Chapter
1.2.3 Programmable Self-Assembly
1.2.4 Self-Assembling Kinetics: Supracolloidal Reaction
Chapter 2 Developing Hybrid Modeling Methods to Simulate Self-Assembly in Polymer Nanocomposites
2.2.1 Dissipative Particle Dynamics
2.2.2 Polymer Chains, Gels, and Nanoparticles
2.2.3 Radical Polymerization Model
2.3 Results and Discussions
2.3.1 Modeling Bulk Polymerization Using FRP and ATRP
2.3.2 Modeling Regeneration of Severed Polymer Gels with Interfacially Active Nanorods
2.3.3 Modeling the Formation of Polymer-Clay Composite Gels
Chapter 3 Theory and Simulation Studies of Self-Assembly of Helical Particles
3.1 Introduction: Why Hard Helices?
3.2 Liquid Crystal Phases
3.3 Hard Helices: A Minimal Model
3.4 Numerical Simulations
3.4.1 Monte Carlo in Various Ensembles
3.4.1.1 Canonical Monte Carlo simulations (NVT-MC)
3.4.1.2 Isothermal-Isobaric Monte Carlo Simulations (NPT-MC)
3.4.2 Details on the MC Simulation of Hard Helices
3.5 Onsager (Density Functional) Theory
3.6 Onsager-Like Theory for the Cholesteric and Screw-Nematic Phases
3.7 Order Parameters and Correlation Functions
3.7.1 Nematic Order Parameter
3.7.2 Screw-Like Nematic Order Parameter
3.7.3 Smectic Order Parameter
3.7.4 Hexatic Order Parameter
3.7.5 Parallel and Perpendicular Pair Correlation Functions
3.8 The Physical Origin of Cholesteric and Screw-Like Order
3.9 The Phase Diagram of Hard Helices
3.9.1 The Equation of State
3.9.2 Phase Diagrams in the Volume Fraction-Pitch Plane
3.9.2.1 Phase Diagram for r=0.1
3.9.2.2 Phase Diagram for r=0.2
3.9.2.3 Phase Diagram for r=0.4
3.10 Helical (Bio)Polymers and Colloidal Particles
3.11 Conclusions and Perspectives
Chapter 4 Self-Consistent Field Theory of Self-Assembling Multiblock Copolymers
4.2 Theoretical Framework: Self-Consistent Field Theory of Block Copolymers
4.3 Numerical Methods of SCFT
4.3.1 Reciprocal-Space Method
4.3.3 Pseudo-Spectral Method
4.3.4 Fourth-Order Pseudo-Spectral Method
4.4 Application of SCFT to Multiblock Copolymers
4.5 Conclusions and Discussions
Chapter 5 Simulation Models of Soft Janus and Patchy Particles
5.2 Soft Janus Particle Models
5.2.1 Soft One-Patch Janus Particle Model
5.2.2 Soft ABA-Type Triblock Janus Particle Model
5.2.3 Soft BAB-Type Triblock Janus Particle Model
5.2.4 Integration Algorithm
5.3 Soft Patchy Particle Models
5.3.2 Integration Algorithm
5.4 Physical Meanings of the Simulation Parameters in Our Models
5.6 Self-Assembly of Soft Janus and Patchy Particles
5.6.1 Self-Assembly of Soft One-Patch Janus Particles
5.6.2 The Role of Particle Softness in Self-Assembling Different Supracolloidal Helices
5.6.3 Self-Assembly of Soft ABA-Type Triblock Janus Particles
5.6.4 Template-Free Fabrication of Two-Dimensional Exotic Nanostructures through the Self-Assembly of Soft BAB-Type Triblock Janus Particles
5.6.5 Self-Assembly of Soft Multi-Patch Particles
Chapter 6 Molecular Models for Hepatitis B Virus Capsid Formation, Maturation, and Envelopment
6.2 Molecular Thermodynamics of Capsid Formation
6.2.1 Energetics of Viral Assembly
6.2.2 Thermodynamics of Capsid Formation and Stability
6.2.2.1 Stability of CTD-Free Empty Capsids
6.2.2.2 Stability of Nucleocapsids
6.3 Electrostatics of Genome Packaging
6.3.1 Thermodynamics of RNA Encapsidation
6.3.2 The Optimal Genome Size of an HBV Nucleocapsid
6.3.3 Charge Balance between Packaged RNA and CTD Tails
6.4 Dynamic Structure of HBV Nucleocapsids
6.4.1 Structure of WT and Mutant Nucleocapsids
6.4.2 The Location of CTD Residues
6.4.3 Implication of the CTD Exposure
6.4.4 The Effect of Phosphorylation of Capsid Structure
6.5 Capsid Envelopment with Surface Proteins
Chapter 7 Simulation Studies of Metal-Ligand Self-Assembly
7.2 Modeling Metal-Ligand Self-Assembly
7.2.1 Modeling Metals, Ligands and their Interactions
7.2.3 Computational Methods
7.3 Self-Assembly of Supramolecular Coordination Complex
