arXiv subjects

Quentin Vagne

Publications and source records attributed to Quentin Vagne.

7 recordsLinked to original sources

arXiv2024

Generic theory of interacting, spinning, active polar particles: a model for cell aggregates

We present a generic framework for describing interacting, spinning, active polar particles, aimed at modelling dense cell aggregates, where cells are treated as polar, rotating objects that interact mechanically with one another and their surrounding environment. Using principles from non-equilibrium thermodynamics, we derive constitutive equations for interaction forces, torques, and polarity dynamics. We subsequently use this framework to analyse the spontaneous motion of cell doublets, uncovering a rich phase diagram of collective behaviours, including steady rotation driven by flow-polarity coupling or interactions between polarity and cell position.

cond-mat.soft↗

arXiv2023

Spontaneous flow instabilities of active polar fluids in three dimensions

Active polar fluids exhibit spontaneous flow when sufficient active stress is generated by internal molecular mechanisms. This is also referred to as an active Fr\'{e}edericksz transition. Experiments have revealed the existence of competing in-plane and out-of-plane instabilities in three-dimensional active matter. So far, however, a theoretical model reconciling all observations is missing. In particular, the role of boundary conditions in these instabilities still needs to be explained. Here, we characterize the spontaneous flow transition in a symmetry-preserving three-dimensional active Ericksen-Leslie model, showing that the boundary conditions select the emergent behavior. Using nonlinear numerical solutions and linear perturbation analysis, we explain the mechanism for both in-plane and out-of-plane instabilities under extensile active stress for perpendicular polarity anchoring at the boundary, whereas parallel anchoring only permits in-plane flows under contractile stress or out-of-plane wrinkling under extensile stress.

cond-mat.soft↗

arXiv2022

Learning deterministic hydrodynamic equations from stochastic active particle dynamics

We present a principled data-driven strategy for learning deterministic hydrodynamic models directly from stochastic non-equilibrium active particle trajectories. We apply our method to learning a hydrodynamic model for the propagating density lanes observed in self-propelled particle systems and to learning a continuum description of cell dynamics in epithelial tissues. We also infer from stochastic particle trajectories the latent phoretic fields driving chemotaxis. This demonstrates that statistical learning theory combined with physical priors can enable discovery of multi-scale models of non-equilibrium stochastic processes characteristic of collective movement in living systems.

cond-mat.soft↗

arXiv2020

Glycan processing in the Golgi -- optimal information coding and constraints on cisternal number and enzyme specificity

Many proteins that undergo sequential enzymatic modification in the Golgi cisternae are displayed at the plasma membrane as cell identity markers. The modified proteins, called glycans, represent a molecular code. The fidelity of this glycan code is measured by how accurately the glycan synthesis machinery realises the desired target glycan distribution for a particular cell type and niche. In this paper, we quantitatively analyse the tradeoffs between the number of cisternae and the number and specificity of enzymes, in order to synthesize a prescribed target glycan distribution of a certain complexity. We find that to synthesize complex distributions, such as those observed in real cells, one needs to have multiple cisternae and precise enzyme partitioning in the Golgi. Additionally, for fixed number of enzymes and cisternae, there is an optimal level of specificity of enzymes that achieves the target distribution with high fidelity. Our results show how the complexity of the target glycan distribution places functional constraints on the Golgi cisternal number and enzyme specificity.

q-bio.SC↗

arXiv2018

Stochastic Models of Vesicular Sorting in Cellular Organelles

The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intra-cellular organisation. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic fluctuations considering the relatively small size of many organelles. We identify the perfect sorting of two membrane components initially mixed in a single compartment as a first passage process, and we show that the mean sorting time exhibits two distinct regimes as a function of the ratio of vesicle fusion to budding rates. Low ratio values lead to fast sorting, but results in a broad size distribution of sorted compartments dominated by small entities. High ratio values result in two well defined sorted compartments but is exponentially slow. Our results suggest an optimal balance between vesicle budding and fusion for the rapid and efficient sorting of membrane components, and highlight the importance of stochastic effects for the steady-state organisation of intra-cellular compartments.

physics.bio-ph↗

arXiv2017

Stochastic Model of Maturation and Vesicular Exchange in Cellular Organelles

The dynamical organization of membrane-bound organelles along intracellular transport pathways relies on vesicular exchange between organelles and on biochemical maturation of the organelle content by specific enzymes. The relative importance of each mechanism in controlling organelle dynamics remains controversial, in particular for transport through the Golgi apparatus. Using a stochastic model, we show that full maturation of membrane-bound compartments can be seen as the stochastic escape from a steady-state in which export is dominated by vesicular exchange. We show that full maturation can contribute a significant fraction of the total out-flux for small organelles such as endosomes and Golgi cisternae.

physics.bio-ph↗

arXiv2014

Finite size effects in non-equilibrium membrane phase separation

The formation of dynamical clusters of proteins is ubiquitous in cellular membranes and is in part regulated by the recycling of membrane components. Mean-field models of out-of-equilibrium cluster formation with recycling predict a broad cluster size distribution for infinite systems and must be corrected for finite-size effects for small systems such as cellular organelles. We show, using stochastic simulations and analytic modelling, that tuning the system size is an efficient way to control the size of lateral membrane heterogeneities. We apply these findings to a chain of enzymatic reaction sensitive to membrane protein clustering. The reaction efficiency is found to be a non-monotonic function of the system size, and can be optimal for sizes comparable to those of cellular organelles.

cond-mat.soft↗