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.

Bacterial ParB partitioning proteins involved in chromosomes and low-copy-number plasmid segregation are CTP-dependent molecular switches. CTP-binding converts ParB dimers to DNA clamps, allowing unidimensional diffusion along the DNA. This sliding property has been proposed to explain the ParB spreading over large distances from parS centromere sites where ParB is specifically loaded. We modeled such a ‘Clamping & sliding’ mechanism as a typical reaction-diffusion system, compared it to the F-plasmid ParB DNA binding pattern, and found that it can account neither for the long range of ParB binding to DNA, nor for the rapid assembly kinetics observed in vivo after parS duplication. Also, it predicts a strong effect on the F-plasmid ParB binding pattern from the presence of a roadblock that is not observed in ChIP-seq. We conclude that although ‘Clamping & sliding’ can occur at short distances from parS, another mechanism must apply for ParB recruitment at larger genomic distances.

Water transport in plant roots is of vital importance: it is a necessary transport to feed the rest of the organism in most vascular plants. To reach the xylem vessels, which ensure the long-distance transport to the aerial parts of the plant, water has first to flow across the root tissues surrounding the xylem. This flow, denoted to as radial transport, is not easily amenable to the experimentation, and has been studied mostly by measurements at a larger scale, and by models that poorly take into account cells and roots geometries. We adopted a continuous description of stationary root radial water transport to investigate how the geometry and the permeability contrasts between root compartments affect the transport of water. We experimentally modeled the root radial section as a two-dimensional and composite porous material with variable water permeabilities. It mimics the most salient water transport features of the root anatomy and allows a direct isualization of the water pathways. We also present 2D continuous numerical simulations of the water flow, in which we systematically varied the permeabilities of the different tissues. Our approach provides the physical premises to explain preferential sub-cellular radial routes from one cell to another and look for the subcellular pattern of structures or molecules involved in water transport.

We investigate the measurement of DNA supercoiling density ($\sigma$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS}. Using this framework, we provide an upper bound for $\sigma$ in the {\it Escherichia coli} chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries.

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.