Computational modeling of membrane bilayers:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2008
|
| Edition: | 1. ed. |
| Series: | Current topics in membranes
60 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXV, 466 S. Ill., graph. Darst. |
| ISBN: | 9780123738936 |
Staff View
MARC
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Record in the Search Index
| _version_ | 1804137940060733440 |
|---|---|
| adam_text | Contents
Contributors
xi
Preface
xvii
Previous Volumes in Series
xxiii
CHAPTER
1
Considerations for Lipid Force Field Development
Jeffery B. Klauda, Richard M.
Venable,
Alexander D. MacKerell and Richard
W. Pastor
I. Introduction
2
II. Quantum Mechanics and Molecular Dynamics Based
Parameter Optimization
4
III. Membrane Targets and Related Issues
20
IV. Summary and Perspectives
39
References
42
CHAPTER
2
Electrostatics in Biomolecular Simulations: Where
Are We Now and Where Are We Heading?
Mikko
Karttunen,
Jörg Rottler,
Upo
Vattulainen and Celeste Sagui
I. Introduction
50
II. Importance of Long-Range Interactions in Simulations
of Biological Systems
51
III. Overview of Methods and Their Applicability
52
IV. Non-Periodic Systems and Different Boundary
Conditions
69
V. Applications and Latest Methodological
Developments
71
VI. Final Notes on Software, Accuracy, and Speed
80
References
81
CHAPTER
3
Time and Length Scales in Lipid Bilayer Simulations
Olle Edholm
I. Introduction
91
II. Area per Lipid and Finite Size Effects
94
VI
Contents
III. Undulations
96
IV. Peristaltic Fluctuations
101
V. Hydrocarbon Chain Dynamics
104
VI. Lateral Diffusion of Lipids
105
References
107
CHAPTER
4
Molecular Dynamics Simulation of Lipid-Protein
Interactions
Nicolas Sapay and D. Peter Tieleman
I. Introduction
112
II. Force Fields
114
III. Combining Force Fields
117
IV. Sampling Concerns
123
V. Validation of Lipid-Protein Simulations
125
VI. Conclusion and Perspective
127
References
128
CHAPTER
5
Implicit Modeling of Membranes
Alan Grossfield
I. Introduction
131
II. Classes of Models
133
III. Interesting Problems in Implicit Membrane
Modeling
146
IV. Conclusion
150
References
150
CHAPTER
6
Blue Matter: Scaling of iV-Body Simulations to One
Atom per Node
Blake G. Fitch,
Aleksandr
Rayshubskiy, Maria Eleftheriou, T.J. Christopher
Ward, Mark Giampapa, Michael C. Pitman, Jed
Pitera,
William
С
Swope
and Robert S. Germain
I. Introduction
160
II. Background on Massively Parallel Biomolecular
Simulation
162
III. Inherent Concurrency of Molecular Dynamics
164
IV. Parallel Decompositions
167
V. Results
171
VI. Summary and Conclusions
177
References
178
Contents
CHAPTER
Vil
7
Multiscale
Simulation of Membranes and Membrane
Proteins: Connecting Molecular Interactions to
Mesoscopic Behavior
Gary S. Ay ton, Sergei lzvekov, W.G. Noid and Gregory A. Voth
I. Multiscale Aspects of Membrane Simulation: A Brief
Review
182
II. New Multiscale Methods for Membrane
Simulations
187
III. Selected Applications
201
IV. Summary
219
References
219
CHAPTER
8
Interactions between Small Molecules and
Lipid
Bilayers
Justin L. MacCallum and D. Peter Tieleman
Abbreviations
228
I. Introduction
228
II. Partitioning of Small Molecules in
Lipid
Bilayers
232
III. Conclusions
252
References
253
CHAPTER
9
On the Nature of
Lipid
Rafts: Insights from
Molecularly Detailed Simulations of Model Biological
Membranes Containing Mixtures of Cholesterol and
Phospholipids
Max Berkowitz
I. Introduction
257
II. Simulations
262
III. Concluding Remarks
275
References
276
CHAPTER
10
Atomistic and Mean Field Simulations of Lateral
Organization in Membranes
SagarA. Pandit, See-Wing
Chiu,
Eric
Jakobsson
and H. Larry Scott
I. Introduction
281
II. Molecular Dynamics Simulation of
Hydrated
Lipid
Bilayers
284
III. General Issues in Force
Feld
Development for
Biomolecular Simulations
285
IV. Simulation of Heterogeneous
Lipid
membranes
293
Vlil
Contents
V. Application:
A Mean Field
Based
Lipid Bilayer
Model
Based
on MD
Simulations
300
VI. Summary
308
References
309
CHAPTER
11
Molecular Modeling of the Structural Properties and
Formation of High-Density Lipoprotein Particles
Amy Y. Shih, Peter L.
