School of Physics and Astronomy
http://hdl.handle.net/10283/246
2020-02-24T04:22:36ZExperimental data for the article "Predictable Properties of Fitness Landscapes Induced by Adaptational Tradeoffs"
http://hdl.handle.net/10283/3558
Experimental data for the article "Predictable Properties of Fitness Landscapes Induced by Adaptational Tradeoffs"
We used strains from Marcusson et al. (2009) (courtesy of Douglas Huseby and Diarmaid Hughes). The strains are isogenic derivatives of MG1655, a K12 strain of the bacterium E. coli, with specific point mutations or gene deletions in five different loci: gyrA:S83L, gyrA:D87N, parC:S80I, ΔmarR, and ΔacrR. There are 32 possible combinations of these alleles, but we only used the wild type, single mutants (5 strains) and double mutants (8 strains of 10 possible combinations): LM179 (00000), LM378 (10000), LM534 (01000), LM792 (00100), LM202 (00010), LM351 (00001), LM625 (11000), LM862 (10100), LM421 (10010), LM647 (10001), LM1124 (01100), LM538 (01010), LM592 (01001), LM367 (00011). A binary sequence after the strain’s name represents the presence/absence of a particular mutated allele (order as in the above list of genetic alterations).
Reference: Marcusson, Linda L., Niels Frimodt-Møller, and Diarmaid Hughes. "Interplay in the selection of fluoroquinolone resistance and bacterial fitness." PLoS pathogens 5.8 (2009).
2020-01-23T14:02:47ZDataset for: "A combined rheometry and imaging study of viscosity reduction in bacterial suspensions"
http://hdl.handle.net/10283/3547
Dataset for: "A combined rheometry and imaging study of viscosity reduction in bacterial suspensions"
Dataset supporting the manuscript "A combined rheometry and imaging study of viscosity reduction in bacterial suspensions" accepted in PNAS.
2020-01-08T13:14:43ZTesting the Wyart-Cates model for non-Brownian shear thickening using bidisperse suspensions [Dataset]
http://hdl.handle.net/10283/3442
Testing the Wyart-Cates model for non-Brownian shear thickening using bidisperse suspensions [Dataset]
Raw simulation data and processed simulation and experimental data to support the article "Testing the Wyart-Cates model for non-Brownian shear thickening using bidisperse suspensions" by Ben M. Guy et al, published in Soft Matter and available on arXiv: https://arxiv.org/abs/1901.02066. Further details are contained in the README files attached.
ABSTRACT:
There is a growing consensus that shear thickening of concentrated dispersions is driven by the formation of stress-induced frictional contacts. The Wyart-Cates (WC) model of this phenomenon, in which the microphysics of the contacts enters solely via the fraction f of contacts that are frictional, can successfully fit flow curves for suspensions of weakly polydisperse spheres. However, its validity for "real-life", polydisperse suspensions has yet to be seriously tested. By performing systematic simulations and experiments on bidisperse mixtures of spheres, we show that the WC model applies only in the monodisperse limit and fails when substantial bidispersity is introduced. Our results prompt new questions about the microphysics of thickening for both monodisperse and polydisperse systems.
## Acknowledgments ##
The full list of funders is:
> EPSRC EP/J007404/1
> EPSRC EP/N025318/1
> Maudslay-Butler Research Fellowship at Pembroke College, Cambridge
> EPSRC SOFI CDT (EP/L015536/1)
> The Royal Academy of Engineering
> The Leverhulme Trust Senior Research Fellowship LTSRF1617/13/2
2019-11-13T16:43:58ZThe role of friction in the yielding of adhesive non-Brownian suspensions
http://hdl.handle.net/10283/3430
The role of friction in the yielding of adhesive non-Brownian suspensions
Yielding behavior is well known in attractive colloidal suspensions. Adhesive non-Brownian suspensions, in which the interparticle bonds are due to finite-size contacts, also show yielding behavior. We use a combination of steady-state, oscillatory and shear-reversal rheology to probe the physical origins of yielding in the latter class of materials, and find that yielding is not simply a matter of breaking adhesive bonds, but involves unjamming from a shear-jammed state in which the micro-structure has adapted to the direction of the applied load. Comparison with a recent constraint-based rheology model shows the importance of friction in determining the yield stress, suggesting novel ways to tune the flow of such suspensions.
2019-10-18T16:37:27ZLiquid Migration in Shear Thickening Suspensions Flowing through Constrictions
http://hdl.handle.net/10283/3413
Liquid Migration in Shear Thickening Suspensions Flowing through Constrictions
Dense suspensions often become more dilute as they move downstream through a constriction. We find that as a shear-thickening suspension is extruded through a narrow die and undergoes such liquid migration, the extrudate maintains a steady concentration, independent of time or initial concentration. At low volumetric flow rate Q, this concentration is a universal function of Q/r^3, a characteristic shear rate in the die of radius r, and coincides with the critical input concentration for the onset of liquid migration. We predict this function by coupling the Wyart-Cates model for shear thickening and the 'suspension balance model' for solvent permeation through particles.
