arXiv subjects

Wilson C. K. Poon

Publications and source records attributed to Wilson C. K. Poon.

52 records · Page 3Linked to original sources

arXiv2015

Escherichia coli as a model active colloid: a practical introduction

The flagellated bacterium Escherichia coli is increasingly used experimentally as a self-propelled swimmer. To obtain meaningful, quantitative results that are comparable between different laboratories, reproducible protocols are needed to control, `tune' and monitor the swimming behaviour of these motile cells. We critically review the knowledge needed to do so, explain methods for characterising the colloidal and motile properties of E.coli, cells, and propose a protocol for keeping them swimming at constant speed at finite bulk concentrations. In the process of establishing this protocol, we use motility as a high-throughput probe of aspects of cellular physiology via the coupling between swimming speed and the proton motive force.

cond-mat.soft↗

arXiv2014

Flagellated bacterial motility in polymer solutions

It is widely believed that the swimming speed, $v$, of many flagellated bacteria is a non-monotonic function of the concentration, $c$, of high-molecular-weight linear polymers in aqueous solution, showing peaked $v(c)$ curves. Pores in the polymer solution were suggested as the explanation. Quantifying this picture led to a theory that predicted peaked $v(c)$ curves. Using new, high-throughput methods for characterising motility, we have measured $v$, and the angular frequency of cell-body rotation, $Ω$, of motile Escherichia coli as a function of polymer concentration in polyvinylpyrrolidone (PVP) and Ficoll solutions of different molecular weights. We find that non-monotonic $v(c)$ curves are typically due to low-molecular weight impurities. After purification by dialysis, the measured $v(c)$ and $Ω(c)$ relations for all but the highest molecular weight PVP can be described in detail by Newtonian hydrodynamics. There is clear evidence for non-Newtonian effects in the highest molecular weight PVP solution. Calculations suggest that this is due to the fast-rotating flagella `seeing' a lower viscosity than the cell body, so that flagella can be seen as nano-rheometers for probing the non-Newtonian behavior of high polymer solutions on a molecular scale.

cond-mat.soft↗

arXiv2014

Effects of the Carnahan-Starling free energy within theories of fluids with short-range attraction

Within the Free-Volume Asakura-Oosawa-Vrij (FVAO) theory of colloid-polymer mixtures, we show that unphysical gas-liquid binodals predicted in the regime of small attraction range (i.e. polymer size) are caused in part by the use of the Carnahan-Starling (CS) hard sphere (HS) reference free energy. Replacement of the CS expression with an alternative dramatically affects predicted phase behaviour and, for polydisperse colloid, the resultant fractionation predictions. Although short-range attractions render FVAO, as a perturbative HS-based theory, less accurate anyway, we argue that the particular effects of CS in this regime are an important consideration -- usually ignored -- in the evaluation of such theories. We refer to a variety of literature exhibiting similarly inaccurate gas-liquid binodals, and suggest CS's status as the de facto choice of hard sphere reference should be carefully considered where short-range attractions are present.

cond-mat.soft↗

arXiv2013

On polydispersity and the hard-sphere glass transition

We simulate the dynamics of polydisperse hard spheres at high packing fractions, $ϕ$, with an experimentally-realistic particle size distribution (PSD) and other commonly-used PSDs such as gaussian or top hat. We find that the mode of kinetic arrest depends on the PSD's shape and not only on its variance. For the experimentally-realistic PSD, the largest particles undergo an ideal glass transition at $ϕ\sim 0.588$ while the smallest particles remain mobile. Such species-specific localisation was previously observed only in asymmetric binary mixtures. Our findings suggest that the recent observation of ergodic behavior up to $ϕ\sim 0.6$ in a hard-sphere system is not evidence for activated dynamics, but an effect of polydispersity.