Freddolino,
Anton Arkhipov, Stephen G. Sligar and
Klaus
Schulten
I. Introduction
313
II. Methods
318
III. Structure of
Discoidal
HDL
322
IV. Formation of
Discoidal
HDL
327
V. Conclusions
336
References
337
CHAPTER
12
Gas Conduction of
Lipid Bilayers
and Membrane
Channels
Yi Wang, Y. Zenmei Ohkubo and Emad Tajkhorshid
I. Introduction
344
II. Computational Methodology
346
HI. Lipid-Mediated Gas Conduction
348
IV. Protein-Mediated Gas Conduction
355
V. Concluding Remarks
362
References
363
CHAPTER
1 3
A Brief Introduction to Voltage-Gated K+ Channels
Benoît Roux
I. Introduction
369
II. Structure of Kv Channels and Gating Mechanisms
III. Free Energy and Membrane Voltage
379
IV. Conclusion
382
References
383
370
CHAPTER
14
Computational Models for Electrified Interfaces
Elizabeth J. Denning and Thomas B,
Woolf
I. Introduction
385
И.
General Concepts of Surface Charge and Co/Counter
Ions
386
III. Continuum Models
387
Contents ix
IV. Bridging from the Continuum to Molecular
Calculations
389
V. All-Atom Models
393
VI.
Long-Term
Trends
397
VII.
Summary
400
References
400
CHAPTER
15
Charged Protein Side Chain Movement in
Lipid
Bilayers Explored with Free Energy Simulation
Libo
Li, Igor Vorobyov, Sudha Dorairaj and Toby W. Allen
I. Introduction
406
II. Theoretical Perspectives
409
III. Experimental Hydrophobicity and Membrane
Partitioning Models
411
IV. Fully Atomistic Computer Simulations
415
V. Reconciling Simulation and Experiment
441
VI. Conclusion and Implications
448
References
453
Index
461
|
| adam_txt |
Contents
Contributors
xi
Preface
xvii
Previous Volumes in Series
xxiii
CHAPTER
1
Considerations for Lipid Force Field Development
Jeffery B. Klauda, Richard M.
Venable,
Alexander D. MacKerell and Richard
W. Pastor
I. Introduction
2
II. Quantum Mechanics and Molecular Dynamics Based
Parameter Optimization
4
III. Membrane Targets and Related Issues
20
IV. Summary and Perspectives
39
References
42
CHAPTER
2
Electrostatics in Biomolecular Simulations: Where
Are We Now and Where Are We Heading?
Mikko
Karttunen,
Jörg Rottler,
Upo
Vattulainen and Celeste Sagui
I. Introduction
50
II. Importance of Long-Range Interactions in Simulations
of Biological Systems
51
III. Overview of Methods and Their Applicability
52
IV. Non-Periodic Systems and Different Boundary
Conditions
69
V. Applications and Latest Methodological
Developments
71
VI. Final Notes on Software, Accuracy, and Speed
80
References
81
CHAPTER
3
Time and Length Scales in Lipid Bilayer Simulations
Olle Edholm
I. Introduction
91
II. Area per Lipid and Finite Size Effects
94
VI
Contents
III. Undulations
96
IV. Peristaltic Fluctuations
101
V. Hydrocarbon Chain Dynamics
104
VI. Lateral Diffusion of Lipids
105
References
107
CHAPTER
4
Molecular Dynamics Simulation of Lipid-Protein
Interactions
Nicolas Sapay and D. Peter Tieleman
I. Introduction
112
II. Force Fields
114
III. Combining Force Fields
117
IV. Sampling Concerns
123
V. Validation of Lipid-Protein Simulations
125
VI. Conclusion and Perspective
127
References
128
CHAPTER
5
Implicit Modeling of Membranes
Alan Grossfield
I. Introduction
131
II. Classes of Models
133
III. Interesting Problems in Implicit Membrane
Modeling
146
IV. Conclusion
150
References
150
CHAPTER
6
Blue Matter: Scaling of iV-Body Simulations to One
Atom per Node
Blake G. Fitch,
Aleksandr
Rayshubskiy, Maria Eleftheriou, T.J. Christopher
Ward, Mark Giampapa, Michael C. Pitman, Jed
Pitera,
William
С
Swope
and Robert S. Germain
I. Introduction
160
II. Background on Massively Parallel Biomolecular
Simulation
162
III. Inherent Concurrency of Molecular Dynamics
164
IV. Parallel Decompositions
167
V. Results
171
VI. Summary and Conclusions
177
References
178
Contents
CHAPTER
Vil
7
Multiscale
Simulation of Membranes and Membrane
Proteins: Connecting Molecular Interactions to
Mesoscopic Behavior
Gary S. Ay ton, Sergei lzvekov, W.G. Noid and Gregory A. Voth
I. Multiscale Aspects of Membrane Simulation: A Brief
Review
182
II. New Multiscale Methods for Membrane
Simulations
187
III. Selected Applications
201
IV. Summary
219
References
219
CHAPTER
8
Interactions between Small Molecules and
Lipid
Bilayers
Justin L. MacCallum and D. Peter Tieleman
Abbreviations
228
I. Introduction
228
II. Partitioning of Small Molecules in
Lipid
Bilayers
232
III. Conclusions
252
References
253
CHAPTER
9
On the Nature of
Lipid
Rafts: Insights from
Molecularly Detailed Simulations of Model Biological
Membranes Containing Mixtures of Cholesterol and
Phospholipids
Max Berkowitz
I. Introduction
257
II. Simulations
262
III. Concluding Remarks
275
References
276
CHAPTER
10
Atomistic and Mean Field Simulations of Lateral
Organization in Membranes
SagarA. Pandit, See-Wing
Chiu,
Eric
Jakobsson
and H. Larry Scott
I. Introduction
281
II. Molecular Dynamics Simulation of
Hydrated
Lipid
Bilayers
284
III. General Issues in Force
Feld
Development for
Biomolecular Simulations
285
IV. Simulation of Heterogeneous
Lipid
membranes
293
Vlil
Contents
V. Application:
A Mean Field
Based
Lipid Bilayer
Model
Based
on MD
Simulations
300
VI. Summary
308
References
309
CHAPTER
11
Molecular Modeling of the Structural Properties and
Formation of High-Density Lipoprotein Particles
Amy Y. Shih, Peter L.
