Rugged Free Energy Landscapes : Common Computational Approaches to Spin Glasses, Structural Glasses and Biological Macromolecules

by Janke, Wolfhard

ISBN13: 9783540740254

ISBN10: 3540740252

Format: Hardcover

Pub. Date: 2008-01-03

Publisher(s): Springer Verlag

Other versions by this Author

List Price: ~~$109.00~~

Rent Textbook

Select for Price

Add to Cart

There was a problem. Please try again later.

New Textbook

We're Sorry
Sold Out

Used Textbook

We're Sorry
Sold Out

eTextbook

We're Sorry
Not Available

Buy from our Marketplace starting at $56.82

Summary

This collection of lectures and tutorial reviews by renowned experts focusses on the common computational approaches in use to unravel the static and dynamical behaviour of complex physical systems at the interface of physics, chemistry and biology. Paradigmatic examples of condensed matter physics are spin and structural glasses and protein folding, as well as their aggregation and adsorption to hard and soft surfaces, in physico-chemical biology. Among the most prominent joint key features of the systems considered in this volume are rugged free-energy landscapes. These generate metastability and are often responsible for very slow dynamics allowing for the system to be trapped in one of the many available local minima. The challenge set forth by the authors of this volume is to provide a common basis and technical language for the (computational) technology transfer between the fields and systems considered.

Rugged Free-Energy Landscapes - An Introduction	p. 1
References	p. 6
Spin Glasses
Some Aspects of Infinite-Range Models of Spin Glasses: Theory and Numerical Simulations	p. 11
Introduction	p. 12
The Sherrington-Kirkpatrick Model	p. 14
Simulations Techniques	p. 29
Finite-Size Effects for the Free Energy and the Internal Energy	p. 36
Conclusions	p. 43
References	p. 44
The Potts Glass Model: A Scenario for the Freezing Transition of Structural Glasses?	p. 47
Introduction: A Brief Survey of Experimental Facts and Theoretical Ideas on Glass Transitions	p. 47
The p-State Potts Glass and Its Properties in the Thermodynamic Limit for Infinite-Range Interactions	p. 51
Monte Carlo Results for the 10-State Mean-Field Potts Glass: Static Properties	p. 54
Finite-Size Scaling for the "Dynamic Transition" of the Potts Glass	p. 57
Monte Carlo Study of the Short-Range 10-State Potts Glass: Do all Transitions Disappear?	p. 60
Concluding Discussion: What have we Learned about Glass Transitions?	p. 62
References	p. 64
Domain Walls, Droplets and Barriers in Two-Dimensional Ising Spin Glasses	p. 67
Experimental Realizations	p. 68
Models	p. 72
Ground States of Two-Dimensional Spin Glasses	p. 76
Droplets and Domain Walls	p. 88
Energy Barriers	p. 96
References	p. 104
Local Scale-Invariance in Disordered Systems	p. 107
Introduction	p. 107
Local Scale-Invariance Without Disorder	p. 115
Disordered Ferromagnets	p. 123
Critical Ising Spin Glasses	p. 131
Discussion	p. 141
Note Added in Proof	p. 143
References	p. 143
Structural Glasses
Transport of Mobile Particles in an Immobile Environment: Computer Simulations of Sodium Silicates	p. 149
Introduction	p. 149
Model and Details of the Simulation	p. 151
The Structure of Sodium Silicates	p. 153
Channel Diffusion	p. 161
Mode-Coupling Theory	p. 165
Conclusions	p. 169
References	p. 170
The Gonihedric Ising Model and Glassiness	p. 173
(Pre-)History of the Model	p. 173
Equilibrium Behaviour, by Various Means	p. 178
Non-equilibrium Behaviour, Mostly by Monte Carlo Simulations	p. 184
Variations on the Glassy and Gonihedric Themes	p. 195
Endpiece	p. 196
References	p. 197
Protein Folding
Thermodynamics of Protein Folding from Coarse-Grained Models' Perspectives	p. 203
Introduction	p. 203
Why Coarse-Graining?	p. 206
The Hydrophobic-Polar Lattice Protein Model	p. 207
Going Off-Lattice: Folding Behavior of Heteropolymers in the AB Continuum Model	p. 234
Peptide Aggregation	p. 240
Summary	p. 242
References	p. 244
Exact Energy Landscapes of Proteins Using a Coarse-Grained Model	p. 247
Introduction	p. 247
Structural Discretization	p. 249
Fragmentation of Protein Structures	p. 251
Energy Function	p. 252
Branch and Bound	p. 256
Results	p. 258
Summary	p. 267
References	p. 267
Protein Folding, Unfolding and Aggregation Studied Using an All-Atom Model with a Simplified Interaction Potential	p. 269
Introduction	p. 269
Model and Methods	p. 271
Results	p. 274
Summary	p. 288
References	p. 289
All-Atom Simulations of Proteins	p. 293
Introduction	p. 293
Energy Landscape Paving	p. 295
Parallel Tempering	p. 297
Multicanonical Sampling	p. 301
Other Generalized-Ensemble Techniques	p. 303
Helix Versus Sheet Formation	p. 304
Structure Predictions of Small Proteins	p. 307
Conclusions	p. 312
References	p. 312
Algorithmic Developments
Markov Chain Monte Carlo Methods for Simulations of Biomolecules	p. 317
Introduction	p. 317
Markov Chain Monte Carlo	p. 318
Statistical Errors of MCMC Data	p. 326
Generalized Ensembles for MCMC Simulations	p. 332
Biased Markov Chain Monte Carlo	p. 341
Conclusions and Outlook	p. 348
References	p. 349
A Different Approach to Monte Carlo Simulations in Systems with Complex Free-Energy Landscapes	p. 353
Introduction	p. 353
Method	p. 354
Applications	p. 359
Conclusions	p. 367
References	p. 367
Generalized-Ensemble Algorithms for Protein Folding Simulations	p. 369
Introduction	p. 369
Generalized-Ensemble Algorithms	p. 372
Simulation Results	p. 396
Conclusions	p. 402
References	p. 403
Index	p. 409
Table of Contents provided by Ingram. All Rights Reserved.

Rugged Free Energy Landscapes : Common Computational Approaches to Spin Glasses, Structural Glasses and Biological Macromolecules

Rent Textbook

New Textbook

Used Textbook

eTextbook

How Marketplace Works:

Summary

Table of Contents

Digital License