The Vesicle Builder - A Membrane Packing Algorithm for the CELLmicrocosmos MembraneEditor

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dc.contributor.authorGiuliari, Beatriceen_US
dc.contributor.authorKösters, Manuelen_US
dc.contributor.authorZhou, Janen_US
dc.contributor.authorDingersen, Timen_US
dc.contributor.authorHeissmann, Andréen_US
dc.contributor.authorRotzoll, Ralfen_US
dc.contributor.authorKrüger, Jensen_US
dc.contributor.authorGiorgetti, Alejandroen_US
dc.contributor.authorSommer, Björnen_US
dc.contributor.editorByška, Jan and Krone, Michael and Sommer, Björnen_US
dc.date.accessioned2020-05-24T13:29:45Z
dc.date.available2020-05-24T13:29:45Z
dc.date.issued2020
dc.description.abstractFor a long time, the major focus of membrane simulations was laid on rectangular membrane patches based on the fluid mosaic model. Because of the computational performance of today's computer hardware, it is now possible to generate and simulate larger structures, such as vesicles or micelles. Yet, there are no approaches available to generate these partly complex structures in a convenient and interactive way using WYSIWYG methods and exporting it to PDB format. The CELLmicrocosmos 2.2 MembraneEditor was originally developed for the interactive computation of heterogeneous rectangular membrane patches, solving 2.5D packing problems. Now, its packing capabilities were extended into the third dimension by introducing the Vesicle Builder which is optimized for the computation of vesicular mono- or bilayer membranes. The shape computation is based on an ellipsoid formula enabling the generation of vesicles featuring different lipid compositions, shapes and sizes. More complex shapes can be generated by combining different shapes. Moreover, extended shape customization is possible by modifying and extending the algorithm. Three application cases are discussed: 1) Different potential vesicular configurations including wavy, ellipsoid, enclosing and modular structures are modelled and shortly discussed; 2) To evaluate the compatibility of the Vesicle Builder with simulation tools, a three-component vesicle was modelled and successfully simulated. 3) To show the capability to generate large structures, a vesicle with a radius of 370 Å was generated, consisting of approx. 50,000 lipids and 2 million atoms, respectively. The MembraneEditor as well as the Vesicle Builder plugin can be downloaded from https://Cm2.CELLmicrocosmos.orgen_US
dc.description.sectionheadersSession 1
dc.description.seriesinformationWorkshop on Molecular Graphics and Visual Analysis of Molecular Data
dc.identifier.doi10.2312/molva.20201096
dc.identifier.isbn978-3-03868-114-4
dc.identifier.pages7-15
dc.identifier.urihttps://doi.org/10.2312/molva.20201096
dc.identifier.urihttps://diglib.eg.org:443/handle/10.2312/molva20201096
dc.publisherThe Eurographics Associationen_US
dc.rightsAttribution 4.0 International License
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/]
dc.subjectSoftware and its engineering
dc.subjectSoftware prototyping
dc.subjectTheory of computation
dc.subjectPacking and covering problems
dc.subjectHuman centered computing
dc.subjectVisualization toolkits
dc.titleThe Vesicle Builder - A Membrane Packing Algorithm for the CELLmicrocosmos MembraneEditoren_US
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MolVa: Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2020