Self-Assembling Systems

Professor Li-Tang Yan, Tsinghua University, ChinaProfessor Yan’s research focuses on computational macromolecular science, materials design and self-assembly. He uses multiscale modeling and simulation methods as well as theoretical analysis to explore the basic science and the fundamental principles in studies spanning polymer science, nanoscience, biomacromolecules and biomembranes.Professor Yan has published more than 60 papers in peer reviewed journals such as Nano Letters, ACS Nano, Biomaterials, Scientific Reports, JPC Lett, Nanoscale; these articles cover some important directions in the field of self-assembling systems, e.g., polymer nanocomposites, self-assembly in biomembranes, and self-assembly of nanoparticles to various suprastructures. In 2013 he published an invited review articles in Progress in Polymer Science, entitled "Computational Modeling and Simulation of Nanoparticle Self-Assembly in Polymeric Systems: Structures, Properties and External Field Effects".In 2014 he received an Excellent Young Investigator Award from NSFC (Natural Science Foundation of China).

• List of Contributors xiiiPreface xvii1 Theoretical Studies and Tailored Computer Simulations in Self-Assembling Systems: A General Aspect 1Zihan Huang and Li-Tang Yan1.1 Introduction 11.2 Emerging Self-Assembling Principles 31.2.1 Predictive Science and Rational Design of Complex Building Blocks 31.2.2 Entropy-Driven Ordering and Self-Assembly 51.2.3 Programmable Self-Assembly 101.2.4 Self-Assembling Kinetics: Supracolloidal Reaction 14Acknowledgments 16References 162 Developing Hybrid Modeling Methods to Simulate Self-Assembly in Polymer Nanocomposites 20Xin Yong, Stephen C. Snow, Olga Kuksenok and Anna C. Balazs2.1 Introduction 202.2 Methodology 212.2.1 Dissipative Particle Dynamics 212.2.2 Polymer Chains, Gels, and Nanoparticles 222.2.3 Radical Polymerization Model 242.3 Results and Discussions 272.3.1 Modeling Bulk Polymerization Using FRP and ATRP 272.3.2 Modeling Regeneration of Severed Polymer Gels with Interfacially Active Nanorods 322.3.3 Modeling the Formation of Polymer–Clay Composite Gels 432.4 Conclusions 47Acknowledgments 48References 493 Theory and Simulation Studies of Self-Assembly of Helical Particles 53Giorgio Cinacchi, Alberta Ferrarini, Elisa Frezza, Achille Giacometti and Hima Bindu Kolli3.1 Introduction: Why Hard Helices? 533.2 Liquid Crystal Phases 553.3 Hard Helices: A Minimal Model 563.4 Numerical Simulations 573.4.1 Monte Carlo in Various Ensembles 573.4.1.1 Canonical Monte Carlo simulations (NVT–MC) 593.4.1.2 Isothermal–Isobaric Monte Carlo Simulations (NPT–MC) 593.4.2 Details on the MC Simulation of Hard Helices 593.5 Onsager (Density Functional) Theory 613.6 Onsager-Like Theory for the Cholesteric and Screw-Nematic Phases 643.7 Order Parameters and Correlation Functions 673.7.1 Nematic Order Parameter ⟨P 2 ⟩ 683.7.2 Screw-Like Nematic Order Parameter 683.7.3 Smectic Order Parameter 703.7.4 Hexatic Order Parameter 703.7.5 Parallel and Perpendicular Pair Correlation Functions 713.8 The Physical Origin of Cholesteric and Screw-Like Order 733.9 The Phase Diagram of Hard Helices 743.9.1 The Equation of State 753.9.2 Phase Diagrams in the Volume Fraction–Pitch Plane 763.9.2.1 Phase Diagram for r = 0.1 773.9.2.2 Phase Diagram for r = 0.2 783.9.2.3 Phase Diagram for r = 0.4 793.10 Helical (Bio)Polymers and Colloidal Particles 793.11 Conclusions and Perspectives 81Acknowledgments 82References 824 Self-Consistent Field Theory of Self-Assembling Multiblock Copolymers 85Weihua Li and An-Chang Shi4.1 Introduction 854.2 Theoretical Framework: Self-Consistent Field Theory of Block Copolymers 884.3 Numerical Methods of SCFT 904.3.1 