Hydrodynamic oscillations and variable swimming speed in squirmers close to repulsive walls.

We present a lattice Boltzmann study of the hydrodynamics of a fully resolved squirmer, confined in a slab of fluid between two no-slip walls. We show that the coupling between hydrodynamics and short-range repulsive interactions between the swimmer and the surface can lead to hydrodynamic trapping of both pushers and pullers at the wall, and to hydrodynamic oscillations in the case of a pusher. We further show that a pusher moves significantly faster when close to a surface than in the bulk, whereas a puller undergoes a transition between fast motion and a dynamical standstill according to the range of the repulsive interaction. Our results critically require near-field hydrodynamics and demonstrate that far-field hydrodynamics is insufficient to give even a qualitatively correct account of swimmer behaviour near walls. Finally our simulations suggest that it should be possible to control the density and speed of squirmers at a surface by tuning the range of steric and electrostatic swimmer-wall interactions.

Quantitative morphological characterization of bicontinuous Pickering emulsions via interfacial curvatures.

Bicontinuous Pickering emulsions (bijels) are a physically interesting class of soft materials with many potential applications including catalysis, microfluidics and tissue engineering. They are created by arresting the spinodal decomposition of a partially-miscible liquid with a (jammed) layer of interfacial colloids. Porosity L (average interfacial separation) of the bijel is controlled by varying the radius (r) and volume fraction (ϕ) of the colloids (L∝r/ϕ). However, to optimize the bijel structure with respect to other parameters, e.g. quench rate, characterizing by L alone is insufficient. Hence, we have used confocal microscopy and X-ray CT to characterize a range of bijels in terms of local and area-averaged interfacial curvatures; we further demonstrate that bijels are bicontinuous using an image-analysis technique known as 'region growing'. In addition, the curvatures of bijels have been monitored as a function of time, which has revealed an intriguing evolution up to 60 minutes after bijel formation, contrary to previous understanding.

Simulating dynamics of ellipsoidal particles using lattice Boltzmann method.

Anisotropic particles are often encountered in different fields of soft matter and complex fluids. In this work, we present an implementation of the coupled hydrodynamics of solid ellipsoidal particles and the surrounding fluid using the lattice Boltzmann method. A standard link-based mechanism is used to implement the solid-fluid boundary conditions. We develop an implicit method to update the position and orientation of the ellipsoid. This exploits the relations between the quaternion which describes the ellipsoid's orientation and the ellipsoid's angular velocity to obtain a stable and robust dynamic update. The proposed algorithm is validated by looking at four scenarios: (i) the steady translational velocity of a spheroid subject to an external force in different orientations, (ii) the drift of an inclined spheroid subject to an imposed force, (iii) three-dimensional rotational motions in a simple shear flow (Jeffrey's orbits), and (iv) developed fluid flows and self-propulsion exhibited by a spheroidal microswimmer. In all cases the comparison of numerical results shows good agreement with known analytical solutions, irrespective of the choice of the fluid properties, geometrical parameters, and lattice Boltzmann model, thus demonstrating the robustness of the proposed algorithm.

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.

Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model.

Circadian clocks generate 24-h rhythms that are entrained by the day/night cycle. Clock circuits include several light inputs and interlocked feedback loops, with complex dynamics. Multiple biological components can contribute to each part of the circuit in higher organisms. Mechanistic models with morning, evening and central feedback loops have provided a heuristic framework for the clock in plants, but were based on transcriptional control. Here, we model observed, post-transcriptional and post-translational regulation and constrain many parameter values based on experimental data. The model's feedback circuit is revised and now includes PSEUDO-RESPONSE REGULATOR 7 (PRR7) and ZEITLUPE. The revised model matches data in varying environments and mutants, and gains robustness to parameter variation. Our results suggest that the activation of important morning-expressed genes follows their release from a night inhibitor (NI). Experiments inspired by the new model support the predicted NI function and show that the PRR5 gene contributes to the NI. The multiple PRR genes of Arabidopsis uncouple events in the late night from light-driven responses in the day, increasing the flexibility of rhythmic regulation.

Bijels containing magnetic particles: a simulation study.