7.3.1 Self-Assembly of M6L8 Spherical Complex
7.3.2 Self-Assembly of M12L24 Spherical Complex
7.4 Self-Assembly of Metal-Organic Frameworks
7.4.1 Self-Assembly of 2D-Like MOF
7.4.2 Self-Assembly of 3D-Like MOF
7.5 Conclusion and Outlook
Chapter 8 Simulations of Cell Uptake of Nanoparticles: Membrane-Mediated Interaction, Internalization Pathways, and Cooperative Effect
8.2 N-Varied DPD Technique
8.2.1 Traditional DPD Method
8.2.2 N-Varied DPD Method
8.3 The Interaction between NP and Membrane
8.3.1 Membrane-Mediated Interaction between NPs
8.3.2 Internalization Pathways of the NPs
8.3.2.1 NP Properties Affecting the NP-Membrane Interaction
8.3.2.2 The Effect of Membrane Properties on NP-Membrane Interaction
8.4 Cooperative Effect between NPs during Internalization
Chapter 9 Theories for Polymer Melts Consisting of Rod-Coil Polymers
9.1.1 Rod-Coil Polymers and Recent Theoretical Progress
9.1.2.1 Molecular Parameters
9.1.2.2 Polymer-Melt Parameters
9.2.1 The Ideal Rod-Coil Diblock Model
9.2.3 The Wormlike-wormlike diblock model
9.2.3.3 Reduction to the Rod-Coil Problem
9.2.4 Numerical Algorithms
9.2.4.4 Pseudo-Spectral Method for GSC Propagator and Finite Difference for Rod Probability
9.2.4.5 Single-Chain Mean-Field Calculation
9.2.4.6 Finite Difference Method for a WLC Problem
9.2.4.7 Combined Finite Difference and Spherical Harmonics Expansion
9.2.4.8 Full Spectral Method for a WLC Problem
9.2.4.9 Pseudospectral Method for a WLC Problem
9.2.4.10 Pseudospectral Backward Differentiation Formula Method for a WLC Problem
Chapter 10 Theoretical and Simulation Studies of Hierarchical Nanostructures Self-Assembled from Soft Matter Systems
10.2 Computational Modeling and Methods
10.2.1 Particle-Based Methods
10.2.2 Field-Based Methods
10.3 Hierarchical Nanostructures of Block Copolymer Melts
10.3.1 Hierarchical Structures Self-Assembled from ABC Terpolymers
10.3.2 Hierarchical Patterns Self-Assembled from Multiblock Copolymers
10.3.3 Hierarchical Structures Self-Assembled from Supramolecular Polymers
10.4 Hierarchical Aggregates of Block Copolymer Solutions
10.4.1 Hierarchical Aggregates Self-Assembled from Block Copolymer Solutions
10.4.2 Multicompartment Aggregates Self-Assembled from Triblock Terpolymer Solutions
10.4.3 Multicompartment Aggregates Self-Assembled from Amphiphilic Copolymer Blends
10.4.3.1 Mixtures of Diblock Copolymers
10.4.3.2 Blends of Terpolymers and Copolymers
10.4.3.3 Blends of Distinct Terpolymers
10.4.3.4 Multicomponent Rigid Homopolymer/Rod-Coil Diblock Copolymer Systems
10.5 Hierarchically Ordered Nanocomposites Self-Assembled from Organic-Inorganic Systems
10.5.1 Hierarchical Self-Assembly of Block Copolymer/Nanoparticle Mixtures
10.5.2 Hierarchical Self-Assembly of Polymer/Nanoparticle/Solvent Systems
10.6 Conclusions and Perspectives
10.6.1 New Theoretical Insights
10.6.2 Horizontal Multiscale Modeling
10.6.3 Inverse Design Strategy
10.6.4 Element-Structure-Property Relationships
Chapter 11 Nucleation in Colloidal Systems: Theory and Simulation
11.2 Theory of Nucleation
11.2.1 Free Energy Barrier
11.2.2 Kinetics of Nucleation
11.2.3 Equilibrium Distribution of Cluster Sizes
11.4 Simulation Methods for Studying Nucleation
11.4.1 Brute Force Molecular Dynamics Simulations
11.4.3 Forward Flux Sampling
11.5 Crystal Nucleation of Hard Spheres: Debates and Progress
11.6 Two-Step Nucleation in Systems of Attractive Colloids
11.7 Nucleation of Anisotropic Colloids
11.8 Crystal Nucleation in Binary Mixtures
11.9 Concluding Remarks and Future Directions
Chapter 12 Atomistic and Coarse-Grained Simulation of Liquid Crystals
12.2 Thermotropic Liquid Crystal
12.2.1 Fully Atomistic Simulation
12.2.2 Coarse-Grained Model
12.3 Discotic Liquid Crystals
12.4 Chromonic Liquid Crystals
12.5 Conclusion and Outlook
Self-Assembling Systems
：Theory and Simulation
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