We use the swap Monte Carlo algorithm to analyse the glassy behaviour of sticky spheres in equilibrium conditions at densities where conventional simulations and experiments fail to reach equilibrium, beyond predicted phase transitions and dynamic singularities. We demonstrate the existence of a unique ergodic region comprising all the distinct phases previously reported, except for a phase-separated region at strong adhesion. All structural and dynamic observables evolve gradually within this ergodic region, the physics evolving smoothly from well-known hard sphere glassy behaviour at small adhesions and large densities, to a more complex glassy regime characterised by unusually-broad distributions of relaxation timescales and lengthscales at large adhesions.

The understanding of thermodynamic glass transition has been hindered by the lack of proper models beyond mean-field theories. Here, we propose a three-dimensional lattice glass model on a simple cubic lattice that exhibits the typical dynamics observed in fragile supercooled liquids such as two-step relaxation, super-Arrhenius growth in the relaxation time, and dynamical heterogeneity. Using advanced Monte Carlo methods, we compute the thermodynamic properties deep inside the glassy temperature regime, well below the onset temperature of the slow dynamics. The specific heat has a finite jump towards the thermodynamic limit with critical exponents close to those expected from the hyperscaling and the random first-order transition theory for the glass transition. We also study an effective free energy of glasses, the Franz-Parisi potential, as a function of the overlap between equilibrium and quenched configurations. The effective free energy indicates the existence of a first-order phase transition, consistent with the random first-order transition theory. These findings strongly suggest that the glassy dynamics of the model has its origin in thermodynamics.

We develop a minimal model to describe growing dense active matter such as biological tissues, bacterial colonies and biofilms, that are driven by a competition between particle division and steric repulsion. We provide a detailed numerical analysis of collective and single particle dynamics. We show that the microscopic dynamics can be understood as the superposition of an affine radial component due to the global growth, and of a more complex non-affine component which displays features typical of driven soft glassy materials, such as aging, compressed exponential decay of time correlation functions, and a crossover from superdiffusive behaviour at short scales to subdiffusive behaviour at larger scales. This analogy emerges because particle division at the microscale leads to a global expansion which then plays a role analogous to shear flow in soft driven glasses. We conclude that growing dense active matter and sheared dense suspensions can generically be described by the same underlying physics.

The swap Monte Carlo algorithm allows the preparation of highly stable glassy configurations for a number of glass-formers, but is inefficient for some models, such as the much studied binary Kob-Andersen (KA) mixture. We have recently developed generalisations to the KA model where swap can be very effective. Here, we show that these models can in turn be used to considerably enhance the stability of glassy configurations in the original KA model at no computational cost. We successfully develop several numerical strategies both in and out of equilibrium to achieve this goal and show how to optimise them. We provide several physical measurements indicating that the proposed algorithms considerably enhance mechanical and thermodynamic stability in the KA model, including a transition towards brittle yielding behaviour. Our results thus pave the way for future studies of stable glasses using the KA model.

Using molecular dynamics simulations we investigate the dependence of the structuraland vibrational properties of the surfaces of sodo-silicate glasses on the sodium content as well as the nature of the surface. Two types of glass surfaces are considered:A melt-formed surface (MS) in which a liquid with a free surface has been cooleddown into the glass phase and a fracture surface (FS) obtained by tensile loadingof a glass sample. We find that the MS is more abundant in Na and non-bridgingoxygen atoms than the FS and the bulk glass, whereas the FS has higher concentration of structural defects such as two-membered rings and under-coordinated Si thanthe MS. We associate these structural differences to the production histories of theglasses and the mobility of the Na ions. It is also found that for Na-poor systems thefluctuations in composition and local atomic charge density decay with a power-lawas a function of distance from the surface while Na-rich systems show an exponentialdecay with a typical decay length of ≈ 2.3 Å. The vibrational density of states showsthat the presence of the surfaces leads to a decrease of the characteristic frequenciesin the system. The two-membered rings give rise to a pronounce band at ≈ 880 cm−1which is in good agreement experimental observations.

The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles carrying biochemical reactants. Crossings between such filaments constitute a key element, as they may serve to alter the destination of such payload. Although motor proteins are known to display a rich behaviour at such crossings, the latter have so far only been modelled as simple branching points. Here we explore a model for a crossing between two microtubules which retains the individual tracks consisting of protofilaments, and we construct a schematic representation of the transport paths. We study collective transport exemplified by the Totally Asymmetric Simple Exclusion Process (TASEP), and provide a full analysis of the transport features and the associated phase diagram, by a generic mean-field approach which we confirm through particle-based stochastic simulations. In particular we show that transport through such a compound crossing cannot be approximated from a coarse-grained structure with a simple branching point. Instead, it gives rise to entirely new and counterintuitive features: the fundamental current-density relation for traffic flow is no longer a single-valued function, and it furthermore differs according to whether it is observed upstream or downstream from the crossing. We argue that these novel features may be directly relevant for interpreting experimental measurements.