cond-mat.soft↗

arXiv2013

Switching of swimming modes in Magnetospirillium gryphiswaldense

The microaerophilic magnetotactic bacterium Magnetospirillum gryphiswaldense swims along magnetic field lines using a single flagellum at each cell pole. It is believed that this magnetotactic behavior enables cells to seek optimal oxygen concentration with maximal efficiency. We analyse the trajectories of swimming M. gryphiswaldense cells in external magnetic fields larger than the earth's field, and show that each cell can switch very rapidly (in < 0.2 s) between a fast and a slow swimming mode. Close to a glass surface, a variety of trajectories was observed, from straight swimming that systematically deviates from field lines to various helices. A model in which fast (slow) swimming is solely due to the rotation of the trailing (leading) flagellum can account for these observations. We determined the magnetic moment of this bacterium using a new method, and obtained a value of (2.0 $\pm$ 0.6) $\times$ $10^{-16}$ Am$^2$. This value is found to be consistent with parameters emerging from quantitative fitting of trajectories to our model.

physics.bio-ph↗

arXiv2012

In Search of Colloidal Hard Spheres

We recently reviewed the experimental determination of the volume fraction, $ϕ$, of hard-sphere colloids, and concluded that the absolute value of $ϕ$ was unlikely to be known to better than $\pm 3$-6%. Here, in a second part to that review, we survey effects due to softness in the interparticle potential, which necessitates the use of an {\em effective} volume fraction. We review current experimental systems, and conclude that the one that most closely approximates hard spheres remains polymethylmethacrylate spheres sterically stabilised by polyhydroxystearic acid `hairs'. For these particles their effective hard sphere diameter is around 1-10% larger than the core diameter, depending on the particle size. We argue that for larger colloids suitable for confocal microscopy, the effect of electrostatic charge cannot be neglected, so that mapping to hard spheres must be treated with caution.

cond-mat.soft↗

arXiv2012

From compact to fractal crystalline clusters in concentrated systems of monodisperse hard spheres

We address the crystallization of monodisperse hard spheres in terms of the properties of finite- size crystalline clusters. By means of large scale event-driven Molecular Dynamics simulations, we study systems at different packing fractions ϕ ranging from weakly supersaturated state points to glassy ones, covering different nucleation regimes. We find that such regimes also result in different properties of the crystalline clusters: compact clusters are formed in the classical-nucleation-theory regime (ϕ \leq 0.54), while a crossover to fractal, ramified clusters is encountered upon increasing packing fraction (ϕ \geq 0.56), where nucleation is more spinodal-like. We draw an analogy between macroscopic crystallization of our clusters and percolation of attractive systems to provide ideas on how the packing fraction influences the final structure of the macroscopic crystals. In our previous work (Phys. Rev. Lett., 106, 215701, 2011), we have demonstrated how crystallization from a glass (at ϕ > 0.58) happens via a gradual (many-step) mechanism: in this paper we show how the mechanism of gradual growth seems to hold also in super-saturated systems just above freezing showing that static properties of clusters are not much affected by dynamics.

cond-mat.soft↗

arXiv2012

Differential Dynamic Microscopy: a High-Throughput Method for Characterizing the Motility of Microorganism

We present a fast, high-throughput method for characterizing the motility of microorganisms in 3D based on standard imaging microscopy. Instead of tracking individual cells, we analyse the spatio-temporal fluctuations of the intensity in the sample from time-lapse images and obtain the intermediate scattering function (ISF) of the system. We demonstrate our method on two different types of microorganisms: bacteria, both smooth swimming (run only) and wild type (run and tumble) Escherichia coli, and the bi-flagellate alga Chlamydomonas reinhardtii. We validate the methodology using computer simulations and particle tracking. From the ISF, we are able to extract (i) for E. coli: the swimming speed distribution, the fraction of motile cells and the diffusivity, and (ii) for C. reinhardtii: the swimming speed distribution, the amplitude and frequency of the oscillatory dynamics. In both cases, the motility parameters are averaged over \approx 10^4 cells and obtained in a few minutes.

physics.bio-ph↗

arXiv2011

On measuring colloidal volume fractions

Hard-sphere colloids are popular as models for testing fundamental theories in condensed matter and statistical physics, from crystal nucleation to the glass transition. A single parameter, the volume fraction (phi), characterizes an ideal, monodisperse hard-sphere suspension. In comparing experiments with theories and simulation, researchers to date have paid little attention to likely uncertainties in experimentally-quoted phi values. We critically review the experimental measurement of phi in hard-sphere colloids, and show that while statistical uncertainties in comparing relative values of phi can be as low as 0.0001, systematic errors of 3-6% are probably unavoidable. The consequences of this are illustrated by way of a case study comparing literature data sets on hard-sphere viscosity and diffusion.

