Biomedical subjects

J M Yeomans

Publications and source records attributed to J M Yeomans.

At least 19 recordsLinked to original sources

PubMed2007

Controlling drop size and polydispersity using chemically patterned surfaces.

We explore numerically the feasibility of using chemical patterning to control the size and polydispersity of micrometer-scale drops. The simulations suggest that it is possible to sort drops by size or wetting properties by using an array of hydrophilic stripes of different widths. We also demonstrate that monodisperse drops can be generated by exploiting the pinning of a drop on a hydrophilic stripe. Our results follow from using a lattice Boltzmann algorithm to solve the hydrodynamic equations of motion of the drops and demonstrate the applicability of this approach as a design tool for micofluidic devices with chemically patterned surfaces.

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PubMed2006

Shear thinning in dilute polymer solutions.

We use bead-spring models for a polymer coupled to a solvent described by multiparticle collision dynamics to investigate shear thinning effects in dilute polymer solutions. First, we consider the polymer motion and configuration in a shear flow. For flexible polymer models we find a sharp increase in the polymer radius of gyration and the fluctuations in the radius of gyration at a Weissenberg number approximately 1. We then consider the polymer viscosity and the effect of solvent quality, excluded volume, hydrodynamic coupling between the beads, and finite extensibility of the polymer bonds. We conclude that the excluded volume effect is the major cause of shear thinning in polymer solutions. Comparing the behavior of semiflexible chains, we find that the fluctuations in the radius of gyration are suppressed when compared to the flexible case. The shear thinning is greater and, as the rigidity is increased, the viscosity measurements tend to those for a multibead rod.

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PubMed2006

Lattice Boltzmann algorithm to simulate isotropic-nematic emulsions.

We present lattice Boltzmann simulations of the dynamical equations of motion of a drop of isotropic fluid in a nematic liquid crystal solvent, both in the absence and in the presence of an electric field. The coupled equations we solve are the Beris-Edward equations for the dynamics of the tensor order parameter describing the nematic solvent, the Cahn-Hilliard equation for the concentration evolution, and the Navier-Stokes equations for the determination of the instantaneous velocity field. We implement the lattice Boltzmann algorithm to ensure that spurious velocities are close to zero in equilibrium. We first study the effects of the liquid crystal elastic constant, K, anchoring strength, W, and surface tension, sigma, on the shape of the droplet and on the director field texture in equilibrium. We then consider how the drop behaves as the director field is switched by an applied electric field. We also show that the algorithm allows us to follow the motion of a drop of isotropic fluid placed in a liquid crystal cell with a tilted director field at the boundaries.

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PubMed2006

Lattice Boltzmann simulations of phase separation in chemically reactive binary fluids.

We use a lattice Boltzmann method to study pattern formation in chemically reactive binary fluids in the regime where hydrodynamic effects are important. The coupled equations solved by the method are a Cahn-Hilliard equation, modified by the inclusion of a reactive source term, and the Navier-Stokes equations for conservation of mass and momentum. The coupling is twofold, resulting from the advection of the order parameter by the velocity field and the effect of fluid composition on pressure. We study the evolution of the system following a critical quench for a linear and for a quadratic reaction source term. Comparison is made between the high and low viscosity regimes to identify the influence of hydrodynamic flows. In both cases hydrodynamics is found to influence the pathways available for domain growth and the eventual steady states.

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PubMed2006

Permeative flows in cholesterics: shear and Poiseuille flows.

By using a lattice Boltzmann scheme that solves the Beris-Edwards equations of motion describing liquid-crystal hydrodynamics, we study the response of cholesterics to shear and Poiseuille flows. The geometry we focus on is a flow along the direction of the helical axis, which is known to give rise to permeation. For both shear and Poiseuille flow we find that the boundary conditions on the director field are crucial in determining the rheological properties of the liquid crystal. For helices pinned at the boundaries, a small forcing leads to a large viscosity increase whereas a stronger forcing induces a sharp decrease towards the Newtonian value. This shear thinning behavior is in agreement with experiments and previous analytic results. If, on the other hand, the director is free to rotate at the walls, different behaviors are found depending on the symmetry of the steady-state primary flow. Some of the cases considered are compared to a similar imposed flow but with the helix lying perpendicular to the plates, for which no viscosity increase is observed.

