AI reveals a damage signalling hierarchy that coordinates different cell behaviours driving wound re-epithelialisation.

One of the key tissue movements driving closure of a wound is re-epithelialisation. Earlier wound healing studies have described the dynamic cell behaviours that contribute to wound re-epithelialisation, including cell division, cell shape changes and cell migration, as well as the signals that might regulate these cell behaviours. Here, we use a series of deep learning tools to quantify the contributions of each of these cell behaviours from movies of repairing wounds in the Drosophila pupal wing epithelium. We test how each is altered following knockdown of the conserved wound repair signals, Ca2+ and JNK, as well as ablation of macrophages which supply growth factor signals believed to orchestrate aspects of the repair process. Our genetic perturbation experiments provide quantifiable insights regarding how these wound signals impact cell behaviours. We find that Ca2+ signalling is a master regulator required for all contributing cell behaviours; JNK signalling primarily drives cell shape changes and divisions, whereas signals from macrophages regulate largely cell migration and proliferation. Our studies show AI to be a valuable tool for unravelling complex signalling hierarchies underlying tissue repair.

Rheology of Suspensions of Flat Elastic Particles.

We consider a suspension of noninteracting flat elastic particles in a Newtonian fluid. We model a flat shape as three beads, carried along by the flow according to Stokes law, and connected by nonlinear springs, chosen such that the energy is quadratic in the area. In analogy with common dumbbell models involving two beads connected by linear springs, we solve the stochastic equations of motion exactly to compute the constitutive law for the stress tensor of a flat elastic particle suspension. A lower convected time derivative naturally arises as part of the constitutive law, but surprisingly the rheological response in strong extensional and strong contracting flows is similar to that of the classical Oldroyd-B model associated with dumbbell suspensions.

Mechanochemical Active Feedback Generates Convergence Extension in Epithelial Tissue.

Convergence extension, the simultaneous elongation of tissue along one axis while narrowing along a perpendicular axis, occurs during embryonic development. A fundamental process that contributes to shaping the organism, it happens in many different species and tissue types. Here, we present a minimal continuum model, that can be directly linked to the controlling microscopic biochemistry, which shows spontaneous convergence extension. It is comprised of a 2D viscoelastic active material with a mechanochemical active feedback mechanism coupled to a substrate via friction. Robust convergent extension behavior emerges beyond a critical value of the activity parameter and is controlled by the boundary conditions and the coupling to the substrate. Oscillations and spatial patterns emerge in this model when internal dissipation dominates over friction, as well as in the active elastic limit.

Necking and failure of a particulate gel strand: signatures of yielding on different length scales.

"Sticky" spheres with a short-ranged attraction are a basic model of a wide range of materials from the atomic to the granular length scale. Among the complex phenomena exhibited by sticky spheres is the formation of far-from-equilibrium dynamically arrested networks which comprise "strands" of densely packed particles. The aging and failure of such gels under load is a remarkably challenging problem, given the simplicity of the model, as it involves multiple length- and time-scales, making a single approach ineffective. Here we tackle this challenge by addressing the failure of a single strand with a combination of methods. We study the mechanical response of a single strand of a model gel-former to deformation, both numerically and analytically. Under elongation, the strand breaks by a necking instability. We analyse this behaviour at three different length scales: a rheological continuum model of the whole strand; a microscopic analysis of the particle structure and dynamics; and the local stress tensor. Combining these different approaches gives a coherent picture of the necking and failure. The strand has an amorphous local structure and has large residual stresses from its initialisation. We find that neck formation is associated with increased plastic flow, a reduction in the stability of the local structure, and a reduction in the residual stresses; this indicates that the system loses its solid character and starts to behave more like a viscous fluid. These results will inform the development of more detailed models that incorporate the heterogeneous network structure of particulate gels.

Active Brownian particles in random and porous environments.

The transport of active particles may occur in complex environments, in which it emerges from the interplay between the mobility of the active components and the quenched disorder of the environment. Here, we explore the structural and dynamical properties of active Brownian particles (ABPs) in random environments composed of fixed obstacles in three dimensions. We consider different arrangements of the obstacles. In particular, we consider two particular situations corresponding to experimentally realizable settings. First, we model pinning particles in (non-overlapping) random positions and, second, in a percolating gel structure and provide an extensive characterization of the structure and dynamics of ABPs in these complex environments. We find that the confinement increases the heterogeneity of the dynamics, with new populations of absorbed and localized particles appearing close to the obstacles. This heterogeneity has a profound impact on the motility induced phase separation exhibited by the particles at high activity, ranging from nucleation and growth in random disorder to a complex phase separation in porous environments.