cond-mat.soft↗

arXiv2011

Crystallization Mechanism of Hard Sphere Glasses

In supercooled liquids, vitrification generally suppresses crystallization. Yet some glasses can still crystallize despite the arrest of diffusive motion. This ill-understood process may limit the stability of glasses, but its microscopic mechanism is not yet known. Here we present extensive computer simulations addressing the crystallization of monodisperse hard-sphere glasses at constant volume (as in a colloid experiment). Multiple crystalline patches appear without particles having to diffuse more than one diameter. As these patches grow, the mobility in neighbouring areas is enhanced, creating dynamic heterogeneity with positive feedback. The future crystallization pattern cannot be predicted from the coordinates alone: crystallization proceeds by a sequence of stochastic micro-nucleation events, correlated in space by emergent dynamic heterogeneity.

physics.chem-ph↗

arXiv2010

Differential Dynamic Microscopy of Bacterial Motility

We demonstrate 'differential dynamic microscopy' (DDM) for the fast, high throughput characterization of the dynamics of active particles. Specifically, we characterize the swimming speed distribution and the fraction of motile cells in suspensions of Escherichia coli bacteria. By averaging over ~10^4 cells, our results are highly accurate compared to conventional tracking. The diffusivity of non-motile cells is enhanced by an amount proportional to the concentration of motile cells.

q-bio.QM↗

arXiv2010

Finding bridges in packings of colloidal spheres

We identify putative load-bearing structures (bridges) in experimental colloidal systems studied by confocal microscopy. Bridges are co-operative structures that have been used to explain stability and inhomogeneous force transmission in simulated granular packings with a range of densities. We show that bridges similar to those found in granular simulations are present in real experimental colloidal packings. We describe critically the bridge-finding procedure for real experimental data and propose a new criterion-Lowest Mean Squared Separation (LSQS)-for selecting optimum stabilisations.

cond-mat.soft↗

arXiv2008

Quantitative imaging of colloidal flows

We present recent advances in the instrumentation and analysis methods for quantitative imaging of concentrated colloidal suspensions under flow. After a brief review of colloidal imaging, we describe various flow geometries for two and and three-dimensional (3D) imaging, including a `confocal rheoscope'. This latter combination of a confocal microscope and a rheometer permits simultaneous characterization of rheological response and 3D microstructural imaging. The main part of the paper discusses in detail how to identify and track particles from confocal images taken during flow. After analyzing the performance of the most commonly used colloid tracking algorithm by Crocker and Grier extended to flowing systems, we propose two new algorithms for reliable particle tracking in non-uniform flows to the level of accuracy already available for quiescent systems. We illustrate the methods by applying it to data collected from colloidal flows in three different geometries (channel flow, parallel plate shear and cone-plate rheometry).

cond-mat.soft↗

arXiv2008

Velocity oscillations in confined channel flows of concentrated colloidal suspensions

We study the pressure-driven flow of concentrated colloids confined in glass micro-channels at the single particle level using fast confocal microscopy. For channel to particle size ratios $a/\bar{D} \lesssim 30$, the flow rate of the suspended particles shows fluctuations. These turn into regular oscillations for higher confinements ($a/\bar{D} \simeq 20$). We present evidence to link these oscillations with the relative flow of solvent and particles (permeation) and the effect of confinement on shear thickening.

cond-mat.soft↗

arXiv2005

Protein crystallization in vivo

Protein crystallization in vivo provides some fascinating examples of biological self-assembly. Here, we provide a selective survey to show the diversity of functions for which protein crystals are used, and the physical properties of the crystals thatare exploited. Where known, we emphasize how the nature of the protein-protein interactions leads to control of the crystallization behaviour.

q-bio.BM↗

arXiv1998

Spinodal-assisted crystallization in polymer melts

Recent experiments in some polymer melts quenched below the melting temperature have reported spinodal kinetics in small-angle X ray scattering before the emergence of crystalline structure. To explain these observations we propose that the coupling between density and chain conformation induces a liquid-liquid binodal within the equilibrium liquid--crystalline solid coexistence region. A simple phenomenological theory is developed to illustrate this idea, and several experimentally testable consequences are discussed. Shear is shown to enhance the kinetic role of the hidden binodal.

cond-mat.soft↗