2019-08-30T16:47:56ZNucleosome positions alone can be used to predict domains in yeast chromosomes
http://hdl.handle.net/10283/3401
Nucleosome positions alone can be used to predict domains in yeast chromosomes
Simulation data related to the project "Nucleosome positions alone can be used to predict domains in yeast chromosomes". DNA is packaged into chromosomes, which are further organized into domains: Regions of the genome which are more likely to self-interact. Domains have been observed in species ranging from bacteria to humans and are thought to play an important role in gene regulation. Yet the mechanisms of domain formation are not fully understood. Here we use computer simulations to investigate domain formation in yeast. Our model reproduces the experimentally observed domains using only nucleosome positioning information as an input, implying that (unlike in higher eukaryotes) domain boundary locations are largely determined at this level. Our results reveal how irregular nucleosome spacing impacts the 3D chromosome organization, pointing to a direct link between nucleosome positioning and genome regulation at the large scale.
2019-08-21T10:26:14ZDynamic optical rectification and delivery of active particles
http://hdl.handle.net/10283/3394
Dynamic optical rectification and delivery of active particles
We use moving light patterns to control the motion of Escherichia coli bacteria whose motility is photoactivated. Varying the pattern speed controls the magnitude and direction of the bacterial flux, and therefore the accumulation of cells in up- and down-stream reservoirs. We validate our results with two-dimensional simulations and a 1-dimensional analytic model, and use these to explore parameter space. We find that cell accumulation is controlled by a competition between directed flux and undirected, stochastic transport. Our results point to a number of design principles for using moving light patterns and light-activated micro-swimmers in a range of practical applications.
2019-08-15T16:50:56ZPolymer Modelling Predicts Chromosome Reorganisation in Senescence
http://hdl.handle.net/10283/3381
Polymer Modelling Predicts Chromosome Reorganisation in Senescence
This dataset contains the data related to the figures and supplemental figures in the manuscript "Polymer Modelling Predicts Chromosome Reorganisation in Senescence". Lamina-associated domains (LADs) cover a large part of the human genome and are thought to play a major role in shaping the nuclear architectural landscape. Here, we perform polymer simulations, microscopy and mass spectrometry to dissect the roles played by heterochromatin- and lamina-mediated interactions in nuclear organisation. Our model explains the conventional organisation of heterochromatin and euchromatin in growing cells and the pathological organisation found in oncogene-induced senescence and progeria. We show that the experimentally observed changes in the locality of contacts in senescent and progeroid cells can be explained as arising due to phase transitions in the system. Within our simulations LADs are highly stochastic, as in experiments. Our model suggests that, once established, the senescent phenotype should be metastable even if lamina-mediated interactions were reinstated. Overall, our simulations uncover a generic physical mechanism that can regulate heterochromatin segregation and LAD formation in a wide range of mammalian nuclei.
2019-07-26T15:09:29ZGranulation and suspension rheology: a unified treatment
http://hdl.handle.net/10283/3375
Granulation and suspension rheology: a unified treatment
Mixing a small amount of liquid into a powder can give rise to dry-looking granules; increasing the amount of liquid eventually produces a flowing suspension. We perform experiments on these phenomena using Spheriglass, an industrially-realistic model powder. Drawing on recent advances in understanding friction-induced shear thickening and jamming in suspensions, we offer a unified description of granulation and suspension rheology. A ‘liquid incorporation phase diagram’ explains the existence of permanent and transient granules and the increase of granule size with liquid content. Our results point to rheology-based design principles for industrial granulation.
2019-07-17T14:50:24ZData associated with publication "Detectability of biosignatures in a low-biomass simulation of martian sediments"
http://hdl.handle.net/10283/3359
Data associated with publication "Detectability of biosignatures in a low-biomass simulation of martian sediments"
Data associated with Stevens et al. "Detectability of biosignatures in a low-biomass simulation of martian sediments" (In submission).
2019-06-19T11:00:14ZCompeting Timescales Lead to Oscillations in Shear-Thickening Suspensions
http://hdl.handle.net/10283/3357
Competing Timescales Lead to Oscillations in Shear-Thickening Suspensions
Competing timescales generate novelty. Here, we show that a coupling between the timescales imposed
by instrument inertia and the formation of interparticle frictional contacts in shear-thickening suspensions
leads to highly asymmetric shear-rate oscillations. Experiments tuning the presence of oscillations by
varying the two timescales support our model. The observed oscillations give access to a shear-jamming
portion of the flow curve that is forbidden in conventional rheometry. Moreover, the oscillation frequency
allows us to quantify an intrinsic relaxation time for particle contacts. The coupling of fast contact network
dynamics to a slower system variable should be generic to many other areas of dense suspension flow, with
instrument inertia providing a paradigmatic example. For further information see the related pre-print: Richards, J. A., et al. "Competing Time Scales Lead to Oscillations in Shear-Thickening Suspensions." arXiv preprint arXiv:1902.07655 (2019).
