A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results.

The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.

Flow of Deformable Droplets: Discontinuous Shear Thinning and Velocity Oscillations.

We study the rheology of a suspension of soft deformable droplets subjected to a pressure-driven flow. Through computer simulations, we measure the apparent viscosity as a function of droplet concentration and pressure gradient, and provide evidence of a discontinuous shear thinning behavior, which occurs at a concentration-dependent value of the forcing. We further show that this response is associated with a nonequilibrium transition between a "hard" (or less deformable) phase, which is nearly jammed and flows very slowly, and a "soft" (or more deformable) phase, which flows much more easily. The soft phase is characterized by flow-induced time dependent shape deformations and internal currents, which are virtually absent in the hard phase. Close to the transition, we find sustained oscillations in both the droplet and fluid velocities. Polydisperse systems show similar phenomenology but with a smoother transition, and less regular oscillations.

A single nucleotide resolution model for large-scale simulations of double stranded DNA.

The computational modelling of DNA is becoming crucial in light of new advances in DNA nano-technology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules - up to a million base pairs - for time-scales which are relevant to physiological processes. This is made possible by an efficient and highly-parallelised implementation of the model which we discuss here. The model captures the main characteristics of DNA, such as the different persistence lengths for double and single strands, pitch, torsional rigidity and the presence of major and minor grooves. The model constitutes a starting point for the future implementation of further features, such as sequence specificity and electrostatic repulsion. We show that the behaviour of the presented model compares favourably with single molecule experiments where dsDNA is manipulated by external forces or torques. We finally present some results on the kinetics of denaturation of linear DNA and supercoiling of closed dsDNA molecules.

Self-assembly of colloid-cholesteric composites provides a possible route to switchable optical materials.

Colloidal particles dispersed in liquid crystals can form new materials with tunable elastic and electro-optic properties. In a periodic 'blue phase' host, particles should template into colloidal crystals with potential uses in photonics, metamaterials and transformational optics. Here we show by computer simulation that colloid/cholesteric mixtures can give rise to regular crystals, glasses, percolating gels, isolated clusters, twisted rings and undulating colloidal ropes. This structure can be tuned via particle concentration, and by varying the surface interactions of the cholesteric host with both the particles and confining walls. Many of these new materials are metastable: two or more structures can arise under identical thermodynamic conditions. The observed structure depends not only on the formulation protocol but also on the history of an applied electric field. This new class of soft materials should thus be relevant to design of switchable, multistable devices for optical technologies such as smart glass and e-paper.

Switching hydrodynamics in liquid crystal devices: a simulation perspective.

In liquid crystal devices it is important to understand the physics underlying their switching between different states, which is usually achieved by applying or removing an electric field. Flow is known to be a key determinant of the timescales and pathways of the switching kinetics. Incorporating hydrodynamic effects into theories for liquid crystal devices is therefore important; however this is also highly non-trivial, and typically requires the use of accurate numerical methods. Here, we review some recent advances in our theoretical understanding of the dynamics of switching in liquid crystal devices, mainly gained through computer simulations. These results, as we shall show, uncover interesting new physics, and may be important for future applications.

Confined cubic blue phases under shear.

We study the behaviour of confined cubic blue phases under shear flow via lattice Boltzmann simulations. We focus on the two experimentally observed phases, blue phase I and blue phase II. The disclination network of blue phase II continuously breaks and reforms under shear, leading to an oscillatory stress response in time. The oscillations are only regular for very thin samples. For thicker samples, the shear leads to a 'stick-slip' motion of part of the network along the vorticity direction. Blue phase I responds very differently: its defect network undergoes seemingly chaotic rearrangements under shear, irrespective of system size.

Structure of blue phase III of cholesteric liquid crystals.

