Scientific Modeling and Simulations

Cover Page......Page 1
Title Page......Page 3
ISBN 1402097409......Page 4
Contents......Page 5
Scientific Modeling and Simulations: Advocacy of computational science (Editors’ preface)......Page 7
A retrospective on the journal of computer-aided materials design (JCAD), 1993--2007......Page 9
1 Introduction......Page 11
1.1 Superconductivity......Page 12
1.2 Low-temperature heat capacity......Page 13
1.3 Crystals modelled as stacking of atomic spheres......Page 14
2 Elastic shear instability and melting......Page 15
3 Shear constants in alloys......Page 16
4 Melting of superheated solids......Page 18
5 Theoretical strength of solids......Page 21
6 Another model---the linear chain......Page 22
7 Four types of extrapolative procedures......Page 23
References......Page 24
1 Introduction......Page 27
2.1 Waves at sea......Page 28
2.3 Terminal velocity......Page 29
2.4 Engineering science versus school physics......Page 30
4 Characteristic quantities......Page 31
5 Buckingham's Π theorem......Page 33
7.1 Gravity waves in deep water......Page 35
7.2 Small hole in a large sheet under stress......Page 36
8 The Lennard-Jones model......Page 37
9 The Lindemann melting criterion......Page 39
10 Saturating conductivities -- a still unsolved problem......Page 40
1.1 Thermal conduction in a semi-infinite medium......Page 42
2.1 Spider silk......Page 43
References......Page 44
1 Introduction......Page 47
2.1 The oil peak problem......Page 48
2.2 The entropy of TiC......Page 49
2.3 Discussion......Page 51
3.1 The CALPHAD method......Page 52
3.2 Separation of contributions to the heat capacity......Page 53
3.3 Discussion......Page 54
4.2 Thermal conduction in insulators......Page 56
5.2 Weakly inhomogeneous materials......Page 57
6.1 The vibrational heat capacity......Page 58
6.2 The electronic heat capacity......Page 59
7 Conclusions......Page 60
Sum of power laws in a log-log plot......Page 61
References......Page 62
1 Introduction......Page 65
2 Two representative examples......Page 66
3 Problems and prospects......Page 69
References......Page 70
Abstract......Page 73
2.1 Rare events and rough energy landscapes......Page 74
2.2 Diving in to rough energy landscapes of alloys, glasses, and biomolecules......Page 76
3.1 Does stiffness matter? Why ks perturbs the accessible molecular rupture forces......Page 79
3.2 Enough is enough: practical requirements of rare event sampling in MD......Page 81
4 Potential advances for chemomechanical analysis of other complex materials......Page 82
5 Summary and outlook......Page 84
References......Page 85
1 Introduction......Page 87
2 Quasi-atomic minimal-basis-sets orbitals......Page 89
3 Tight-binding matrix elements in terms of QUAMBOs......Page 92
4 Large-scale electronic calculations using the QUAMBO scheme......Page 95
5 Concluding remarks......Page 99
Acknowledgements......Page 100
References......Page 101
1 Introduction......Page 103
2.1 General formalism of tight-binding potential model......Page 104
2.2 EDTB potential model formalism......Page 105
3.1 EDTB potential for carbon......Page 107
3.2 TBMD simulation of vacancy diffusion and reconstruction in grapheme......Page 109
3.3 TBMD simulation of junction formation in carbon nanotubes......Page 112
4.1 EDTB potential for silicon......Page 114
4.2 TBMD simulation studies of addimer diffusion on Si(100) surface......Page 115
4.2.1 Diffusion between trough and the top of dimer row......Page 119
4.2.2 Diffusion along the trough between the dimmer rows......Page 121
4.3 TBMD study of dislocation core structure in Si......Page 123
Acknowledgment......Page 125
References......Page 126
1 Introduction......Page 129
2 Molecular point defects......Page 134
3 Bjerrum defect/molecular point defect interactions......Page 140
4 Summary......Page 145
References......Page 146
1 Introduction......Page 149
2 Overview of multi-scale simulations in ductile metals......Page 150
3 Mechanical experiments at small length scales......Page 151
4 Mechanical experiments on monolayer graphene......Page 153
5 Analysis of experiments......Page 157
6 Suggestions for further simulations......Page 159
7 Conclusions......Page 160
References......Page 161
Abstract......Page 165
1 Introduction......Page 166
2 Approaches to in situ studies of atomic processes under dynamic compression......Page 167
2.1.1 Laser-based systems for x-ray diffraction......Page 168
2.1.3 Computation-simulation......Page 169
3.1 Inelastic response to shock loading (1D to 3D transition)......Page 170
3.2.1 Phase transition pathways......Page 176
3.2.3 Calculated observables for the α--ε phase transition......Page 177
3.2.4 In situ, Real-time diffraction measurements during the shock......Page 179
3.2.5 The transformation mechanism......Page 180
4.1 Dynamic melt: simulation and experiment......Page 182
4.2 Damage: in situ void nucleation and growth......Page 184
5 Conclusion......Page 187
References......Page 189
