Title Page

Contents

Preface

Course group shot

Basic concepts in self-assembly

Thermodynamic description of the clustering process

The need of low temperatures (compared to the bonding energy)

The need of directional attractive interactions

Analogies with chemical reactions

The simplest self-assembly process. Equilibrium polymerization

Equilibrium polimerization in chemical language

Cooperative polymerization: slaved equilibrium polymerization

Micelles

How do we ``exactly'' calculate Qn

Conclusions

Self-assembly from colloids to biology

Reversible adsorption and allostery: The MWC model

Introduction

Statistical mechanics of self-assembly onto templates

Allostery: MWC model

Oxygen binding to hemoglobin

Collective adsorption and the Hill coefficient

MWC and genome accessibility

Statistical mechanics of genetic regulation

Introduction

Simple repression in the grand ensemble

Calculating the fugacity

Complex behavior by simple adsorption

Comparison with experiments: Data collapse in gene expression

Virus capsid assembly

Introduction: Viruses as equilibrium objects

Association equilibria: critical aggregate concentration

Interactions in virus capsids

Hydrophobic interactions

Electrostatic self-energy of a virus capsid

Predictions: temperature and ionic strength dependence of virus capsid formation

Finite-size objects stabilized by electrostatic interactions

Introduction

Equilibrium clusters of colloids and proteins

Very large protein clusters

Liposome-polyelectrolyte clusters

Non-equilibrium clusters

Beyond clusters: Higher colloid concentrations

Conclusions

Depletion interactions on soft colloids: Glass formation, melting and demixing

Depletion interactions: the Asakura-Oosawa paradigm

Mixtures of star polymers and linear homopolymer chains

Mixtures of soft and hard colloids

Concentrated solutions: glasses and demixing

Summary and concluding remarks

Driven self-assembly

Introduction

Colloidal building blocks for driven self-assembly

The available toolbox of interparticle interactions

Technical interlude: how to quantitatively compare confocal microscopy and computer simulation results

Electric field-driven self-assembly of soft dipolar particles

Using field-driven self-assembly to investigate phase transition kinetics for ultrasoft colloids

Shape matters: electric field-driven self-assembly in ellipsoidal particle suspensions

Anisotropic magnetic particles in a magnetic field --- what can we learn from SAXS

Magnetic field-driven assembly of hematite particles

Conclusions

The influence of self-assembly on the magnetic response of dipolar soft systems

Introduction

Back to the 19th century

Need for correlations

Self-assembly as a tool to design the magnetic response: chains

Crosslinked chains

When the temperature goes down

Branching

Beyond spheres

Conclusions

Capillary interactions on fluid interfaces: Opportunities for directed assembly

Introduction

The interactions of microparticles in confined systems: It is all about the boundaries

The trapping of isolated particles on planar interfaces

Particle with an equilibrium contact angle

Particle with a pinned, undulated contact line

Non-spherical particles

Isolated particles trapped on curved interfaces

Pair interaction on planar interfaces

Method of reflections

Exact solution in bipolar coordinate

Capillary curvature energy

Local expansion of the curvature field in terms of matched asymptotics

Electrostatic analogies

A grounded disk in an external potential

A charged disk in an external potential: Handle with care

Experimental observations

Near-field repulsion

Curved interface

Molding of the fluid interface

Observations of microdisk migration on curved interfaces around a circular micropost

Observations of microsphere migration on curved interfaces around a circular micropost

Observations of microcylinders on curved interfaces around a circular micropost

Cylinders on interfaces with more complex curvature fields

Interface shape

Shape of the interface in the presence of a particle

Conclusions

Pathways to self-organization: Crystallization via nucleation and growth

Introduction

Classical nucleation theory

General picture

Kramers problem and mean first-passage times

Nucleation rate of CNT

When does CNT fail?

Setting the stage

Phase diagrams and free energy calculations

Order parameter and reaction coordinate(s) for crystallization

Free energy landscapes are not unique

Computing nucleation rates

Macroscopic view

A pedestrian approach

Mean first-passage time

Transition state theory (TST)

Bennett-Chandler method (TST-BC)

Transition path sampling

Transition interface sampling (TIS)

Forward flux sampling

Evolution of methods

Crystallization rates of a supercooled LJ fluid

Transition rates are unique

Analyzing the nucleation mechanism

Reaction coordinate

Committor

Committor distribution and transition state ensemble

Likelihood maximization

Applications

Hard sphere freezing

Water freezing

Summary and outlook

Static and dynamic properties of inverse patchy colloids

Introduction

Model

Simulation techniques

Results

Confined, two-dimensional system with and without external field

Three-dimensional system

Conclusions

A geometric view of structure formation in soft colloids

Introduction

2D minimal-enthalpy structures

Canonical lattices

Semi-canonical and non-canonical lattices

Intermediate and large shoulder-to-core ratios

Phase coexistence

Phase separation

Quasicrystals

Conclusions

DNA-based nanoscale self-assembly

DNA for nanotechnology

Advantages of DNA as a nanomaterial

DNA tiles and crystalline arrays

Three-dimensional (3D) DNA Nano-objects

Scaffolded DNA origami

DNA bricks

Approaches for DNA-nanoparticles conjugates

Direct replacement method

Non-covalent attachment method

Conjugation approaches

Functional group grafting and subsequent conjugation method

Approaches for DNA-microparticles conjugates

DNA-assembled nanoparticle clusters

One (1D)- and two (2D)-dimensional nanoparticle arrays

1D arrays

2D arrays

DNA-driven three-dimensional nanoparticle superlattices

Dynamic systems

Some applications of DNA-NP systems

Conclusions

The hydrodynamics of active systems

Introduction

Single swimmer hydrodynamics: background

Swimming at low Reynolds number

The Scallop Theorem

Far flow fields

Single swimmer hydrodynamics: applications

Tracers: loops and entrainment

Swimmers in Poiseuille flow

Surfaces

Collective hydrodynamics of active entities

Nematic liquid crystals

Beris-Edwards equations

Adding activity

Collective hydrodynamics: applications

Active turbulence

Microtubules and molecular motors

Lyotropic active nematics

Discussion

Colloidal inclusions in liquid crystals

Introduction and summary

Warmup in flatland

The boojums

The hedgehog

Two further readings

List of participants