biocurvature
download: biocurvature_0112.rar
biocurvature
3D contour maps of the mean curvature of a sinusoidal membrane network (left) and a MD model of the red blood cell membrane (right). Refer to sections 3.1 and 3.3 of Fraternali et al., JOURNAL OF COMPUTATIONAL PHYSICS, 231, 528-540, 2012.
Release notes for biocurvature
Developers:
  • main code: Fernando Fraternali(*)
  • graphics: Fernando Fraternali and Vincenzo Ciancia
University of Salerno and King’s College, London
© 2011-2012 All Rights Reserved
(*) corresponding author, f.fraternali@unisa.it

The “biocurvature” code performs the Local Maximum-Entropy (LME) regularization of a fluctuating membrane network, estimating the curvatures and in-plane strains of the mean shape of such a membrane.

The adopted LME scheme is fully described in the following reference:
Fraternali, F., Lorenz, C.D., Marcelli, G. On the estimation of the curvatures and bending rigidity of membrane networks via a local maximum-entropy approach. JOURNAL OF COMPUTATIONAL PHYSICS, 231, 528-540, 2012. ISSN: 0021-9991. DOI:10.1016/j.jcp.2011.09.017.

The compressed file biocurvature_0112.rar includes the following subfolders:
  • main: providing a read_me file; the executable biocurvature_01112.exe for windows; the associated Matlab plotting code biocurvature_plot_0112.m; the Matlab library MyCrustOpen (needed for plotting purposes); and the current release notes;
  • examples: providing input/output files for the illustrative examples described in sections 3.1 (sinusoidal membrane) and 3.3 (red blood cell membrane) of Fraternali et al., JCOMP 2011;
  • papers: providing some reference papers about the LME regularization scheme; the given demonstrative examples and related topics (limiting elastic energies and elastic coefficients of fluctuating membrane networks).

Animated example
Area stretching fluctuations of a molecular dynamics model of the red blood cell membrane (bibliographic reference)