1 Introduction......Page 193
2 Model and computations......Page 195
2.1 The simulation set up and its validation......Page 197
2.2 Collective variables for the local H-vacancy diffusion......Page 198
3 Methods......Page 201
3.1 Temperature accelerated molecular dynamics......Page 202
3.2 Radial basis representation of the free energy......Page 203
4.1 Local hydrogen diffusion......Page 204
4.2.1 The TAMD trajectory......Page 206
4.2.2 Radial basis reconstruction of the free energy......Page 207
4.2.3 Calculation of the activation barrier......Page 210
References......Page 211
1 Introduction......Page 213
2 What is materials design?......Page 221
2.1 Hierarchy of scales in concurrent design of materials and products......Page 222
2.2 Goals of materials design......Page 225
3.2 Challenges for top-down, inductive design......Page 227
3.3 Uncertainty in materials design......Page 228
3.4 Microstructure-mediated design......Page 231
4 Applications of materials design......Page 232
4.1 High strength and toughness steels......Page 233
4.2 Integrating advances in 3D characterization and modeling tools......Page 235
5 Educational imperatives for materials design......Page 237
6 Future prospects......Page 239
Acknowledgements......Page 241
References......Page 242
Abstract......Page 247
1 Introduction......Page 248
2 The glass transition......Page 249
3 The enthalpy landscape approach......Page 253
3.1 Potential energy landscapes......Page 254
3.2 Enthalpy landscapes......Page 257
3.3 Nonequilibrium statistical mechanics......Page 259
4 Simulation techniques......Page 260
4.1 Locating inherent structures and transition points......Page 261
4.2 Inherent structure density of states......Page 266
4.3 Master equation dynamics......Page 267
5.1 Continuously broken ergodicity and the residual entropy of glass......Page 270
5.2 Supercooled liquid fragility......Page 274
5.3 The Kauzmann paradox and the ideal glass transition......Page 276
5.4 Fictive temperature and the glassy state......Page 281
References......Page 285
1 Introduction and background......Page 289
2.1 The electro-optic effect......Page 290
2.3 Amplitude modulators......Page 291
2.3.1 Mach-Zehnder modulation with an ideal branching ratio......Page 292
2.3.2 Mach-Zehnder modulation with a non-ideal branching ratio......Page 294
2.3.3 Calculation of extinction ratio......Page 295
2.3.4 Chirp induced by Mach-Zehnder modulation......Page 296
3.1 Nonreturn-to-zero (NRZ)......Page 298
3.2 Return-to-zero (RZ)......Page 299
3.2.1 RZ with 50% duty cycle......Page 300
3.2.2 RZ with 33% duty cycle......Page 302
3.2.3 Carrier-suppressed RZ (CSRZ) with 67% duty cycle......Page 304
3.2.4 Chirped RZ (CRZ)......Page 306
3.3 Duobinary......Page 307
3.4 Modified duobinary......Page 308
3.5 Differential phase-shift keyed (DPSK)......Page 309
4 Impact on system performance......Page 312
4.1 Amplified spontaneous emission (ASE) noise......Page 314
4.2 Fiber nonlinearities......Page 315
5 Conclusions......Page 316
References......Page 317
1 Introduction......Page 319
2.1 Seismic imaging for exploration and production......Page 320
2.2 Towards inversion for reservoir properties......Page 324
2.3 Evolution to 4-D (time lapse) seismic and reservoir simulations......Page 325
2.4 Inversion of seismic and electromagnetic wavefields......Page 327
3.2 Drilling and geosteering......Page 329
3.3.1 Introduction......Page 330
3.3.2 What do we want to achieve?......Page 331
3.3.3 Porescale simulations......Page 333
4.2 Illuminating the oilfield with new sensor systems......Page 337
4.3 Computational materials......Page 338
4.3.1 High temperature polymer composites......Page 339
5 Summary......Page 340
References......Page 342
Abstract......Page 345
1 Cell mechanics and adhesion......Page 349
2 Modelling molecules inside cells......Page 353
3 Mechanical loading of single molecules......Page 356
4 Nanomechanics of living polymers......Page 359
5 Perspectives: physics, mechanics, and the multiscale modelling of biomolecules......Page 361
References......Page 365
Abstract......Page 369
1 Introduction......Page 370
2 Order parameters for connected structures......Page 373
3 Order parameter fields for disconnected subsystems......Page 375
4 Multiscale integration for enveloped virus modeling......Page 376
5 Multiscale computations and the NanoX platform......Page 380
6 Applications and conclusions......Page 382
References......Page 385
Abstract......Page 387
1 Introduction......Page 388
2 In silico brain tumor modeling: objectives & challenges......Page 389
3.1 Discrete modeling......Page 390
3.2 Continuum modeling......Page 392
4 Conclusions and perspectives......Page 394
References......Page 396
Editorial Policy......Page 400
General Remarks......Page 401
Lecture Notes in Computational Science and Engineering......Page 402
Monographs in Computational Science and Engineering......Page 404
Texts in Computational Science and Engineering......Page 405