Self-Assembling Systems : Theory and Simulation.
Yan, Li-Tang.
Self-Assembling Systems : Theory and Simulation. - 1st ed. - 1 online resource (392 pages)
Cover -- Title Page -- Copyright -- Contents -- List of Contributors -- Preface -- Chapter 1 Theoretical Studies and Tailored Computer Simulations in Self-Assembling Systems: A General Aspect -- 1.1 Introduction -- 1.2 Emerging Self-Assembling Principles -- 1.2.1 Predictive Science and Rational Design of Complex Building Blocks -- 1.2.2 Entropy-Driven Ordering and Self-Assembly -- 1.2.3 Programmable Self-Assembly -- 1.2.4 Self-Assembling Kinetics: Supracolloidal Reaction -- Acknowledgments -- References -- Chapter 2 Developing Hybrid Modeling Methods to Simulate Self-Assembly in Polymer Nanocomposites -- 2.1 Introduction -- 2.2 Methodology -- 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 -- 2.4 Conclusions -- Acknowledgments -- References -- 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 < -- P2> -- -- 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 -- Acknowledgments -- References -- Chapter 4 Self-Consistent Field Theory of Self-Assembling Multiblock Copolymers -- 4.1 Introduction -- 4.2 Theoretical Framework: Self-Consistent Field Theory of Block Copolymers -- 4.3 Numerical Methods of SCFT -- 4.3.1 Reciprocal-Space Method -- 4.3.2 Real-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 -- Acknowledgments -- References -- Chapter 5 Simulation Models of Soft Janus and Patchy Particles -- 5.1 Introduction -- 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 -- 5.3.1 The Model -- 5.3.2 Integration Algorithm -- 5.4 Physical Meanings of the Simulation Parameters in Our Models -- 5.5 GPU Acceleration -- 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 -- 5.7 Conclusions -- Acknowledgments -- References -- Chapter 6 Molecular Models for Hepatitis B Virus Capsid Formation, Maturation, and Envelopment -- 6.1 Introduction -- 6.2 Molecular Thermodynamics of Capsid Formation -- 6.2.1 Energetics of Viral Assembly -- 6.2.1.1 Rigid Capsids -- 6.2.1.2 Nucleocapsids -- 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 -- 6.2.3 Modulation Effects -- 6.2.4 T3/T4 Dimorphism -- 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 -- 6.6 Summary and Outlook -- Acknowledgments -- References -- Chapter 7 Simulation Studies of Metal-Ligand Self-Assembly -- 7.1 Introduction -- 7.2 Modeling Metal-Ligand Self-Assembly -- 7.2.1 Modeling Metals, Ligands and their Interactions -- 7.2.2 Modeling Solvents -- 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 -- Acknowledgments -- References -- Chapter 8 Simulations of Cell Uptake of Nanoparticles: Membrane-Mediated Interaction, Internalization Pathways, and Cooperative Effect -- 8.1 Introduction -- 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 -- 8.5 Conclusions -- References -- Chapter 9 Theories for Polymer Melts Consisting of Rod-Coil Polymers -- 9.1 Introduction -- 9.1.1 Rod-Coil Polymers and Recent Theoretical Progress -- 9.1.2 Basic Parameters -- 9.1.2.1 Molecular Parameters -- 9.1.2.2 Polymer-Melt Parameters -- 9.1.2.3 Other Parameters -- 9.2 Theoretical Models -- 9.2.1 The Ideal Rod-Coil Diblock Model -- 9.2.1.1 Comments -- 9.2.1.2 Formalism -- 9.2.2 The Lattice Model -- 9.2.2.1 Comments -- 9.2.2.2 Formalism -- 9.2.3 The Wormlike-wormlike diblock model -- 9.2.3.1 Comments -- 9.2.3.2 Formalism -- 9.2.3.3 Reduction to the Rod-Coil Problem -- 9.2.4 Numerical Algorithms -- 9.2.4.1 Comments -- 9.2.4.2 Lattice Sampling -- 9.2.4.3 Spectral Method -- 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 -- 9.3 Concluding Remarks -- References -- Chapter 10 Theoretical and Simulation Studies of Hierarchical Nanostructures Self-Assembled from Soft Matter Systems -- 10.1 Introduction -- 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 -- Acknowledgments -- References -- Chapter 11 Nucleation in Colloidal Systems: Theory and Simulation -- 11.1 Introduction -- 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 -- 11.3 Order Parameter -- 11.4 Simulation Methods for Studying Nucleation -- 11.4.1 Brute Force Molecular Dynamics Simulations -- 11.4.2 Umbrella Sampling -- 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.
9781119113157
Self-assembly (Chemistry).
Electronic books.
