1,721,037 research outputs found
Dataset for "High-throughput characterisation of bull semen motility using differential dynamic microscopy"
No full textDataset supporting the manuscript "High-throughput characterisation of bull semen motility using differential dynamic microscopy" published in PLOSone.Jepson, Alys; Arlt, Jochen; Martinez, Vincent. (2019). Dataset for "High-throughput characterisation of bull semen motility using differential dynamic microscopy", [dataset]. University of Edinburgh. School of Physics & Astronomy. Institute for Condensed Matter and Complex Systems. https://doi.org/10.7488/ds/2492
Probing the dynamics of turbid colloidal suspensions using Differential Dynamic Microscopy
No full textDataset for the manuscript entitled 'Probing the dynamics of turbid colloidal suspensions using Differential Dynamic Microscopy': Few techniques can reliably measure the dynamics of colloidal suspensions or other soft materials over a wide range of turbidities. Here we systematically investigate the capability of Differential Dynamic Microscopy (DDM) to characterise particle dynamics in turbid colloidal suspensions based on brightfield optical microscopy. We measure the Intermediate Scattering Function (ISF) of polystyrene microspheres suspended in water over a range of concentrations, turbidities, and up to 4 orders of magnitude in time-scales. These DDM results are compared to data obtained from both Dynamic Light Scattering (DLS) and Two-colour Dynamic Light Scattering (TCDLS). The latter allows for suppression of multiple scattering for moderately turbid suspensions. We find that DDM can obtain reliable diffusion coefficients at up to 10 and 1000 times higher particle concentrations than TCDLS and standard DLS, respectively. Additionally, we investigate the roles of the four length-scales relevant when imaging a suspension: the sample thickness , the imaging depth , the imaging depth of field DoF, and the photon mean free path . More detailed experiments and analysis reveal the appearance of a short-time process as turbidity is increased, which we associate with multiple scattering events within the imaging depth of field. The long-time process corresponds to the particle dynamics from which particle-size can be estimated in the case of non-interacting particles. Finally, we provide a simple theoretical framework, ms-DDM, for turbid samples, which accounts for multiple scattering
Painting with bacteria: Smart templated self assembly using motile bacteria
No full textDataset supporting the manuscript entitled 'Painting with bacteria: Smart templated self assembly using motile
bacteria':
External control of the swimming speed of ‘active particles’ can be used to self assemble designer structures in situ on the µm to mm scale. We demonstrate such reconfigurable templated active self assembly in a fluid environment using light powered strains of Escherichia coli. The physics and biology controlling the sharpness and formation speed of patterns is investigated using a bespoke fast-responding strain
Self-diffusion in Isotropic and Liquid Crystalline Phases of fd Virus Colloidal Rods: a Combined Single Particle Tracking and Differential Dynamic Microscopy Study
No full textDataset for the manuscript entitled 'Self-diffusion in Isotropic and Liquid Crystalline Phases of fd Virus Colloidal Rods: a Combined Single Particle Tracking and Differential Dynamic Microscopy Study':
In this study, we investigate the dynamics of self-organised suspensions formed by rod-like fd virus colloids. Two methods have been employed for analysing fluorescence microscopy movies: single particle tracking (SPT) in direct space and differential dynamic microscopy (DDM) in reciprocal space. We perform a quantitative analysis on this anisotropic system with complex diffusion across different self-assembled states, ranging from dilute and semi-dilute liquids to nematic and smectic organisations. By leveraging the complementary strengths of SPT and DDM, we provide new insights in the dynamics of viral colloidal rods, such as long time diffusion coefficients in the smectic phase. We further discuss the advantages and limitations of both methods for studying the intricate dynamics of anisotropic colloidal systems
Dataset for: "A combined rheometry and imaging study of viscosity reduction in bacterial suspensions"
No full textDataset supporting the manuscript "A combined rheometry and imaging study of viscosity reduction in bacterial suspensions" accepted in PNAS.Martinez, Vincent; Clement, Eric; Arlt, Jochen; Douarche, Carine; Dawson, Angela; Schwarz-Linek, Jana; Creppy, Adama; Skultety, Viktor; Morozov, Alexander; Auradou, Harold; Poon, Wilson. (2020). Dataset for: "A combined rheometry and imaging study of viscosity reduction in bacterial suspensions", [dataset]. University of Edinburgh. School of Physics and Astronomy. Institute for Condensed Matter and Complex Systems. https://doi.org/10.7488/ds/2748
Dynamics-dependent density distribution in active suspensions
No full textDataset for the manuscript entitled 'Dynamics-dependent density distribution in active suspensions': Self-propelled colloids constitute an important class of intrinsically non-equilibrium matter. Typically, such a particle moves ballistically at short times, but eventually changes its orientation, and displays random-walk behaviour in the long-time limit. Theory predicts that if the velocity of non-interacting swimmers varies spatially in 1D, v(x), then their density ρ(x) satisfies ρ(x) = ρ(0)v(0)/v(x), where x = 0 is an arbitrary reference point. Such a dependence of steady-state ρ(x) on the particle dynamics, which was the qualitative basis of recent work demonstrating how to ‘paint’ with bacteria, is forbidden in thermal equilibrium. We verify this prediction quantitatively by constructing bacteria that swim with an intensity-dependent speed when illuminated and implementing spatially-resolved differential dynamic microscopy (sDDM) for quantitative analysis over ∼ mm length-scales. A spatial light pattern therefore creates a speed profile, along which we find that, indeed, ρ(x)v(x) = constant, provided that steady state is reached
Dynamic and static quenching of 2-aminopurine fluorescence by the natural DNA nucleotides in solution
