Coarse-graining of condensed phase and biomolecular systems:
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| Other Authors: | |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Boca Raton, Fla. [u.a.]
CRC Press, Taylor & Francis
2009
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVIII, 455 S., [8] Bl. zahlr. Ill. und graph. Darst. |
| ISBN: | 9781420059557 |
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Record in the Search Index
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| adam_text | Table
of Contents
Acknowledgments
...........................................................................................................................ix
Editor
...............................................................................................................................................xi
Contributors
.................................................................................................................................xiii
Chapter
1
Introduction
..................................................................................................................1
Gregory
A. Vot h
Chapter
2
The MARTINI Force Field
..........................................................................................5
Siewert J. Marrink, Marc Fuhrmans, H. Jelger
Risselada,
and
Xavier Periole
Chapter
3
The Multiscale Coarse-Graining Method:
A Systematic Approach to Coarse-Graining
.............................................................21
W. G. Noid, Gary S. Ayton, Sergei Izvekov, and Gregory A. Voth
Chapter
4
A Model for
Lipid Bilayers
in Implicit Solvent
..........................................................41
Grace Brannigan and Frank L.H. Brown
Chapter
5
Coarse-Grained Dynamics of
Anisotropie
Systems
..................................................59
L. Paramonov, M.G. Burke, andS.N. Yaliraki
Chapter
6
State-Point Dependence and Transferability of
Potentials in Systematic Structural Coarse-Graining
................................................69
Qi Sun, Jayeeta Ghosh, and Roland
Faller
Chapter
7
Systematic Approach to Coarse-Graining of Molecular Descriptions and
Interactions with Applications to
Lipid
Membranes
..................................................83
Teemu
Murtola,
Про
Vattulainen, and
Mikko Karttunen
Chapter
8
Simulation of Protein Structure and Dynamics with the
Coarse-Grained UNRES Force Field
......................................................................107
Adam
Liwo, Cezary Czaplewski, Stanisław Ołdziej,
Ana
V.
Rojas,
Rajmund Kaźmierkiewicz, Mariusz Makowski, Rajesh K. Murarka,
and Harold
A. Scheraga
Chapter
9
Coarse-Grained
Structure-Based Simulations of Proteins and
RNA......................
123
Alexander Schug, Changbong Hyeon, and
José
N.
Onuchic
vi
Table of Contents
Chapter
10
On the Development of Coarse-Grained Protein Models: Importance of
Relative Side-Chain Orientations and Backbone Interactions
...............................141
N.-V
Buchete,
J.E. Sträub,
and
D.
Thirumalai
Chapter
11
Characterization of Protein-Folding Landscapes by
Coarse-Grained Models Incorporating Experimental Data
...................................157
Silvina Matysiak and Cecilia dementi
Chapter
12
Principles and Practicalities of Canonical Mixed-Resolution
Sampling of Biomolecules
......................................................................................171
Daniel M. Zuckerman
Chapter
13
Pathways of Conformational Transitions in Proteins
.............................................185
Peter
Májek,
Ron Elber, and
Harel
Weinstein
Chapter
14
Insights into the Sequence-Dependent Macromolecular
Properties of
DNA
from Base-Pair Level Modeling
..............................................205
Wilma
К.
Olson, Andrew V. Colasanti, Luke
Czapla,
and Guohui Zheng
Chapter
15
Coarse-Grained Models for Nucleic Acids and Large
Nucleoprotein Assemblies
......................................................................................225
Robert K.-Z. Tan, Anton S.
Petrov,
Batsal Devkota, and Stephen C. Harvey
Chapter
16
Elastic Network Models of Coarse-Grained Proteins Are Effective for
Studying the Structural Control Exerted over Their Dynamics
.............................237
Robert L. Jernigan, Lei Yang, Guang Song, Ozge Kurkcuoglu, and Pemra Doruker
Chapter
17
Coarse-Grained Elastic Normal Mode Analysis and Its Applications in
Х
-Ray Crystallographic Refinement at Moderate Resolutions
...............................255
Jianpeng Ma
Chapter
18
Coarse-Grained Normal Mode Analysis to Explore Large-Scale
Dynamics of Biological Molecules
.........................................................................267
Osamu
Miyashita and Florence
Tama
Chapter
19
One-Bead Coarse-Grained Models for Proteins
....................................................285
Valentina
Tozzini and J. Andrew McCammon
Chapter
20
Application of Residue-Based and Shape-Based Coarse-Graining to
Biomolecular Simulations
.......................................................................................299
Peter L.
Freddolino,
Amy Y. Shih, Anton Arkhipov, Ying Ying,
Zhongzhou Chen, and Klaus
Schulten
Table
of Contents
vii
Chapter
21
Coarse-Graining Protein Mechanics
......................................................................317
Richard Lavery and Sophie Sacquin-Mora
Chapter
22
Self-Assembly of Surfactants in Bulk Phases and at
Interfaces Using Coarse-Grain Models
..................................................................329
Wataru Shinoda, Russell DeVane, and Michael L. Klein
Chapter
23
Coarse-Grained Simulations of Polyelectrolytes
...................................................343
Mark J. Stevens
Chapter
24
Monte Carlo Simulations of a Coarse-Grain
Model for Block Copolymer Systems
.....................................................................361
F.A. Detcheverry, K.Ch. Daoulas, M.
