MemRBC - a numerical modeling laboratory for the stomatocyte-discocyte-echinocyte-transformation of Red Blood Cell shape
Authors/Creators
Contributors
Project leader:
-
1.
University of Bremen
-
2.
Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung
Description
Abstract
MemRBC is a result of open science research. It demonstrates the use of hi-level apps in a light-weight object oriented approach in R, keeping metadata and lineage recorded systematically for reproducibility and self-documentation.
Many studies have been published on the modeling of the transformation of stomatocyte to discocyte to echinocyte shape of red blood cells. However, not many details and result data of the different numerical simulation approaches have been given, hindering a systematic comparison and the selection of an optimal approach. With the present work, the software package MembraneRBC is published that facilitates a couple of numerical approaches to be explored and combined in modeling workflows. Results of exemplary applications are given to explain some features of the implementations and their effects in modeling practice of RBC shape transformation.
A spectral membrane shape model implementation is adapted here for RBC. It is based on the Spontaneous Curvature Model (SCM), extended by an area difference term, but no preferred area difference, such that membrane asymmetry is completely under control of the spontaneous curvature parameter C_0. Furthermore, the shear-elastic network (SEN) implementation is included, allowing for modeling spicule formation and redistribution.
Implemented methods are: constraint Newton-based energy minimization, Monte Carlo dynamics, Newtonian dynamics, augmented Lagrangian minimization. The major advantage of the used object-oriented multi-method software package is the seamless data exchange between different approaches, with restart and protocol facility. This enables the combination of several modeling sub-tasks, like initial constraint energy minimization, dynamics simulation, and stability analyses in a few lines of code.
Previously published related work
Frickenhaus, S., & Woelper, C. (2024). MembraneR - a membrane shape modeling environment in R. Zenodo. https://doi.org/10.5281/zenodo.13354043
Software package given here
- MemRBR_0.1.22.tar.gz R-package source code, e.g., use install.packages("MemRBC_0.1.20.tar.gz"), having additional standard packages from CRAN. For Windows you need Rtools installed.
Prepare your R installation with
install.packages(c("fields","rgl","igraph","RSpectra","crayon","tictoc","Rcpp",
"RcppEigen","Rvcg","pracma"))
3d-plots under WSL (Windows Subsystem Linux) may not be working, or even lead to crash. Use "plt=FALSE" in the apps to suppress 3d plots and avid using plot() on membrane objects.
LIMITATIONS
Most of the low-level functions used in the documented apps are undocumented yet. Most of them are self-explaining when looking, e.g., how they are used in the apps code. Type, for example, PSD to see the code for Panylized Steepest Descend app.
REPOSITORY
MemRBC is registered on Helmholtz Software under https://helmholtz.software/software/memrbc
and version managed on github: https://github.com/atfric/MemRBC
The value of constraint/reference area given in the introduction must be 140 mu^2, not 100.
Citation
citation.MemRBC()
Frickenhaus, S. (2025). MemRBC - a numerical modeling laboratory for the stomatocyte-discocyte-echinocyte-transformation of Red Blood Cell shape, ZENODO, DOI: https://doi.org/10.5281/zenodo.15103741
Files
MemRBC-preprint_2.pdf
Files
(328.3 MB)
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Additional details
Additional titles
- Alternative title (English)
- MemRBC with Apps for Red Blood Cells
Software
- Programming language
- R , C++
- Development Status
- Unsupported