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Collective behaviour in living systems is observed across many scales, from bacteria to insects, to fish shoals. Zebrafish have emerged as a model system amenable to laboratory study. Here we report a three-dimensional study of the collective dynamics of fifty zebrafish. We observed the emergence of collective behaviour changing between \yy{ordered} to randomised, upon \yy{adaptation} to new environmental conditions. We quantify the spatial and temporal correlation functions of the fish and identify two length scales, the persistence length and the nearest neighbour distance, that capture the essence of the behavioural changes. The ratio of the two length scales correlates robustly with the polarisation of collective motion that we explain with a reductionist model of self--propelled particles with alignment interactions., Comment: PLOS Comp. Biol. 18 e1009394

Measurements of local density fluctuations are crucial to characterizing the interfacial properties of equilibrium fluids. A specific case that has been well-explored involves the heightened compressibility of water near hydrophobic entities. Commonly, a spatial profile of local fluctuation strength is constructed from measurements of the mean and variance of solvent particle number fluctuations in a set of contiguous sub-volumes of the system adjacent to the solvo/hydrophobe. An alternative measure proposed by Evans and Stewart (J. Phys.: Condens. Matter 27, 194111 (2015)) defines a local compressibility profile in terms of the chemical potential derivative of the spatial number density profile. Using Grand Canonical Monte Carlo simulation, we compare and contrast the efficacy of these two approaches for a Lennard-Jones solvent at spherical and planar solvophobic interfaces, and SPC/E water at a hydrophobic spherical solute. Our principal findings are that: (i) the local compressibility profile $\chi({\bf r})$ of Evans and Stewart is considerably more sensitive to variations in the strength of local density fluctuations than the spatial fluctuation profile $F({\bf r})$ and can resolve much more detailed structure; (ii) while the local compressibility profile is essentially independent of the choice of spatial discretization used to construct the profile, the spatial fluctuation profile exhibits strong systematic dependence on the size of the subvolumes on which the profile is defined. We clarify the origin and nature of this finite-size effect., Comment: 12 pages, 6 figures

We study wetting droplets formed of active Brownian particles in contact with a repulsive potential barrier, in a wedge geometry. Our numerical results demonstrate a transition between partially wet and completely wet states, as a function of the barrier height, analogous to the corresponding surface phase transition in passive fluids. We analyse partially wet configurations characterised by a nonzero contact angle $\theta$ between the droplet surface and the barrier, including the average density profile and its fluctuations. These findings are compared with two equilibrium systems: a Lennard-Jones fluid and a simple contour model for a liquid-vapour interface. We locate the wetting transition where $\cos(\theta)=1$, and the neutral state where $\cos(\theta)=0$. We discuss the implications of these results for possible definitions of surface tensions in active fluids.

Inverse Ising inference allows pairwise interactions of complex binary systems to be reconstructed from empirical correlations. Typical estimators used for this inference, such as Pseudo-likelihood maximization (PLM), are biased. Using the Sherrington-Kirkpatrick (SK) model as a benchmark, we show that these biases are large in critical regimes close to phase boundaries, and may alter the qualitative interpretation of the inferred model. In particular, we show that the small-sample bias causes models inferred through PLM to appear closer-to-criticality than one would expect from the data. Data-driven methods to correct this bias are explored and applied to a functional magnetic resonance imaging (fMRI) dataset from neuroscience. Our results indicate that additional care should be taken when attributing criticality to real-world datasets.

Colloidal dispersions are prized as model systems to understand basic properties of materials, and are central to a wide range of industries from cosmetics to foods to agrichemicals. Among the key developments in using colloids to address challenges in condensed matter is to resolve the particle coordinates in 3D, allowing a level of analysis usually only possible in computer simulation. However in amorphous materials, relating mechanical properties to microscopic structure remains problematic. This makes it rather hard to understand, for example, mechanical failure. Here we address this challenge by studying the contacts and the forces between particles, as well as their positions. To do so, we use a colloidal model system (an emulsion) in which the interparticle forces and local stress can be linked to the microscopic structure. We demonstrate the potential of our method to reveal insights into the failure mechanisms of soft amorphous solids by determining local stress in a colloidal gel. In particular, we identify `force chains' of load-bearing droplets, and local stress anisotropy, and investigate their connection with locally rigid packings of the droplets., Comment: 12 pages

We study non-equilibrium analogues of surface phase transitions in a minimal model of active particles in contact with a purely repulsive potential barrier that mimics a thin porous membrane. Under conditions of bulk motility-induced phase separation, the interaction strength $\varepsilon_w$ of the barrier controls the affinity of the dense phase for the barrier region. We uncover clear signatures of a wetting phase transition as $\varepsilon_w$ is varied. In common with its equilibrium counterpart, the character of this transition depends on the system dimensionality: a continuous transition with large density fluctuations and gas bubbles is uncovered in 2d while 3d systems exhibit a sharp transition absent of large correlations.

