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E-raamat: Coarse-Graining of Condensed Phase and Biomolecular Systems

Edited by (University of Utah, Salt Lake City, USA)
  • Formaat: 456 pages
  • Ilmumisaeg: 22-Sep-2008
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781420059564
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  • Formaat: 456 pages
  • Ilmumisaeg: 22-Sep-2008
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781420059564

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Exploring recent developments in the field, Coarse-Graining of Condensed Phase and Biomolecular Systems examines systematic ways of constructing coarse-grained representations for complex systems. It explains how this approach can be used in the simulation and modeling of condensed phase and biomolecular systems.

Each chapter focuses on specific examples of evolving coarse-graining methodologies and presents results for a variety of complex systems. The contributors carefully detail their own coarse-graining approach, exploring its motivation, strengths, weaknesses, and important application examples. They discuss two of the most successful coarse-graining schemes for soft matter: inverse and multiscale coarse-graining. The book also describes current coarse-grained model development for peptides and proteins at the amino acid level and larger length scales.

Assembling the work of some of the most influential, world-renowned researchers in the field, this book provides a unified, in-depth overview of all the coarse-grained schemes developed for condensed phase and biomolecular systems. It shows the promise of coarse-graining as a revolutionary advancement in the scientific community.
Acknowledgments ix
Editor xi
Contributors xiii
Introduction
1(4)
Gregory A. Voth
The MARTINI Force Field
5(16)
Siewert J. Marrink
Marc Fuhrmans
H. Jelger Risselada
Xavier Periole
The Multiscale Coarse-Graining Method: A Systematic Approach to Coarse-Graining
21(20)
W. G. Noid
Gary S. Ayton
Sergei Izvekov
Gregory A. Voth
A Model for Lipid Bilayers in Implicit Solvent
41(18)
Grace Brannigan
Frank L.H. Brown
Coarse-Grained Dynamics of Anisotropic Systems
59(10)
L. Paramonov
M.G. Burke
S.N. Yaliraki
State-Point Dependence and Transferability of Potentials in Systematic Structural Coarse-Graining
69(14)
Qi Sun
Jayeeta Ghosh
Roland Faller
Systematic Approach to Coarse-Graining of Molecular Descriptions and Interactions with Applications to Lipid Membranes
83(24)
Teemu Murtola
Ilpo Vattulainen
Mikko Karttunen
Simulation of Protein Structure and Dynamics with the Coarse-Grained UNRES Force Field
107(16)
Adam Liwo
Cezary Czaplewski
Stanislaw Oldziej
Ana V. Rojas
Rajmund Kazmierkiewicz
Mariusz Makowski
Rajesh K. Murarka
Harold A. Scheraga
Coarse-Grained Structure-Based Simulations of Proteins and RNA
123(18)
Alexander Schug
Changbong Hyeon
Jose N. Onuchic
On the Development of Coarse-Grained Protein Models: Importance of Relative Side-Chain Orientations and Backbone Interactions
141(16)
N.-V. Buchete
J.E. Straub
D. Thirumalai
Characterization of Protein-Folding Landscapes by Coarse-Grained Models Incorporating Experimental Data
157(14)
Silvina Matysiak
Cecilia Clementi
Principles and Practicalities of Canonical Mixed-Resolution Sampling of Biomolecules
171(14)
Daniel M. Zuckerman
Pathways of Conformational Transitions in Proteins
185(20)
Peter Majek
Ron Elber
Harel Weinstein
Insights into the Sequence-Dependent Macromolecular Properties of DNA from Base-Pair Level Modeling
205(20)
Wilma K. Olson
Andrew V. Colasanti
Luke Czapla
Guohui Zheng
Coarse-Grained Models for Nucleic Acids and Large Nucleoprotein Assemblies
225(12)
Robert K.-Z. Tan
Anton S. Petrov
Batsal Devkota
Stephen C. Harvey
Elastic Network Models of Coarse-Grained Proteins Are Effective for Studying the Structural Control Exerted over Their Dynamics
237(18)
Robert L. Jernigan
Lei Yang
Guang Song
Ozge Kurkcuoglu
Pemra Doruker
Coarse-Grained Elastic Normal Mode Analysis and Its Applications in X-Ray Crystallographic Refinement at Moderate Resolutions
255(12)
Jianpeng Ma
Coarse-Grained Normal Mode Analysis to Explore Large-Scale Dynamics of Biological Molecules
267(18)
Osamu Miyashita
Florence Tama
One-Bead Coarse-Grained Models for Proteins
285(14)
Valentina Tozzini
J. Andrew McCammon
Application of Residue-Based and Shape-Based Coarse-Graining to Biomolecular Simulations
299(18)
Peter L. Freddolino
Amy Y. Shih
Anton Arkhipov
Ying Ying
Zhongzhou Chen
Klaus Schulten
Coarse-Graining Protein Mechanics
317(12)
Richard Lavery
Sophie Sacquin-Mora
Self-Assembly of Surfactants in Bulk Phases and at Interfaces Using Coarse-Grain Models
329(14)
Wataru Shinoda
Russell DeVane
Michael L. Klein
Coarse-Grained Simulations of Polyelectrolytes
343(18)
Mark J. Stevens
Monte Carlo Simulations of a Coarse-Grain Model for Block Copolymer Systems
361(18)
F.A. Detcheverry
K. Ch. Daoulas
M. Muller
P.F. Nealey
J.J. de Pablo
Structure-Based Coarse- and Fine-Graining in Soft Matter Simulations
379(20)
Nico F.A. van der Vegt
Christine Peter
Kurt Kremer
From Atomistic Modeling of Macromolecules Toward Equations of State for Polymer Solutions and Melts: How Important Is the Accurate Description of the Local Structure?
399(16)
Kurt Binder
Wolfgang Paul
Peter Virnau
Leonid Yelash
Marcus Muller
Luis Gonzalez MacDowell
Effective Interaction Potentials for Coarse-Grained Simulations of Polymer-Tethered Nanoparticle Self-Assembly in Solution
415(18)
Elaine R. Chan
Alberto Striolo
Clare McCabe
Peter T. Cummings
Sharon C. Glotzer
Coarse-Graining in Time: From Microscopics to Macroscopics
433(16)
Angela Violi
Index 449
University of Utah, Salt Lake City, USA