Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 2

Contents......Page 9
Computer Simulations of Supercooled Liquids......Page 17
1. Introduction......Page 19
2. Salient Features of Glass-Forming Systems......Page 20
2.1 Theoretical Approaches......Page 27
3. Computer Simulations of Glass-Forming Liquids......Page 34
References......Page 44
Numerical Simulations of Spin Glasses: Methods and Some Recent Results......Page 47
1. Introduction......Page 49
2. Model and Theory......Page 52
3.1 Speeding Up the Dynamics......Page 53
3.2 Test for Equilibration......Page 54
3.3 Finite Size Scaling......Page 55
3.4 Evidence for a Finite Transition Temperature......Page 56
4. Absence of a Phase Transition in a Magnetic Field......Page 57
5. Conclusions......Page 59
References......Page 60
Dipolar Fluctuations in the Bulk and at Interfaces......Page 61
1. Polar Fluids: A Closed Chapter?......Page 63
2. Bulk Behaviour of Point and Extended Dipole Molecules......Page 64
3. Dipolar Fluctuations in Confined Fluids......Page 67
4. Slab Geometry......Page 70
5. Spherical Geometry......Page 72
6. Polarisation Effects......Page 74
7. Summary and Outlook......Page 76
References......Page 77
Theory and Simulation of Friction and Lubrication......Page 80
1. Introduction......Page 82
2. Theoretical Background......Page 83
2.1 Friction Mechanisms......Page 84
2.2 Velocity-Dependence of Friction......Page 87
2.3 Load-Dependence of Friction and Contact Mechanics......Page 89
2.4 Role of Interfacial Symmetry......Page 90
2.5 Common Toy Models......Page 92
3.1 Imposing Load and Shear......Page 93
3.2 Including Surface Roughness and Elastic Deformations......Page 95
3.3 Imposing Constant Temperature......Page 99
3.4 Determination of Bulk Viscosities......Page 104
4.1 Superlubricity and the Role of Roughness at the Nanometer Scale......Page 110
4.2 Physics and Chemistry of Lubricant Additives......Page 114
References......Page 116
Simulation of Nanodroplets on Solid Surfaces: Wetting, Spreading and Bridging......Page 120
1. Introduction......Page 122
2. Theoretical Model......Page 123
3. Nanodroplets on Flat Structureless Substrates......Page 124
3.2 Estimation of γωι from the Local Pressure Tensor Anisotropy......Page 126
4. Nanodroplets Adsorbed on Nanofibers......Page 127
5. Spreading of Droplets on Horizontal Surfaces......Page 129
6. Liquid Bridges and Induced Forces on Chemically Decorated Droplets with Varying Wettability......Page 132
7. Film Rupture......Page 135
8. Conclusions and Outlook......Page 138
References......Page 139
Monte Carlo Simulations of Compressible Ising Models: Do We Understand Them?......Page 142
1. Introduction......Page 144
2. Model and Method......Page 145
3. Results......Page 147
References......Page 152
Computer Simulation of Colloidal Suspensions......Page 154
1. Introduction......Page 156
2. Effective Interactions......Page 158
3. Approximative Density Functionals......Page 163
4. Charged Colloidal Dispersions......Page 164
5. Star Polymers......Page 168
6. Colloids and Polymers: Depletion Interactions......Page 170
7. Conclusions......Page 172
References......Page 173
Phase Transitions of Model Colloids in External Fields......Page 177
1. Introduction......Page 179
2.1 The Method......Page 181
2.2 Two-Dimensional Systems......Page 183
3. Melting of Hard Disks in Two Dimensions......Page 185
4.1 Model and Method......Page 189
4.2 Results and Discussion......Page 194
References......Page 200
Computer Simulation of Liquid Crystals......Page 204
1. Introduction......Page 206
1.2 Order in Nematic Phases......Page 207
1.4 Onsager Theory......Page 208
