Kevin Stratford

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 models 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.

Fluctuating lattice Boltzmann

The lattice Boltzmann algorithm efficiently simulates the Navier-Stokes equation of isothermal fluid flow, but ignores thermal fluctuations of the fluid, important in mesoscopic flows. We show how to adapt the algorithm to include noise, satisfying a fluctuation-dissipation theorem (FDT) directly at lattice level: this gives correct fluctuations for mass and momentum densities, and for stresses, at all wave vectors k. Unlike previous work, which recovers FDT only as k → 0, our algorithm offers full statistical mechanical consistency in mesoscale simulations of, e.g., fluctuating colloidal hydrodynamics.

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 stabilised over crystalline blue phases at intermediate chiralities. This amorphous network becomes ordered under an applied electric field, as seen in experiments.

Lattice Boltzmann simulations of liquid crystalline fluids: active gels and blue phases

Lattice Boltzmann simulations have become the method of choice to solve the hydrodynamic equations of motion of a number of complex fluids. Here we review some recent applications of lattice Boltzmann to study the hydrodynamics of liquid crystalline materials. In particular, we focus on the study of (a) the exotic blue phases of cholesteric liquid crystals, and (b) active gels—a model system for actin plus myosin solutions or bacterial suspensions. In both cases lattice Boltzmann studies have proved useful to provide new insights into these complex materials.

Simulating colloid hydrodynamics with lattice Boltzmann methods

We present a progress report on our work on lattice Boltzmann methods for colloidal suspensions. We focus on the treatment of colloidal particles in binary solvents and on the inclusion of thermal noise. For a benchmark problem of colloids sedimenting and becoming trapped by capillary forces at a horizontal interface between two fluids, we discuss the criteria for parameter selection, and address the inevitable compromise between computational resources and simulation accuracy.

Parallel simulation of particle suspensions with the lattice Boltzmann method

A description of the steps taken to produce a massively parallel code for particle suspension problems using the lattice Boltzmann method is presented. A number of benchmarks based on a binary fluid lattice Boltzmann model are used to assess the performance of the code in terms of the computational overhead required for the particle problem compared with the fluid-only problem, and for the scaling of the code to large processor numbers. On the Blue Gene/L architecture, the additional computational cost of particle suspensions of up to 40% solid volume fraction (here over a million particles) is negligible compared with the fluid-only code.

Lattice Boltzmann for Binary Fluids with Suspended Colloids

A new description of the binary fluid problem via the lattice Boltzmann method is presented which highlights the use of the moments in constructing two equilibrium distribution functions. This offers a number of benefits, including better isotropy, and a more natural route to the inclusion of multiple relaxation times for the binary fluid problem. In addition, the implementation of solid colloidal particles suspended in the binary mixture is addressed, which extends the solid–fluid boundary conditions for mass and momentum to include a single conserved compositional order parameter. A number of simple benchmark problems involving a single particle at or near a fluid–fluid interface are undertaken and show good agreement with available theoretical or numerical results

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.

Modelling changes in Mediterranean thermohaline circulation 1987–1995

Abstract The observed changes in the eastern Mediterranean thermohaline circulation between 1987 and 1995 are investigated using an ocean general circulation model. A number of different surface forcing regimes are imposed to investigate the possible causes of the formation of new Aegean deep water. The formation and spreading of the Aegean deep water is assessed in terms of chlorofluorocarbon distributions and the changes in salt content in comparison with observation. It is found that three observed cold winters (of 1987, 1992 and 1993) are enough to generate new Aegean deep water in the model. The addition of anomalous winter wind stresses for the period 1988–1995 increases the southward transport of cool north Aegean water, but does not lead to a significant extra outflow of deep water. The modelled water properties agree well with the observation, but the overall volume of the new deep water is too low and there is no outflow at the straits to the west of Crete. The salt budget is examined to highlight the roles of both vertical redistribution and net inflow of salt at Sicily.

Colloidal templating at a cholesteric-oil interface: assembly guided by an array of disclination lines.

We simulate colloids (radius R ~ 1 μm) trapped at the interface between a cholesteric liquid crystal and an immiscible oil at which the helical order (pitch p) in the bulk conflicts with the orientation induced at the interface, stabilizing an ordered array of disclinations. For a weak anchoring strength W of the director field at the colloidal surface, this creates a template, favoring particle positions either on top of or midway between defect lines, depending on α=R/p. For small α, optical microscopy experiments confirm this picture, but for larger α no templating is seen. This may stem from the emergence at moderate W of a rugged energy landscape associated with defect reconnections.