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- Alexandra Pokhilko, Sarah K Hodge, +5 authors Andrew J Millar
- Molecular systems biology
- 2010

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)

- Alan Gray, Alistair Hart, Alan Richardson, Kevin Stratford
- PARCO
- 2011

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)

- R Adhikari, K Stratford, M E Cates, A J Wagner
- 2005

– 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… (More)

- K Stratford, R Adhikari, I Pagonabarraga, J-C Desplat, M E Cates
- Science
- 2005

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)

- Mike Ashworth, Ian J. Bush, +6 authors Alessandro Curioni
- Concurrency - Practice and Experience
- 2005

- K. Stratford
- 2005

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… (More)

- Kevin Stratford, Ignacio Pagonabarraga
- Computers & Mathematics with Applications
- 2008

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)

- J S Lintuvuori, K Stratford, M E Cates, D Marenduzzo
- Physical review letters
- 2010

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)

- Anna Flis, Aurora Piñas Fernández, +11 authors Andrew J Millar
- Open biology
- 2015

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)

- K Stratford, J-C Desplat, P Stansell, M E Cates
- Physical review. E, Statistical, nonlinear, and…
- 2007

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)