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PubMed2006

Polymer packaging and ejection in viral capsids: shape matters.

We use a mesoscale simulation approach to explore the impact of different capsid geometries on the packaging and ejection dynamics of polymers of different flexibility. We find that both packing and ejection times are faster for flexible polymers. For such polymers a sphere packs more quickly and ejects more slowly than an ellipsoid. For semiflexible polymers, however, the case relevant to DNA, a sphere both packs and ejects more easily. We interpret our results by considering both the thermodynamics and the relaxational dynamics of the polymers. The predictions could be tested with biomimetic experiments with synthetic polymers inside artificial vesicles. Our results suggest that phages may have evolved to be roughly spherical in shape to optimize the speed of genome ejection, which is the first stage in infection.

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PubMed2005

Polymer translocation: the effect of backflow.

We investigate the effect of backflow on the translocation dynamics of short, flexible polymer chains threading through a small hole in a wall. We find that hydrodynamic interactions between polymer beads play an important role in determining the translocation time distribution: as a monomer moves through the hole it sets up a flow field which transfers momentum to neighboring monomers, thus helping them to move in the same direction. Translocation times are calculated by using the velocity-Verlet algorithm to solve the equations of motion of a polymer which moves in a fluid described by the stochastic rotation algorithm, a particle-based Navier-Stokes solver.

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PubMed2005

Rheology of cholesteric blue phases.

Cholesteric blue phases are a spectacular example of disclination line networks. Here we numerically investigate their response to an imposed Poiseuille flow. We show that shear forces bend and twist and can unzip the disclination lines. Under gentle forcing the network opposes the flow and the apparent viscosity is large. With increased forcing we find strong shear thinning corresponding to the disruption of the network. As the viscosity starts to drop, the imposed flow sets the network into motion. Disclinations break up and re-form with their neighbors along the flow.

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PubMed2005

Pattern formation arising from condensation of a homogeneous gas into a binary, phase-separating liquid.

We examine the nucleated growth of a binary, immiscible liquid drop within a homogeneous gas. The system couples the growth of the liquid drop with the phase separation of the immiscible components and, thus, can potentially reveal novel pattern formation. To carry out this study, we first characterize the thermodynamic properties of the system in terms of an appropriate Ginzburg-Landau free energy density. By minimizing this free energy, we construct the equilibrium phase diagram for the system. We then use a lattice Boltzmann algorithm to solve the hydrodynamic equations describing the dynamical evolution of the fluid. We observe intriguing tentaclelike structures within the nucleation and growth regime and explore how the formation of these structures depends on the thermodynamic and transport properties of the system. We give scaling laws describing domain growth in both the diffusion- and flow-limited regimes. The results highlight the novel physics that can emerge when there is interplay between the ordering of a density and a concentration field.

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PubMed2005

Kinetics of the polymer collapse transition: the role of hydrodynamics.

We investigate numerically the dynamical behavior of a polymer chain collapsing in a dilute solution. The rate of collapse is measured with and without the presence of hydrodynamic interactions. We find that hydrodynamic interactions accelerate polymer collapse. We present a scaling theory describing the physical process responsible for the collapse kinetics. Predicted collapse times in a hydrodynamic (tauH approximately N(4/3)) and a Brownian heat bath (tauB approximately N2) agree well with the numerical results (tauH approximately N(1.40+/-0.08) and tauB approximately N(1.89+/-0.09)) where N denotes chain length. The folding kinetics of Go models of proteins is also examined. We show that for these systems, where many free energy minima compete, hydrodynamics has little effect on the kinetics.

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PubMed2005

Modeling a tethered polymer in Poiseuille flow.

We investigate the behavior of a tethered polymer in Poiseuille flow using a multiscale algorithm. The polymer, treated using molecular dynamics, is coupled to a solvent modeled by the stochastic rotation algorithm, a particle-based Navier-Stokes integrator. The expected series of morphological transitions of the polymer: sphere to distorted sphere to trumpet to stem and flower to rod are recovered, and we discuss how the polymer extension depends on the flow velocity. Backflow effects cause an effective increase in viscosity, which appears to be primarily due to the fluctuations of the free end of the polymer.

