Computer Simulation of Polymeric Materials (eBook)

The Japan Association for Chemical Innovation (JACI), a public interest incorporated association, is composed of members from the chemical industry, user industries, academia, and leading national research institutions in Japan. This public interest corporation carries out activities with the aim of promoting various projects with highly public nature concerning chemical technology innovation.

Preface 5
Contents 7
Part I Introduction of Computer Simulation of Polymeric Materials 10
1 Expected Target of Polymer Simulation 11
2 Coarse-Grained Simulation 13
2.1 Coarse-Graining of Polymers 13
2.2 Examples of Coarse-Grained Molecular Models 14
2.2.1 United Atom Model 14
2.2.2 Rigid-Body Model 15
2.2.3 Bead–Spring Model 16
2.2.4 Ideal Chain Model 17
2.2.5 Slip-Link Model 17
2.3 Relation Between Coarse-Grained Models and Real Polymer Chains 18
2.3.1 Coarse-Graining from Chemical Structures 18
2.3.2 Mapping Using the Scaling Concept 19
References 20
Part II OCTA: Mesoscale Polymer Simulation System 21
3 Overview of OCTA 22
3.1 What is OCTA? 22
3.2 UDF File and Python 25
3.3 Action Mechanism 28
3.4 Unit Conversion 29
3.5 3D Graphics and the Select Mechanism 30
3.6 Record and Animation 32
3.7 Closing Remarks 34
4 COGNAC: Coarse-Grained Molecular Dynamics Simulator 35
4.1 What Is COGNAC? 35
4.2 Potential Functions 35
4.2.1 Bond-Stretching Potential Functions 36
4.2.2 Angle Bending Potential Functions 37
4.2.3 Torsion Potential Functions 37
4.2.4 Nonbonding Potential Functions 37
4.2.5 External Potential Functions 38
4.2.6 Electrostatic Interaction 38
4.3 Equations of Motion 38
4.4 Ensembles 39
4.4.1 Temperature Control 39
4.4.2 Pressure/Stress Control 40
4.5 Boundary Conditions 40
4.6 Generation of Initial Coordinates 41
4.7 SILK 42
4.8 Extended Functions to Study Polymeric Materials 42
4.8.1 Deformation 42
4.8.2 Bond Formation and Breakage 43
4.8.3 Zooming 44
4.8.4 Data Conversion 45
4.9 Output Information 46
4.10 Analysis of Results 46
4.11 Total Flow of COGNAC Execution 50
4.11.1 Step 1: Generation of a COGNAC Input UDF File 51
4.11.2 Step 2: Editing of Simulation Conditions 52
4.11.3 Step 3: Execution of COGNAC 52
4.11.4 Step 4: Visualization and Analysis 53
4.12 Example: Study of the Molecular Shape and Size of a Polymer 53
4.12.1 Step 1: Generation of COGNAC Input UDF File Using Action SILK 53
4.12.2 Step 1': Generation of a COGNAC Input UDF File Using SILK Script 57
4.12.3 Step 2: Editing of Simulation Conditions 58
4.12.4 Step 3: Execution of COGNAC 62
4.12.5 Step 4: Visualization and Analysis of the Simulation Results 63
Visualization of Molecular Structure 63
Calculation of < R2>
Pair Distribution Function 66
Autocorrelation Function of Normal Coordinates 68
4.13 Download Instruction 70
References 70
5 SUSHI: Density Functional Theory Simulator 72
5.1 Introduction 72
5.2 Overview of DFT for Polymer Blends 73
5.3 Flory–Huggins Free Energy Model 74
5.4 Phenomenological Flory–Huggins Free Energy Model 74
5.5 Gaussian Chain Model 76
5.6 Linear SCF Theory with RPA 78
5.6.1 Application of the RPA to a Polymer Blend 79
5.7 Ginzburg–Landau Theory 79
5.8 Flory–Huggins–de Gennes Model 80
5.9 Combination of Ginzburg–Landau Theory and the RPA 81
5.10 SCF Theory 81
5.10.1 Path Integral 82
5.10.2 Calculation of Segment Density 83
Canonical Ensemble 83
Grand Canonical Ensemble 84
5.10.3 Free Energy 84
5.10.4 Practical Method of Calculating the Path Integral 84
5.10.5 SCF Calculation 85
5.11 Hydrodynamics Effect 86
5.11.1 Coupling with the Navier–Stokes Equation 86
5.12 Example: Phase Diagram Generated with the Flory–Huggins Free Energy Model 87