Bicontinuous, interfacially jammed emulsion gels (bijels) represent a class of soft solid materials in which interpenetrating domains of two immiscible fluids are stabilized by an interfacial colloidal monolayer. Such structures can be formed by arrested spinodal decomposition from an initially single-phase colloidal suspension. Here, we explore by lattice Boltzmann simulation the possible effects of using magnetic colloids in bijels. This may allow additional control over the structure, during or after formation, by application of a magnetic field or field gradient. These effects are modest for typical parameters based on the magnetic nanoparticles used in conventional ferrofluids, although significantly larger particles might be appropriate here. Field gradient effects, which are cumulative across a sample, could then allow a route for controlled breakdown of bijels as they do for particle-stabilized droplet emulsions.

Hydrodynamic interactions in colloidal ferrofluids: a lattice Boltzmann study.

We use lattice Boltzmann simulations, in conjunction with Ewald summation methods, to investigate the role of hydrodynamic interactions in colloidal suspensions of dipolar particles, such as ferrofluids. Our work addresses volume fractions phi of up to 0.20 and dimensionless dipolar interaction parameters lambda of up to 8. We compare quantitatively with Brownian dynamics simulations, in which many-body hydrodynamic interactions are absent. Monte Carlo data are also used to check the accuracy of static properties measured with the lattice Boltzmann technique. At equilibrium, hydrodynamic interactions slow down both the long-time and the short-time decays of the intermediate scattering function S(q, t), for wavevectors close to the peak of the static structure factor S(q), by a factor of roughly two. The long-time slowing is diminished at high interaction strengths, whereas the short-time slowing (quantified via the hydrodynamic factor H(q)) is less affected by the dipolar interactions, despite their strong effect on the pair distribution function arising from cluster formation. Cluster formation is also studied in transient data following a quench from lambda = 0; hydrodynamic interactions slow the formation rate, again by a factor of roughly two.

Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.

Our understanding of the complex, transcriptional feedback loops in the circadian clock mechanism has depended upon quantitative, timeseries data from disparate sources. We measure clock gene RNA profiles in Arabidopsis thaliana seedlings, grown with or without exogenous sucrose, or in soil-grown plants and in wild-type and mutant backgrounds. The RNA profiles were strikingly robust across the experimental conditions, so current mathematical models are likely to be broadly applicable in leaf tissue. In addition to providing reference data, unexpected behaviours included co-expression of PRR9 and ELF4, and regulation of PRR5 by GI. Absolute RNA quantification revealed low levels of PRR9 transcripts (peak approx. 50 copies cell(-1)) compared with other clock genes, and threefold higher levels of LHY RNA (more than 1500 copies cell(-1)) than of its close relative CCA1. The data are disseminated from BioDare, an online repository for focused timeseries data, which is expected to benefit mechanistic modelling. One data subset successfully constrained clock gene expression in a complex model, using publicly available software on parallel computers, without expert tuning or programming. We outline the empirical and mathematical justification for data aggregation in understanding highly interconnected, dynamic networks such as the clock, and the observed design constraints on the resources required to make this approach widely accessible.

Field-induced breakup of emulsion droplets stabilized by colloidal particles.

We simulate the response of a particle-stabilized emulsion droplet in an external force field, such as gravity, acting equally on all N particles. We show that the field strength required for breakup (at fixed initial area fraction) decreases markedly with droplet size, because the forces act cumulatively, not individually, to detach the interfacial particles. The breakup mode involves the collective destabilization of a solidified particle raft occupying the lower part of the droplet, leading to a critical force per particle that scales approximately as N(-1/2).

Cultural hitchhiking on the wave of advance of beneficial technologies.

The wave-of-advance model was introduced to describe the spread of advantageous genes in a population. It can be adapted to model the uptake of any advantageous technology through a population, such as the arrival of neolithic farmers in Europe, the domestication of the horse, and the development of the wheel, iron tools, political organization, or advanced weaponry. Any trait that preexists alongside the advantageous one could be carried along with it, such as genetics or language, regardless of any intrinsic superiority. Decoupling of the advantageous trait from other "hitchhiking" traits depends on its adoption by the preexisting population. Here, we adopt a similar wave-of-advance model based on food production on a heterogeneous landscape with multiple populations. Two key results arise from geographic inhomogeneity: the "subsistence boundary," land so poor that the wave of advance is halted, and the temporary "diffusion boundary" where the wave cannot move into poorer areas until its gradient becomes sufficiently large. At diffusion boundaries, farming technology may pass to indigenous people already in those poorer lands, allowing their population to grow and resist encroachment by farmers. Ultimately, this adoption of technology leads to the halt in spread of the hitchhiking trait and establishment of a permanent "cultural boundary" between distinct cultures with equivalent technology.