Self-assembling systems : theory and simulation

385 Pages·2016·24.657 MB·English

by  Yan, Li-Tang

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Self-AssemblingSystems
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Self-Assembling Systems
TheoryandSimulation
Editedby
Li-TangYan
DepartmentofChemicalEngineering,
(cid:2) TsinghuaUniversity,China (cid:2)
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Thiseditionfirstpublished2017
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LibraryofCongressCataloging-in-PublicationData
Names:Yan,Li-Tang,1978–
Title:Self-assemblingsystems:theoryandsimulation/Li-TangYan.
Description:Chichester,WestSussex:JohnWiley&Sons,Inc.,2016.|
Includesbibliographicalreferencesandindex.
Identifiers:LCCN2016024926(print)|LCCN2016028669(ebook)|ISBN
9781119113140(cloth)|ISBN9781119113157(pdf)|ISBN9781119113164
(epub)
Subjects:LCSH:Self-assembly(Chemistry)|Colloidalcrystals.|Polymers.
Classification:LCCQD475.Y362016(print)|LCCQD475(ebook)|DDC
547/.2–dc23
LCrecordavailableathttps://lccn.loc.gov/2016024926
AcataloguerecordforthisbookisavailablefromtheBritishLibrary.
Setin10/12ptWarnockProbySPiGlobal,Chennai,India
10987654321
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v
Contents
ListofContributors xiii
Preface xvii
1 TheoreticalStudiesandTailoredComputerSimulationsin
Self-AssemblingSystems:AGeneralAspect 1
ZihanHuangandLi-TangYan
1.1 Introduction 1
1.2 EmergingSelf-AssemblingPrinciples 3
1.2.1 PredictiveScienceandRationalDesignofComplexBuildingBlocks 3
1.2.2 Entropy-DrivenOrderingandSelf-Assembly 5
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1.2.3 ProgrammableSelf-Assembly 10
1.2.4 Self-AssemblingKinetics:SupracolloidalReaction 14
Acknowledgments 16
References 16
2 DevelopingHybridModelingMethodstoSimulateSelf-Assemblyin
PolymerNanocomposites 20
XinYong,StephenC.Snow,OlgaKuksenokandAnnaC.Balazs
2.1 Introduction 20
2.2 Methodology 21
2.2.1 DissipativeParticleDynamics 21
2.2.2 PolymerChains,Gels,andNanoparticles 22
2.2.3 RadicalPolymerizationModel 24
2.3 ResultsandDiscussions 27
2.3.1 ModelingBulkPolymerizationUsingFRPandATRP 27
2.3.2 ModelingRegenerationofSeveredPolymerGelswithInterfaciallyActive
Nanorods 32
2.3.3 ModelingtheFormationofPolymer–ClayCompositeGels 43
2.4 Conclusions 47
Acknowledgments 48
References 49
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vi Contents
3 TheoryandSimulationStudiesofSelf-AssemblyofHelical
Particles 53
GiorgioCinacchi,AlbertaFerrarini,ElisaFrezza,AchilleGiacomettiand
HimaBinduKolli
3.1 Introduction:WhyHardHelices? 53
3.2 LiquidCrystalPhases 55
3.3 HardHelices:AMinimalModel 56
3.4 NumericalSimulations 57
3.4.1 MonteCarloinVariousEnsembles 57
3.4.1.1 CanonicalMonteCarlosimulations(NVT–MC) 59
3.4.1.2 Isothermal–IsobaricMonteCarloSimulations(NPT–MC) 59
3.4.2 DetailsontheMCSimulationofHardHelices 59