2019-06-18T10:15:09ZSupplementary data for the manuscript "Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic"
http://hdl.handle.net/10283/3351
Supplementary data for the manuscript "Quantitative modelling predicts the impact of DNA methylation on RNA polymerase II traffic"
Patterns of gene expression are primarily determined by proteins that locally enhance or repress transcription. While many transcription factors target a restricted number of genes, others appear to modulate transcription levels globally. An example is MeCP2, an abundant methylated-DNA binding protein that is mutated in the neurological disorder Rett Syndrome. Despite much research, the molecular mechanism by which MeCP2 regulates gene expression is not fully resolved. Here we integrate quantitative, multi-dimensional experimental analysis and mathematical modelling to show that MeCP2 is a novel type of global transcriptional regulator whose binding to DNA creates "slow sites" in gene bodies. Waves of slowed-down RNA polymerase II formed behind these sites travel backward and indirectly affect initiation, reminiscent of defect-induced shock waves in non-equilibrium physics transport models. This mechanism differs from conventional gene regulation mechanisms, which often involve direct modulation of transcription initiation. Our findings point to a genome-wide function of DNA methylation that may account for the reversibility of Rett syndrome in mice. Moreover, our combined theoretical and experimental approach provides a general method for understanding how global gene expression patterns are choreographed.
2019-06-07T16:17:30ZDynamics-dependent density distribution in active suspensions
http://hdl.handle.net/10283/3330
Dynamics-dependent density distribution in active suspensions
Dataset 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.
2019-05-16T11:19:26ZDataset for "Helical and oscillatory microswimmer motility statistics from differential dynamic microscopy"
http://hdl.handle.net/10283/3327
Dataset for "Helical and oscillatory microswimmer motility statistics from differential dynamic microscopy"
Raw data (i.e. simulated videos) supporting the manuscript "Helical and oscillatory microswimmer motility statistics from differential dynamic microscopy" published in New Journal of Physics. Research grant: ERC-AdG-340877 PHYSAPS .
2019-05-13T16:04:39ZMD simulations Phase IV-V H2
http://hdl.handle.net/10283/3326
MD simulations Phase IV-V H2
Data supporting the thesis "Theoretical investigation of solid hydrogen and deuterium" Magdau, Ioan-Bogdan (2016) [PhD thesis].
2019-05-13T10:32:25ZOn the chain-melted phase of matter
http://hdl.handle.net/10283/3300
On the chain-melted phase of matter
Various single elements form incommensurate crystal structures under pressure, where a zeolite-type “host” sublattice surrounds a “guest” sublattice comprising 1D chains of atoms. On “chain melting,” diffraction peaks from the guest sublattice vanish, while those from the host remain. Diffusion of the guest atoms is expected to be confined to the channels in the host sublattice, which suggests 1D melting. Here, we present atomistic simulations of potassium to investigate this phenomenon and demonstrate that the chain-melted phase has no long-ranged order either along or between the chains. This 3D disorder provides the extensive entropy necessary to make the chain melt a true thermodynamic phase of matter, yet with the unique property that diffusion remains confined to 1D only. Calculations necessitated the development of an interatomic forcefield using machine learning, which we show fully reproduces potassium’s phase diagram, including the chain-melted state and 14 known phase transitions.
2019-04-05T10:39:12ZConching chocolate is a prototypical transition from frictionally jammed solid to flowable suspension with maximal solid content
http://hdl.handle.net/10283/3281
Conching chocolate is a prototypical transition from frictionally jammed solid to flowable suspension with maximal solid content
The mixing of a powder of 10-50μm primary particles into a liquid to form a dispersion with the highest possible solid content is a common industrial operation. Building on recent advances in the rheology of such 'granular dispersions', we study a paradigmatic example of such powder incorporation: the conching of chocolate, in which a homogeneous, flowing suspension is prepared from an inhomogeneous mixture of particulates, triglyceride oil and dispersants. Studying the rheology of a simplified formulation, we find that the input of mechanical energy and staged addition of surfactants combine to effect a considerable shift in the jamming volume fraction of the system, thus increasing the maximum flowable solid content. We discuss the possible microscopic origins of this shift, and suggest that chocolate conching exemplifies a ubiquitous class of powder-liquid mixing.
2019-03-25T16:59:19ZCode and accessories for 'Subcritical instabilities in plane Poiseuille flow of an Oldroyd-B fluid'
http://hdl.handle.net/10283/3276
Code and accessories for 'Subcritical instabilities in plane Poiseuille flow of an Oldroyd-B fluid'
Recently, detailed experiments on visco-elastic channel flow have provided convincing evidence for a nonlinear instability scenario which we had argued for based on calculations for visco-elastic Couette flow. Motivated by these experiments we extend the previous calculations to the case of visco-elastic Poiseuille flow, using the Oldroyd-B constitutive model. Our results confirm that the subcritical instability scenario is similar for both types of flow, and that the nonlinear transition occurs for Weissenberg numbers somewhat larger than one. We provide detailed results for the convergence of our expansion and for the spatial structure of the mode that drives the instability. This also gives insight into possible similarities with the mechanism of the transition to turbulence in Newtonian pipe flow.
2019-03-13T09:38:16ZInteracting Particles in 1D and 2D
http://hdl.handle.net/10283/3261
Interacting Particles in 1D and 2D
Codes for Joshua Hellier's PhD thesis "On Interacting Particles in 1D and 2D" (Python). Related to https://arxiv.org/abs/1803.09712 .
