• The vesicle builder - A membrane packing algorithm for the CELLmicrocosmos MembraneEditor

Giuliari, Beatrice, Kösters, Manuel, Zhou, Jan, Dingersen, Tim, Heissmann, André, Rotzoll, Ralf, Krüger, Jens, Giorgetti, Alejandro and Sommer, Bjorn ORCID: https://orcid.org/0000-0003-1514-9898, 2020, Book Section, The vesicle builder - A membrane packing algorithm for the CELLmicrocosmos MembraneEditor In: Byška, Jan, Krone, Michael and Sommer, Bjorn ORCID: https://orcid.org/0000-0003-1514-9898, (eds.) Workshop on Molecular Graphics and Visual Analysis of Molecular Data. The Eurographics Association, pp. 7-15. ISBN 978-3-03868-114-4

Abstract or Description:

For 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.org

Official URL: https://diglib.eg.org/handle/10.2312/molva20201096...
Subjects: Other > Biological Sciences > C100 Biology
Other > Biological Sciences > C900 Others in Biological Sciences > C910 Applied Biological Sciences
Other > Mathematical and Computer Sciences > G400 Computer Science > G440 Human-computer Interaction
Creative Arts and Design > W200 Design studies
School or Centre: School of Design
Identification Number or DOI: https://doi.org/10.2312/molva.20201096
Date Deposited: 08 Jul 2021 17:20
Last Modified: 08 Jul 2021 17:20
URI: https://researchonline.rca.ac.uk/id/eprint/4831
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