Abstract
The shapes of phospholipid bilayer biomembranes are modeled by the celebrated Canham-Evans-Helfrich model as constrained Willmore minimizers. Several numerical treatments of the model have been proposed in the literature, one of which was used extensively by biophysicists over two decades ago to study real lipid bilayer membranes. While the key ingredients of this algorithm are implemented in Brakke’s well-known surface evolver software, some of its glory details were never explained by either the geometers who invented it or the biophysicists who used it. As such, most of the computational results claimed in the biophysics literature are difficult to reproduce. In this note, we give an exposition of this method, connect it with some related ideas in the literature, and propose a modification of the original method based on replacing mesh smoothing with harmonic energy regularization. We present a theoretical finding and related computational observations explaining why such a smoothing or regularization step is indispensable for the success of the algorithm. A software package called WMINCON is available for reproducing the experiments in this and related articles.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Notes
- 1.
We assume that the normal of any closed orientable surface points outward. In particular, it means H < 0 for a sphere.
- 2.
The paper [17] derived the same formula based on the characterization of mean curvature by the Laplace-Beltrami operator: Δ S X(x) = H(x), x ∈ S, where \(\mathbf {X}: S \rightarrow {\mathbb {R}}^3\) is the position function of the surface S.
References
A. I. Bobenko, A conformal energy for simplicial surfaces. Comb. Comput. Geom. 52, 135–145 (2005)
A.I. Bobenko, P. Schröder, Discrete Willmore flow, in The Eurographics Symposium on Geometry Processing (2005), pp. 101–110
A. