicals and Materials answers this important question via a simple and practical approach to the MM paradigm. Using case studies, it highlights the importance and usability of MM tools and techniques in various industrial applications. The book presents detailed case studies demonstrating diverse applications such as mineral processing, pharmaceuticals, ceramics, energy storage, electronic materials, paints, coatings, agrochemicals, and personal care. The book is divided into themed chapters covering a diverse range of industrial case studies, from pharmaceuticals to cement. While not going too in-depth into fundamental aspects, the book covers almost all paradigms of MM, and references are provided for further learning. The text includes more than 100 color illustrations of molecular models.