2019-02-21T15:28:10ZDataset for "High-throughput characterisation of bull semen motility using differential dynamic microscopy"
http://hdl.handle.net/10283/3252
Dataset for "High-throughput characterisation of bull semen motility using differential dynamic microscopy"
Dataset supporting the manuscript "High-throughput characterisation of bull semen motility using differential dynamic microscopy" published in PLOSone.
2019-02-04T14:47:46ZNovel phases in ammonia-water mixtures under pressure
http://hdl.handle.net/10283/3229
Novel phases in ammonia-water mixtures under pressure
While ammonia and water readily form hydrogen-bonded molecular mixtures at ambient conditions, their miscibility under pressure is not well understood, yet crucial e.g. to model the interior of icy planets. We report here on the behaviour of ammonia-water mixtures under extreme pressure conditions, based on first-principles calculations of 15 stoichiometries in the pressure range of 1 atm to 10 Mbar. We show that compression facilitates proton transfer from water to ammonia in all relevant mixtures. This favors ammonia-rich hydrates above 1 Mbar, stabilized by complete de-protonation of water and the formation of the unusual structural motifs O2−·(NH4+)2 and O2−·(N2H7+)2. The hydronitrogen cations persist to the highest pressures studied. We predict a new ammonia-rich 4:1-hydrate at intermediate pressures and find that by 5.5 Mbar, close to the core-mantle boundary of Neptune, all cold ammonia-water mixtures are unstable against decomposition into their constituents.
2018-12-10T09:55:34ZStructural and electronic properties of the alkali metal incommensurate phases
http://hdl.handle.net/10283/3212
Structural and electronic properties of the alkali metal incommensurate phases
Under pressure, the alkali elements sodium, potassium, and rubidium adopt nonperiodic structures based on two incommensurate interpenetrating lattices. While all elements form the same “host” lattice, their “guest” lattices are all distinct. The physical mechanism that stabilizes these phases is not known, and detailed calculations are challenging due to the incommensurability ofthe lattices. Using a series of commensurate approximant structures, we tackle this issue using density functional theory calculations. In Na and K, the calculations prove accurate enough to reproduce not only the stability of the host-guest phases, but also the complicated pressure dependence of the host-guest ratio and the two guest-lattice transitions. We find Rb-IV to be metastable at all pressures, and suggest it is a high-temperature phase. The electronic structure of these materials is unique: they exhibit two distinct, coexisting types of electride behavior, with both fully localized pseudoanions and electrons localized in 1D wells in the host lattice, leading to low conductivity. While all phases feature pseudogaps in the electronic density of states, the perturbative free-electron picture applies to Na, but not to K and Rb, due to significant d-orbital population in the latter.
2018-11-06T13:17:43ZUnusually complex phase of dense nitrogen at extreme conditions
http://hdl.handle.net/10283/3193
Unusually complex phase of dense nitrogen at extreme conditions
This dataset contains DFT enthalpies (PBE and PBE+TS), Raman spectra and AIRSS search generators supporting the paper “Unusually Complex Phase of Dense Nitrogen at Extreme Conditions” published in Nature Communications.
2018-10-01T16:09:30ZData accompanying 'A growing bacterial colony in two dimensions as an active nematic'
http://hdl.handle.net/10283/3188
Data accompanying 'A growing bacterial colony in two dimensions as an active nematic'
How a single bacterium becomes a colony of many thousand cells is important in biomedicine and food safety. Much is known about the molecular and genetic bases of this process, but less about the underlying physical mechanisms. Here we study the growth of single-layer micro-colonies of rod-shaped Escherichia coli bacteria confined to just under the surface of soft agarose by a glass slide. Analysing this system as a liquid crystal, we find that growth-induced activity fragments the colony into microdomains of well-defined size, whilst the associated flow orients it tangentially at the boundary. Topological defect pairs with charges ± 1/2 are produced at a constant rate, with the +1/2 defects being propelled to the periphery. Theoretical modelling suggests that these phenomena have different physical origins from similar observations in other extensile active nematics, and a growing bacterial colony belongs to a new universality class, with features reminiscent of the expanding universe.
2018-09-24T13:53:16ZStability of Hydrogen Hydrates from Second-Order Møller-Plesset Perturbation Theory
http://hdl.handle.net/10283/3179
Stability of Hydrogen Hydrates from Second-Order Møller-Plesset Perturbation Theory
The formation of gas hydrates and clathrates critically depends on the interaction between the host water network and the guest gas species. Density functional calculations can struggle to quantitatively capture these dispersion-type interactions. Here, we report wave function-based calculations on hydrogen hydrates that combine periodic Hartree−Fock with a localized treatment of electronic correlation. We show that local second-order Møller−Plesset perturbation theory (LMP2) reproduces the stability of the different filled-ice-like hydrates in excellent agreement with experimental data. In contrast to various dispersion-corrected density functional theory implementations, LMP2 correctly identifies the pressures needed to stabilize the C0, C1, and C2 hydrates and does not find a spurious region of stability for an ice-Ih-based dihydrate. Our results suggest that LMP2 or similar approaches can provide quantitative insights into the mechanisms of formation and eventual decomposition of molecular host−guest compounds.