Steady-state running rate sets the speed and accuracy of accumulation of swimming bacteria.

We study the chemotaxis of a population of genetically identical swimming bacteria undergoing run and tumble dynamics driven by stochastic switching between clockwise and counterclockwise rotation of the flagellar rotary system, where the steady-state rate of the switching changes in different environments. Understanding chemotaxis quantitatively requires that one links the measured steady-state switching rates of the rotary system, as well as the directional changes of individual swimming bacteria in a gradient of chemoattractant/repellant, to the efficiency of a population of bacteria in moving up/down the gradient. Here we achieve this by using a probabilistic model, parametrized with our experimental data, and show that the response of a population to the gradient is complex. We find the changes to the steady-state switching rate in the absence of gradients affect the average speed of the swimming bacterial population response as well as the width of the distribution. Both must be taken into account when optimizing the overall response of the population in complex environments.

The nonlinear motion of cells subject to external forces.

To develop a minimal model for a cell moving in a crowded environment such as in tissue, we investigate the response of a liquid drop of active matter moving on a flat rigid substrate to forces applied at its boundaries. We consider two different self-propulsion mechanisms, active stresses and treadmilling polymerisation, and we investigate how the active drop motion is altered by these surface forces. We find a highly non-linear response to forces that we characterise using drop velocity, drop shape, and the traction between the drop and the substrate. Each self-propulsion mechanism gives rise to two main modes of motion: a long thin drop with zero traction in the bulk, mostly occurring under strong stretching forces, and a parabolic drop with finite traction in the bulk, mostly occurring under strong squeezing forces. In each case there is a sharp transition between parabolic, and long thin drops as a function of the applied forces and indications of drop break-up where large forces stretch the drop.

Crystallisation and polymorph selection in active Brownian particles.

We explore crystallisation and polymorph selection in active Brownian particles with numerical simulation. In agreement with previous work (Wysocki et al. in Europhys Lett 105:48004, 2014), we find that crystallisation is suppressed by activity and occurs at higher densities with increasing Péclet number ([Formula: see text]). While the nucleation rate decreases with increasing activity, the crystal growth rate increases due to the accelerated dynamics in the melt. As a result of this competition, we observe the transition from a nucleation and growth regime at high [Formula: see text] to "spinodal nucleation" at low [Formula: see text]. Unlike the case of passive hard spheres, where preference for FCC over HCP polymorphs is weak, activity causes the annealing of HCP stacking faults, thus strongly favouring the FCC symmetry at high [Formula: see text]. When freezing occurs more slowly, in the nucleation and growth regime, this tendency is much reduced and we see a trend towards the passive case of little preference for either polymorph.

How many ways a cell can move: the modes of self-propulsion of an active drop.

Numerous physical models have been proposed to explain how cell motility emerges from internal activity, mostly focused on how crawling motion arises from internal processes. Here we offer a classification of self-propulsion mechanisms based on general physical principles, showing that crawling is not the only way for cells to move on a substrate. We consider a thin drop of active matter on a planar substrate and fully characterize its autonomous motion for all three possible sources of driving: (i) the stresses induced in the bulk by active components, which allow in particular tractionless motion, (ii) the self-propulsion of active components at the substrate, which gives rise to crawling motion, and (iii) a net capillary force, possibly self-generated, and coupled to internal activity. We determine travelling-wave solutions to the lubrication equations as a function of a dimensionless activity parameter for each mode of motion. Numerical simulations are used to characterize the drop motion over a wide range of activity magnitudes, and explicit analytical solutions in excellent agreement with the simulations are derived in the weak-activity regime.

Beyond icosahedral symmetry in packings of proteins in spherical shells.