Reciprocal-Space Method 904.3.2 Real-Space Method 934.3.3 Pseudo-Spectral Method 954.3.4 Fourth-Order Pseudo-Spectral Method 984.4 Application of SCFT to Multiblock Copolymers 984.5 Conclusions and Discussions 104Acknowledgments 107References 1075 Simulation Models of Soft Janus and Patchy Particles 109Zhan-Wei Li, Zhao-Yan Sun and Zhong-Yuan Lu5.1 Introduction 1095.2 Soft Janus Particle Models 1115.2.1 Soft One-Patch Janus Particle Model 1115.2.2 Soft ABA-Type Triblock Janus Particle Model 1135.2.3 Soft BAB-Type Triblock Janus Particle Model 1145.2.4 Integration Algorithm 1165.3 Soft Patchy Particle Models 1175.3.1 The Model 1175.3.2 Integration Algorithm 1185.4 Physical Meanings of the Simulation Parameters in Our Models 1215.5 GPU Acceleration 1215.6 Self-Assembly of Soft Janus and Patchy Particles 1225.6.1 Self-Assembly of Soft One-Patch Janus Particles 1225.6.2 The Role of Particle Softness in Self-Assembling Different Supracolloidal Helices 1235.6.3 Self-Assembly of Soft ABA-Type Triblock Janus Particles 1245.6.4 Template-Free Fabrication of Two-Dimensional Exotic Nanostructures through the Self-Assembly of Soft BAB-Type Triblock Janus Particles 1255.6.5 Self-Assembly of Soft Multi-Patch Particles 1265.7 Conclusions 127Acknowledgments 128References 1286 Molecular Models for Hepatitis B Virus Capsid Formation, Maturation, and Envelopment 134Jehoon Kim and Jianzhong Wu6.1 Introduction 1346.2 Molecular Thermodynamics of Capsid Formation 1406.2.1 Energetics of Viral Assembly 1416.2.1.1 Rigid Capsids 1416.2.1.2 Nucleocapsids 1446.2.2 Thermodynamics of Capsid Formation and Stability 1476.2.2.1 Stability of CTD-Free Empty Capsids 1476.2.2.2 Stability of Nucleocapsids 1506.2.3 Modulation Effects 1526.2.4 T3/T4 Dimorphism 1536.3 Electrostatics of Genome Packaging 1546.3.1 Thermodynamics of RNA Encapsidation 1556.3.2 The Optimal Genome Size of an HBV Nucleocapsid 1576.3.3 Charge Balance between Packaged RNA and CTD Tails 1576.4 Dynamic Structure of HBV Nucleocapsids 1596.4.1 Structure of WT and Mutant Nucleocapsids 1596.4.2 The Location of CTD Residues 1616.4.3 Implication of the CTD Exposure 1656.4.4 The Effect of Phosphorylation of Capsid Structure 1656.5 Capsid Envelopment with Surface Proteins 1676.6 Summary and Outlook 171Acknowledgments 173References 1747 Simulation Studies of Metal–Ligand Self-Assembly 186Makoto Yoneya7.1 Introduction 1867.2 Modeling Metal–Ligand Self-Assembly 1877.2.1 Modeling Metals, Ligands and their Interactions 1877.2.2 Modeling Solvents 1897.2.3 Computational Methods 1907.3 Self-Assembly of Supramolecular Coordination Complex 1907.3.1 Self-Assembly of M 6 L 8 Spherical Complex 1907.3.2 Self-Assembly of M 12 L 24 Spherical Complex 1947.4 Self-Assembly of Metal–Organic Frameworks 1987.4.1 Self-Assembly of 2D-Like MOF 1987.4.2 Self-Assembly of 3D-Like MOF 2007.5 Conclusion and Outlook 203Acknowledgments 204References 2048 Simulations of Cell Uptake of Nanoparticles: Membrane-Mediated Interaction, Internalization Pathways, and Cooperative Effect 208Falin Tian, Tongtao Yue, Ye Li and Xianren Zhang8.1 Introduction 2088.2 N-Varied DPD Technique 2108.2.1 Traditional DPD Method 2108.2.2 N-Varied DPD Method 2108.3 The Interaction between NP and Membrane 2118.3.1 Membrane-Mediated Interaction between NPs 2118.3.2 Internalization Pathways of the NPs 2148.3.2.1 NP Properties Affecting the NP–Membrane Interaction 2168.3.2.2 The Effect of Membrane Properties on NP–Membrane Interaction 2218.4 Cooperative Effect between NPs during Internalization 2228.5 Conclusions 226References 2269 Theories for Polymer Melts Consisting of Rod–Coil Polymers 230Ying Jiang and Jeff Z. Y. Chen9.1 Introduction 2309.1.1 Rod–Coil Polymers and Recent Theoretical