Biology subjects

Allier, C.

Publications and source records attributed to Allier, C..

4 recordsLinked to original sources

bioRxiv2025

Chromatix: a differentiable, GPU-accelerated wave-optics library

Modern microscopy methods incorporate computational modeling as an integral part of the imaging process, either to solve inverse problems or optimize the optical system design itself. These methods often depend on differentiable optics simulations, yet no standardized framework exists--forcing computational optics researchers to repeatedly and independently implement simulations with limited reusability and performance. These common problems limit the potential impact of computational optics as a field. Here we present Chromatix: an open-source, GPU-accelerated, differentiable wave optics simulation library. Chromatix builds on JAX to democratize fast, parallelized simulation of diverse optical systems and expand the design space in computational optics. Chromatix standardizes a growing collection of optical elements and propagation methods allowing a broad range of applications, which we demonstrate here for snapshot microscopy, holography, and phase retrieval. We demonstrate speed improvements of 2-6x on a single GPU and up to 22x on 8 GPUs.

bioinformatics↗

bioRxiv2019

A New Ultradian Rhythm Linked to Protein Degradation and Synthesis in Mammalian Cells

We describe a new ultradian rhythm that occurs during the interphase of the cell cycle in a wide range of mammalian cells, including both primary and transformed cells. The rhythm was detected by holographic lens-free microscopy that follows the individual histories of the dry mass of thousands of live cells simultaneously, each at a resolution of five minutes. Importantly, the rhythm was observed in inherently heterogeneous cell populations, thus eliminating synchronization and labeling bias. The rhythm is independent of circadian rhythm, has a period of 4 hours and is temperature-compensated. We demonstrated that the 4 hr rhythm is suppressed by proteostasis disruptors and is detected only in proliferating cells, suggesting that it represents the periodic dynamics of protein mass in growing cells. Brief teaserWe have revealed a 4 hr rhythm in cell dry mass dynamics that seems to be general in proliferating mammalian cells.

cell biology↗

bioRxiv2018

Confinement-induced transition between wave-like collective cell migration modes

The structural and functional organization of biological tissues relies on the intricate interplay between chemical and mechanical signaling. Whereas the role of constant and transient mechanical perturbations is generally accepted, several studies recently highlighted the existence of long-range mechanical excitations (i.e., waves) at the supracellular level. Here, we confine epithelial cell mono-layers to quasi-one dimensional geometries, to force the establishment of tissue-level waves of well-defined wavelength and period. Numerical simulations based on a self-propelled Voronoi model reproduce the observed waves and exhibit a phase transition between a global and a multi-nodal wave, controlled by the confinement size. We confirm experimentally the existence of such a phase transition, and show that wavelength and period are independent of the confinement length. Together, these results demonstrate the intrinsic origin of tissue oscillations, which could provide cells with a mechanism to accurately measure distances at the supracellular level.

biophysics↗

bioRxiv2018

Curvature Dependent constraints drive remodeling of epithelia

Epithelial tissues are essential to keep a proper barrier for the organism. They usually have highly curved shapes, such as tubules or cysts. However, interplays between the environment and cell mechanical properties to set the shape are not known. In this study, we encapsulated two epithelial cell lineages, MDCK and J3B1A, into hollow alginate tubes and grew them under cylindrical confinement. Once formed, the epithelial MDCK layer detached from the alginate shell, while J3B1A layer remained adherent. Detachment resulted from contractile forces within cell layers that pulled cells away from the shell. We concluded that J3B1A cells have lower contractility than MDCK cells. As the pulling forces depend on the radius of the tube, we induced detachment of J3B1A cells by reducing the size of the hollow tube by two. Moreover, in bent tubes, detachment was more pronounced on the outer side of the turn, while extrusion occurred in the inner side, further highlighting the coupling between curvature and cell contractility.

bioengineering↗