3.5 Onsager(DensityFunctional)Theory 61
3.6 Onsager-LikeTheoryfortheCholestericandScrew-NematicPhases 64
3.7 OrderParametersandCorrelationFunctions 67
3.7.1 NematicOrderParameter⟨P ⟩ 68
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3.7.2 Screw-LikeNematicOrderParameter 68
3.7.3 SmecticOrderParameter 70
3.7.4 HexaticOrderParameter 70
3.7.5 ParallelandPerpendicularPairCorrelationFunctions 71
3.8 ThePhysicalOriginofCholestericandScrew-LikeOrder 73
3.9 ThePhaseDiagramofHardHelices 74
(cid:2) 3.9.1 TheEquationofState 75 (cid:2)
3.9.2 PhaseDiagramsintheVolumeFraction–PitchPlane 76
3.9.2.1 PhaseDiagramforr =0.1 77
3.9.2.2 PhaseDiagramforr =0.2 78
3.9.2.3 PhaseDiagramforr =0.4 79
3.10 Helical(Bio)PolymersandColloidalParticles 79
3.11 ConclusionsandPerspectives 81
Acknowledgments 82
References 82
4 Self-ConsistentFieldTheoryofSelf-AssemblingMultiblock
Copolymers 85
WeihuaLiandAn-ChangShi
4.1 Introduction 85
4.2 TheoreticalFramework:Self-ConsistentFieldTheoryofBlock
Copolymers 88
4.3 NumericalMethodsofSCFT 90
4.3.1 Reciprocal-SpaceMethod 90
4.3.2 Real-SpaceMethod 93
4.3.3 Pseudo-SpectralMethod 95
4.3.4 Fourth-OrderPseudo-SpectralMethod 98
4.4 ApplicationofSCFTtoMultiblockCopolymers 98
4.5 ConclusionsandDiscussions 104
Acknowledgments 107
References 107
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Contents vii
5 SimulationModelsofSoftJanusandPatchyParticles 109
Zhan-WeiLi,Zhao-YanSunandZhong-YuanLu
5.1 Introduction 109
5.2 SoftJanusParticleModels 111
5.2.1 SoftOne-PatchJanusParticleModel 111
5.2.2 SoftABA-TypeTriblockJanusParticleModel 113
5.2.3 SoftBAB-TypeTriblockJanusParticleModel 114
5.2.4 IntegrationAlgorithm 116
5.3 SoftPatchyParticleModels 117
5.3.1 TheModel 117
5.3.2 IntegrationAlgorithm 118
5.4 PhysicalMeaningsoftheSimulationParametersinOurModels 121
5.5 GPUAcceleration 121
5.6 Self-AssemblyofSoftJanusandPatchyParticles 122
5.6.1 Self-AssemblyofSoftOne-PatchJanusParticles 122
5.6.2 TheRoleofParticleSoftnessinSelf-AssemblingDifferentSupracolloidal
Helices 123
5.6.3 Self-AssemblyofSoftABA-TypeTriblockJanusParticles 124
5.6.4 Template-FreeFabricationofTwo-DimensionalExoticNanostructures
throughtheSelf-AssemblyofSoftBAB-TypeTriblockJanusParticles 125
5.6.5 Self-AssemblyofSoftMulti-PatchParticles 126
5.7 Conclusions 127
(cid:2) Acknowledgments 128 (cid:2)
References 128
6 MolecularModelsforHepatitisBVirusCapsidFormation,Maturation,
andEnvelopment 134
JehoonKimandJianzhongWu
6.1 Introduction 134
6.2 MolecularThermodynamicsofCapsidFormation 140
6.2.1 EnergeticsofViralAssembly 141
6.2.1.1 RigidCapsids 141
6.2.1.2 Nucleocapsids 144
6.2.2 ThermodynamicsofCapsidFormationandStability 147
6.2.2.1 StabilityofCTD-FreeEmptyCapsids 147
6.2.2.2 StabilityofNucleocapsids 150
6.2.3 ModulationEffects 152
6.2.4 T3/T4Dimorphism 153
6.3 ElectrostaticsofGenomePackaging 154
6.3.1 ThermodynamicsofRNAEncapsidation 155