Freddolino,
Anton Arkhipov, Stephen G. Sligar and
Klaus
Schulten
I. Introduction
313
II. Methods
318
III. Structure of
Discoidal
HDL
322
IV. Formation of
Discoidal
HDL
327
V. Conclusions
336
References
337
CHAPTER
12
Gas Conduction of
Lipid Bilayers
and Membrane
Channels
Yi Wang, Y. Zenmei Ohkubo and Emad Tajkhorshid
I. Introduction
344
II. Computational Methodology
346
HI. Lipid-Mediated Gas Conduction
348
IV. Protein-Mediated Gas Conduction
355
V. Concluding Remarks
362
References
363
CHAPTER
1 3
A Brief Introduction to Voltage-Gated K+ Channels
Benoît Roux
I. Introduction
369
II. Structure of Kv Channels and Gating Mechanisms
III. Free Energy and Membrane Voltage
379
IV. Conclusion
382
References
383
370
CHAPTER
14
Computational Models for Electrified Interfaces
Elizabeth J. Denning and Thomas B,
Woolf
I. Introduction
385
И.
General Concepts of Surface Charge and Co/Counter
Ions
386
III. Continuum Models
387
Contents ix
IV. Bridging from the Continuum to Molecular
Calculations
389
V. All-Atom Models
393
VI.
Long-Term
Trends
397
VII.
Summary
400
References
400
CHAPTER
15
Charged Protein Side Chain Movement in
Lipid
Bilayers Explored with Free Energy Simulation
Libo
Li, Igor Vorobyov, Sudha Dorairaj and Toby W. Allen
I. Introduction
406
II. Theoretical Perspectives
409
III. Experimental Hydrophobicity and Membrane
Partitioning Models
411
IV. Fully Atomistic Computer Simulations
415
V. Reconciling Simulation and Experiment
441
VI. Conclusion and Implications
448
References
453
Index
461 |
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| index_date | 2024-07-02T21:45:41Z |
| indexdate | 2024-07-09T21:20:16Z |
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| series2 | Current topics in membranes |
| spelling | Computational modeling of membrane bilayers ed. by Scott E. Feller 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2008 XXV, 466 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Current topics in membranes 60 Bilayer lipid membranes Computer simulation Membranlipide (DE-588)4203814-5 gnd rswk-swf Computersimulation (DE-588)4148259-1 gnd rswk-swf Doppelschicht (DE-588)4150451-3 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Membranlipide (DE-588)4203814-5 s Doppelschicht (DE-588)4150451-3 s Computersimulation (DE-588)4148259-1 s DE-604 Feller, Scott Edward Sonstige oth Current topics in membranes 60 (DE-604)BV036839511 60 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016685793&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Computational modeling of membrane bilayers Current topics in membranes Bilayer lipid membranes Computer simulation Membranlipide (DE-588)4203814-5 gnd Computersimulation (DE-588)4148259-1 gnd Doppelschicht (DE-588)4150451-3 gnd |
| subject_GND | (DE-588)4203814-5 (DE-588)4148259-1 (DE-588)4150451-3 (DE-588)4143413-4 |
| title | Computational modeling of membrane bilayers |
| title_auth | Computational modeling of membrane bilayers |
| title_exact_search | Computational modeling of membrane bilayers |
| title_exact_search_txtP | Computational modeling of membrane bilayers |
| title_full | Computational modeling of membrane bilayers ed. by Scott E. Feller |
| title_fullStr | Computational modeling of membrane bilayers ed. by Scott E. Feller |
| title_full_unstemmed | Computational modeling of membrane bilayers ed. by Scott E. Feller |
| title_short | Computational modeling of membrane bilayers |
| title_sort | computational modeling of membrane bilayers |
| topic | Bilayer lipid membranes Computer simulation Membranlipide (DE-588)4203814-5 gnd Computersimulation (DE-588)4148259-1 gnd Doppelschicht (DE-588)4150451-3 gnd |
| topic_facet | Bilayer lipid membranes Computer simulation Membranlipide Computersimulation Doppelschicht Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016685793&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV036839511 |
| work_keys_str_mv | AT fellerscottedward computationalmodelingofmembranebilayers |