Building Simulation Models of Developing Plant Organs Using VirtualLeaf

Merks, Roeland; Guravage, Michael

doi:10.1007/978-1-62703-221-6_23

Cited by 12 publications

(12 citation statements)

References 15 publications

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“…In this paper, we have introduced extensions of our plant tissue simulation environment VirtualLeaf (Merks et al. 2011; Merks and Guravage 2012), adopting it for the simulation of animal tissues. The key novelty is a method to simulate relative movement of cells, the ‘sliding operator.’ This operator is applied alongside node displacements in a Metropolis-based energy minimization approach.…”

Section: Discussionmentioning

confidence: 99%

“…The model is an extension of the open-source package VirtualLeaf (Merks et al. 2011; Merks and Guravage 2012) (also see the re-engineered derivative Virtual Plant Tissue ; De Vos et al. 2017), which was initially developed to simulate plant tissue morphogenesis where cells do not move relative to one another.…”

Section: Introductionmentioning

confidence: 99%

“…In this paper we introduce a variant of the VM in which these three limitations have been resolved. The model is an extension of the open-source package VirtualLeaf [45,47] (also see the re-engineered derivative Virtual Plant Tissue [15]), which was initially developed to simulate plant tissue morphogenesis where cells do not move relative to one another. VirtualLeaf differs from traditional VMs in that (a) cell interfaces are represented by multiple nodes that allow membrane fluctuations; (b) tissue topology changes exclusively through cell division with no T1 or T2 transitions; and (c) tissue dynamics are advanced used a Metropolis algorithm that incorporates membrane fluctuations.…”

Section: Introductionmentioning

confidence: 99%

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Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf

2019

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Cell-based, mathematical modeling of collective cell behavior has become a prominent tool in developmental biology. Cell-based models represent individual cells as single particles or as sets of interconnected particles and predict the collective cell behavior that follows from a set of interaction rules. In particular, vertex-based models are a popular tool for studying the mechanics of confluent, epithelial cell layers. They represent the junctions between three (or sometimes more) cells in confluent tissues as point particles, connected using structural elements that represent the cell boundaries. A disadvantage of these models is that cell–cell interfaces are represented as straight lines. This is a suitable simplification for epithelial tissues, where the interfaces are typically under tension, but this simplification may not be appropriate for mesenchymal tissues or tissues that are under compression, such that the cell–cell boundaries can buckle. In this paper, we introduce a variant of VMs in which this and two other limitations of VMs have been resolved. The new model can also be seen as on off-the-lattice generalization of the Cellular Potts Model. It is an extension of the open-source package VirtualLeaf, which was initially developed to simulate plant tissue morphogenesis where cells do not move relative to one another. The present extension of VirtualLeaf introduces a new rule for cell–cell shear or sliding, from which cell rearrangement (T1) and cell extrusion (T2) transitions emerge naturally, allowing the application of VirtualLeaf to problems of animal development. We show that the updated VirtualLeaf yields different results than the traditional vertex-based models for differential adhesion-driven cell sorting and for the neighborhood topology of soft cellular networks. Electronic supplementary material The online version of this article (10.1007/s11538-019-00599-9) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf

2019

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“…Simulations were performed as recommended previously [30]. To be able to see established models in action, the VirtualLeaf software was installed according to the following instructions described in the supplementary information and as described previously [56]. All simulations within Model 1, Model 2, and Model 3, respectively, were conducted for the same VirtualLeaf time duration.…”

Section: Virtualleaf Simulationsmentioning

confidence: 99%

Computational modelling of cambium activity provides a regulatory framework for simulating radial plant growth

Lebovka

Mele

Zakieva

et al. 2020

Preprint

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Precise organization of growing structures is a fundamental problem in developmental biology. In plants, radial growth is mediated by the cambium, a stem cell niche continuously producing wood (xylem) and bast (phloem) in a strictly bidirectional manner. While this process contributes large parts to terrestrial biomass, cambium dynamics eludes direct experimental access due to obstacles in live cell imaging. Here, we present a cell-based computational model visualizing cambium activity and integrating the function of central cambium regulators. Performing iterative comparisons of plant and model anatomies, we conclude that an intercellular signaling module consisting of the receptor-like kinase PXY and its ligand CLE41 constitutes a minimal framework sufficient for instructing tissue organization. Employing genetically encoded markers for different cambium domains in backgrounds with altered PXY/CLE41 activity, we furthermore propose that the module is part of a larger regulatory circuit using the phloem as a morphogenetic center. Our model highlights the importance of intercellular communication along the radial sequence of tissues within the cambium area and shows that a limited number of factors is sufficient to create a stable bidirectional tissue production.

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“…Computer models of plants have generally been implemented in computer graphics (Habel et al, 2009), for accurate modeling of plant dynamics (Runions et al, 2014;Cournède et al, 2008;Merks and Guravage, 2013;Prusinkiewicz and Runions, 2012) and for assessing the role of evolution on the emergence of plant traits (Valladares and Pearcy, 2000). Moreover, evolutionary computations and generative encodings have been implemented to efficiently simulate plant models Brest, 2012, 2014) with some biological accuracy.…”

Section: Simulated Modelsmentioning

confidence: 99%

Generating Artificial Plant Morphologies for Function and Aesthetics through Evolving L-Systems

Veenstra¹,

Faa²,

Støy³

et al. 2016

Proceedings of the Artificial Life Conference 2016

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Due to the replacement of natural flora and fauna with urban environments, a significant part of the earth's organisms that function as primary producers have been dispelled. To compensate for the reduction in the amount of primary producers, robotic systems that mimic plant-like organisms are interesting to mimic for their potential functional and aesthetic value in urban environments. To investigate how to utilize plant developmental strategies in order to engender urban artificial plants, we built a simple evolutionary model that applies an L-System based grammar as an abstraction of plant development. In the presented experiments, phytomorphologies (plant morphologies) are iteratively constructed using a context sensitive L-System. The genomic representation of the L-System is subject to mutation by an evolutionary algorithm. These mutations thus alter the developmental rules of these phytomorphologies. We compare the differences between the light absorption of evolving virtual plants that remain static during their life and virtual plants that possess the possibility to move joints that link the separate parts of the virtual plants. Our results show that our evolutionary algorithm did not exploit potential beneficial joint actuation, instead, mostly static structures evolved. The results of our evolving L-System show that it is able to create various phytomorphologies, albeit that the results are preliminary and will be more thoroughly investigated in the future.

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Building Simulation Models of Developing Plant Organs Using VirtualLeaf

Cited by 12 publications

References 15 publications

Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf

Adapting a Plant Tissue Model to Animal Development: Introducing Cell Sliding into VirtualLeaf

Computational modelling of cambium activity provides a regulatory framework for simulating radial plant growth

Generating Artificial Plant Morphologies for Function and Aesthetics through Evolving L-Systems

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