Biology subjects

Demircigil, M.

Publications and source records attributed to Demircigil, M..

3 recordsLinked to original sources

bioRxiv2026

Microscopic collisions govern macroscopic aerotactic spreading through emergent transport coefficients

Collective migration is often attributed to complex cell-cell communication, yet coordinated multicellular dynamics can also emerge in organisms lacking social interactions. Continuum descriptions successfully capture such behaviors but generally rely on phenomenological transport coefficients whose microscopic origin remains elusive. Here we show that these coefficients emerge from cell-cell collisions and can be independently determined from experiments. We investigate the aerotactic dispersal of confined colonies of the solitary amoeba Acanthamoeba castellanii, in which oxygen consumption continuously reshapes the local environment to generate self-organized guidance cues. Combining quantitative videomicroscopy, oxygen mapping with phosphorescent sensing films, and oxygen-controlled microfluidics, we directly measure both the oxygen landscape and the aerotactic response governing colony expansion. We then develop a Patlak-Keller-Segel (PKS) -type drift-diffusion model whose transport coefficients are entirely determined from independent experiments and microscopic-to-macroscopic modeling approach, without adjustable parameters. The model quantitatively reproduces the observed dynamics, including the coexistence of a fast ballistic front and a trailing transient accumulation band. We show that both diffusion and aerotactic transport are modulated by the same collision-controlled mechanism through density-dependent changes in cell persistence. More generally, our results establish transport coefficients as measurable emergent properties bridging microscopic cell dynamics and macroscopic collective behavior, providing a predictive framework for oxygen-guided migration in living active matter.

biophysics↗

bioRxiv2025

Density-Dependent Cell Migration in the Absence of Social Interactions: A Case Study of Acanthamoeba castellanii

Cell migration is often influenced by intercellular or social interactions, ranging from long-range diffusive cues to direct contacts that can trigger biochemical signaling within the cell and affect the cell protruding activity or direction of turns. Here we study the density-dependent migration of the amoeba Acanthamoeba castellanii (Ac), a unicellular eukaryote that moves without social interactions. Using experiments and mean free path theory, we characterize how collisions affect motility parameters in crowded environments. We identify the collision rate as a key parameter linking cell density to the collision-induced reorientation rate, and we show its consistency across multiple independent approaches. Our findings reveal that the intrinsic migration speed remains constant, while persistence time and effective diffusion are entirely governed by collisions. At high densities, cells exhibit nearly ballistic trajectories between collisions, a behavior rarely reported in eukaryotes. These results establish Ac as a minimal model for motility in the absence of biochemical signaling, with implications for testing behaviors in complex crowded environments and pre-jamming dynamics.

biophysics↗

bioRxiv2020

Hypoxia triggers collective aerotactic migration in Dictyostelium discoideum

It is well known that eukaryotic cells can sense oxygen (O2) and adapt their metabolism accordingly. It is less known that they can also move towards regions of higher oxygen level (aerotaxis). Using a self-generated hypoxic assay, we show that the social amoeba Dictyostelium discoideum displays a spectacular aerotactic behavior. When a cell colony is covered by a coverglass, cells quickly consume the available O2 and the ones close to the periphery move directionally outward forming a dense ring keeping a constant speed and density. To confirm that O2 is the main molecular player in this seemingly collective process, we combined two technological developments, porphyrin based O2 sensing films and microfluidic O2 gradient generators. We showed that Dictyostelium cells exhibit aerotactic and aerokinetic (increased speed at low O2) response in an extremely low range of O2 concentration (0-1.5%) indicative of a very efficient detection mechanism. The various cell behaviors under self-generated or imposed O2 gradients were modeled with a very satisfactory quantitative agreement using an in silico cellular Potts model built on experimental observations. This computational model was complemented with a parsimonious Go or Grow partial differential equation (PDE) model. In both models, we found that the collective migration of a dense ring can be explained by the interplay between cell division and the modulation of aerotaxis, without the need for cell-cell communication.

biophysics↗