The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral cage. In turn, this has inspired synthetic biologists to design de novo protein cages. We use simple models, on multiple scales, to investigate the self-assembly of a spherical cage, focusing on the regularity of the packing of protein-like objects on the surface. Using building blocks, which are able to pack with icosahedral symmetry, we examine how stable these highly symmetric structures are to perturbations that may arise from the interplay between flexibility of the interacting blocks and entropic effects. We find that, in the presence of those perturbations, icosahedral packing is not the most stable arrangement for a wide range of parameters; rather disordered structures are found to be the most stable. Our results suggest that (i) many designed, or even natural, protein cages may not be regular in the presence of those perturbations and (ii) optimizing those flexibilities can be a possible design strategy to obtain regular synthetic cages with full control over their surface properties.

Tractionless Self-Propulsion of Active Drops.

We report on a new mode of self-propulsion exhibited by compact drops of active liquids on a substrate which, remarkably, is tractionless, i.e., which imparts no mechanical stress locally on the surface. We show, both analytically and by numerical simulation, that the equations of motion for an active nematic drop possess a simple self-propelling solution, with no traction on the solid surface and in which the direction of motion is controlled by the winding of the nematic director field across the drop height. The physics underlying this mode of motion has the same origins as that giving rise to the zero viscosity observed in bacterial suspensions. This topologically protected tractionless self-propusion provides a robust physical mechanism for efficient cell migration in crowded environments like tissues.

Exact results for sheared polar active suspensions with variable liquid crystalline order.

We consider a confined sheared active polar liquid crystal with a uniform orientation and study the effect of variations in the magnitude of polarization. Restricting our analysis to one-dimensional geometries, we demonstrate that with asymmetric boundary conditions, this system is characterized, macroscopically, by a linear shear stress vs. shear strain relationship that does not pass through the origin: At a zero strain rate, the fluid sustains a non-zero stress. Analytic solutions for the polarization, density, and velocity fields are derived for asymptotically large or small systems and are shown by comparison with precise numerical solutions to be good approximations for finite-size systems.

Active Suspensions have Nonmonotonic Flow Curves and Multiple Mechanical Equilibria.

We point out unconventional mechanical properties of confined active fluids, such as bacterial suspensions, under shear. Using a minimal model of an active liquid crystal with no free parameters, we predict the existence of a window of bacteria concentration for which a suspension of E. Coli effectively behaves, at steady-state, as a negative viscosity fluid and reach a quantitative agreement with experimental measurements. Our theoretical analysis further shows that a negative apparent viscosity is due to a nonmonotonic local velocity profile, and it is associated with a nonmonotonic stress versus strain rate flow curve. This implies that fixed stress and fixed strain rate ensembles are not equivalent for active fluids.

From hydrodynamic lubrication to many-body interactions in dense suspensions of active swimmers.

We study how hydrodynamic interactions affect the collective behaviour of active particles suspended in a fluid at high concentrations, with particular attention to lubrication forces which appear when the particles are very close to one another. We compute exactly the limiting behaviour of the hydrodynamic interactions between two spherical (circular) active swimmers in very close proximity to one another in the general setting in both three and (two) dimensions. Combining this with far-field interactions, we develop a novel numerical scheme which allows us to study the collective behaviour of large numbers of active particles with accurate hydrodynamic interactions when close to one another. We study active swimmers whose intrinsic flow fields are characterised by force dipoles and quadrupoles. Using this scheme, we are able to show that lubrication forces when the particles are very close to each other can play as important a role as long-range hydrodynamic interactions in determining their many-body behaviour. We find that when the swimmer force dipole is large, finite clusters and open gel-like clusters appear rather than complete phase separation. This suppression is due to near-field lubrication interactions. For swimmers with small force dipoles, we find surprisingly that a globally polar-ordered phase appears because near-field lubrication rather than long-range hydrodynamics dominates the alignment mechanism. Polar order is present for very large system sizes and is stable to fluctuations with a finite noise amplitude. We explain the emergence of polar order using a minimal model in which only the leading rotational effect of the near-field interaction is included. These phenomena are also reproduced in two dimensions.

The dynamical interplay between a megadalton peptide nanocage and solutes probed by microsecond atomistic MD; implications for design.

