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Using cellzilla for plant growth simulations at the cellular level

Shapiro, Bruce E. and Meyerowitz, Elliot M. and Mjolsness, Eric (2013) Using cellzilla for plant growth simulations at the cellular level. Frontiers in Plant Science, 4 . Art. No. 408. ISSN 1664-462X. PMCID PMC3797531. doi:10.3389/fpls.2013.00408. https://resolver.caltech.edu/CaltechAUTHORS:20131028-083534657

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Abstract

Cellzilla is a two-dimensional tissue simulation platform for plant modeling utilizing Cellerator arrows. Cellerator describes biochemical interactions with a simplified arrow-based notation; all interactions are input as reactions and are automatically translated to the appropriate differential equations using a computer algebra system. Cells are represented by a polygonal mesh of well-mixed compartments. Cell constituents can interact intercellularly via Cellerator reactions utilizing diffusion, transport, and action at a distance, as well as amongst themselves within a cell. The mesh data structure consists of vertices, edges (vertex pairs), and cells (and optional intercellular wall compartments) as ordered collections of edges. Simulations may be either static, in which cell constituents change with time but cell size and shape remain fixed; or dynamic, where cells can also grow. Growth is controlled by Hookean springs associated with each mesh edge and an outward pointing pressure force. Spring rest length grows at a rate proportional to the extension beyond equilibrium. Cell division occurs when a specified constituent (or cell mass) passes a (random, normally distributed) threshold. The orientation of new cell walls is determined either by Errera's rule, or by a potential model that weighs contributions due to equalizing daughter areas, minimizing wall length, alignment perpendicular to cell extension, and alignment perpendicular to actual growth direction.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.3389/fpls.2013.00408DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3797531/PubMed CentralArticle
ORCID:
AuthorORCID
Meyerowitz, Elliot M.0000-0003-4798-5153
Additional Information:© 2013 Shapiro, Meyerowitz and Mjolsness. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Received: 31 May 2013; Accepted: 26 September 2013; Published online: 16 October 2013. We would like to thank Sergey Nikolaev for valuable suggestions. This work was supported by grants from the Beckman Institute, the Division of Biology, and the Provost's Office at Caltech; a gift from Peter Cross to Caltech; by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation (through Grant GBMF3406) to Elliot M. Meyerowitz; and by NIH Grant R01 GM086883 to Eric D. Mjolsness at UCI.
Funders:
Funding AgencyGrant Number
Caltech Beckman InstituteUNSPECIFIED
Caltech Division of BiologyUNSPECIFIED
Caltech Provost's OfficeUNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Gordon and Betty Moore FoundationGBMF3406
NIHR01 GM086883
Subject Keywords:mathematical model, computational model, software, meristem, cellerator, cellzilla, wuschel, clavata
PubMed Central ID:PMC3797531
DOI:10.3389/fpls.2013.00408
Record Number:CaltechAUTHORS:20131028-083534657
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20131028-083534657
Official Citation:Shapiro BE, Meyerowitz EM and Mjolsness E (2013) Using cellzilla for plant growth simulations at the cellular level. Front. Plant Sci. 4:408. doi: 10.3389/fpls.2013.00408
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:42084
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:28 Oct 2013 20:53
Last Modified:10 Nov 2021 04:38

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