How environment affects active particle swarms: a case study.

We investigate the collective motion of self-propelled agents in an environment filled with obstacles that are tethered to fixed positions via springs. The active particles are able to modify the environment by moving the obstacles through repulsion forces. This creates feedback interactions between the particles and the obstacles from which a breadth of patterns emerges (trails, band, clusters, honey-comb structures, etc.). We will focus on a discrete model first introduced in Aceves-Sanchez P et al. (2020, Bull. Math. Biol. 82, 125 (doi:10.1007/s11538-020-00805-z)), and derived into a continuum PDE model. As a first major novelty, we perform an in-depth investigation of pattern formation of the discrete and continuum models in two dimensions: we provide phase-diagrams and determine the key mechanisms for bifurcations to happen using linear stability analysis. As a result, we discover that the agent-agent repulsion, the agent-obstacle repulsion and the obstacle's spring stiffness are the key forces in the appearance of patterns, while alignment forces between the particles play a secondary role. The second major novelty lies in the development of an innovative methodology to compare discrete and continuum models that we apply here to perform an in-depth analysis of the agreement between the discrete and continuum models.

Mechanical constraints to cell-cycle progression in a pseudostratified epithelium.

As organs and tissues approach their normal size during development or regeneration, growth slows down, and cell proliferation progressively comes to a halt. Among the various processes suggested to contribute to growth termination,1-10 mechanical feedback, perhaps via adherens junctions, has been suggested to play a role.11-14 However, since adherens junctions are only present in a narrow plane of the subapical region, other structures are likely needed to sense mechanical stresses along the apical-basal (A-B) axis, especially in a thick pseudostratified epithelium. This could be achieved by nuclei, which have been implicated in mechanotransduction in tissue culture.15 In addition, mechanical constraints imposed by nuclear crowding and spatial confinement could affect interkinetic nuclear migration (IKNM),16 which allows G2 nuclei to reach the apical surface, where they normally undergo mitosis.17-25 To explore how mechanical constraints affect IKNM, we devised an individual-based model that treats nuclei as deformable objects constrained by the cell cortex and the presence of other nuclei. The model predicts changes in the proportion of cell-cycle phases during growth, which we validate with the cell-cycle phase reporter FUCCI (Fluorescent Ubiquitination-based Cell Cycle Indicator).26 However, this model does not preclude indefinite growth, leading us to postulate that nuclei must migrate basally to access a putative basal signal required for S phase entry. With this refinement, our updated model accounts for the observed progressive slowing down of growth and explains how pseudostratified epithelia reach a stereotypical thickness upon completion of growth.

Layer-by-Layer Growth of Complex-Shaped Three-Dimensional Nanostructures with Focused Electron Beams.

The fabrication of three-dimensional (3D) nanostructures is of great interest to many areas of nanotechnology currently challenged by fundamental limitations of conventional lithography. One of the most promising direct-write methods for 3D nanofabrication is focused electron beam-induced deposition (FEBID), owing to its high spatial resolution and versatility. Here we extend FEBID to the growth of complex-shaped 3D nanostructures by combining the layer-by-layer approach of conventional macroscopic 3D printers and the proximity effect correction of electron beam lithography. This framework is based on the continuum FEBID model and is capable of adjusting for a wide range of effects present during deposition, including beam-induced heating, defocusing, and gas flux anisotropies. We demonstrate the capabilities of our platform by fabricating free-standing nanowires, surfaces with varying curvatures and topologies, and general 3D objects, directly from standard stereolithography (STL) files and using different precursors. Real 3D nanoprinting as demonstrated here opens up exciting avenues for the study and exploitation of 3D nanoscale phenomena.