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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(More)
We describe the enablement of the Ludwig lattice Boltzmann parallel fluid dynamics application, designed specifically for complex problems, for massively parallel GPU-accelerated architectures. NVIDIA CUDA is introduced into the existing C/MPI framework, and we have given careful consideration to maintainability in addition to performance. Significant(More)
Colloidal particles or nanoparticles, with equal affinity for two fluids, are known to adsorb irreversibly to the fluid-fluid interface. We present large-scale computer simulations of the demixing of a binary solvent containing such particles. The newly formed interface sequesters the colloidal particles; as the interface coarsens, the particles are forced(More)
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(More)
We simulate a colloidal particle (radius R) in a cholesteric liquid crystal (pitch p) with tangential order parameter alignment at the particle surface. The local defect structure evolves from a dipolar pair of surface defects (boojums) at small R/p to a pair of twisted disclination lines wrapping around the particle at larger values. On dragging the(More)
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(More)
We simulate by the lattice Boltzmann method the steady shearing of a binary fluid mixture with full hydrodynamics in three dimensions. Contrary to some theoretical scenarios, a dynamical steady state is attained with finite correlation lengths in all three spatial directions. Using large simulations, we obtain at moderately high Reynolds numbers apparent(More)