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Hybrid Biomolecular Modeling
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Book Synopsis Hybrid Biomolecular Modeling by : Slavica Jonic
Download or read book Hybrid Biomolecular Modeling written by Slavica Jonic and published by Frontiers Media SA. This book was released on 2019-01-24 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: Models of biomolecular structure and dynamics are often obtained by combining simulation or prediction approaches (e.g., comparative modeling, Molecular Dynamics (MD) simulations, Normal Mode Analysis (NMA), etc.) with experimental approaches (e.g., Nuclear Magnetic Resonance (NMR), X-ray crystallography, Small-Angle X-ray Scattering (SAXS), Electron Microscopy (EM), etc.). Such hybrid modeling extends the capabilities of experimental techniques, by enriching structural information and facilitating dynamics studies of biomolecules. This eBook contains articles on methodological developments, applications, and challenges of hybrid biomolecular modeling that have been collected in the framework of the Frontiers Research Topic entitled “Hybrid Biomolecular Modeling”.
Book Synopsis Hybrid Methods of Molecular Modeling by : Andrei L. Tchougréeff
Download or read book Hybrid Methods of Molecular Modeling written by Andrei L. Tchougréeff and published by Springer Science & Business Media. This book was released on 2008-08-01 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis A Practical Introduction to the Simulation of Molecular Systems by : Martin J. Field
Download or read book A Practical Introduction to the Simulation of Molecular Systems written by Martin J. Field and published by Cambridge University Press. This book was released on 2007-07-19 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
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 Integrative Structural Biology with Hybrid Methods by : Haruki Nakamura
Download or read book Integrative Structural Biology with Hybrid Methods written by Haruki Nakamura and published by Springer. This book was released on 2019-01-08 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Molecular Modeling of Self-assembling Hybrid Materials by : Alessandro Patti
Download or read book Molecular Modeling of Self-assembling Hybrid Materials written by Alessandro Patti and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Molecular Modelling for Beginners by : Alan Hinchliffe
Download or read book Molecular Modelling for Beginners written by Alan Hinchliffe and published by Wiley-Blackwell. This book was released on 2008-11-17 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: Updated to appeal to today's student, 'Molecular Modeling for Beginners', provides a concise, basic introduction to this evolving and developing field. It includes many real chemical applications combined with worked problems and solutions in each chapter.
Book Synopsis A Hybrid Explicit/implicit Solvent Technique for Biomolecular Simulations by : Michael S. Lee
Download or read book A Hybrid Explicit/implicit Solvent Technique for Biomolecular Simulations written by Michael S. Lee and published by . This book was released on 2004 with total page 18 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this work, we design and use a new biomolecular simulation technique that combines explicit solvent molecules and implicit solvent theory. We employ a multigrid approach to speed up the computationally expensive long-range electrostatic energy terms ubiquitous to the classical simulation of biomolecules. It is shown that the multigrid technique affords an order-of-magnitude speedup over conventional cutoff approaches. Our algorithm makes possible a new class of biomolecular simulations that was previously untenable (i.e., the calculation of solvation energies of entire proteins using explicit water molecules). We present comparisons of protein solvation energies obtained from our method and a popular implicit solvent model.
Book Synopsis Innovations in Biomolecular Modeling and Simulations by : Tamar Schlick
Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012-05-24 with total page 381 pages. Available in PDF, EPUB and Kindle. Book excerpt: The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.
Book Synopsis Molecular Modeling by : Hans-Dieter Höltje
Download or read book Molecular Modeling written by Hans-Dieter Höltje and published by John Wiley & Sons. This book was released on 2008-07-11 with total page 206 pages. Available in PDF, EPUB and Kindle. Book excerpt: Written by experienced experts in molecular modeling, this books describes the basics to the extent that is necessary if one wants to be able to reliably judge the results from molecular modeling calculations. Its main objective is the description of the various pitfalls to be avoided. Without unnecessary overhead it leads the reader from simple calculations on small molecules to the modeling of proteins and other relevant biomolecules. A textbook for beginners as well as an invaluable reference for all those dealing with molecular modeling in their daily work!