Müller,
P.F.
Nealey, and
J. J.
de
Pablo
Chapter
25
Structure-Based Coarse- and Fine-Graining in
Soft Matter Simulations
..........................................................................................379
Meo
F.A. van
der
Vegt, Christine Peter, and Kurt Kremer
Chapter
26
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
Kurt Binder, Wolfgang Paul, Peter Virnau, Leonid Yelash,
Marcus
Müller,
and
Luis González MacDowell
Chapter
27
Effective Interaction Potentials for Coarse-Grained Simulations of
Polymer-Tethered Nanoparticle Self-Assembly in Solution
...................................415
Elaine R. Chan, Alberto Striolo, Clare McCabe,
Peter T. Cummings, and Sharon C.
Glotzer
Chapter
28
Coarse-Graining in Time: From Microscopies to Macroscopics
...........................433
Angela
Violi
Index
..................................................................................................................................449
|
| adam_txt |
Table
of Contents
Acknowledgments
.ix
Editor
.xi
Contributors
.xiii
Chapter
1
Introduction
.1
Gregory
A. Vot h
Chapter
2
The MARTINI Force Field
.5
Siewert J. Marrink, Marc Fuhrmans, H. Jelger
Risselada,
and
Xavier Periole
Chapter
3
The Multiscale Coarse-Graining Method:
A Systematic Approach to Coarse-Graining
.21
W. G. Noid, Gary S. Ayton, Sergei Izvekov, and Gregory A. Voth
Chapter
4
A Model for
Lipid Bilayers
in Implicit Solvent
.41
Grace Brannigan and Frank L.H. Brown
Chapter
5
Coarse-Grained Dynamics of
Anisotropie
Systems
.59
L. Paramonov, M.G. Burke, andS.N. Yaliraki
Chapter
6
State-Point Dependence and Transferability of
Potentials in Systematic Structural Coarse-Graining
.69
Qi Sun, Jayeeta Ghosh, and Roland
Faller
Chapter
7
Systematic Approach to Coarse-Graining of Molecular Descriptions and
Interactions with Applications to
Lipid
Membranes
.83
Teemu
Murtola,
Про
Vattulainen, and
Mikko Karttunen
Chapter
8
Simulation of Protein Structure and Dynamics with the
Coarse-Grained UNRES Force Field
.107
Adam
Liwo, Cezary Czaplewski, Stanisław Ołdziej,
Ana
V.
Rojas,
Rajmund Kaźmierkiewicz, Mariusz Makowski, Rajesh K. Murarka,
and Harold
A. Scheraga
Chapter
9
Coarse-Grained
Structure-Based Simulations of Proteins and
RNA.
123
Alexander Schug, Changbong Hyeon, and
José
N.
Onuchic
vi
Table of Contents
Chapter
10
On the Development of Coarse-Grained Protein Models: Importance of
Relative Side-Chain Orientations and Backbone Interactions
.141
N.-V
Buchete,
J.E. Sträub,
and
D.
Thirumalai
Chapter
11
Characterization of Protein-Folding Landscapes by
Coarse-Grained Models Incorporating Experimental Data
.157
Silvina Matysiak and Cecilia dementi
Chapter
12
Principles and Practicalities of Canonical Mixed-Resolution
Sampling of Biomolecules
.171
Daniel M. Zuckerman
Chapter
13
Pathways of Conformational Transitions in Proteins
.185
Peter
Májek,
Ron Elber, and
Harel
Weinstein
Chapter
14
Insights into the Sequence-Dependent Macromolecular
Properties of
DNA
from Base-Pair Level Modeling
.205
Wilma
К.
Olson, Andrew V. Colasanti, Luke
Czapla,
and Guohui Zheng
Chapter
15
Coarse-Grained Models for Nucleic Acids and Large
Nucleoprotein Assemblies
.225
Robert K.-Z. Tan, Anton S.
Petrov,
Batsal Devkota, and Stephen C. Harvey
Chapter
16
Elastic Network Models of Coarse-Grained Proteins Are Effective for
Studying the Structural Control Exerted over Their Dynamics
.237
Robert L. Jernigan, Lei Yang, Guang Song, Ozge Kurkcuoglu, and Pemra Doruker
Chapter
17
Coarse-Grained Elastic Normal Mode Analysis and Its Applications in
Х
-Ray Crystallographic Refinement at Moderate Resolutions
.255
Jianpeng Ma
Chapter
18
Coarse-Grained Normal Mode Analysis to Explore Large-Scale
Dynamics of Biological Molecules
.267
Osamu
Miyashita and Florence
Tama
Chapter
19
One-Bead Coarse-Grained Models for Proteins
.285
Valentina
Tozzini and J. Andrew McCammon
Chapter
20
Application of Residue-Based and Shape-Based Coarse-Graining to
Biomolecular Simulations
.299
Peter L.