Among the challenges in discriminating between theoretical approaches to the glass transition is obtaining suitable data. In particular, particle--resolved data in liquids supercooled past the mode--coupling crossover has until recently been hard to obtain. Here we combine nano-particle resolved experiments and GPU simulation data which addresses this and investigate the predictions of differing theoretical approaches. We find support for both dynamic facilitation and thermodynamic approaches. In particular, excitations, the elementary units of relaxation in dynamic facilitation theory follow the predicted scaling behaviour and the properties of cooperatively rearranging regions (CRRs) are consistent with RFOT theory. At weak supercooling there is limited correlation between particles identified in excitations and CRRs, but this increases very substantially at deep supercooling. We identify a timescale related to the CRRs which is coupled to the structural relaxation time and thus decoupled from the excitation timescale, which remains microscopic., Comment: 10 pages

Simulation studies of the phase diagram of repulsive active Brownian particles in three dimensions reveal that the region of motility-induced phase separation between a high and low density phase is enclosed by a region of gas-crystal phase separation. Near-critical loci and structural crossovers can additionally be identified in analogy with simple fluids. Motivated by the striking similarity to the behaviour of equilibrium fluids with short-ranged pair-wise attractions, we show that a direct mapping to pair potentials in the dilute limit implies interactions that are insufficiently attractive to engender phase separation. Instead, this is driven by the emergence of multi-body effects associated with particle caging that occurs at sufficiently high number density. We quantify these effects via information-theoretical measures of $n$-body effective interactions extracted from the configurational structure.

We review recent developments in structural-dynamical phase transitions in trajectory space. An open question is how the dynamic facilitation theory of the glass transition may be reconciled with thermodynamic theories that posit a vanishing configurational entropy. Dynamic facilitation theory invokes a dynamical phase transition, between an active phase (close to the normal liquid) and an inactive phase which is glassy, whose order parameter is either dynamic or a time-averaged structural quantity. In particular, the dynamical phase transition in systems with non-trivial thermodynamics manifests signatures of a lower critical point, which lies close to the putative Kauzmann temperature, where any thermodynamic phase transition to an ideal glass state might occur. We discuss these findings, and suggest that the lower critical point of the structural-dynamical phase transition may be related to the large drop in configurational entropy that occurs in the inactive phase of the dynamical phase transition. Increasing supercooling thus brings configurational entropy of the normal liquid much lower, along with the temperature., Comment: accepted in J. Chem. Phys

Colloidal suspensions have long been studied as a model for atomic and molecular systems, due to the ability to fluorescently label and individually track each particle, yielding particle-resolved structural information. This allows various local order parameters to be probed that are otherwise inaccessible for a comparable molecular system. For phase transitions such as crystallisation, appropriate order parameters which emphasise 6-fold symmetry are a natural choice, but for vitrification the choice of order parameter is less clear cut. Previous work has highlighted the importance of icosahedral local structure as the glass transition is approached. However, counting icosahedra or related motifs is not a continuous order parameter in the same way as, for example, the bond-orientational order parameters $Q_{6}$ and $W_6$. In this work we investigate the suitability of using pentagonal bipyramid membership, a structure which can be assembled into larger, five-fold symmetric structures, as a finer order parameter to investigate the glass transition. We explore various structural and dynamic properties and show that this new approach produces many of the same findings as simple icosahedral membership, but we also find that large instantaneous displacements are often correlated with significant changes in pentagonal bipyramid membership, and unlike the population of defective icosahedra, the pentagonal bypyramid membership and spindle number do not saturate for any measured volume fraction, but continues to increase., Comment: accepted by JStat Mech: Theory and Experiment 2019

In a recent letter we presented a framework for predicting the concentrations of many-particle local structures inside the bulk liquid as a route to assessing changes in the liquid approaching dynamical arrest. Central to this framework was the morphometric approach, a synthesis of integral geometry and liquid state theory, which has traditionally been derived from fundamental measure theory. We present the morphometric approach in a new context as a generalisation of scaled particle theory, and derive several morphometric theories for hard spheres of fundamental and practical interest. Our central result is a new theory which is particularly suited to the treatment of many-body correlation functions in the hard sphere liquid, which we demonstrate by numerical tests against simulation., Comment: 12 pages, 6 figures

