arXiv subjects

Christophe Godin

Publications and source records attributed to Christophe Godin.

6 recordsLinked to original sources

arXiv2025

Towards an active matter theory of plant morphogenesis

Plant morphogenesis relies on dynamic growth deformations at the cell and tissue scales driven by osmotic fluxes. A mechanistic understanding of this phenomenon demands a physical framework that integrates cell imbibition, tissue mechanics, and water fluxes, as well as their biophysical and molecular regulations, within a theory of plant active matter capturing the open-system and out-of-equilibrium properties of tissues. Building on historical insights into growth geometry, physics, and mechanics, combined with recent experimental results, we outline the key challenges in modelling plant growth and propose steps towards a unified physical theory of plant morphogenesis, in which biological regulation, mechanical forces, and water fluxes interact to shape biological form through the fundamental principles of living matter.

physics.bio-ph↗

arXiv2025

Learning to Infer Parameterized Representations of Plants from 3D Scans

Plants frequently contain numerous organs, organized in 3D branching systems defining the plant's architecture. Reconstructing the architecture of plants from unstructured observations is challenging because of self-occlusion and spatial proximity between organs, which are often thin structures. To achieve the challenging task, we propose an approach that allows to infer a parameterized representation of the plant's architecture from a given 3D scan of a plant. In addition to the plant's branching structure, this representation contains parametric information for each plant organ, and can therefore be used directly in a variety of tasks. In this data-driven approach, we train a recursive neural network with virtual plants generated using a procedural model. After training, the network allows to infer a parametric tree-like representation based on an input 3D point cloud. Our method is applicable to any plant that can be represented as binary axial tree. We quantitatively evaluate our approach on Chenopodium Album plants on reconstruction, segmentation and skeletonization, which are important problems in plant phenotyping. In addition to carrying out several tasks at once, our method achieves results on-par with strong baselines for each task. We apply our method, trained exclusively on synthetic data, to 3D scans and show that it generalizes well.

cs.CV↗

arXiv2024

Riemannian L-systems: Modeling growing forms in curved spaces

In the past 50 years, the formalism of L-systems has been successfully used and developed to model the growth of filamentous and branching biological forms. These simulations take place in classical 2-D or 3-D Euclidean spaces. However, various biological forms actually grow in curved, non-Euclidean, spaces. This is for example the case of vein networks growing within curved leaf blades, of unicellular filaments, such as pollen tubes, growing on curved surfaces to fertilize distant ovules, of teeth patterns growing on folded epithelia of animals, of diffusion of chemical or mechanical signals at the surface of plant or animal tissues, etc. To model these forms growing in curved spaces, we thus extended the formalism of L-systems to non-Euclidean spaces. In a first step we show that this extension can be carried out by integrating concepts of differential geometry in the notion of turtle geometry. We then illustrate how this extension can be applied to model and program the development of both mathematical and biological forms on curved surfaces embedded in our Euclidean space. We provide various examples applied to plant development. We finally show that this approach can be extended to more abstract spaces, called abstract Riemannian spaces, that are not embedded into any higher space, while being intrinsically curved. We suggest that this abstract extension can be used to provide a new approach for effective modeling of tropism phenomena and illustrate this idea on a few conceptual examples.

q-bio.QM↗

arXiv2023

Characterization of random walks on space of unordered trees using efficient metric simulation

The simple random walk on $\mathbb{Z}^p$ shows two drastically different behaviours depending on the value of $p$: it is recurrent when $p\in\{1,2\}$ while it escapes (with a rate increasing with $p$) as soon as $p\geq3$. This classical example illustrates that the asymptotic properties of a random walk provides some information on the structure of its state space. This paper aims to explore analogous questions on space made up of combinatorial objects with no algebraic structure. We take as a model for this problem the space of unordered unlabeled rooted trees endowed with Zhang edit distance. To this end, it defines the canonical unbiased random walk on the space of trees and provides an efficient algorithm to evaluate its escape rate. Compared to Zhang algorithm, it is incremental and computes the edit distance along the random walk approximately 100 times faster on trees of size $500$ on average. The escape rate of the random walk on trees is precisely estimated using intensive numerical simulations, out of reasonable reach without the incremental algorithm.

cs.DS↗

arXiv2020

Bipartite non-locality beyond Bell inequalities by means of multivariable correlations

We give a set of necessary conditions for locality in bipartite systems, which include and generalize known Bell's inequalities. Each condition corresponds to a specific order of the expansion of random variables defined on graphs, in terms of genuinely n-variable correlation functions. The first non-trivial order leads to known Bell inequalities, while higher orders produce additional, non-equivalent conditions. In particular, in CHSH settings, we obtain at least two additional tight conditions which do not reduce to the CHSH inequality. This shows that tight Bell inequalities are sufficient but not necessary conditions for the non-locality of bipartite quantum correlations.

quant-ph↗

arXiv2018

Approximation of trees by self-nested trees

The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of trees. In particular, we show from both theoretical and practical viewpoints that complex queries can be quickly answered in self-nested trees compared to general trees. We also present an approximation algorithm of a tree by a self-nested one that can be used in fast prediction of edit distance between two trees.

cs.DS↗