QD475.S454 2017
547.2
Self-Assembling Systems : Theory and Simulation. - 1st ed. - 1 online resource (392 pages)
Cover -- Title Page -- Copyright -- Contents -- List of Contributors -- Preface -- Chapter 1 Theoretical Studies and Tailored Computer Simulations in Self-Assembling Systems: A General Aspect -- 1.1 Introduction -- 1.2 Emerging Self-Assembling Principles -- 1.2.1 Predictive Science and Rational Design of Complex Building Blocks -- 1.2.2 Entropy-Driven Ordering and Self-Assembly -- 1.2.3 Programmable Self-Assembly -- 1.2.4 Self-Assembling Kinetics: Supracolloidal Reaction -- Acknowledgments -- References -- Chapter 2 Developing Hybrid Modeling Methods to Simulate Self-Assembly in Polymer Nanocomposites -- 2.1 Introduction -- 2.2 Methodology -- 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 -- 2.4 Conclusions -- Acknowledgments -- References -- 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 < -- P2> -- -- 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 -- Acknowledgments -- References -- Chapter 4 Self-Consistent Field Theory of Self-Assembling Multiblock Copolymers -- 4.1 Introduction -- 4.2 Theoretical Framework: Self-Consistent Field Theory of Block Copolymers -- 4.3 Numerical Methods of SCFT -- 4.3.1 Reciprocal-Space Method -- 4.3.2 Real-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 -- Acknowledgments -- References -- Chapter 5 Simulation Models of Soft Janus and Patchy Particles -- 5.1 Introduction -- 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 -- 5.3.1 The Model -- 5.3.2 Integration Algorithm -- 5.4 Physical Meanings of the Simulation Parameters in Our Models -- 5.5 GPU Acceleration -- 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 -- 5.7 Conclusions -- Acknowledgments -- References -- Chapter 6 Molecular Models for Hepatitis B Virus Capsid Formation, Maturation, and Envelopment -- 6.1 Introduction -- 6.2 Molecular Thermodynamics of Capsid Formation -- 6.2.1 Energetics of Viral Assembly -- 6.2.1.1 Rigid Capsids -- 6.2.1.2 Nucleocapsids -- 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 -- 6.2.3 Modulation Effects -- 6.2.4 T3/T4 Dimorphism -- 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 -- 6.6 Summary and Outlook -- Acknowledgments -- References -- Chapter 7 Simulation Studies of Metal-Ligand Self-Assembly -- 7.1 Introduction -- 7.2 Modeling Metal-Ligand Self-Assembly -- 7.2.1 Modeling Metals, Ligands and their Interactions -- 7.2.2 Modeling Solvents -- 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 -- Acknowledgments -- References -- Chapter 8 Simulations of Cell Uptake of Nanoparticles: Membrane-Mediated Interaction, Internalization Pathways, and Cooperative Effect -- 8.1 Introduction -- 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 -- 8.5 Conclusions -- References -- Chapter 9 Theories for Polymer Melts Consisting of Rod-Coil Polymers -- 9.1 Introduction -- 9.1.1 Rod-Coil Polymers and Recent Theoretical Progress -- 9.1.2 Basic Parameters -- 9.1.2.1 Molecular Parameters -- 9.1.2.2 Polymer-Melt Parameters -- 9.1.2.3 Other Parameters -- 9.2 Theoretical Models -- 9.2.1 The Ideal Rod-Coil Diblock Model -- 9.2.1.1 Comments -- 9.2.1.2 Formalism -- 9.2.2 The Lattice Model -- 9.2.2.1 Comments -- 9.2.2.2 Formalism -- 9.2.3 The Wormlike-wormlike diblock model -- 9.2.3.1 Comments -- 9.2.3.2 Formalism -- 9.2.3.3 Reduction to the Rod-Coil Problem -- 9.2.4 Numerical Algorithms -- 9.2.4.1 Comments -- 9.2.4.2 Lattice Sampling -- 9.2.4.3 Spectral Method -- 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 -- 9.3 Concluding Remarks -- References -- Chapter 10 Theoretical and Simulation Studies of Hierarchical Nanostructures Self-Assembled from Soft Matter Systems -- 10.1 Introduction -- 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 -- Acknowledgments -- References -- Chapter 11 Nucleation in Colloidal Systems: Theory and Simulation -- 11.1 Introduction -- 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 -- 11.3 Order Parameter -- 11.4 Simulation Methods for Studying Nucleation -- 11.4.1 Brute Force Molecular Dynamics Simulations -- 11.4.2 Umbrella Sampling -- 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.
9781119113157
Self-assembly (Chemistry).
Electronic books.
QD475.S454 2017
547.2