5.12.1 Critical Point 88
5.12.2 Spinodal Points 88
5.12.3 Binodal Points 89
5.12.4 Tool for the Flory–Huggins Phase Diagram 90
5.13 Example: Estimation of the Critical Point of Spinodal Decomposition of a Diblock Copolymer 91
5.14 Example: Estimation of ? Parameters 93
5.15 Example: Macrophase Separation and Microphase Separation 96
5.15.1 Macrophase Separation (Static SCF Calculation) 96
5.15.2 Microphase Separation (Dynamic SCF Method) 98
5.16 Example: Microphase Separated Structures of Diblock Copolymers 100
5.16.1 Lamellar Structure 101
5.16.2 Cylinder Structure 101
5.16.3 BCC Sphere Structure 101
5.16.4 Gyroid Structure 102
5.16.5 Fddd Structure 102
5.16.6 Phase Diagram of Microphase Separation of Diblock Copolymers Generated by SUSHI 102
5.17 Conclusion 103
5.18 Download Instruction 104
References 104
6 PASTA and NAPLES: Rheology Simulator 106
6.1 Introduction 106
6.2 Model 108
6.2.1 Slip-Link Model 108
6.2.2 Slip-Link Model for PASTA 109
6.2.3 Slip-Link Model for NAPLES 111
6.2.4 Stress Tensor 112
6.3 Model Parameters 113
6.3.1 Overview 113
6.3.2 Molecular Weight 113
6.3.3 Unit Modulus 114
6.3.4 Unit Time 116
6.4 Example 1: Calculation of Linear Viscoelasticity and Determination of Unit Time 117
6.4.1 Overview 117
6.4.2 Input UDF File for PASTA 117
6.4.3 Running PASTA 119
6.4.4 Analysis of the Output UDF File for PASTA 121
6.4.5 Input UDF File for NAPLES 124
6.4.6 Running NAPLES 126
6.4.7 Analysis of the Output File for NAPLES 127
6.5 Example 2: Calculation of Nonlinear Viscoelasticity Under Fast Flow 128
6.5.1 Overview 128
6.5.2 Input UDF file 129
6.5.3 NAPLES Simulation 129
6.5.4 Data Processing 130
6.6 Download Instruction 131
References 131
7 MUFFIN: Multiphase Simulator 133
7.1 Introduction 133
7.1.1 Multi-fluid Phase Dynamics Simulator 134
7.1.2 Electrolyte Fluid Dynamics Simulator 135
7.1.3 Micro Electrochemical Fluidics Chip Simulator 135
7.1.4 Multiphase Elasticity Simulator 136
7.1.5 Gel Dynamics Simulator 136
7.1.6 Light Transmittance Simulator 138
7.1.7 Mesh Generator 138
7.2 Theoretical Background 139
7.2.1 Multi-fluid Phase Dynamics Simulator 139
7.2.2 Multiphase Elasticity Simulator 140
7.3 Tutorial 142
7.3.1 Multi-fluid Phase Dynamics Simulator 142
7.3.2 Multiphase Elasticity Simulator 144
Appendix 151
References 151
8 KAPSEL: Colloidal Dispersion Simulator 152
8.1 What Is KAPSEL? 152
8.2 KAPSEL Installation and Basic Operations 154
8.2.1 OCTA Installation 154
8.2.2 KAPSEL Installation 155
8.2.3 Analysis with GOURMET 156
8.2.4 Analysis Without GOURMET 156
8.2.5 Sample Simulations 158
8.3 Dynamics of Particle Dispersions 160
8.3.1 Basic Equations 160
8.3.2 A Note on the Units 162
8.3.3 Particle Types 162
8.3.4 Input UDF File 163
8.4 Electrophoresis of Charged Colloidal Particles 165
8.4.1 Basic Equations 165
8.4.2 Electric Double-Layer Properties 167
8.4.3 UDF Description 169
References 170
Part III Examples of the Application of OCTA 171
9 Melt Viscoelasticity 172
9.1 Introduction 172
9.2 Calculation Model 173
9.3 Calculation of Stress Relaxation by COGNAC 173
9.4 Creation of the Initial Structure 174
9.5 Start of Simulation 174
9.6 Output and Plotting of Simulation Results 174
9.7 Analysis of Simulation Results 175
9.8 Concluding Remarks 178
9.9 Download Instruction 178
References 178
10 Crystallization of Polymers 179
10.1 Introduction 179
10.2 Molecular Models and Simulation Conditions 180
10.3 Results of Simulations 181
10.3.1 Chain-Folded Crystallization of a Single Molecule 181
10.3.2 Crystallization from a Highly Stretched Melt 184
10.3.3 Crystal Growth of the Chain-Folded Lamellae 186
