arXiv subjects

Ilyas Djafer-Cherif

Publications and source records attributed to Ilyas Djafer-Cherif.

3 recordsLinked to original sources

arXiv2026

An Affordable Fiducial Marker Strategy for Reliable Autofocus in Long-Term Live Microscopy

Long-term time-lapse imaging of biological samples requires correcting for focal drift, which would otherwise gradually push the sample out of focus. We present a software-based method that eliminates this time-dependent blur using only a motorized Z-drive, with no additional hardware. The method relies on imaging marks made on the side of the coverslip opposite to the sample. We provide a Beanshell script implementation, evaluate its performance across multiple objectives, and benchmark it against a hardware autofocus system, finding comparable results. Finally, we demonstrate its effectiveness in live imaging of growing bacterial colonies.

physics.bio-ph↗

arXiv2022

Generating active T1 transitions through mechanochemical feedback

Convergence-extension in embryos is controlled by chemical and mechanical signalling. A key cellular process is the exchange of neighbours via T1 transitions. We propose and analyse a model with positive feedback between recruitment of myosin motors and mechanical tension in cell junctions. The model produces active T1 events, which act to elongate the tissue perpendicular to external pulling. Using an idealized tissue patch comprising several active cells embedded in a matrix of passive hexagonal cells we identified an optimal range of pulling forces to trigger an active T1 event. We show that pulling also generates tension chains in a realistic patch made entirely of active cells of random shapes, and leads to convergence-extension over a range of parameters. Our findings show that active intercalations can generate stress that activates T1 events in neighbouring cells resulting in tension dependent tissue re-organisation, in qualitative agreement with experiments on gastrulation in chick embryos.

physics.bio-ph↗

arXiv2019

Understanding dense active nematics from microscopic models

We study dry, dense active nematics at both particle and continuous levels. Specifically, extending the Boltzmann-Ginzburg-Landau approach, we derive well-behaved hydrodynamic equations from a Vicsek-style model with nematic alignment and pairwise repulsion. An extensive study of the phase diagram shows qualitative agreement between the two levels of description. We find in particular that the dynamics of topological defects strongly depends on parameters and can lead to ``arch'' solutions forming a globally polar, smectic arrangement of Néel walls. We show how these configurations are at the origin of the defect ordered states reported previously. This work offers a detailed understanding of the theoretical description of dense active nematics directly rooted in their microscopic dynamics.

cond-mat.soft↗