Christopher Pooley

Transport coefficients of a mesoscopic fluid dynamics model

We investigate the properties of stochastic rotation dynamics, a mesoscopic model used for simulating fluctuating hydrodynamics. Analytical results are given for the shear viscosity and the friction exerted on a massive solute particle moving within the fluid. We discuss an efficient way of measuring the shear viscosity and viscous friction, and obtain excellent agreement between the theoretical and numerical calculations.

Eliminating spurious velocities in the free-energy lattice Boltzmann method.

Spurious velocities are unphysical currents that appear close to curved interfaces in diffuse interface methods. We analyze the causes of these spurious velocities in the free-energy lattice Boltzmann algorithm. By making a suitable choice of the equilibrium distribution, and by finding the best way to numerically calculate derivatives, we show that these velocities may be decreased by an order of magnitude compared to previous models. Furthermore, we propose a momentum conserving forcing method that reduces spurious velocities by another factor of approximately 5. In three dimensions we find that 19 velocity vectors is the minimum number necessary.

Capillary filling in patterned channels.

We show how the capillary filling of microchannels is affected by posts or ridges on the sides of the channels. Ridges perpendicular to the flow direction introduce contact line pinning, which slows, or sometimes prevents, filling, whereas ridges parallel to the flow provide extra surface that may enhance filling. Patterning the microchannel surface with square posts has little effect on the ability of a channel to fill for equilibrium contact angle theta_{e} less than approximately 30 degrees . For theta_{e} greater than approximately 60 degrees , however, even a small number of posts can pin the advancing liquid front.

Modeling microscopic swimmers at low Reynolds number.

The authors employ three numerical methods to explore the motion of low Reynolds number swimmers, modeling the hydrodynamic interactions by means of the Oseen tensor approximation, lattice Boltzmann simulations, and multiparticle collision dynamics. By applying the methods to a three bead linear swimmer, for which exact results are known, the authors are able to compare and assess the effectiveness of the different approaches. They then propose a new class of low Reynolds number swimmers, generalized three bead swimmers that can change both the length of their arms and the angle between them. Hence they suggest a design for a microstructure capable of moving in three dimensions. They discuss multiple bead, linear microstructures and show that they are highly efficient swimmers. They then turn to consider the swimming motion of elastic filaments. Using multiparticle collision dynamics the authors show that a driven filament behaves in a qualitatively similar way to the micron-scale swimming device recently demonstrated by Dreyfus et al. [Nature (London) 437, 862 (2005)].

Contact line dynamics in binary lattice Boltzmann simulations

We show that, when a single relaxation time lattice Boltzmann algorithm is used to solve the hydrodynamic equations of a binary fluid for which the two components have different viscosities, strong spurious velocities in the steady state lead to incorrect results for the equilibrium contact angle. We identify the origins of these spurious currents and demonstrate how the results can be greatly improved by using a lattice Boltzmann method based on a multiple-relaxation-time algorithm. By considering capillary filling we describe the dependence of the advancing contact angle on the interface velocity.

Hydrodynamics of linked sphere model swimmers.

We describe in detail the hydrodynamics of a simple model of linked sphere swimmers. We calculate the asymptotic form of both the time averaged flow field generated by a single swimmer and the interactions between swimmers in a dilute suspension, showing how each depends on the parameters describing the swimmer and its swimming stroke. We emphasize the importance of time reversal symmetry in determining the far field flow around a swimmer and show that the interactions between swimmers are highly dependent on the relative phase of their swimming strokes.

Scattering of low-Reynolds-number swimmers

We describe the consequences of time-reversal invariance of the Stokes equations for the hydrodynamic scattering of two low-Reynolds-number swimmers. For swimmers that are related to each other by a time-reversal transformation, this leads to the striking result that the angle between the two swimmers is preserved by the scattering. The result is illustrated for the particular case of a linked-sphere model swimmer. For more general pairs of swimmers, not related to each other by time reversal, we find that hydrodynamic scattering can alter the angle between their trajectories by several tens of degrees. For two identical contractile swimmers, this can lead to the formation of a bound state.

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells

The generation of myeloid cells from their progenitors is regulated at the level of transcription by combinatorial control of key transcription factors influencing cell‐fate choice. To unravel the global dynamics of this process at the transcript level, we generated transcription profiles for 91 human cell types of myeloid origin by use of CAGE profiling. The CAGE sequencing of these samples has allowed us to investigate diverse aspects of transcription control during myelopoiesis, such as identification of novel transcription factors, miRNAs, and noncoding RNAs specific to the myeloid lineage. We further reconstructed a transcription regulatory network by clustering coexpressed transcripts and associating them with enriched cis‐regulatory motifs. With the use of the bidirectional expression as a proxy for enhancers, we predicted over 2000 novel enhancers, including an enhancer 38 kb downstream of IRF8 and an intronic enhancer in the KIT gene locus. Finally, we highlighted relevance of these data to dissect transcription dynamics during progressive maturation of granulocyte precursors. A multifaceted analysis of the myeloid transcriptome is made available (www.myeloidome.roslin.ed.ac.uk). This high‐quality dataset provides a powerful resource to study transcriptional regulation during myelopoiesis and to infer the likely functions of unannotated genes in human innate immunity.

Modeling the flow of complex fluids through heterogeneous channels

Computational modeling of the driven flow of multi-component fluids past chemically, physically and thermally heterogeneous substrates can provide insight into a variety of processes, from flow in microfluidic devices to polymer processing in reaction chambers. One of the challenges in modeling these systems is capturing the close interplay between hydrodynamics and thermodynamics. The lattice Boltzmann method (LBM) provides a computationally efficient method for carrying out such investigations. We review recent studies using the LBM to examine the flow of partially miscible binary fluids through channels that contain chemically, topographically or thermally patterned substrates. The findings highlight how the substrates can be modified to yield the required behavior at fluid/surface and fluid/fluid interfaces and consequently, the desired macroscopic properties. Specifically, the results provide guidelines for optimizing processes in microfluidic devices and in creating microemulsions with well-controlled morphologies. The studies also reveal new phenomena that arise from the interplay between flowing complex fluids and chemically, physically and thermally patterned confining walls.

Stripe formation in differentially forced binary systems

We consider pattern formation in periodically forced binary systems. In particular, we focus on systems in which the two species are differentially forced, one being accelerated with respect to the other. Using a continuum model consisting of two isothermal ideal gases which interact via a frictional force we demonstrate analytically that stripes form spontaneously above a critical forcing amplitude. The wavelength of the stripes is found to be close to the wavelength of sound in the limit of small viscosity. The results are confirmed numerically. We suggest that the same mechanism may contribute to the formation of stripes in experiments on horizontally oscillated granular mixtures.