Swimmers and self-propelled particles are physical models for the collective behaviour and motility of a wide variety of living systems, such as bacteria colonies, bird flocks and fish schools. Such artificial active materials are amenable to physical models which reveal the microscopic mechanisms underlying the collective behaviour. Here we study colloids in a DC electric field. Our quasi-two-dimensional system of electrically-driven particles exhibits a rich and exotic phase behaviour. At low field strengths, electrohydrodynamic flows lead to self-organisation into crystallites with hexagonal order. Upon self-propulsion of the particles due to Quincke rotation, we find an ordered phase of active matter in which the motile crystallites constantly change shape and collide with one another. At higher field strengths, this "dissolves" to an active gas. We parameterise a particulate simulation model which reproduces the experimentally observed phases and, at higher field strengths predicts an activity-driven demixing to band-like structures.

Starting from an ideal crystalline state, we numerically study a nonequilibrium dynamical order- disorder transition promoted by the application of a periodic shearing protocol at low temperatures in model systems in two and three dimensions. We observe a continuous (2D) and discontinuous (3D) dynamical transition from an ordered to a disordered steady state. Through the analysis of large-scale simulations, we show that the amorphization mechanism around the discontinuous transition is reminiscent of spinodal decomposition.

The discrepancy in nucleation rate densities between simulated and experimental hard spheres remains staggering and unexplained. Suggestively, more strongly sedimenting colloidal suspensions of hard spheres nucleate much faster than weakly sedimenting systems. In this work we consider firstly the effect of sedimentation on the structure of colloidal hard spheres, by tuning the density mismatch between solvent and colloidal particles. In particular we investigate the effect on the degree of five fold symmetry present. Secondly we study the size of density fluctuations in these experimental systems in comparison to simulations. The density fluctuations are measured by assigning each particle a local density, which is related to the number of particles within a distance of 3.25 particle diameters. The standard deviation of these local densities gives an indication of the fluctuations present in the system. Five fold symmetry is suppressed by a factor of two when sedimentation is induced in our system. Density fluctuations are also increased by a factor of two in experiments compared to simulations. The change in five fold symmetry makes a difference to the expected nucleation rates, but we demonstrate that it is ultimately too small to resolve the discrepancy between experiment and simulation, while the fluctuations are shown to be an artefact of 3d particle tracking., Comment: 8 pages

We model the thermodynamics of local structures within the hard sphere liquid at arbitrary volume fractions through the \textit{morphometric} calculation of $n$-body correlations. We calculate absolute free energies of local geometric motifs in excellent quantitative agreement with molecular dynamics simulations across the liquid and supercooled liquid regimes. We find a bimodality in the density library of states where five-fold symmetric structures appear lower in free energy than four-fold symmetric structures, and from a single reaction path predict a relaxation barrier which scales linearly in the compressibility factor. The method provides a new route to assess changes in the free energy landscape at volume fractions dynamically inaccessible to conventional techniques., Comment: 6+17 pages, 3 figures

Supercooled liquids are kinetically trapped materials in which the transition to a thermodynamically more stable state with long-range order is strongly suppressed. To assess the glass-forming abilities of a liquid empirical rules exist, but a comprehensive microscopic picture of devitrification is still missing. Here we study the crystallization of a popular model glass former, the binary Kob-Andersen mixture, in small systems. We perform trajectory sampling employing the population of the locally favored structure as order parameter. While for large population a dynamical phase transition has been reported, here we show that biasing towards a small population of locally favored structures induces crystallization, and we estimate the free energy difference. This result sheds new light on the competition between local and global structure in glass-forming liquids and its implications for crystallization.

In trajectory space, dynamical heterogeneities in glass-forming liquids correspond to the emergence of a dynamical phase transition between an active phase poor in local structure and an inactive phase which is rich in local structure. We support this scenario with the study of a model additive mixture of Lennard-Jones particles, quantifying how the choice of the relevant structural and dynamical observable affects the transition in trajectory space. We find that the low mobility, structure-rich phase is dominated by icosahedral order. Applying a nonequilibrium rheological protocol, we connect local order to the emergence of mechanical rigidity.

A quasi two-dimensional colloidal suspension is studied under the influence of immobilisation (pinning) of a random fraction of its particles. We introduce a novel experimental method to perform random pinning and, with the support of numerical simulation, we find that increasing the pinning concentration smoothly arrests the system, with a cross-over from a regime of high mobility and high entropy to a regime of low mobility and low entropy. At the local level, we study fluctuations in area fraction and concentration of pins and map them to entropic structural signatures and local mobility, obtaining a measure for the local entropic fluctuations of the experimental system.