10.4 Conclusions and Comments 188
10.5 Download Instruction 188
References 188
11 Polymer Blends: Bulk Property 189
11.1 Introduction 189
11.2 Method of Generating the Bulk Structure 190
11.3 Calculation of the Morphology with SUSHI 190
11.4 Procedure for Calculating Bulk Physical Properties 191
11.5 Display of Calculation Results 195
11.6 Concluding Remarks 196
11.7 Download Instruction 197
References 199
12 Polymer Blends: Interfacial Strength 200
12.1 Introduction 200
12.2 Calculation Model 201
12.3 Calculation Results 204
12.4 Conclusion 207
12.5 Download Instruction 208
References 209
13 Composites: Morphology 210
13.1 Introduction 210
13.2 Modeling 210
13.3 Results and Discussion 212
13.4 Application 216
13.5 Conclusion 216
13.6 Download Instruction 217
References 218
14 Composites: Interfacial Strength 219
14.1 Introduction 219
14.2 Simulation Conditions 219
14.3 Results and Discussion 223
14.4 Conclusion 225
14.5 Download Instruction 226
References 226
15 Cross-Linked Rubber 227
15.1 Introduction 227
15.2 Formation of Cross-Linked Structures 228
15.2.1 Formation Method 228
15.2.2 Procedure for Creating a Cross-Linked Structure 229
15.2.3 Creation of an Input UDF File 230
15.2.4 Calculation of Equilibration (1) 232
15.2.5 Calculation of the Cross-Linking Reaction 233
15.2.6 Calculation of Equilibration (2) 236
15.3 Elongational Physical Properties 237
15.3.1 Calculation of Elongational Deformation 237
15.3.2 Observation of the Deformed State 239
15.3.3 Calculation of the Stress–Strain Property 239
15.3.4 Example of Calculating the Elongational Physical Property (1): Method Using Cross-Linking Particles 241
15.3.5 Example of Calculating the Elongational Physical Property (2): Method for end Cross-Linking 244
15.4 Download Instruction 246
References 246
16 Thermoplastic Elastomers 247
16.1 Introduction 247
16.2 Initial Structure Preparation 248
16.2.1 Selection of a Calculation Model 249
16.2.2 Generation of BCC Structure 249
16.2.3 Setup for Zooming 253
16.2.4 Setup for Simulation Conditions of COGNAC 255
16.2.5 COGNAC Execution 257
16.3 Elongational Properties 258
16.3.1 Setup for Elongational Deformation 259
16.3.2 Preparation of the Initial Structure 260
16.3.3 Performing Uniaxial Elongation 261
16.3.4 Analyzing Results 261
16.4 Download Instruction 265
References 265
17 Filler-Filled Rubbers 266
17.1 Introduction 266
17.2 Filler Dispersion Structure 267
17.2.1 Calculation Model 267
17.2.2 Tips in Creating Input Data 268
17.2.3 Analysis of Output Data 270
17.2.4 Analysis of Results: Dispersion Structure 270
17.3 Elongational Properties 272
17.3.1 Calculation Model 272
17.3.2 Tips in Creating Input Data 273
17.3.3 Analysis of Output Data 275
17.3.4 Analysis of Results: Analysis of Stress–Strain Curves 275
17.4 Download Instruction 277
References 278
18 Structures of the Surface and Interface 279
18.1 Experimental Methods for the Estimation of Surface and Interface Structures of Polymers and the Simulation 279
18.2 The Distribution of Polymer Ends at the Surface of a Thin Film 280
18.3 Summary 285
18.4 Download Instruction 285
References 285
19 Glass Transition at the Surface and Interface 286
19.1 Introduction 286
19.2 Calculation Model 287
19.3 Tips in Creating Input Data 287
19.4 Analysis of Results: Glass Transition Temperatures of the Thin Film, Surface, and Interface 289
19.5 Download Instruction 291
References 291
20 Evaporation from Polymer Solution 292
20.1 Introduction 292
20.2 Calculation Model 293
20.3 Tips in Creating Input Data 294
20.4 Analysis of Output Data 294
20.5 Analysis of Results: Structural Analysis of Solvent Evaporation 295
20.6 Download Instruction 299