Freddolino,
Amy Y. Shih, Anton Arkhipov, Ying Ying,
Zhongzhou Chen, and Klaus
Schulten
Table
of Contents
vii
Chapter
21
Coarse-Graining Protein Mechanics
.317
Richard Lavery and Sophie Sacquin-Mora
Chapter
22
Self-Assembly of Surfactants in Bulk Phases and at
Interfaces Using Coarse-Grain Models
.329
Wataru Shinoda, Russell DeVane, and Michael L. Klein
Chapter
23
Coarse-Grained Simulations of Polyelectrolytes
.343
Mark J. Stevens
Chapter
24
Monte Carlo Simulations of a Coarse-Grain
Model for Block Copolymer Systems
.361
F.A. Detcheverry, K.Ch. Daoulas, M.
Müller,
P.F.
Nealey, and
J. J.
de
Pablo
Chapter
25
Structure-Based Coarse- and Fine-Graining in
Soft Matter Simulations
.379
Meo
F.A. van
der
Vegt, Christine Peter, and Kurt Kremer
Chapter
26
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
Kurt Binder, Wolfgang Paul, Peter Virnau, Leonid Yelash,
Marcus
Müller,
and
Luis González MacDowell
Chapter
27
Effective Interaction Potentials for Coarse-Grained Simulations of
Polymer-Tethered Nanoparticle Self-Assembly in Solution
.415
Elaine R. Chan, Alberto Striolo, Clare McCabe,
Peter T. Cummings, and Sharon C.
Glotzer
Chapter
28
Coarse-Graining in Time: From Microscopies to Macroscopics
.433
Angela
Violi
Index
.449 |
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| spelling | Coarse-graining of condensed phase and biomolecular systems ed. by Gregory A. Voth Boca Raton, Fla. [u.a.] CRC Press, Taylor & Francis 2009 XVIII, 455 S., [8] Bl. zahlr. Ill. und graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biomolecules Computer simulation Computational Biology methods Computer Simulation Condensed matter Computer simulation Models, Molecular Models, Statistical Molecular Biology methods Molecular dynamics Computer simulation Molekulardynamik (DE-588)4170370-4 gnd rswk-swf Coarse graining (DE-588)4487765-1 gnd rswk-swf Biomolekül (DE-588)4135124-1 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content (DE-588)4173536-5 Patentschrift gnd-content Molekulardynamik (DE-588)4170370-4 s Biomolekül (DE-588)4135124-1 s Coarse graining (DE-588)4487765-1 s DE-604 Voth, Gregory A. edt Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016377742&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Coarse-graining of condensed phase and biomolecular systems Biomolecules Computer simulation Computational Biology methods Computer Simulation Condensed matter Computer simulation Models, Molecular Models, Statistical Molecular Biology methods Molecular dynamics Computer simulation Molekulardynamik (DE-588)4170370-4 gnd Coarse graining (DE-588)4487765-1 gnd Biomolekül (DE-588)4135124-1 gnd |
| subject_GND | (DE-588)4170370-4 (DE-588)4487765-1 (DE-588)4135124-1 (DE-588)4143413-4 (DE-588)4173536-5 |
| title | Coarse-graining of condensed phase and biomolecular systems |
| title_auth | Coarse-graining of condensed phase and biomolecular systems |
| title_exact_search | Coarse-graining of condensed phase and biomolecular systems |
| title_exact_search_txtP | Coarse-graining of condensed phase and biomolecular systems |
| title_full | Coarse-graining of condensed phase and biomolecular systems ed. by Gregory A. Voth |
| title_fullStr | Coarse-graining of condensed phase and biomolecular systems ed. by Gregory A. Voth |
| title_full_unstemmed | Coarse-graining of condensed phase and biomolecular systems ed. by Gregory A. Voth |
| title_short | Coarse-graining of condensed phase and biomolecular systems |
| title_sort | coarse graining of condensed phase and biomolecular systems |
| topic | Biomolecules Computer simulation Computational Biology methods Computer Simulation Condensed matter Computer simulation Models, Molecular Models, Statistical Molecular Biology methods Molecular dynamics Computer simulation Molekulardynamik (DE-588)4170370-4 gnd Coarse graining (DE-588)4487765-1 gnd Biomolekül (DE-588)4135124-1 gnd |
| topic_facet | Biomolecules Computer simulation Computational Biology methods Computer Simulation Condensed matter Computer simulation Models, Molecular Models, Statistical Molecular Biology methods Molecular dynamics Computer simulation Molekulardynamik Coarse graining Biomolekül Aufsatzsammlung Patentschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016377742&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT vothgregorya coarsegrainingofcondensedphaseandbiomolecularsystems |