2.1 Bulk Elastic Constants......Page 209
2.2 Helical Twisting Power......Page 210
3.2 Solid Surface Anchoring......Page 212
3.3 Fluctuations in Confined Geometry......Page 213
3.4 Nematic-Isotropic Interface......Page 214
4.1 Colloidal Suspensions......Page 216
4.2 Single Spherical Macroparticle......Page 217
4.3 Two Spherical Macroparticles......Page 219
5. Conclusions......Page 220
References......Page 221
Coarse-Grained Models of Complex Fluids at Equilibrium and Under Shear......Page 224
1. Introduction......Page 226
2.1 Introduction......Page 227
2.2 Coarse-Grained Molecular Models......Page 230
2.3 Mesoscopic Membrane Models......Page 241
2.4 Summary......Page 245
3.1 Introduction......Page 246
3.2 Simulating Shear on the Particle Level: NEMD......Page 252
3.3 Simulations at the Mesoscopic Level......Page 261
4. Conclusions......Page 263
References......Page 264
Mesoscopic Simulations of Biological Membranes......Page 272
1. Introduction......Page 274
2.1 Dissipative Particle Dynamics......Page 276
2.2 Surface Tension in Lipid Bilayers......Page 277
3. Phase Behavior of Coarse-Grained Lipid Bilayers......Page 279
3.1 Single-Tail Lipid Bilayers......Page 280
3.2 Double-Tail Lipid Bilayers......Page 285
4. Perturbations of the Membrane Structure......Page 287
4.1 Effect of Alcohol......Page 288
4.2 Bilayers with Transmembrane Proteins......Page 291
5. Concluding Remarks......Page 293
References......Page 294
Microscopic Elasticity of Complex Systems......Page 300
2. Some Definitions......Page 302
3. Finite Temperature Elastic Constants: Born and Fluctuation Terms......Page 304
4. Amorphous Systems at Zero Temperature: Nonaffine Deformation......Page 305
5. Numerical Results......Page 307
6. Polymeric Systems: Stresses and Self Consistent Field Theory......Page 312
A. Expression for the Stress Tensor in SCFT......Page 317
References......Page 318
Mesoscopic Simulations for Problems with Hydrodynamics, with Emphasis on Polymer Dynamics......Page 321
1.1 Overview......Page 323
1.2 Static Scaling in Polymer Solutions......Page 325
1.3 Rouse Model......Page 327
1.4 Zimm Model......Page 332
1.5 Hydrodynamic Screening and Dynamic Crossover......Page 334
2.1 Overview......Page 335
2.2 Dissipative Particle Dynamics (DPD)......Page 338
2.3 Multi-Particle Collision Dynamics (MPCD)......Page 342
2.4 Lattice Boltzmann (LB)......Page 343
3. Some Final Remarks......Page 347
References......Page 348
Polymer Dynamics: Long Time Simulations and Topological Constraints......Page 353
1. Introduction......Page 355
2. Polymer Dynamics and Network Elasticity......Page 357
3.1 Unentangled Chains – Rouse Regime......Page 360
3.2 Entangled Chains......Page 362
4. Simulation Models, Equilibrated Melts......Page 366
4.1 Preparing an Equilibrated Melt, Specific Systems......Page 368
5.1 "Visual" Inspection of Melts and Networks......Page 372
5.2 Analysis of Chain Motion......Page 374
5.3 Structure and Property Relations: Specific Polymers......Page 378
6. Primitive Path Analysis: PPA......Page 381
References......Page 386
Reaction Kinetics of Coarse-Grained Equilibrium Polymers: A Brownian Dynamics Study......Page 391
1. Introduction......Page 393
2.1 Statistical Mechanics Derivation of the Distribution of Chain Lengths......Page 396
2.2 A Kinetic Model for Scissions and Recombinations......Page 401
3. The Mesoscopic Model and Its Brownian Dynamics Implementation......Page 404
4.1 List of Experiments and Chain Length Distributions......Page 410
4.2 Chain Length Conformational Analysis......Page 413
5. Kinetics Analysis......Page 415
5.1 Distribution of First Recombination Times......Page 416
5.2 Cumulative Hazard Analysis......Page 418