2018-09-10T15:00:54ZPolymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci
http://hdl.handle.net/10283/3178
Polymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci
This dataset contains data corresponding to the figures and supplemental figures of the manuscript "Polymer Simulations of Heteromorphic Chromatin Predict the 3-D Folding of Complex Genomic Loci". Data sets from next generation sequencing experiments (including full raw sequence data) will be deposited separately in the Gene Expression Omnibus.
Chromatin folded into 3-D macromolecular structures is often analysed by 3C and FISH techniques, but these frequently provide contradictory results. Chromatin can be modelled as a simple polymer comprised of a connected chain of units. By embedding data for epigenetic marks (H3K27ac), chromatin accessibility (ATAC-seq) and structural anchors (CTCF) we developed a highly predictive heteromorphic polymer (HiP-HoP) model, where the chromatin fibre varied along its length; combined with diffusing protein bridges and loop extrusion this model predicted the 3-D organisation of genomic loci at a population and single cell level. The model was validated at several gene loci, including the complex Pax6 gene, and was able to determine locus conformations across cell types with varying levels of transcriptional activity and explain different mechanisms of enhancer use. Minimal a priori knowledge of epigenetic marks is sufficient to recapitulate complex genomic loci in 3-D and enable predictions of chromatin folding paths.
2018-09-04T17:35:04ZChaotic behaviour of Eulerian MHD turbulence
http://hdl.handle.net/10283/3152
Chaotic behaviour of Eulerian MHD turbulence
We study the chaos of a turbulent conducting fluid using direct numerical simulation in the Eulerian frame. We predict that the Lyapunov exponent, which measures the exponential separation of initially close solutions of the magnetohydrodynamic equations, is proportional to the inverse of the Kolmogorov microscale time and also obtain new results for this relation in hydrodynamic turbulence, specifically deriving a previously unknown co-efficient. These predictions agree with simulation results. The simulations also show a diminution of chaos from the introduction of magnetic helicity, which is expected to be eliminated at maximum helicity. Linear growth of the difference between fields was recently found in hydrodynamics and we find here that it extends to the magnetic and velocity fields, with growth rates dependent on the dissipation rate of the relevant field. We infer that the chaos in the system is totally dominated by the velocity field and connect this work to real magnetic systems such as solar weather and confined plasmas.
2018-08-10T16:37:16ZCritical mode and band-gap-controlled bipolar thermoelectric properties of SnSe
http://hdl.handle.net/10283/3143
Critical mode and band-gap-controlled bipolar thermoelectric properties of SnSe
From the related article: The reliable calculation of electronic structures and understanding of electrical properties depends on an accurate model of the crystal structure. Here, we have reinvestigated the crystal structure of the high-zT thermoelectric material tin selenide, SnSe, between 4 and 1000 K using high-resolution neutron powder diffraction. Symmetry analysis reveals the presence of four active structural distortion modes, one of which is found to be active over a relatively wide range of more than ±200 K around the symmetry-breaking Pnma--Cmcm transition at 800~K. Density functional theory calculations on the basis of the experimental structure parameters show that the unusual, step-like temperature dependencies of the electrical transport properties of SnSe are caused by the onset of intrinsic bipolar conductivity, amplified and shifted to lower temperatures by a rapid reduction of the band gap between 700 and 800 K. The calculated band gap is highly sensitive to small out-of-plane Sn displacements observed in the diffraction experiments. SnSe with a sufficiently controlled acceptor concentration is predicted to produce simultaneously a large positive and a large negative Seebeck effect along different crystal directions. https://doi.org/10.1103/PhysRevMaterials.2.085405
2018-08-02T17:20:03ZData for "Mixtures of blue phase liquid crystal with simple liquids: elastic emulsions and cubic fluid cylinders"
http://hdl.handle.net/10283/3137
Data for "Mixtures of blue phase liquid crystal with simple liquids: elastic emulsions and cubic fluid cylinders"
We numerically investigate the behavior of a phase-separating mixture of a blue phase I liquid crystal with an isotropic fluid. The resulting morphology is primarily controlled by an inverse capillary number, χ, setting the balance between interfacial and elastic forces. When χ and the concentration of the isotropic component are both low, the blue phase disclination lattice templates a cubic array of fluid cylinders. For larger χ, the isotropic phase arranges primarily into liquid emulsion droplets which coarsen very slowly, rewiring the blue phase disclination lines into an amorphous elastic network. Our blue phase-simple fluid composites can be externally manipulated: an electric field can trigger a morphological transition between cubic fluid cylinder phases with different topologies.
2018-07-27T16:07:12ZDynamical analysis of bacteria in microscopy movies
http://hdl.handle.net/10283/3134
Dynamical analysis of bacteria in microscopy movies
This repository contains data and code related to the manuscript
"Dynamical analysis of bacteria in microscopy movies", PloS One, 14,
6, e0217823, 2019 (https://doi.org/10.1371/journal.pone.0217823).
Please find more information on the contents and structure of the
files in the corresponding readme files.
2018-07-25T12:06:53ZProbing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy (Part 2)
http://hdl.handle.net/10283/3115
Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy (Part 2)
Part 2 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.