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PubMed2005

Kinetic theory derivation of the transport coefficients of stochastic rotation dynamics.

We use a kinetic theory approach to derive the continuum Navier-Stokes and heat conduction equations for stochastic rotation dynamics, a particle based algorithm for simulating a fluid. Hence we obtain expressions for the viscosity and thermal conductivity in two and three dimensions. The predictions are tested numerically and good agreement is found.

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PubMed2005

Modeling droplets on superhydrophobic surfaces: equilibrium states and transitions.

We present a lattice Boltzmann solution of the equations of motion describing the spreading of droplets on topologically patterned substrates. We apply it to model superhydrophobic behavior on surfaces covered by an array of micrometer-scale posts. We find that the patterning results in a substantial increase in contact angle, from 110 degrees to 156 degrees. The dynamics of the transition from drops suspended on top of the posts to drops collapsed in the grooves is described.

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PubMed2005

Numerical calculations of the phase diagram of cubic blue phases in cholesteric liquid crystals.

We study the static properties of cubic blue phases by numerically minimizing the three-dimensional, Landau-de Gennes free energy for a cholesteric liquid crystal close to the isotropic-cholesteric phase transition. Thus we are able to refine the powerful but approximate, semianalytic frameworks that have been used previously. We obtain the equilibrium phase diagram and discuss it in relation to previous results. We find that the value of the chirality above which blue phases appear is shifted by 20% (toward experimentally more accessible regions) with respect to previous estimates. We also find that the region of stability of the O5 structure-which has not been observed experimentally-shrinks, while that of blue phase I ( O-8 ) increases thus giving the correct order of appearance of blue phases at small chirality. We also study the approach to equilibrium starting from the infinite chirality solutions and we find that in some cases the disclination network has to assemble during the equilibration. In these situations disclinations are formed via the merging of isolated aligned defects.

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PubMed2004

Dynamics of polymer packaging.

We use the stochastic rotation dynamics algorithm to investigate the packaging of flexible and semiflexible polymers into a capsid that is permeable to solvent molecules. The model takes into account hydrodynamic interactions arising due to local flow. The flexible chain maintains a random configuration as it is being fed into the capsid, in contrast to the semiflexible chain, whose configuration is initially spool-like, becoming more random at high packing. We measure the packing rate, which is found to decrease with the percentage of the chain packed and highlight the difference between the flexible and semiflexible chains. Reflecting experiments, we find pauses in the packing process for individual chains as the motor loses grip of the fluctuating beads. We also find that hydrodynamics is important, in that the packaging rate is faster when flow is included.

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PubMed2004

Pattern formation in binary fluids confined between rough, chemically heterogeneous surfaces.

Using a mesoscale model for hydrodynamics, we simulate driven flow of AB binary fluids past surfaces that contain well-defined roughness or asperities. The geometry and wetting properties of the asperities are found to have a dramatic effect on the flow patterns. We isolate conditions where the A fluid forms vertical bands that bridge the asperities and an imposed shear (or pressure gradient) drives the system to form monodisperse droplets of A within the B fluid. The size of the droplets can be tailored by varying the morphology of the asperities. The surfaces needed to create this rich dynamical behavior are used as the stamps in microcontact printing; thus, the parameter space can readily be accessed experimentally, and the predictions suggest an efficient method for forming emulsions with well-controlled morphologies.

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PubMed2004

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.

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PubMed2004

Lattice Boltzmann algorithm for three-dimensional liquid-crystal hydrodynamics.

We describe a lattice Boltzmann algorithm to simulate liquid-crystal hydrodynamics in three dimensions. The equations of motion are written in terms of a tensor order parameter. This allows both the isotropic and the nematic phases to be considered. Backflow effects and the hydrodynamics of topological defects are naturally included in the simulations, as are viscoelastic effects such as shear-thinning and shear-banding. We describe the implementation of velocity boundary conditions and show that the algorithm can be used to describe optical bounce in twisted nematic devices and secondary flow in sheared nematics with an imposed twist.

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