6.3.2 TheOptimalGenomeSizeofanHBVNucleocapsid 157
6.3.3 ChargeBalancebetweenPackagedRNAandCTDTails 157
6.4 DynamicStructureofHBVNucleocapsids 159
6.4.1 StructureofWTandMutantNucleocapsids 159
6.4.2 TheLocationofCTDResidues 161
6.4.3 ImplicationoftheCTDExposure 165
6.4.4 TheEffectofPhosphorylationofCapsidStructure 165
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6.5 CapsidEnvelopmentwithSurfaceProteins 167
6.6 SummaryandOutlook 171
Acknowledgments 173
References 174
7 SimulationStudiesofMetal–LigandSelf-Assembly 186
MakotoYoneya
7.1 Introduction 186
7.2 ModelingMetal–LigandSelf-Assembly 187
7.2.1 ModelingMetals,LigandsandtheirInteractions 187
7.2.2 ModelingSolvents 189
7.2.3 ComputationalMethods 190
7.3 Self-AssemblyofSupramolecularCoordinationComplex 190
7.3.1 Self-AssemblyofM L SphericalComplex 190
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7.3.2 Self-AssemblyofM L SphericalComplex 194
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7.4 Self-AssemblyofMetal–OrganicFrameworks 198
7.4.1 Self-Assemblyof2D-LikeMOF 198
7.4.2 Self-Assemblyof3D-LikeMOF 200
7.5 ConclusionandOutlook 203
Acknowledgments 204
References 204
(cid:2) 8 SimulationsofCellUptakeofNanoparticles:Membrane-Mediated (cid:2)
Interaction,InternalizationPathways,andCooperativeEffect 208
FalinTian,TongtaoYue,YeLiandXianrenZhang
8.1 Introduction 208
8.2 N-VariedDPDTechnique 210
8.2.1 TraditionalDPDMethod 210
8.2.2 N-VariedDPDMethod 210
8.3 TheInteractionbetweenNPandMembrane 211
8.3.1 Membrane-MediatedInteractionbetweenNPs 211
8.3.2 InternalizationPathwaysoftheNPs 214
8.3.2.1 NPPropertiesAffectingtheNP–MembraneInteraction 216
8.3.2.2 TheEffectofMembranePropertiesonNP–MembraneInteraction 221
8.4 CooperativeEffectbetweenNPsduringInternalization 222
8.5 Conclusions 226
References 226
9 TheoriesforPolymerMeltsConsistingofRod–CoilPolymers 230
YingJiangandJeffZ.Y.Chen
9.1 Introduction 230
9.1.1 Rod–CoilPolymersandRecentTheoreticalProgress 230
9.1.2 BasicParameters 235
9.1.2.1 MolecularParameters 235
9.1.2.2 Polymer-MeltParameters 236
9.1.2.3 OtherParameters 236
9.2 TheoreticalModels 237
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9.2.1 TheIdealRod–CoilDiblockModel 237
9.2.1.1 Comments 237
9.2.1.2 Formalism 237
9.2.2 TheLatticeModel 240
9.2.2.1 Comments 240
9.2.2.2 Formalism 240
9.2.3 TheWormlike–wormlikediblockmodel 242
9.2.3.1 Comments 242
9.2.3.2 Formalism 242
9.2.3.3 ReductiontotheRod–CoilProblem 244
9.2.4 NumericalAlgorithms 245
9.2.4.1 Comments 245
9.2.4.2 LatticeSampling 245
9.2.4.3 SpectralMethod 245
9.2.4.4 Pseudo-SpectralMethodforGSCPropagatorandFiniteDifferenceforRod
Probability 246
9.2.4.5 Single-ChainMean-FieldCalculation 246
9.2.4.6 FiniteDifferenceMethodforaWLCProblem 247
9.2.4.7 CombinedFiniteDifferenceandSphericalHarmonicsExpansion 247
9.2.4.8 FullSpectralMethodforaWLCProblem 247
9.2.4.9 PseudospectralMethodforaWLCProblem 248
