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9783540255420

New Algorithms For Molecular Simulation

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  • ISBN13:

    9783540255420

  • ISBN10:

    3540255427

  • Format: Paperback
  • Copyright: 2006-02-28
  • Publisher: Springer-Verlag New York Inc
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Summary

Molecular simulation is a widely used tool in biology, chemistry, physics and engineering. This book contains a collection of articles by leading researchers who are developing new methods for molecular modelling and simulation. Topics addressed here include: multiscale formulations for biomolecular modelling, such as quantum-classical methods and advanced solvation techniques; protein folding methods and schemes for sampling complex landscapes; membrane simulations; free energy calculation; and techniques for improving ergodicity. The book is meant to be useful for practitioners in the simulation community and for those new to molecular simulation who require a broad introduction to the state of the art.

Table of Contents

Part I Macromolecular Models: From Theories to Effective Algorithms
Membrane Protein Simulations: Modelling a Complex Environment
3(18)
P.J. Bond
J. Cuthbertson
S.S. Deol
L.R. Forrest
J. Johnston
G. Patargias
M.S.P. Sansom
Introduction -- Membrane Proteins and Their Importance
3(2)
Membrane Protein Environments in Vivo and in Vitro
5(1)
Simulation Methods for Membranes
6(1)
Using Simulations to Explore Membrane Protein Systems
6(1)
Complex Solvents
7(3)
Detergent Micelles
10(2)
Lipid Bilayers
12(2)
Self-Assembly and Complex Systems
14(7)
References
16(5)
Modeling and Simulation Based Approaches for Investigating Allosteric Regulation in Enzymes
21(14)
M.Q. Ma
K. Sugino
Y. Wang
N. Gehani
A.V. Beuve
Introduction
21(4)
Modeling and Simulation of sGC
25(4)
Future Work
29(6)
References
31(4)
Exploring the Connection Between Synthetic and Natural RNAs in Genomes via a Novel Computational Approach
35(22)
U. Laserson
H.H. Gan
T. Schlick
Introduction: Importance of RNA Structure and Function
35(1)
Exploring the Connection between Synthetic and Natural RNAs
36(1)
Methods
37(4)
Results
41(7)
Conclusions and Future Directions
48(9)
References
53(4)
Learning to Align Sequences: A Maximum-Margin Approach
57(16)
T. Joachims
T. Galor
R. Elber
Introduction
57(1)
Sequence Alignment
58(1)
Inverse Sequence Alignment
59(1)
A Maximum-Margin Approach to Learning the Cost Parameters
60(3)
Training Algorithm
63(3)
Experiments
66(2)
Conclusions
68(5)
References
68(5)
Part II Minimization of Complex Molecular Landscapes
Overcoming Energetic and Time Scale Barriers Using the Potential Energy Surface
73(16)
D.J. Wales
J.M. Carr
T. James
Introduction
73(1)
Discrete Path Sampling
74(5)
Basin-Hopping Global Optimisation
79(10)
References
83(6)
The Protein Folding Problem
89(14)
H.A. Scheraga
A. Liwo
S. Oldziej
C. Czaplewski
J. Pillardy
J. Lee
D.R. Ripoll
J.A. Vila
R. Kazmierkiewicz
J.A. Saunders
Y.A. Arnautova
K.D. Gibson
A. Jagielska
M. Khalili
M. Chinchio
M. Nanias
Y.K. Kang
H. Schafroth
A. Ghosh
R. Elber
M. Makowski
Introduction
89(1)
Early Approaches to Structure Prediction
89(1)
Global Optimization of Crystal Structures
90(1)
All-atom Treatment of Protein A and the Villin Headpiece
91(1)
Hierarchical Approach to Predict Structures of Large Protein Molecules
91(1)
Performance in CASP Tests
92(1)
Computation of Folding Pathways
93(2)
Molecular Dynamics with the UNRES Model
95(1)
Conclusions
96(7)
References
97(6)
Part III Dynamical and Stochastic-Dynamical Foundations for Macromolecular Modelling