We study the joint variability of structural information in a hard sphere fluid biased to avoid crystallisation and form fivefold symmetric geometric motifs. We show that the structural covariance matrix approach, originally proposed for on-lattice liquids [Ronceray and Harrowell, JCP 2016], can be meaningfully employed to understand structural relationships between different motifs and can predict, within the linear-response regime, structural changes related to motifs distinct from that used to bias the system.

Key to resolving the scientific challenge of the glass transition is to understand the origin of the massive increase in viscosity of liquids cooled below their melting temperature (avoiding crystallisation). A number of competing and often mutually exclusive theoretical approaches have been advanced to describe this phenomenon. Some posit a bona fide thermodynamic phase to an "ideal glass", an amorphous state with exceptionally low entropy. Other approaches are built around the concept of the glass transition as a primarily dynamic phenomenon. These fundamentally different interpretations give equally good descriptions of the data available, so it is hard to determine which -- if any -- is correct. Recently however this situation has begun to change. A consensus has emerged that one powerful means to resolve this longstanding question is to approach the putative thermodynamic transition sufficiently closely, and a number of techniques have emerged to meet this challenge. Here we review the results of some of these new techniques and discuss the implications for the existence -- or otherwise -- of the thermodynamic transition to an ideal glass., Comment: 42 pages

We consider the sedimentation of a colloidal gel under confinement in the direction of gravity. The confinement allows us to compare directly experiments and computer simulations, for the same system size in the vertical direction. The confinement also leads to qualitatively different behaviour compared to bulk systems: in large systems gelation suppresses sedimentation, but for small systems sedimentation is enhanced relative to non-gelling suspensions, although the rate of sedimentation is reduced when the strength of the attraction between the colloids is strong. We map interaction parameters between a model experimental system (observed in real space) and computer simulations. Remarkably, we find that when simulating the system using Brownian dynamics in which hydrodynamic interactions between the particles are neglected, we find that sedimentation occurs on the same timescale as the experiments, however the thickness of the "arms" of the gel is rather larger in the experiments, compared with the simulations. An analysis of local structure in the simulations showed similar behaviour to gelation in the absence of gravity.

Geometric frustration describes the inability of a local molecular arrangement, such as icosahedra found in metallic glasses and in model atomic glass-formers, to tile space. Local icosahedral order however is strongly frustrated in Euclidean space, which obscures any causal relationship with the observed dynamical slowdown. Here we relieve frustration in a model glass-forming liquid by curving 3-dimensional space onto the surface of a 4-dimensional hypersphere. For sufficient curvature, frustration vanishes and the liquid freezes in a fully icosahedral structure via a sharp `transition'. Frustration increases upon reducing the curvature, and the transition to the icosahedral state smoothens while glassy dynamics emerges. Decreasing the curvature leads to decoupling between dynamical and structural length scales and the decrease of kinetic fragility. This sheds light on the observed glass-forming behavior in the Euclidean space., Comment: 5 pages + supplementary material

Among the key insights into the glass transition has been the identification of a non-equilibrium phase transition in trajectory space which reveals phase coexistence between the normal supercooled liquid (active phase) and a glassy state (inactive phase). Here we present evidence that such a transition occurs in experiment. In colloidal hard spheres we find a non-Gaussian distribution of trajectories leaning towards those rich in locally favoured structures (LFS), associated with the emergence of slow dynamics. This we interpret as evidence for an non-equilibrium transition to an inactive LFS-rich phase. Reweighting trajectories reveals a first-order phase transition in trajectory space between a normal liquid and a LFS-rich phase. We further find evidence of a purely dynamical transition in trajectory space., Comment: 5 pages

The formation of colloidal gels is strongly dependent on the volume fraction of the system and the strength of the interactions between the colloids. Here we explore very dilute solutions by the means of numerical simulations, and show that, in the absence of hydrodynamic interactions and for sufficiently strong interactions, percolating colloidal gels can be realised at very low values of the volume fraction. Characterising the structure of the network of the arrested material we find that, when reducing the volume fraction, the gels are dominated by low-energy local structures, analogous to the isolated clusters of the interaction potential. Changing the strength of the interaction allows us to tune the compactness of the gel as characterised by the fractal dimension, with low interaction strength favouring more chain-like structures.

