Defect-influenced particle advection in highly confined liquid crystal flows.

We study the morphology of the Saturn ring defect and director structure around a colloidal particle with normal anchoring conditions and within the flow of the nematic host phase through a rectangular duct of comparable size to the particle. The changes in the defect structures and director profile influence the advection behaviour of the particle, which we compare to that in a simple Newtonian host phase. These effects lead to a non-monotonous dependence of the differential velocity of particle and fluid, also known as retardation ratio, on the Ericksen number.

Heterogeneous migration routes of DNA triplet repeat slip-outs.

It is unclear how the length of a repetitive DNA tract determines the onset and progression of repeat expansion diseases, but the dynamics of secondary DNA structures formed by repeat sequences are believed to play an important role. It was recently shown that three-way DNA junctions containing slip-out hairpins of CAG or CTG repeats and contiguous triplet repeats in the adjacent duplex displayed single-molecule FRET (smFRET) dynamics that were ascribed to both local conformational motions and longer-range branch migration. Here we explore these so-called "mobile" slip-out structures through a detailed kinetic analysis of smFRET trajectories and coarse-grained modeling. Despite the apparent structural simplicity, with six FRET states resolvable, most smFRET states displayed biexponential dwell-time distributions, attributed to structural heterogeneity and overlapping FRET states. Coarse-grained modeling for a (GAC)10 repeat slip-out included trajectories that corresponded to a complete round of branch migration; the structured free energy landscape between slippage events supports the dynamical complexity observed by smFRET. A hairpin slip-out with 40 CAG repeats, which is above the repeat length required for disease in several triplet repeat disorders, displayed smFRET dwell times that were on average double those of 3WJs with 10 repeats. The rate of secondary-structure rearrangement via branch migration, relative to particular DNA processing pathways, may be an important factor in the expansion of triplet repeat expansion diseases.

Controllable particle migration in liquid crystal flows.

We observe novel positional control of a colloidal particle in microchannel flow of a nematic liquid crystal. Lattice Boltzmann simulations show multiple equilibrium particle positions, the existence and position of which are tunable using the driving pressure, in direct contrast to the classical Segré-Silberberg effect in isotropic liquids. In addition, particle migration in nematic flow occurs an order of magnitude faster. These new equilibria are determined through a balance of elastic forces, hydrodynamic lift and drag as well as order-flow interactions through the defect structure around the particle.

Shear-enhanced elasticity in the cubic blue phase I.

We present results of the linear and nonlinear rheology of the cubic blue phase I (BPI). The elasticity of BPI is dominated by double-twist cylinders assembled in a body-centered cubic lattice, which can be specified by disclination lines. We find that the elasticity of BPI is enhanced by an order of magnitude by applying pre-shear. The shear-enhanced elasticity is attributed to a rearrangement of the disclination lines that are arrested in a metastable state. Our results are relevant for the understanding of the dynamics of disclinations in the cubic blue phases.

Coarse-grained simulation of DNA using LAMMPS : An implementation of the oxDNA model and its applications.

During the last decade coarse-grained nucleotide models have emerged that allow us to study DNA and RNA on unprecedented time and length scales. Among them is oxDNA, a coarse-grained, sequence-specific model that captures the hybridisation transition of DNA and many structural properties of single- and double-stranded DNA. oxDNA was previously only available as standalone software, but has now been implemented into the popular LAMMPS molecular dynamics code. This article describes the new implementation and analyses its parallel performance. Practical applications are presented that focus on single-stranded DNA, an area of research which has been so far under-investigated. The LAMMPS implementation of oxDNA lowers the entry barrier for using the oxDNA model significantly, facilitates future code development and interfacing with existing LAMMPS functionality as well as other coarse-grained and atomistic DNA models.

Mesoscopic modelling and simulation of soft matter.

The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We review a number of the most popular simulation methods that have emerged, such as Langevin dynamics, dissipative particle dynamics, multi-particle collision dynamics, sometimes also referred to as stochastic rotation dynamics, and the lattice-Boltzmann method. We conclude this review with a short glance at current compute architectures for high-performance computing and community codes for soft matter simulation.

Microfluidic flow of cholesteric liquid crystals.

We explore the rheology and flow-induced morphological changes of cholesteric liquid crystal patterns subject to Poiseuille flow within a slab geometry, and under different anchoring conditions at the wall. Our focus is particularly on the behaviour of "Cholesteric Fingers of the first kind" and of Blue Phase II. Depending on the applied pressure gradient, we observe a number of dynamic regimes with different rheological properties. Our results provide the first insight into the flow response of cholesteric phases with fully two- or three-dimensional director field patterns and normal and planar degenerate anchoring conditions as commonly realised in experiments. They are also of high relevance for a fundamental understanding of complex liquid crystals in confinement and an important step towards future microfluidic applications that are based on cholesteric liquid crystals.

Ordering dynamics of blue phases entails kinetic stabilization of amorphous networks.

The cubic blue phases of liquid crystals are fascinating and technologically promising examples of hierarchically structured soft materials, comprising ordered networks of defect lines (disclinations) within a liquid crystalline matrix. We present large-scale simulations of their domain growth, starting from a blue phase nucleus within a supercooled isotropic or cholesteric background. The nucleated phase is thermodynamically stable; one expects its slow orderly growth, creating a bulk cubic phase. Instead, we find that the strong propensity to form disclinations drives the rapid disorderly growth of a metastable amorphous defect network. During this process, the original nucleus is destroyed; reemergence of the stable phase may therefore require a second nucleation step. Our findings suggest that blue phases exhibit hierarchical behavior in their ordering dynamics, to match the hierarchy in their structure.

Hard discs under steady shear: comparison of Brownian dynamics simulations and mode coupling theory.

Brownian dynamics simulations of bidisperse hard discs moving in two dimensions in a given steady and homogeneous shear flow are presented close to and above the glass transition density. The stationary structure functions and stresses of shear-melted glass are compared quantitatively to parameter-free numerical calculations of monodisperse hard discs using mode coupling theory within the integration through transients framework. Theory qualitatively explains the properties of the yielding glass but quantitatively overestimates the shear-driven stresses and structural anisotropies.