2018-07-10T15:53:38ZProbing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy (Part 1)
http://hdl.handle.net/10283/3114
Probing the spatiotemporal dynamics of catalytic Janus particles with single-particle tracking and differential dynamic microscopy (Part 1)
Part 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.
2018-07-10T15:53:14ZFully-resolved array of simulations investigating the influence of the magnetic Prandtl number
http://hdl.handle.net/10283/3099
Fully-resolved array of simulations investigating the influence of the magnetic Prandtl number
This dataset is for a paper which is currently in submission.
We explore the effect of the magnetic Prandtl number Pr_M on energy and dissipation in fully-resolved direct numerical simulations of steady-state, mechanically-forced homogeneous magnetohydrodynamic turbulence in the range Pr_M=1/32 to 32. We compare the spectra and show that if the simulations are not fully-resolved, the steepness of the scaling of the kinetic-to-magnetic dissipation ratio with Pr_M is overestimated. We also present results of decaying turbulence with helical and nonhelical magnetic fields, where we find nonhelical reverse spectral transfer for Pr_M<1 for the first time. The results of this systematic analysis have applications ranging from tokamak reactors to black hole accretion disks.
2018-06-15T10:56:22ZMonte Carlo simulation of and active interface with diffusing activators
http://hdl.handle.net/10283/3048
Monte Carlo simulation of and active interface with diffusing activators
C source code for a Monte Carlo simulation of a system of particles diffusing onto a fluctuating interface. This code has been developed in the context of my PhD project and it simulates a stochastic process I built to mimic the dynamics of a living cell membrane. The code can be run by giving values to the model parameters, and it will produce a series of system configurations (position of the particles and the membrane) plus some average quantities (interface mean height, mean width, particles mean squared displacement). Details of the model are under publication in Physical Review Letters.
2018-03-16T14:47:45ZBacteria as living patchy colloids: Phenotypic heterogeneity in surface adhesion
http://hdl.handle.net/10283/3037
Bacteria as living patchy colloids: Phenotypic heterogeneity in surface adhesion
This dataset contains data corresponding to the figures in the main text of the manuscript "Bacteria as living patchy colloids: Phenotypic heterogeneity in surface adhesion" (Science Advances, 4, 4, eaao1170, 2018). Data is from experiments of bacteria on a glass surface. From movies recorded in time, we follow many individual cells in time and quantify their dynamics. Our results show that even in a clonal population (genetically identical cells), there are differences between individual cells in adhesion properties. The observations can be explained with a model, where cells have various numbers of adhesive patches. Cells with zero patches never adhere, cells with one patch adhere weakly and cells with multiple patches can adhere strongly. More details and background information on the data can be found in the manuscript and its figure captions and SI, and/or in the readme.txt file attached to this dataset.
2018-03-06T12:32:00ZY-Mars Analogue Characterisation
http://hdl.handle.net/10283/3019
Y-Mars Analogue Characterisation
This dataset contains a range of analytical characterisations of the Y-Mars analogue, which is intended to simulate a mudstone found in Gale Crater, Mars.
2018-02-13T10:29:14ZRaw DFT data for "Post-aragonite phases of CaCO3 at lower mantle pressures"
http://hdl.handle.net/10283/3001
Raw DFT data for "Post-aragonite phases of CaCO3 at lower mantle pressures"
This dataset contains DFT enthalpies and phonon spectra, computed with PBEsol, that together produce the theoretical static, and P-T quasiharmonic phase diagrams seen in the paper "Post-aragonite phases of CaCO3 at lower mantle pressures".
2018-01-16T14:27:30ZPainting with bacteria: Smart templated self assembly using motile bacteria
http://hdl.handle.net/10283/2964
Painting with bacteria: Smart templated self assembly using motile bacteria
Dataset 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.
2017-12-01T17:45:48ZDirac cones in two-dimensional borane
http://hdl.handle.net/10283/2949
Dirac cones in two-dimensional borane
We introduce two-dimensional borane, a single-layered material of BH stoichiometry, with promising electronic properties. We show that, according to Density Functional Theory calculations, two-dimensional borane is semimetallic, with two symmetry-related Dirac cones meeting right at the Fermi energy E_f. The curvature of the cones is lower than in graphene, thus closer to the ideal linear dispersion. Its structure, formed by a puckered trigonal boron network with hydrogen atoms connected to each boron atom, can be understood as distorted, hydrogenated borophene (Science {350}, 1513 (2015)). Chemical bonding analysis reveals the boron layer in the network being bound by delocalized four-center two-electron {\sigma} bonds. Finally, we suggest high-pressure could be a feasible route to synthesise two-dimensional borane.