No full text2-aminopurine (2AP) is a responsive fluorescent base analogue that is used widely as a probe of the local molecular environment in DNA. The ability of 2AP to report changes in local conformation and base-stacking interactions arises from the efficient quenching of its fluorescence by the natural DNA bases. However, the mechanism of this inter-base quenching remains imperfectly understood. Two previous studies of the collisional quenching of 2AP by the natural bases, in different buffer solutions, showed that dynamic quenching efficiency depends on the identity of the natural base, but disagreed on the relative quenching efficiencies of the bases. We report a comprehensive investigation of inter-base quenching of 2AP by the natural nucleoside monophosphates (NMPs), replicating the buffer conditions used in the previous studies. Using time-resolved fluorescence measurements to distinguish between dynamic and static quenching, we find that the dynamic quenching rate constants of the different bases show a consistent trend across both buffers, and this is in line with a charge-transfer mechanism. Time-resolved measurements also provide insight into static quenching, revealing formation of 2AP-NMP ground-state complexes in which 2AP displays a very short fluorescence lifetime, comparable to that seen in oligonucleotides. In these complexes, the dependence of the rate of quenching on the partner base also supports a charge-transfer mechanism.Jones, Anita; Paterson, Kyle; Arlt, Jochen. (2019). Dynamic and static quenching of 2-aminopurine fluorescence by the natural DNA nucleotides in solution, [dataset]. University of Edinburgh. School of Chemistry. https://doi.org/10.7488/ds/2717
Characterising shear-induced dynamics in flowing complex fluids using differential dynamic microscopy
No full textMicroscopic dynamics reveal the origin of the bulk rheological response in complex fluids. In model systems particle motion can be tracked, but for industrially relevant samples this is often impossible. Here we adapt differential dynamic microscopy (DDM) to study flowing highly-concentrated samples without particle resolution. By combining an investigation of oscillatory flow, using a novel "echo-DDM" analysis, and steady shear, through flow-DDM, we characterise the yielding of a silicone oil emulsion on both the microscopic and bulk level. Through measuring the rate of shear-induced droplet rearrangements and the flow velocity, the transition from a solid-like to liquid-like state is shown to occur in two steps: with droplet mobilisation marking the limit of linear visco-elasticity, followed by the development of shear localisation and macroscopic yielding. Using this suite of techniques, such insight could be developed for a wide variety of challenging complex fluids.Richards, James A; Martinez, Vincent A; Arlt, Jochen. (2021). Characterising shear-induced dynamics in flowing complex fluids using differential dynamic microscopy, [dataset]. University of Edinburgh. School of Physics and Astronomy. Institute of Condensed Matter and Complex Systems. https://doi.org/10.7488/ds/3132
Part 1: Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy
No full textPart 1 of datasets supporting the manuscript "Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy". Abstract: We demonstrate differential dynamic microscopy and particle tracking for the characterization of the spatiotemporal behavior of active Janus colloids in terms of the intermediate scattering function (ISF). We provide an analytical solution for the ISF of the paradigmatic active Brownian particle model and find striking agreement with experimental results from the smallest length scales, where translational diffusion and self-propulsion dominate, up to the largest ones, which probe effective diffusion due to rotational Brownian motion. At intermediate length scales, characteristic oscillations resolve the crossover between directed motion to orientational relaxation and allow us to discriminate active Brownian motion from other reorientation processes, e.g., run-and-tumble motion. A direct comparison to theoretical predictions reliably yields the rotational and translational diffusion coefficients of the particles, the mean and width of their speed distribution, and the temporal evolution of these parameters.Kurzthaler, Christina; Devailly, Clemence; Arlt, Jochen; Franosch, Thomas; Poon, Wilson; Martinez, Vincent; Brown, Aidan. (2018). Part 1: Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy, [dataset]. University of Edinburgh. School of Physics and Astronomy. Institute of Complex Matter and Complex Systems. http://dx.doi.org/10.7488/ds/2373
Particle sizing for flowing colloidal suspensions using flow-differential dynamic microscopy
No full textDataset for "Particle sizing for flowing colloidal suspensions using flow-differential dynamic microscopy". Particle size is a key variable in understanding the behaviour of the particulate products that underpin much of our modern lives. Typically obtained from suspensions at rest, measuring the particle size under flowing conditions would enable advances for in-line testing during manufacture and high-throughput testing during development. However, samples are often turbid, multiply scattering light and preventing the direct use of common sizing techniques. Differential dynamic microscopy (DDM) is a powerful technique for analysing video microscopy of such samples, measuring diffusion and hence particle size without the need to resolve individual particles while free of substantial user input. However, when applying DDM to a flowing sample, diffusive dynamics are rapidly dominated by flow effects, preventing particle sizing. Here, we develop ``flow-DDM'', a novel analysis scheme that combines optimised imaging conditions, a drift-velocity correction and modelling of the impact of flow. Flow-DDM allows a decoupling of flow from diffusive motion that facilitates successful particle size measurements at flow speeds an order of magnitude higher than for DDM. We demonstrate the generality of the technique by applying flow-DDM to two separate microscopy methods and flow geometries.Richards, James A; Martinez, Vincent A; Arlt, Jochen. (2021). Particle sizing for flowing colloidal suspensions using flow-differential dynamic microscopy, [dataset]. University of Edinburgh. School of Physics and Astronomy. Institute for Condensed Matter and Complex Systems. https://doi.org/10.7488/ds/2987
- …