Biomolecular Sampling: Algorithms, Test Molecules, and Metrics
103(22)
S.S. Hampton
P. Brenner
A. Wenger
S. Chatterjee
J.A. Izaguirre
Introduction
103(2)
Sampling Algorithms
105(6)
Test Systems, Methods, and Metrics
111(3)
Simulation Results
114(5)
Discussion
119(6)
References
121(4)
Approach to Thermal Equilibrium in Biomolecular Simulation
125(16)
E. Barth
B. Leimkuhler
C. Sweet
Introduction
125(3)
Molecular Dynamics Formulation
128(2)
Thermostatting using Nose-Hoover Chains, Nose-Poincare and RMT Methods
130(7)
Conclusions
137(4)
References
139(2)
The Targeted Shadowing Hybrid Monte Carlo (TSHMC) Method
141(14)
E. Akhmatskaya
S. Reich
Introduction
141(1)
Description of the Basic HMC Method
142(1)
Stormer-Verlet Time-Stepping Method and Modified Hamiltonian
143(1)
Targeted Shadowing HMC
144(4)
Computer Experiment
148(3)
Conclusion
151(4)
References
151(4)
The Langevin Equation for Generalized Coordinates
155(12)
R.L.C. Akkermans
Introduction
155(2)
Generalized Coordinates
157(1)
Generalized Langevin Equation
158(2)
Point Transformations
160(3)
Conclusions
163(4)
References
164(3)
Metastability and Dominant Eigenvalues of Transfer Operators
167(18)
W. Huisinga
B. Schmidt
Introduction
167(2)
Markovian Molecular Dynamics
169(1)
Markov Chains, Transfer Operators, and Metastability
170(2)
Upper and Lower Bounds
172(4)
Illustrative Examples
176(4)
Outlook
180(5)
References
180(5)
Part IV Computation of the Free Energy
Free Energy Calculations in Biological Systems. How Useful Are They in Practice?
185(28)
C. Chipot
Introduction
185(1)
Methodological Background
186(8)
Free Energy Calculations and Drug Design
194(5)
Free Energy Calculations and Signal Transduction
199(2)
Free Energy Calculations and Peptide Folding
201(3)
Free Energy Calculations and Membrane Protein Association
204(2)
Conclusion
206(7)
References
207(6)
Numerical Methods for Calculating the Potential of Mean Force
213(38)
E. Darve
Introduction
213(5)
Generalized Coordinates and Lagrangian Formulation
218(5)
Derivative of the Free Energy
223(3)
Potential of Mean Constraint Force
226(7)
Adaptive Biasing Force
233(5)
Numerical Results
238(6)
Conclusion
244(7)
References
246(5)
Replica-Exchange-Based Free-Energy Methods
251(12)
C.J. Woods
M.A. King
J.W. Essex
Introduction
251(1)
Free Energy Calculations
251(2)
Hydration of Water and Methane
253(2)
Halide Binding to a Calix[4]Pyrrole Derivative
255(2)
Conclusion
257(6)
References
257(6)
Part V Fast Electrostatics and Enhanced Solvation Models
Implicit Solvent Electrostatics in Biomolecular Simulation
263(34)
N.A. Baker
D. Bashford
D.A. Case
Introduction
263(3)
Poisson-Boltzmann Methods
266(7)
Generalized Born and Related Approximations
273(5)
Applications
278(7)
Conclusions
285(12)
References
286(11)
New Distributed Multipole Methods for Accurate Electrostatics in Large-Scale Biomolecular Simulations
297(18)
C. Sagui
C. Roland
L.G. Pedersen
T.A. Darden
Introduction
297(3)
Calculations
300(2)
Results and Discussion
302(7)
Conclusion
309(6)
References
310(5)
Part VI Quantum-Chemical Models for Macromolecular Simulation
Towards Fast and Reliable Quantum Chemical Modelling of Macromolecules
315(28)
Y. Tu
A. Laaksonen
Introduction
315(2)
Extended NDDO Approximation (PART I)
317(8)
An Efficient ab initio Tight-Binding Method (PART II)
325(13)
Conclusion
338(5)
References
338(5)
Quantum Chemistry Simulations of Glycopeptide Antibiotics
343(10)
J.-G. Lee
C. Sagui
C. Roland
Introduction
343(1)
Calculations
344(1)
Results and Discussion
345(5)
Conclusion
350(3)
References
350(3)
Panel Discussion 353

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