2017-11-21T13:54:12ZData and movies accompanying 'Kinetic theory of pattern formation in mixtures of microtubules and molecular motors'
http://hdl.handle.net/10283/2944
Data and movies accompanying 'Kinetic theory of pattern formation in mixtures of microtubules and molecular motors'
In this study we formulate a theoretical approach, based on a Boltzmann-like kinetic equation, to describe pattern formation in two-dimensional mixtures of microtubular filaments and molecular motors. Following the previous work by Aranson and Tsimring [Phys. Rev. E {\bf 74}, 031915 (2006) https://doi.org/10.1103/PhysRevE.74.031915 ] we model the motor-induced reorientation of microtubules as collision rules, and devise a semi-analytical method to calculate the corresponding interaction integrals. This procedure yields an infinite hierarchy of kinetic equations that we terminate by employing a well-established closure strategy, developed in the pattern-formation community and based on a power-counting argument. We thus arrive at a closed set of coupled equations for slowly varying local density and orientation of the microtubules, and study its behaviour by performing a linear stability analysis and direct numerical simulations. By comparing our method with the work of Aranson and Tsimring, we assess the validity of the assumptions required to derive their and our theories. We demonstrate that our approximation-free evaluation of the interaction integrals and our choice of a systematic closure strategy result in a rather different dynamical behaviour than was previously reported. Based on our theory, we discuss the ensuing phase diagram and the patterns observed.
2017-11-09T09:48:43ZStacking characteristics of close packed materials
http://hdl.handle.net/10283/2932
Stacking characteristics of close packed materials
It is shown that the enthalpy of any close packed structure for a given element can be characterized as a linear expansion in a set of continuous variables α_n, which describe the stacking configuration. This enables us to represent the infinite, discrete set of stacking sequences within a finite, continuous space of the expansion parameters H_n. These H_n determine the stable structure and vary continuously in the thermodynamic space of pressure, temperature, or composition. The continuity of both spaces means that only transformations between stable structures adjacent in the H_n space are possible, giving the model predictive as well as descriptive ability. We calculate the H_n using density functional theory and interatomic potentials for a range of materials. Some striking results are found: e.g. the Lennard-Jones potential model has 11 possible stable structures and over 50 phase transitions as a function of cutoff range. The very different phase diagrams of Sc, Tl, Y, and the lanthanides are understood within a single theory. We find that the widely reported 9R-fcc transition is not allowed in equilibrium thermodynamics, and in cases where it has been reported in experiments (Li, Na), we show that DFT theory is also unable to predict it.
2017-10-24T10:30:38ZNonequilibrium chromosome looping via molecular slip links
http://hdl.handle.net/10283/2812
Nonequilibrium chromosome looping via molecular slip links
We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of cohesinlike molecules, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred 'loading site'. This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.
2017-09-04T09:16:26ZStabilization of ammonia-rich hydrate inside icy planets
http://hdl.handle.net/10283/2777
Stabilization of ammonia-rich hydrate inside icy planets
The interior structure of the giant ice planets Uranus and Neptune, but also of newly discovered exoplanets, is loosely constrained, because limited observational data can be satisfied with various interior models. Although it is known that their mantles comprise large amounts of water, ammonia, and methane ices, it is unclear how these organize themselves within the planets -- as homogeneous mixtures, with continuous concentration gradients, or as well-separated layers of specific composition. While individual ices have been studied very detailed under pressure, the properties of their mixtures are much less explored. We show here, using first-principles calculations, that the 2:1 ammonia hydrate, (H2O)(NH3)2, is stabilized at icy planet mantle conditions due to a remarkable structural evolution. Above 65 GPa, we predict it to transform from a hydrogen-bonded molecular solid into a fully ionic phase O2-(NH4+)2, where all water molecules are completely deprotonated, an unexpected bonding phenomenon not seen before. Ammonia hemihydrate is stable in a sequence of ionic phases up to 500 GPa, pressures found deep within Neptune-like planets, and thus at higher pressures than any other ammonia-water mixture. This suggests it precipitates out of any ammonia-water mixture at sufficiently high pressures and thus forms an important component of icy planets.
2017-07-26T15:48:51ZImages used to calculate the pressure dependence of the saturated methane concentration in water as a function of pressure
http://hdl.handle.net/10283/2771
Images used to calculate the pressure dependence of the saturated methane concentration in water as a function of pressure
We have measured the maximum concentration of methane dissolved in water as a function of pressure using a diamond anvil cell. These images show the sample space with regions of methane (darker) and water+methane (lighter). From the relative areas of these regions we estimated the concentration.
2017-07-12T15:06:26ZQuantum and isotope effects in lithium metal
http://hdl.handle.net/10283/2715
Quantum and isotope effects in lithium metal
The crystal structure of elements at zero pressure and temperature is the most fundamental information in condensed matter physics. For decades it has been believed that lithium, the simplest metallic element, has a complicated ground-state structure. Using synchrotron X-ray diffraction in diamond-anvil-cells and multiscale simulations with density functional theory and molecular dynamics we show that the previously accepted martensitic ground-state is metastable. The actual ground-state is face-centered-cubic. We find that isotopes of lithium, under identical thermal paths, exhibit a large difference in martensitic transition temperature. Lithium exhibits large quantum mechanical effects, serving as a metallic intermediate between helium, with its quantum-effect-dominated structures, and the higher mass elements. By disentangling the quantum-kinetic complexities, we prove that fcc lithium is the groundstate, and we synthesize it by decompression.
