ArticleJournal of computational biology : a journal of computational molecular cell biology2010
Cytopede: a three-dimensional tool for modeling cell motility on a flat surface.
Article in Journal of computational biology : a journal of computational molecular cell biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- A predictive mechanochemical modeling framework for the deformation and remodeling of the nuclear lamina.bioRxiv : the preprint server for biology · 2026Article
- Spatial modeling algorithms for reactions and transport in biological cells.Nature computational science · 2025Article
- A minimal computational model for three-dimensional cell migration.Journal of the Royal Society, Interface · 2019Article
- Parameter identification problems in the modelling of cell motility.Journal of mathematical biology · 2015Article
- A conservative algorithm for parabolic problems in domains with moving boundaries.Journal of computational physics · 2014Article
- High-resolution traction force microscopy.Methods in cell biology · 2014Article
- Matrix geometry determines optimal cancer cell migration strategy and modulates response to interventions.Nature cell biology · 2013Article
- Damped and persistent oscillations in a simple model of cell crawling.Journal of the Royal Society, Interface · 2012Article
- A comparison of computational models for eukaryotic cell shape and motility.PLoS computational biology · 2012Review
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
When cultured on flat surfaces, fibroblasts and many other cells spread to form thin lamellar sheets. Motion then occurs by extension of the sheet at the leading edge and retraction at the trailing edge. Comprehensive quantitative models of these phenomena have so far been lacking and to address this need, we have designed a three-dimensional code called Cytopede specialized for the simulation of the mechanical and signaling behavior of plated cells. Under assumptions by which the cytosol and the cytoskeleton are treated from a continuum mechanical perspective, Cytopede uses the finite element method to solve mass and momentum equations for each phase, and thus determine the time evolution of cellular models. We present the physical concepts that underlie Cytopede together with the algorithms used for their implementation. We then validate the approach by a computation of the spread of a viscous sessile droplet. Finally, to exemplify how Cytopede enables the testing of ideas about cell mechanics, we simulate a simple fibroblast model. We show how Cytopede allows computation, not only of basic characteristics of shape and velocity, but also of maps of cell thickness, cytoskeletal density, cytoskeletal flow, and substratum tractions that are readily compared with experimental data.
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