R. Dilão | Searcharxiv

arXiv2025

Properties of Hagen-Poiseuille flow in channel networks

We derive the main properties of adaptive Hagen-Poiseuille flows in elastic microchannel networks similar to biological veins found in organisms. We demonstrate that adaptive Hagen-Poiseuille flows effectively simulate key features of \textit{Physarum polycephalum} networks, replicating physiological out-of-equilibrium phenomena such as peristalsis and shuttle streaming, which are associated with the mechanism of nutrient transport in \textit{Physarum}. A new topological steady state has been identified for asynchronous adaptation, supporting out-of-equilibrium laminar fluxes. Adaptive Hagen-Poiseuille flows exhibit saturation effects on the fluxes in contractile veins, as observed in both animal and artificial contractile veins. These results suggest that the non-equilibrium effects observed in \textit{Physarum} have a hydrodynamic origin

q-bio.CB↗

arXiv2009

Calibration and validation of a genetic regulatory network model describing the production of the gap gene protein Hunchback in \emph{Drosophila} early development

We fit the parameters of a differential equations model describing the production of gap gene proteins Hunchback and Knirps along the antero-posterior axis of the embryo of \emph{Drosophila}. As initial data for the differential equations model, we take the antero-posterior distribution of the proteins Bicoid, Hunchback and Tailless at the beginning of cleavage cycle 14. We calibrate and validate the model with experimental data using single- and multi-objective evolutionary optimization techniques. In the multi-objective optimization technique, we compute the associated Pareto fronts. We analyze the cross regulation mechanism between the gap-genes protein pair Hunchback-Knirps and we show that the posterior distribution of Hunchback follow the experimental data if Hunchback is negatively regulated by the Huckebein protein. This approach enables to predict the posterior localization on the embryo of the protein Huckebein, and we validate with the experimental data the genetic regulatory network responsible for the antero-posterior distribution of the gap gene protein Hunchback. We discuss the importance of Pareto multi-objective optimization techniques in the calibration and validation of biological models.

q-bio.MN↗