5.3 The Reactive Flux Correlation Function and the Transmission Coefficient......Page 421
5.4 Estimation of Rate Constants: Comparison of the Various Methods......Page 423
5.5 Analysis of the Monomer Diffusion......Page 424
5.6 Analysis of the First Recombination Times Distribution and Corresponding Diffusive Steps......Page 426
6. Summary and Conclusions......Page 428
References......Page 429
Equilibration and Coarse-Graining Methods for Polymers......Page 431
1. Introduction......Page 433
2. Connectivity-Altering Algorithms for the Efficient Equilibration of Polymer Melts......Page 435
3. Coarse-Graining of Polymer Models......Page 438
3.1 Iterative Boltzmann Inversion......Page 439
3.2 Coarse-Graining Using Pretabulated Potentials......Page 443
4. Chain Entanglements in Polymer Melts......Page 448
5. Topological Analysis of Atomistic Melt Configurations and Reduction to Entanglement Networks......Page 451
6. Concluding Remarks......Page 456
References......Page 458
Drug-Target Binding Investigated by Quantum Mechanical/Molecular Mechanical (QM/MM) Methods......Page 461
1. Introduction......Page 463
2.1 Non-covalent Drug-Target Interactions......Page 464
2.2 Covalent Drug-Target Interactions......Page 465
3.1 The Basic Idea......Page 466
3.3 Formalism of Hybrid Car-Parrinello QM/MM Simulations......Page 468
3.4 Possible Problems and Pitfalls......Page 476
3.5 Newest Developments and Current Limitations......Page 480
4. Covalent Drug-Target Binding: Examples......Page 481
References......Page 486
Redox Free Energies from Vertical Energy Gaps: Ab Initio Molecular Dynamics Implementation......Page 492
1. Introduction......Page 494
2.1 The Diabatic Energy Gap as Reaction Coordinate......Page 495
2.2 Reaction Free Energies......Page 498
2.3 Free Energy Perturbation Method......Page 500
2.4 Relation to Marcus Theory......Page 502
3.1 Ab Initio MD Considerations......Page 504
3.2 Parallel to Electrode Reactions......Page 506
4.1 Overview......Page 507
4.2 Two Examples: The Ru and Ag Aqua Cations......Page 508
4.3 Conclusion......Page 514
References......Page 515
Advanced Car–Parrinello Techniques: Path Integrals and Nonadiabaticity in Condensed Matter Simulations......Page 518
1. Setting the Stage: Basic Car–Parrinello Molecular Dynamics......Page 520
2.2 Dealing with Quantum Nuclei......Page 523
2.3 Dealing with Excited Electronic States......Page 533
3. Summary and Outlook......Page 545
References......Page 546
Evolutionary Design in Biological Physics and Materials Science......Page 551
1. Introduction......Page 553
1.1 The Polytopic Vaccination Experiment......Page 554
2.1 Generalized NK Model......Page 557
2.2 TCR Selection Dynamics......Page 562
4. Discussion......Page 565
References......Page 569
Monte-Carlo Methods in Studies of Protein Folding and Evolution......Page 573
1. Protein Design – Practical and Evolutionary Aspects......Page 576
2. Prebiotic Discovery of Protein Folds – Wonderfolds and All That......Page 580
3. From Coarse Grained to All-Atom Studies of Protein Folding......Page 585
3.1 Long-Time Side-Chain and Backbone Dynamics – A Glassy Story......Page 586
3.2 Analyzing Folding Nucleus at Atomic Detail......Page 587
4. Sequence or Structure: Insight from High-Resolution Simulations......Page 590
5. How Dynamically Realistic is MC? – Comparison with Discrete Molecular Dynamics Simulations......Page 591
6. Towards Realistic Transferable Sequence-Based Potentials for Folding Simulations and Protein Design......Page 592
7. Concluding Remarks......Page 595
References......Page 596
D......Page 604
L......Page 605
S......Page 606
Z......Page 607