Book Synopsis Experimental and Theoretical Studies in Biomolecular Structure and Catalysis by : Joseph W. Kurutz
Download or read book Experimental and Theoretical Studies in Biomolecular Structure and Catalysis written by Joseph W. Kurutz and published by . This book was released on 1998 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Hybrid Molecular Dynamics Simulation by : Qiong Cai
Download or read book Hybrid Molecular Dynamics Simulation written by Qiong Cai and published by . This book was released on 2007 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer by : Ilia A. Solov’yov
Download or read book Multiscale Modeling of Complex Molecular Structure and Dynamics with MBN Explorer written by Ilia A. Solov’yov and published by Springer. This book was released on 2017-05-16 with total page 460 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book introduces readers to MesoBioNano (MBN) Explorer – a multi-purpose software package designed to model molecular systems at various levels of size and complexity. In addition, it presents a specially designed multi-task toolkit and interface – the MBN Studio – which enables the set-up of input files, controls the simulations, and supports the subsequent visualization and analysis of the results obtained. The book subsequently provides a systematic description of the capabilities of this universal and powerful software package within the framework of computational molecular science, and guides readers through its applications in numerous areas of research in bio- and chemical physics and material science – ranging from the nano- to the mesoscale. MBN Explorer is particularly suited to computing the system’s energy, to optimizing molecular structure, and to exploring the various facets of molecular and random walk dynamics. The package allows the use of a broad variety of interatomic potentials and can, e.g., be configured to select any subset of a molecular system as rigid fragments, whenever a significant reduction in the number of dynamical degrees of freedom is required for computational practicalities. MBN Studio enables users to easily construct initial geometries for the molecular, liquid, crystalline, gaseous and hybrid systems that serve as input for the subsequent simulations of their physical and chemical properties using MBN Explorer. Despite its universality, the computational efficiency of MBN Explorer is comparable to that of other, more specialized software packages, making it a viable multi-purpose alternative for the computational modeling of complex molecular systems. A number of detailed case studies presented in the second part of this book demonstrate MBN Explorer’s usefulness and efficiency in the fields of atomic clusters and nanoparticles, biomolecular systems, nanostructured materials, composite materials and hybrid systems, crystals, liquids and gases, as well as in providing modeling support for novel and emerging technologies. Last but not least, with the release of the 3rd edition of MBN Explorer in spring 2017, a free trial version will be available from the MBN Research Center website (mbnresearch.com).
Book Synopsis Innovations in Biomolecular Modeling and Simulations by : Tamar Schlick
Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012-05-24 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.
Book Synopsis A Hybrid Explicit/implicit Solvent Technique for Biomolecular Simulations by :
Download or read book A Hybrid Explicit/implicit Solvent Technique for Biomolecular Simulations written by and published by . This book was released on 2004 with total page 18 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this work, we design and use a new biomolecular simulation technique that combines explicit solvent molecules and implicit solvent theory. We employ a multigrid approach to speed up the computationally expensive long-range electrostatic energy terms ubiquitous to the classical simulation of biomolecules. It is shown that the multigrid technique affords an order-of-magnitude speedup over conventional cutoff approaches. Our algorithm makes possible a new class of biomolecular simulations that was previously untenable (i.e., the calculation of solvation energies of entire proteins using explicit water molecules). We present comparisons of protein solvation energies obtained from our method and a popular implicit solvent model.
Book Synopsis Innovations in Biomolecular Modeling and Simulations by : Tamar Schlick
Download or read book Innovations in Biomolecular Modeling and Simulations written by Tamar Schlick and published by Royal Society of Chemistry. This book was released on 2012 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts.
Download or read book Enzyme Technology written by Ashok Pandey and published by Springer Science & Business Media. This book was released on 2006-04-28 with total page 774 pages. Available in PDF, EPUB and Kindle. Book excerpt: Publisher Description