References 299
21 Crystallization in Thin Films of N-Alkanes 300
21.1 Introduction 300
21.2 Molecular Models and Simulation Conditions 301
21.3 Results of Simulations 303
21.3.1 Thin-Film Crystallization of C11 on the Flat Wall 303
21.3.2 Crystallization of C19 on Atomic Walls: The Effect of Commensuration on the Structure of the Film 304
21.4 Conclusions and Remarks 306
21.5 Download Instruction 308
References 308
22 Improvement of Adhesive Properties Through the Segregation of Oligomers and an Investigation of the Mechanism Using SUSHI Simulation 309
22.1 Introduction 309
22.2 Development Flow 310
22.2.1 Estimation of the Bubble Generation Mechanism 310
22.2.2 Investigation of Oligomers 311
22.2.3 Segregation of Oligomers into the Interface 312
22.3 Investigation of the Bubbling Suppression Mechanism Using SUSHI Simulation 313
22.3.1 Setting of the Interaction Parameter ? in Accordance with Experimental Results 314
22.3.2 Simulation Conditions for SUSHI 315
22.3.3 Simulation Results for OL-2 (?AB = 0.3) 316
22.3.4 Consistency with XPS Results 316
22.3.5 Local Tg Near the Interface 317
22.3.6 Summary of the Simulation 318
22.4 Conclusions 319
23 Adsorption of Polyelectrolytes 320
23.1 Introduction 320
23.2 Method and Model Used by van de Steeg et al. 320
23.3 System Modeling Using SUSHI 321
23.4 Determination of SUSHI Parameters 322
23.5 Calculation and Analysis 324
23.6 Comparison of Calculation Results 325
23.6.1 Effect of Segment Charge 326
23.6.2 Effect of the Concentration of Added Salt 327
23.7 Concluding Remarks 328
23.8 Download Instruction 328
References 328
24 Adsorbed Structures and Surface Forces 329
24.1 Introduction 329
24.2 Background and Purpose of the Example Analysis 330
24.3 Method for Modeling the Adsorbed Structure 330
24.4 Calculation Conditions 331
24.4.1 Structure of Comb Block Chains 331
24.4.2 Adsorbed Structure Models 331
24.4.3 Adsorbed (Grafted) Amount 332
24.4.4 System Conditions 333
24.5 Method for Analyzing the Calculation Results (Generation of the Force Curve) 333
24.6 Results and Discussion 334
24.6.1 Concentration Distribution 334
24.6.2 Force Curve 335
24.6.3 Effect of the Adsorbed Amount 335
24.7 Conclusions 337
24.8 Download Instruction 337
Reference 337
25 Analysis of Relaxation Mechanism of Thread-LikeMicelle Solution 338
25.1 Introduction 338
25.2 Viscoelastic Behavior of the Thread-Like Micellar System 339
25.3 Dissipative Particle Dynamics (DPD) Model of the Thread-Like Micelle 340
25.4 Simulation of the Crossing Dynamics 342
25.5 Results and Discussion 343
25.6 Conclusions 345
25.7 OCTA Example Run 345
25.8 Download Instruction 348
References 349
26 Vesicle Formation 350
26.1 Introduction 350
26.2 DPD Model for Amphiphiles 351
26.3 Simulation Conditions 352
26.4 Results and Discussion 353
26.5 Conclusions 357
26.6 OCTA Example Run 357
26.7 Download Instruction 359
References 359
27 Electrolyte Membranes 360
27.1 Introduction 360
27.2 Method 361
27.3 Results and Discussion 363
27.4 Conclusion 364
27.5 OCTA Example Run 365
27.6 Calculation of Parameters 367
27.7 Download Instruction 368
References 368
28 Orientation Birefringence 369
28.1 Introduction 369
28.2 Method of Calculating Orientation Birefringence 370
28.3 Input Data 371
28.4 Output Data 372
28.5 Results and Discussion 376
28.6 Download Instruction 376
References 377
29 Lithography 378
29.1 Introduction 378
29.2 Calculation Model 379
29.3 Tips in Creating Input Data 380
29.4 Analysis of Output Data 382
29.5 Analysis of Results: Structural Analysis of Solvent Evaporation 382
29.6 Download Instruction 384
References 385
Erratum 386
Index 388