Nonreciprocity as a generic route to traveling states

We examine a non-reciprocally coupled dynamical model of a mixture of two diffusing species. We demonstrate that nonreciprocity, which is encoded in the model via antagonistic cross diffusivities, provides a generic mechanism for the emergence of traveling patterns in purely diffusive systems with conservative dynamics. In the absence of non-reciprocity, the binary fluid mixture undergoes a phase transition from a homogeneous mixed state to a demixed state with spatially separated regions rich in one of the two components. Above a critical value of the parameter tuning non-reciprocity, the static demixed pattern acquires a finite velocity, resulting in a state that breaks both spatial and time translational symmetry, as well as the reflection parity of the static pattern. We elucidate the generic nature of the transition to traveling patterns using a minimal model that can be studied analytically. Our work has direct relevance to nonequilibrium assembly in mixtures of chemically interacting colloids that are known to exhibit non-reciprocal effective interactions, as well as to mixtures of active and passive agents where traveling states of the type predicted here have been observed in simulations. It also provides insight on transitions to traveling and oscillatory states seen in a broad range of nonreciprocal systems with non-conservative dynamics, from reaction-diffusion and prey-predators models to multispecies mixtures of microorganisms with antagonistic interactions.Comment: 8 pages, 3 figure

Geometry and mechanics of microdomains in growing bacterial colonies

Bacterial colonies are abundant on living and nonliving surfaces and are known to mediate a broad range of processes in ecology, medicine, and industry. Although extensively researched, from single cells to demographic scales, a comprehensive biomechanical picture, highlighting the cell-to-colony dynamics, is still lacking. Here, using molecular dynamics simulations and continuous modeling, we investigate the geometrical and mechanical properties of a bacterial colony growing on a substrate with a free boundary and demonstrate that such an expanding colony self-organizes into a "mosaic" of microdomains consisting of highly aligned cells. The emergence of microdomains is mediated by two competing forces: the steric forces between neighboring cells, which favor cell alignment, and the extensile stresses due to cell growth that tend to reduce the local orientational order and thereby distort the system. This interplay results in an exponential distribution of the domain areas and sets a characteristic length scale proportional to the square root of the ratio between the system orientational stiffness and the magnitude of the extensile active stress. Our theoretical predictions are finally compared with experiments with freely growing E. coli microcolonies, finding quantitative agreement.Comment: 10 pages, 7 figure

Vorticity phase separation and defect lattices in the isotropic phase of active liquid crystals

We use numerical simulations and linear stability analysis to study the dynamics of an active liquid crystal film on a substrate in the regime where the passive system would be isotropic. Extensile activity builds up local orientational order and destabilizes the quiescent isotropic state above a critical activity value, eventually resulting in spatiotemporal chaotic dynamics akin to the one observed ubiquitously in the nematic state. Here we show that tuning substrate friction yields a variety of emergent structures at intermediate activity, including lattices of flow vortices with associated regular arrangements of topological defects and a new state where flow vortices trap pairs of $+1/2$ defect that chase each other tail. These chiral units spontaneously pick the sense of rotation and organize in a hexagonal lattice, surrounded by a diffuse flow of opposite rotation to maintain zero net vorticity. The length scale of these emergent structures is set by the screening length $l_\eta=\sqrt{\eta/\Gamma}$ of the flow, controlled by the shear viscosity $\eta$ and the substrate friction $\Gamma$, and can be captured by simple mode selection of the vortical flows. We demonstrate that the emergence of coherent structures can be interpreted as a phase separation of vorticity, where friction plays a role akin to that of birth/death processes in breaking conservation of the phase separating species and selecting a characteristic scale for the patterns. Our work shows that friction provides an experimentally accessible tuning parameter for designing controlled active flows

Confinement-induced self-organization in growing bacterial colonies

We investigate the emergence of global alignment in colonies of dividing rod-shaped cells under confinement. Using molecular dynamics simulations and continuous modeling, we demonstrate that geometrical anisotropies in the confining environment give rise to imbalance in the normal stresses, which, in turn, drives a collective rearrangement of the cells. This behavior crucially relies on the colony's solid-like mechanical response at short time scales and can be recovered within the framework of active hydrodynamics upon modeling bacterial colonies as growing viscoelastic gels characterized by Maxwell-like stress relaxation.Comment: 10 pages, 8 figure

Spontaneous stable rotation of flocking flexible active matter

In nature, active matter, such as worms or dogs, tend to spontaneously form a stable rotational cluster when they flock to the same food source on an unregulated and unconfined surface. {In this paper we present an $n$-node flexible active matter model to study the collective motion due to the flocking of individual agents on a two-dimensional surface, and confirm that there exists a spontaneous stable cluster rotation synchronizing with a chirality produced by the alignment of their bodies under the impetus of the active force.} A prefactor of 1.86 is obtained for the linear relationship between normalized angular velocity and chirality. The angular velocity of such a rotation is found to be dependent on the individual flexibility, the number of nodes in each individual, and the magnitude of the active force. The conclusions well explain the spontaneous stable rotation of clusters that exists in many flexible active matter, like worms or {dogs}, when they flock to the same single source

APETALA2 antagonizes the transcriptional activity of AGAMOUS in regulating floral stem cells in Arabidopsis thaliana.

APETALA2 (AP2) is best known for its function in the outer two floral whorls, where it specifies the identities of sepals and petals by restricting the expression of AGAMOUS (AG) to the inner two whorls in Arabidopsis thaliana. Here, we describe a role of AP2 in promoting the maintenance of floral stem cell fate, not by repressing AG transcription, but by antagonizing AG activity in the center of the flower. We performed a genetic screen with ag-10 plants, which exhibit a weak floral determinacy defect, and isolated a mutant with a strong floral determinacy defect. This mutant was found to harbor another mutation in AG and was named ag-11. We performed a genetic screen in the ag-11 background to isolate mutations that suppress the floral determinacy defect. Two suppressor mutants were found to harbor mutations in AP2. While AG is known to shut down the expression of the stem cell maintenance gene WUSCHEL (WUS) to terminate floral stem cell fate, AP2 promotes the expression of WUS. AP2 does not repress the transcription of AG in the inner two whorls, but instead counteracts AG activity

Mono-to-multilayer transition in growing bacterial colonies

The transition from monolayers to multilayered structures in bacterial colonies is a fundamental step in biofilm development. Observed across different morphotypes and species, this transition is triggered within freely growing bacterial microcolonies comprising a few hundred cells. Using a combination of numerical simulations and analytical modeling, here we demonstrate that this transition originates from the competition between growth-induced in-plane active stresses and vertical restoring forces, due to the cell-substrate interactions. Using a simple chainlike colony of laterally confined cells, we show that the transition sets when individual cells become unstable to rotations; thus it is localized and mechanically deterministic. Asynchronous cell division renders the process stochastic, so that all the critical parameters that control the onset of the transition are continuously distributed random variables. Here we demonstrate that the occurrence of the first division in the colony can be approximated as a Poisson process in the limit of large cell numbers. This allows us to approximately calculate the probability distribution function of the position and time associated with the first extrusion. The rate of such a Poisson process can be identified as the order parameter of the transition, thus highlighting its mixed deterministic-stochastic nature