Contents -- Foreword -- Preface -- Introduction Role of Modeling in Soft Matter Physics -- References -- Chapter 1 Applications of Density Functional Theory in Soft Condensed Matter -- Introduction -- 1. Freezing of Spheres -- 1.1. Phenomenological results -- i) Lindemann-criterion of melting -- ii) Hansen-Verlet rule of freezing -- 1.2. Independent treatment of the different phases -- 1.3. Unifying Microscopic theories -- 1.4. Phase diagrams of simple potentials -- a) Hard spheres -- b) Plasma -- d) Yukawa-system -- e) Lennard-Jones-system -- f) Sticky hard spheres -- g) Ultrasoft interactions -- 1.5. Density Functional Theory (DFT) -- a) Basics -- b) Approximations for the density functional -- 2. Brownian Dynamics -- 2.1. Brownian dynamics (BD) -- 2.2. BD computer simulations -- 2.3. Dynamical density functional theory (DDFT) -- 2.4. An example: Crystal growth at imposed nucleation clusters -- 2.5. Hydrodynamic interactions -- 3. Rod-Like Particles -- 3.1. Statistical mechanics of rod-like particles -- 1) Fluid (disordered) phase, isotropic phase -- 2) Nematic phase -- 3) Smectic-A phase -- 4) Smectic-B phase -- 5) Columnar phase -- 6) Plastic crystal -- 7) Full crystalline phases -- 3.2. Simple models -- A) Analytical results by Onsager -- B) Computer simulations -- C) Density functional theory -- 3.3. Brownian dynamics of rod-like particles -- 3.4. "Active" (self-propelled) Brownian particles -- 4. Conclusions -- Acknowledgement -- References -- Chapter 2 Polymer Phase Separation -- 1. Introduction -- 2. Phase Behavior in the Bulk -- 2.1. Predictions of the mean-field theory -- 2.2. Estimating the Flory-Huggins parameter for simulation models -- 2.3. Simulation techniques for computing the bulk phase behavior -- 2.4. Compressible mixtures -- 3. Outlook: Interfacial Properties, Phase Boundaries in Confined Geometry, and Wetting -- References.

Chapter 3 Self-Consistent Field Theory of Block Copolymers -- 1. Introduction -- 2. Self-Consistent Field Theory of Block Copolymers -- 2.1. Polymer model and partition function -- 2.2. Chain propagators -- 2.3. Self-consistent mean-field theory -- 3. Reciprocal-Space Formulation -- 4. Applications of the Reciprocal-Space Method -- 5. Summary -- Acknowledgments -- References -- Chapter 4 Dynamic Self-Consistent Field Theories for Polymer Blends and Block Copolymers -- 1. Introduction -- 2. Basic Formalism for Dynamic SCF Theory -- 2.1. Diffusion flux -- 2.2. Convection flux -- 2.3. Flux induced by external fields -- 3. Dynamic SCF Theories in Slow Diffusion Regime -- 3.1. Formulation -- 3.2. Formation process of mesophases of block copolymer melt -- 3.3. Dynamics and non-equilibrium domain structures in thin films and near solid surfaces -- 3.4. Structural phase transitions induced by external fields -- 4. Beyond Diffusion Dynamics - Hydrodynamics, Viscoelasticity and Hybrid Techniques -- 4.1. Hydrodynamic effects on domain formation -- 4.2. Dynamic SCF with viscoelastic properties -- 4.2.1. Non-local kinetic coefficients with chain deformations -- 4.2.2. Full dynamic SCF theory with Rouse dynamics -- 4.2.3. Full dynamic SCF theory with reptation dynamics -- 4.3. Hybrid simulations with particles and fields -- 5. Conclusion -- Acknowledgments -- References -- Chapter 5 Molecular Dynamics in Crystallization of Helical Polymers: Crystal Ordering and Chirality Selection -- 1. Introduction -- 2. Our Strategies for Simulating Crystallization in Helical Polymers -- 3. Molecular Models and Simulation Methods -- 3.1 MD simulations -- 3.2 MC simulation -- 4. Crystallization of the Bare Helix -- 4.1. A primary nucleation of a single polymer in vacuo -- 4.2 Crystallization of a single polymer on a growth front.

