Membrane modeling results from Surface Evolver
DOI10.5281/zenodo.12805964Zenodo12805964MaRDI QIDQ6695229FDOQ6695229
Dataset published at Zenodo repository.
Jigar Maheshbhai Parmar, Roghayeh Mardomkhah, Stephan Frickenhaus, Parham Asadian
Publication date: 24 July 2024
Copyright license: Creative Commons Attribution 4.0 International
Summary Three sets of membrane shapes of genus 0 generated in Surface Evolver (Brakke, 1992) are published here. The first set "ZS" reproduces the shapes that were published in Ziherl Svetina (2005) (bi-layer energy with fixed integrated mean curvature, volume and area). In addition we report on energy values and deliver the shapes as .obj-files. The .dmp files are dumps from the Evolver runs, derived from Frickenhaus (2024). With the same approach, the second set "ST" was created, focusing on axisymmetric stick-like shapes, such as the UnduStick that has been investigated in detail in Frickenhaus Wlper (2024). The third set "SC" deals with a Helfrich-flow energy functional, where instead of setting a mean curvature constraint, spontaneous curvature $H_0$ enters the bending energy functional. In all three sets energy minimization was done as much as possible, using Newton iteration (hessian_seek) along the surface normals, and gradient decent iterations until energy remained constant. The triangulation was adapted (see command macro gogo in .dmp files) by allowing tangential moves for some steps, equiangulation, vertex averaging, as well as edge length adaptation. File names may indicate non-equilibrium (-ne) or a saddle point (-saddle). Constraint target values are changed in a step-wise manner, writing out the complete data and macros for restarts after every step in a Surface Evolver dump-file automatically. Macros govu and gocu are for volume and curvature change, respectively. dv and dc are the corresponding volume/ curvature change per govo/ gocu cycle. If the triangulation becomes degenerate narrow, it may lead to automatic popping off (budding), i.e. seperation into two bodies. However, quantities volume, curvature and energy are not split up accordingly. The data was created during a project week on Scientific Programming at the University of Bremen, Germany (Mathematics, Summer 2024). License/ Citation The data is licensed CC-BY-4.0. When using the code, please cite appropriatly: Frickenhaus, S., Parmar, J. M.,Mardomkhah, R., Asadian, P. (2024). Membrane modeling results from Surface Evolver [Data set]. Zenodo. https://doi.org/10.5281/zenodo.12805964 Contributions RM and PA created the ZS data; JMP created the ST data, and SF created the SC data. References K.A. Brakke (1992) The Surface Evolver. Exp. Math. 1(2) https://dblp.org/db/journals/em/em1.html#Brakke92141-165 P. Ziherl and S. Svetina (2005), Nonaxisymmetric phospholipid vesicles: Rackets, boomerangs, and starfish. EPL 70 690, doi: 10.1209/epl/i2004-10527-4 S. Frickenhaus, (2024). Exploration of extreme vesicle shapes and their modular structure (1.0). Zenodo. doi: 10.5281/zenodo.11199344 S. Frickenhaus, C. Wlper, (2024). MembraneR - a membrane modeling environment in R (Version 1). Zenodo. doi: 10.5281/zenodo.12721406
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