2017-05-25T14:13:25ZLinking particle properties to dense suspension extrusion flow characteristics using discrete element simulations
http://hdl.handle.net/10283/2664
Linking particle properties to dense suspension extrusion flow characteristics using discrete element simulations
Extrusion is a widely used process for forming suspensions and pastes into designed shapes, and is central to the manufacture of many products. In this article, the extrusion through a square-entry die of non-Brownian spheres suspended in Newtonian fluid is investigated using discrete element simulations, capturing individual particle-particle contacts and hydrodynamic interactions. The simulations reveal inhomogeneous velocity and stress distributions, originating in the inherent microstructure formed by the constituent particles. Such features are shown to be relevant to paste extrusion behaviour, such as extrudate swell. The pressure drop across the extruder is correlated with the extrudate flow rate, with the empirical fitting parameters being linked directly to particle properties such as surface friction, and processing conditions such as extruder wall roughness. Our model and results bring recent advances in suspension rheology into an industrial setting, laying foundations for future model development, predictive paste formulation and extrusion design.
2017-04-26T09:18:18ZComparison of forcing functions in magnetohydrodynamics
http://hdl.handle.net/10283/2658
Comparison of forcing functions in magnetohydrodynamics
Results are presented of direct numerical simulations of incompressible, homogeneous magnetohydrodynamic turbulence without a mean magnetic field, subject to different kinetic forcing functions commonly used in the literature. Specifically, the forces are negative damping (which uses the large-scale field as a forcing function), a nonhelical random force, and a nonhelical static sinusoidal force (analogous to helical ABC forcing). The time evolution of the three ideal invariants (energy, magnetic helicity and cross helicity), the time-averaged energy spectra, the energy ratios and the dissipation ratios are examined. The effect of the number of grid points and Reynolds number on the performance of the forces is also considered. All three forces produce qualitatively similar steady states with some differences. In particular, the magnetic helicity is well-conserved in all cases but the sinusoidal method of energy injection has a tendency to introduce cross helicity into the system. Indeed, an ensemble of sinusoidally-forced simulations with identical parameters shows large variations in the cross helicity over long time periods, casting some doubt on the validity of the principle of ergodicity in systems where the injection of helicity cannot be controlled. Cross helicity can unexpectedly enter the system through the forcing function and must be carefully monitored. N.B. a description of the software which ran the simulations can be found in the PhD theses of the two people who designed and implemented the majority of it: Sam Yoffe ( https://arxiv.org/abs/1306.3408 ) and Moritz Linkmann respectively ( https://www.era.lib.ed.ac.uk/handle/1842/19572).
2017-04-14T15:47:36ZInterfacial rheology of sterically stabilized colloids at liquid interfaces and its effect on the stability of Pickering emulsions
http://hdl.handle.net/10283/2654
Interfacial rheology of sterically stabilized colloids at liquid interfaces and its effect on the stability of Pickering emulsions
Particle-laden interfaces can be used to stabilize a variety of high-interface systems, from foams over emulsions to polymer blends. The relation between the particle interactions, the structure and rheology of the interface, and the stability of the system remains unclear. In the present work, we experimentally investigate how micron-sized, near-hard-sphere-like particles affect the mechanical properties of liquid interfaces. In particular, by comparing dried and undried samples, we investigate the effect of aggregation state on the properties of the particle-laden liquid interface and its relation to the stability of the corresponding Pickering emulsions. Partially aggregated suspensions give rise to a soft-solid-like response under shear, whereas for stable PMMA particulate layers a liquid-like behaviour is observed. For interfacial creep-recovery measurements, we present an empirical method to correct for the combined effect of the subphase drag and the compliance of the double-wall ring geometry, which makes a significant contribution to the apparent elasticity of weak interfaces. We further demonstrate that both undried and dried PMMA particles can stabilize emulsions for months, dispelling the notion that particle aggregation, in bulk or at the interface, is required to create stable Pickering emulsions. Our results indicate that shear rheology is a sensitive probe of colloidal interactions, but is not necessarily a predictor of the stability of interfaces, e.g.~in quiescent Pickering emulsions, as in the latter the response to dilatational deformations can be of prime importance.
2017-04-12T11:25:46ZChaotic properties of a turbulent isotropic fluid
http://hdl.handle.net/10283/2650
Chaotic properties of a turbulent isotropic fluid
By tracking the divergence of two initially close trajectories in phase space of forced turbulence,
the relation between the maximal Lyapunov exponent λ, and the Reynolds number Re is measured
using direct numerical simulations, performed on up to 2048^3 collocation points. The Lyapunov
exponent is found to solely depend on the Reynolds number with λ ∝ Re^0.53 and that after a
transient period the divergence of trajectories grows at the same rate at all scales. Finally a linear
divergence is seen that is dependent on the energy forcing rate. Links are made with other chaotic
systems.
2017-04-03T15:26:40ZInfrared peak splitting from phonon localization in solid hydrogen
http://hdl.handle.net/10283/2648
Infrared peak splitting from phonon localization in solid hydrogen
Dataset contain CASTEP input and output for calculations of localization of phonons in C2c hydrogen under pressure. Also contains codes written in the project to extend the lattice dynamics calculation to large disordered unit cells representing post-DISREC hydrogen-deuterium mixtures as reported by Silvera in PRL (http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.116.145501).
2017-03-24T16:59:05Z