9.2.4.10 PseudospectralBackwardDifferentiationFormulaMethodforaWLC
(cid:2) Problem 248 (cid:2)
9.3 ConcludingRemarks 250
References 251
10 TheoreticalandSimulationStudiesofHierarchicalNanostructures
Self-AssembledfromSoftMatterSystems 254
LiangshunZhangandJiapingLin
10.1 Introduction 254
10.2 ComputationalModelingandMethods 255
10.2.1 Particle-BasedMethods 255
10.2.2 Field-BasedMethods 256
10.3 HierarchicalNanostructuresofBlockCopolymerMelts 256
10.3.1 HierarchicalStructuresSelf-AssembledfromABCTerpolymers 257
10.3.2 HierarchicalPatternsSelf-AssembledfromMultiblockCopolymers 259
10.3.3 HierarchicalStructuresSelf-AssembledfromSupramolecular
Polymers 262
10.4 HierarchicalAggregatesofBlockCopolymerSolutions 264
10.4.1 HierarchicalAggregatesSelf-AssembledfromBlockCopolymer
Solutions 265
10.4.2 MulticompartmentAggregatesSelf-AssembledfromTriblockTerpolymer
Solutions 267
10.4.3 MulticompartmentAggregatesSelf-AssembledfromAmphiphilicCopolymer
Blends 270
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10.4.3.1 MixturesofDiblockCopolymers 270
10.4.3.2 BlendsofTerpolymersandCopolymers 270
10.4.3.3 BlendsofDistinctTerpolymers 271
10.4.3.4 MulticomponentRigidHomopolymer/Rod–CoilDiblockCopolymer
Systems 272
10.5 HierarchicallyOrderedNanocompositesSelf-Assembledfrom
Organic–InorganicSystems 272
10.5.1 HierarchicalSelf-AssemblyofBlockCopolymer/NanoparticleMixtures 273
10.5.2 HierarchicalSelf-AssemblyofPolymer/Nanoparticle/SolventSystems 275
10.6 ConclusionsandPerspectives 277
10.6.1 NewTheoreticalInsights 277
10.6.2 HorizontalMultiscaleModeling 278
10.6.3 InverseDesignStrategy 278
10.6.4 Element–Structure–PropertyRelationships 278
Acknowledgments 278
References 279
11 NucleationinColloidalSystems:TheoryandSimulation 288
RanNi
11.1 Introduction 288
11.2 TheoryofNucleation 289
11.2.1 FreeEnergyBarrier 291
(cid:2) 11.2.2 KineticsofNucleation 293 (cid:2)
11.2.3 EquilibriumDistributionofClusterSizes 295
11.3 OrderParameter 296
11.4 SimulationMethodsforStudyingNucleation 298
11.4.1 BruteForceMolecularDynamicsSimulations 299
11.4.2 UmbrellaSampling 299
11.4.3 ForwardFluxSampling 301
11.5 CrystalNucleationofHardSpheres:DebatesandProgress 304
11.6 Two-StepNucleationinSystemsofAttractiveColloids 308
11.7 NucleationofAnisotropicColloids 310
11.8 CrystalNucleationinBinaryMixtures 313
11.9 ConcludingRemarksandFutureDirections 316
Acknowledgments 316
References 316
12 AtomisticandCoarse-GrainedSimulationofLiquidCrystals 320
SaientanBag,SumanSaurabh,YvesLansacandPrabalK.Maiti
12.1 Introduction 320
12.2 ThermotropicLiquidCrystal 321
12.2.1 FullyAtomisticSimulation 321
12.2.2 Coarse-GrainedModel 328
12.3 DiscoticLiquidCrystals 339
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12.4 ChromonicLiquidCrystals 344
12.5 ConclusionandOutlook 347
Acknowledgment 347
References 348
Index 353
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