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5 results for “Vertex Model”
Differences in boundary behavior in the 3D vertex and Voronoi models
<p>An important open question in the modeling of biological tissues is how to identify the right scale for coarse-graining, or equivalently, the right number of degrees of freedom. For confluent biological tissues, both vertex and Voronoi models, which differ only in their representation of the degrees of freedom, have effectively been used to predict behavior, including fluid-solid transitions and cell tissue compartmentalization, which are important for biological function. However, recent work in 2D has hinted that there may be differences between the two models in systems with heterotypic interfaces between two tissue types, and there is a burgeoning interest in 3D tissue models. Therefore, we compare the geometric structure and dynamic sorting behavior in mixtures of two cell types in both 3D vertex and Voronoi models. We find that while the cell shape indices exhibit similar trends in both models, the registration between cell centers and cell orientation at the boundary are significantly different between the two models. We demonstrate that these macroscopic differences are caused by changes to the cusp-like restoring forces introduced by the different representations of the degrees of freedom at the boundary and that the Voronoi model is more strongly constrained by forces that are an artifact of the way the degrees of freedom are represented. This suggests that vertex models may be more appropriate for 3D simulations of tissues with heterotypic contacts.</p>
Differences in boundary behavior in the 3D vertex and Voronoi models
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Experimental dataset: "Minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure"
<p>This repository contains experimental data supporting our paper "Minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure".</p> <p><strong>Original Publication:</strong><br>Tah, I., Haertter, D., et al. (2024). Minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure. PNAS (in press).<br>Preprint available at: <a href="https://doi.org/10.1101/2023.12.20.572544">https://doi.org/10.1101/2023.12.20.572544</a></p> <h2>Dataset Structure</h2> <h2>amnioserosa_time_lapses/</h2> <p>This directory contains confocal microscopy time-lapse recordings of eCadherin-labeled Drosophila melanogaster embryos during dorsal closure:</p> <ul> <li><strong>Imaging parameters:</strong> <ul> <li>Frame interval: 15 seconds</li> <li>Pixel size: 0.158 µm</li> </ul> </li> <li><strong>Data files:</strong> <ul> <li><code>*_data.p</code>: Morphometric features of individual amnioserosa cells during closure</li> <li><code>*_junctions.p</code>: Morphometric features of individual cell-cell adherens junctions</li> <li><code>read_filter_data.py</code>: Python script demonstrating data reading and filtering procedures</li> </ul> </li> </ul> <h2>junction_laser_cuts/</h2> <p>This directory contains high-speed recordings of UV-laser junction ablation experiments:</p> <ul> <li><strong>Imaging parameters:</strong> <ul> <li>Frame rate: 5 Hz</li> <li>Pixel size: 0.364 µm</li> </ul> </li> <li><strong>Content:</strong> Time series of eCadherin-labeled embryos before, during, and after precise UV-laser severing of individual junctions</li> </ul> <h2>data_figures/</h2> <p>This directory contains processed data and analysis results presented in Figures 1-3 of the main manuscript. The data are organized by figure number and include all measurements and simulation results used to generate the plots shown in these figures.</p> <p> </p> <p>For detailed experimental methods and protocols, please refer to the published paper.</p>
Universality in the mechanical behavior of vertex models for biological tissues
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Approximating Bipartite Minimum Vertex Cover in the CONGEST model
Full video presentation of the paper: Approximating Bipartite Minimum Vertex Cover in the CONGEST model.<br><br>Appears in Session 4 of the 24th International Conference on Principles of Distributed Systems OPODIS 2020<br><a href="https://opodis2020.unistra.fr">https://opodis2020.unistra.fr</a>
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