Understanding the assembly and dynamics of protein-based supramolecular capsids and cages is of fundamental importance and could lead to applications in synthetic biology and biotechnology. Here we present long and large atomistic molecular dynamics simulations of de novo designed self-assembling protein nanocages (SAGEs) in aqueous media. Microsecond simulations, comprised of ≈42 million atoms for three pre-formed SAGEs of different charges, in the presence of solutes and solvent have been completed. Here, the dynamics, stability and porosity of the peptide networks are explored along with their interactions with ions, small molecules and macromolecular solutes. All assemblies are stable over the µs timescale, and the solutes show a mixture of transport behaviour across or adherence to the fabric of the SAGE particles. Solute proteins largely retained native-like conformation on contact with SAGE. Certain residues of the SAGE peptides are identified as "repeat offenders" for contacting many different solutes, which suggest modifications to reduce non-specific binding. These studies highlight how molecular dynamics can aid the design process of SAGE and similar assemblies for potential applications as diverse as platforms for drug and vaccine delivery and nanoreactors to encapsulate enzyme pathways.

Structure in sheared supercooled liquids: Dynamical rearrangements of an effective system of icosahedra.

We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of particles organized into icosahedra under simple steady state shear. We recast this glassformer as an effective system of icosahedra [Pinney et al., J. Chem. Phys. 143, 244507 (2015)]. From the observed population of icosahedra in each steady state, we obtain an effective temperature which is linearly dependent on the shear rate in the range considered. Upon shear banding, the system separates into a region of high shear rate and a region of low shear rate. The effective temperatures obtained in each case show that the low shear regions correspond to a significantly lower temperature than the high shear regions. Taking a weighted average of the effective temperature of these regions (weight determined by region size) yields an estimate of the effective temperature which compares well with an effective temperature based on the global mesocluster population of the whole system.

Recasting a model atomistic glassformer as a system of icosahedra.

We consider a binary Lennard-Jones glassformer whose super-Arrhenius dynamics are correlated with the formation of icosahedral structures. Upon cooling, these icosahedra organize into mesoclusters. We recast this glassformer as an effective system of icosahedra which we describe with a population dynamics model. This model we parameterize with data from the temperature regime accessible to molecular dynamics simulations. We then use the model to determine the population of icosahedra in mesoclusters at arbitrary temperature. Using simulation data to incorporate dynamics into the model, we predict relaxation behavior at temperatures inaccessible to conventional approaches. Our model predicts super-Arrhenius dynamics whose relaxation time remains finite for non-zero temperature.

Stress reorganization and response in active solids.

We present a microscopic model of a disordered viscoelastic active solid, i.e., an active material whose long time behavior is elastic as opposed to viscous. It is composed of filaments, passive cross-links, and molecular motors powered by stored chemical energy, e.g., actomyosin powered by adenosine triphosphate. Our model allows us to study the collective behavior of contractile active elements and how their interaction with each other and the passive elastic elements determines the macroscopic mechanical properties of the active material. As a result of the (un)binding dynamics of the active elements, we find that this system provides a highly responsive material with a dynamic mechanical response strongly dependent on the amount of deformation.

Equation of state for active matter.

We characterize the steady states of a suspension of two-dimensional active Brownian particles (ABPs). By approximating the first-order correction to the steady-state probability distribution to lowest order in Peclet number, we show that macroscopic quantities can be calculated in analogous way to equilibrium systems using this probability distribution. We then derive expressions for the macroscopic pressure and position-orientation correlation functions. We check our results by direct comparison with extensive numerical simulations. A key finding is the importance of many-body effective interactions even at very low densities.

Dynamics and interactions of Quincke roller clusters: From orbits and flips to excited states.

Active matter systems may be characterized by the conversion of energy into active motion, e.g., the self-propulsion of microorganisms. Artificial active colloids form models that exhibit essential properties of more complex biological systems but are amenable to laboratory experiments. While most experimental models consist of spheres, active particles of different shapes are less understood. Furthermore, interactions between these anisotropic active colloids are even less explored. Here, we investigate the motion of active colloidal clusters and the interactions between them. We focus on self-assembled dumbbells and trimers powered by an external dc electric field. For dumbbells, we observe an activity-dependent behavior of spinning, circular, and orbital motions. Moreover, collisions between dumbbells lead to the hierarchical self-assembly of tetramers and hexamers, both of which form rotational excited states. On the other hand, trimers exhibit flipping motion that leads to trajectories reminiscent of a honeycomb lattice.