We report large scale simulations of the blue phases of cholesteric liquid crystals. Our results suggest a structure for blue phase III, the blue fog, which has been the subject of a long debate in liquid crystal physics. We propose that blue phase III is an amorphous network of disclination lines, which is thermodynamically and kinetically stabilized over crystalline blue phases at intermediate chiralities. This amorphous network becomes ordered under an applied electric field, as seen in experiments.

Thermodynamics of blue phases in electric fields.

We present extensive numerical studies to determine the phase diagrams of cubic and hexagonal blue phases in an electric field. We confirm the earlier prediction that hexagonal phases, both two and three dimensional, are stabilized by a field, but we significantly refine the phase boundaries, which were previously estimated by means of a semianalytical approximation. In particular, our simulations show that the blue phase I-blue phase II transition at fixed chirality is largely unaffected by electric field, as observed experimentally.

Shear stresses of colloidal dispersions at the glass transition in equilibrium and in flow.

We consider a model dense colloidal dispersion at the glass transition, and investigate the connection between equilibrium stress fluctuations, seen in linear shear moduli, and the shear stresses under strong flow conditions far from equilibrium, viz., flow curves for finite shear rates. To this purpose, thermosensitive core-shell particles consisting of a polystyrene core and a cross-linked poly(N-isopropylacrylamide) shell were synthesized. Data over an extended range in shear rates and frequencies are compared to theoretical results from integrations through transients and mode coupling approaches. The connection between nonlinear rheology and glass transition is clarified. While the theoretical models semiquantitatively fit the data taken in fluid states and the predominant elastic response of glass, a yet unaccounted dissipative mechanism is identified in glassy states.

Bond formation and slow heterogeneous dynamics in adhesive spheres with long-ranged repulsion: quantitative test of mode coupling theory.

A colloidal system of spheres interacting with both a deep and narrow attractive potential and a shallow long-ranged barrier exhibits a prepeak in the static structure factor. This peak can be related to an additional mesoscopic length scale of clusters and/or voids in the system. Simulation studies of this system have revealed that it vitrifies upon increasing the attraction into a gel-like solid at intermediate densities. The dynamics at the mesoscopic length scale corresponding to the prepeak represents the slowest mode in the system. Using mode coupling theory with all input directly taken from simulations, we reveal the mechanism for glassy arrest in the system at 40% packing fraction. The effects of the low-q peak and of polydispersity are considered in detail. We demonstrate that the local formation of physical bonds is the process whose slowing down causes arrest. It remains largely unaffected by the large-scale heterogeneities, and sets the clock for the slow cluster mode. Results from mode-coupling theory without adjustable parameters agree semiquantitatively with the local density correlators but overestimate the lifetime of the mesoscopic structure (voids).

Thermosensitive core-shell particles as model systems for studying the flow behavior of concentrated colloidal dispersions.

We report on a comprehensive investigation of the flow behavior of colloidal thermosensitive core-shell particles at high densities. The particles consist of a solid core of poly(styrene) onto which a network of cross-linked poly(N-isopropylacrylamide) is affixed. Immersed in water the shell of these particles will swell if the temperature is low. Raising the temperature above 32 degrees C leads to a volume transition within this shell which leads to a marked shrinking of the shell. The particles have well-defined core-shell structure and a narrow size distribution. The remaining electrostatic interactions due to a small number of charges affixed to the core particles can be screened by adding 0.05M KCl to the suspensions. Below the lower critical solution temperature at 32 degrees C the particles are purely repulsive. Above this transition, a thermoreversible coagulation takes place. Lowering the temperature again leads to full dissociation of the aggregates formed by this process. The particles crystallize for effective volume fractions between 0.48 and 0.55. The crystallites can be molten by shear in order to reach a fluid sample again. The reduced shear stress measured in this metastable disordered state was found to be a unique function of the shear rate and the effective volume fraction. These reduced flow curves thus obtained can be described quantitatively by the theory of Fuchs and Cates [Phys. Rev. Lett. 89, 248304 (2002)] which is based on the mode-coupling theory of the glass transition.