We consider a model of self-propelled dynamics for athermal active particles, where the non-equilibrium active forces are modelled by a Ornstein-Uhlenbeck process. In the limit of no-driving force, the model reduces to the passive, Brownian dynamics of an atomistic glass forming fluid, the Wahnstr\"om binary mixture. The Wahnstr\"om mixture is known to show strong correlations between the emergence of slow dynamics and the formation of locally favoured structures based on icosahedra. Here, we study how the non-equilibrium forces affect the local structure of the system, and find that these strongly promote icosahedral order. The phases rich in local icosahedral order correspond to configurations of very low potential energy, suggesting that the non-equilibrium dynamics in the self propelled model can be effectively exploited to explore the potential energy surface of the binary mixture and have access to states that are difficult to attain using passive dynamics.

We investigate the effects of the reversal of the gravitational field onto a sedimented and partially crystallised suspension of nearly-hard sphere colloids. We analyse the structural changes that take place during the melting of the crystalline regions and the reorganisation and assembly of the sedimenting particles. Through a comparison with numerical simulation, we access the single-particle kinetics and identify the key structural mechanism in the competition between five-fold symmetric and cubic crystalline structures. With the use of a coarse-grained, discrete model, we reproduce the kinetic network of reactions underpinning crystallisation and highlight the main microscopic transitions.

For binary fluid mixtures of spherical particles in which the two species are sufficiently different in size, the dominant wavelength of oscillations of the pair correlation functions is predicted to change from roughly the diameter of the large species to that of the small species along a sharp crossover line in the phase diagram [C. Grodon, M. Dijkstra, R. Evans & R. Roth, J.Chem.Phys. 121, 7869 (2004)]. Using particle-resolved colloid experiments in 3d we demonstrate that crossover exists and that its location in the phase diagram is in quantitative agreement with the results of both theory and our Monte-Carlo simulations. In contrast with previous work [J. Baumgartl, R. Dullens, M. Dijkstra, R. Roth & C. Bechinger, Phys.Rev.Lett. 98, 198303 (2007)], where a correspondence was drawn between crossover and percolation of both species, in our 3d study we find that structural crossover is unrelated to percolation.

Tackling the low-temperature fate of supercooled liquids is challenging due to the immense timescales involved, which prevent equilibration and lead to the operational glass transition. Relating glassy behaviour to an underlying, thermodynamic phase transition is a long-standing open question in condensed matter physics. Like experiments, computer simulations are limited by the small time window over which a liquid can be equilibrated. Here we address the challenge of low temperature equilibration using trajectory sampling in a system undergoing a nonequilibrium phase transition. This transition occurs in trajectory space between the normal supercooled liquid and a glassy state rich in low-energy geometric motifs. Our results indicate that this transition might become accessible in equilibrium configurational space at a temperature close to the so-called Kauzmann temperature, and provide a possible route to unify dynamical and thermodynamical theories of the glass transition., Comment: accepted in Physical. Rev. X

Geometric frustration is an approach to the glass transition based upon the consideration of locally favoured structures (LFS), which are geometric motifs which minimise the local free energy. Geometric frustration proposes that a transition to a crystalline state is frustrated because these LFS do not tile space. However, this concept is based on icosahedra which are not always the LFS for a given system. The LFS of the popular Kob-Andersen (KA) model glassformer is the bicapped square antiprism, which does tile space. Such an LFS-crystal is indeed realised in the $\mathrm{Al_{2}Cu}$ structure, which is predicted to be a low energy state for the KA model with a 2:1 composition. We therefore hypothesise that upon changing the composition in the KA model towards 2:1, geometric frustration may be progressively relieved, leading to larger and larger domains of LFS which would ultimately correspond to the $\mathrm{Al_{2}Cu}$ crystal. Remarkably, rather than an increase, upon changing composition we find a small decrease in the LFS population, and the system remains impervious to nucleation of LFS crystals. We suggest that this may be related to the composition of the LFS, as only a limited subset are compatible with the crystal. We further demonstrate that the $\mathrm{Al_{2}Cu}$ crystal will grow from a seed in the KA model with 2:1 composition and identify the melting temperature to be 0.447(2)., Comment: submitted to JCP

Charged colloids can behave as Yukawa systems, with similar phase behaviour. Using particle- resolved studies, we consider a system with an unusually long Debye screening length which forms crystals at low colloid volume fraction {\phi} ~ 0.01. We quantitatively compare this system with the Yukawa model and find that its freezing point is compatible with the theoretical prediction but that the crystal polymorph is not always that expected. In particular we find body-centred cubic crystals where face-centred cubic crystals are expected., Comment: To appear in the special issue of Contributions to Plasma Physics for Strongly Coupled Coulomb Systems 2014