Progress 2309.1.2 Basic Parameters 2359.1.2.1 Molecular Parameters 2359.1.2.2 Polymer-Melt Parameters 2369.1.2.3 Other Parameters 2369.2 Theoretical Models 2379.2.1 The Ideal Rod–Coil Diblock Model 2379.2.1.1 Comments 2379.2.1.2 Formalism 2379.2.2 The Lattice Model 2409.2.2.1 Comments 2409.2.2.2 Formalism 2409.2.3 The Wormlike–wormlike diblock model 2429.2.3.1 Comments 2429.2.3.2 Formalism 2429.2.3.3 Reduction to the Rod–Coil Problem 2449.2.4 Numerical Algorithms 2459.2.4.1 Comments 2459.2.4.2 Lattice Sampling 2459.2.4.3 Spectral Method 2459.2.4.4 Pseudo-Spectral Method for GSC Propagator and Finite Difference for Rod Probability 2469.2.4.5 Single-Chain Mean-Field Calculation 2469.2.4.6 Finite Difference Method for a WLC Problem 2479.2.4.7 Combined Finite Difference and Spherical Harmonics Expansion 2479.2.4.8 Full Spectral Method for a WLC Problem 2479.2.4.9 Pseudospectral Method for a WLC Problem 2489.2.4.10 Pseudospectral Backward Differentiation Formula Method for a WLC Problem 2489.3 Concluding Remarks 250References 25110 Theoretical and Simulation Studies of Hierarchical Nanostructures Self-Assembled from Soft Matter Systems 254Liangshun Zhang and Jiaping Lin10.1 Introduction 25410.2 Computational Modeling and Methods 25510.2.1 Particle-Based Methods 25510.2.2 Field-Based Methods 25610.3 Hierarchical Nanostructures of Block Copolymer Melts 25610.3.1 Hierarchical Structures Self-Assembled from ABC Terpolymers 25710.3.2 Hierarchical Patterns Self-Assembled from Multiblock Copolymers 25910.3.3 Hierarchical Structures Self-Assembled from Supramolecular Polymers 26210.4 Hierarchical Aggregates of Block Copolymer Solutions 26410.4.1 Hierarchical Aggregates Self-Assembled from Block Copolymer Solutions 26510.4.2 Multicompartment Aggregates Self-Assembled from Triblock Terpolymer Solutions 26710.4.3 Multicompartment Aggregates Self-Assembled from Amphiphilic Copolymer Blends 27010.4.3.1 Mixtures of Diblock Copolymers 27010.4.3.2 Blends of Terpolymers and Copolymers 27010.4.3.3 Blends of Distinct Terpolymers 27110.4.3.4 Multicomponent Rigid Homopolymer/Rod–Coil Diblock Copolymer Systems 27210.5 Hierarchically Ordered Nanocomposites Self-Assembled from Organic–Inorganic Systems 27210.5.1 Hierarchical Self-Assembly of Block Copolymer/Nanoparticle Mixtures 27310.5.2 Hierarchical Self-Assembly of Polymer/Nanoparticle/Solvent Systems 27510.6 Conclusions and Perspectives 27710.6.1 New Theoretical Insights 27710.6.2 Horizontal Multiscale Modeling 27810.6.3 Inverse Design Strategy 27810.6.4 Element–Structure–Property Relationships 278Acknowledgments 278References 27911 Nucleation in Colloidal Systems: Theory and Simulation 288Ran Ni11.1 Introduction 28811.2 Theory of Nucleation 28911.2.1 Free Energy Barrier 29111.2.2 Kinetics of Nucleation 29311.2.3 Equilibrium Distribution of Cluster Sizes 29511.3 Order Parameter 29611.4 Simulation Methods for Studying Nucleation 29811.4.1 Brute Force Molecular Dynamics Simulations 29911.4.2 Umbrella Sampling 29911.4.3 Forward Flux Sampling 30111.5 Crystal Nucleation of Hard Spheres: Debates and Progress 30411.6 Two-Step Nucleation in Systems of Attractive Colloids 30811.7 Nucleation of Anisotropic Colloids 31011.8 Crystal Nucleation in Binary Mixtures 31311.9 Concluding Remarks and Future Directions 316Acknowledgments 316References 31612 Atomistic and Coarse-Grained Simulation of Liquid Crystals 320Saientan Bag, Suman Saurabh, Yves Lansac and Prabal K. Maiti12.1 Introduction 32012.2 Thermotropic Liquid Crystal 32112.2.1 Fully Atomistic Simulation 32112.2.2 Coarse-Grained Model 32812.3 Discotic Liquid Crystals 33912.4 Chromonic Liquid Crystals 34412.5 Conclusion and Outlook 347Acknowledgment 347References 348Index 353