4.3 Order-disorder transition and crystal chirality -- 4.4 Development of chiral crystal -- 5. Simulations for iPP, a Helical Polymer with Side Groups -- 5.1 Collapsing of a single iPP chain in vacuo -- 5.2 Crystallization of a single chain with definite chiral recognition -- 5.3 Crystallization and polymorph selection -- 6. Conclusions -- References -- Chapter 6 Interplay of Liquid-Liquid Demixing and Polymer Crystallization -- 1. Introduction -- 2. Theoretical Model -- 3. Simulation Techniques -- 4. Results and Discussion -- 4.1. Liquid-liquid demixing enhanced by crystallizability -- 4.2. Crystal nucleation enhanced by prior L-L demixing -- 4.3. Crystal nucleation enhanced by prior L-L demixing in the single-chain systems -- Acknowledgments -- References -- Chapter 7 Elucidation of Single Molecular Observation of a Giant DNA -- 1. Polymer Physics Aspect of DNA Conformation -- 2. Manipulation and Measurement DNA Conformation In Vitro -- 2.1 Condensing agents -- 2.2 Single molecular images -- 2.3 Limitation of traditional light scattering -- 3. All-or-none Conformation Transition of DNA -- 3.1 Discrete conformational transition of DNA -- 3.2 Chain stiffness and discrete conformational transition -- 4. Dynamics of Conformational Relaxation -- 4.1 Time dependent conformational behavior -- 4.2 Folding and unfolding kinetics -- 5. Conformational Hysteresis -- 5.1 Characterization of hysteresis -- 5.2 Thermodynamics in conformational hysteresis -- 5.3 Hysteresis under mechanical forces -- 6. Effect of Charge on DNA Conformation -- 6.1 Conditions to induce intramolecular segregation -- 6.2 Polyelectrolyte analogy -- 6.3 Phase diagram of intermolecular and intramolecular segregation -- 7. Temperature Effect of DNA Conformation -- 7.1 Temperature induced conformational change -- 7.2 Competition of smaller ions on compaction -- 8. Applications.

9. Concluding Remarks -- Acknowledgments -- References -- Chapter 8 Theoretical Modeling of Hydrogen Bonding in Macromolecular Solutions: The Combination of Quantum Mechanics and Molecular Mechanics -- 1. Introduction -- 2. Fragmentation-Based QM/MM Simulations -- 2.1. Solvent models -- 2.2. Energy-based fragmentation QM -- 2.3. Fragmentation QM/MM: Basic idea and formalisms -- 2.4. Fragmentation QM/MM simulations on poly (ethyleneoxide) polyethylene -- 3. Simulations of Solvated Peptides Using Polarizable Force Field Model -- 3.1. Fragmentation-based polarization model -- 3.2. Configurations of solvated α-conotoxin GI and its analogues -- 4. Concluding Remarks -- Acknowledgments -- References -- Chapter 9 Exotic Electrostatics: Unusual Features of Electrostatic Interactions between Macroions -- 1. Introduction -- 2. Scenery -- 2.1. Colloids, polymers and membranes: The mesoscopic scale -- 2.2. Charges: From industry to biology -- 2.3. Theoretical challenge and coarse-grained models -- 3. Length Scales in a Classical Charged System -- 4. From Mean-Field to Strong Coupling Regime -- 4.1. Weak coupling or mean-field regime -- 4.2. Strong coupling regime -- 5. Interactions between Like-Charged Surfaces -- 5.1. WC regime: Repulsion -- 5.2. SC regime: Attraction -- 6. Counterions with Salt -- 6.1. Functional integral formalism -- 6.2. Dressed counterions -- 6.3. WC dressed counterion theory -- 6.4. SC dressed counterion theory -- 7. Counterions between Randomly Charged Surfaces -- 7.1. General formalism: The replica method -- 7.2. Disorder effects in the WC regime -- 7.3. Disorder effects in the SC regime -- 8. Lessons -- Acknowledgments -- References -- Chapter 10 Computer Modeling of Liquid Crystals -- 1. Introduction -- 1.1. What is a liquid crystal? -- 1.2. Theoretical approach to understanding liquid crystals -- 1.2.1. The order parameter.

1.2.2. Liquid crystal theories -- 2. Introduction to the Computer Simulation -- 2.1. Computer simulation techniques -- 2.2. Simulation limitations -- 3. Liquid Crystal Models -- 3.1. The lattice class -- 3.1.1. General techniques -- 3.1.2. Limitations and advantages of the lattice class -- 3.1.3. Some results and applications -- 3.1.4. LL-chiral nematic model -- 3.1.5. LL-mixture models -- 3.1.6. Final comment on LL-like models -- 3.2. The Gay-Berne class -- 3.2.1. Some results and applications -- 3.2.2. Gay-Berne variant models -- 3.3. Full atomistic class -- 3.4. Conclusion -- Acknowledgments -- References -- Chapter 11 Drop Dynamics in Complex Fluids -- 1. Introduction -- 2. Partial Coalescence in Polymer Solutions -- 2.1. Experimental observations -- 2.2. Numerical simulations -- 3. Droplet Self-Assembly in Nematic Liquid Crystals -- 3.1. Experimental observations -- 3.2. Numerical simulations -- 4. Summary -- Acknowledgments -- References -- Index.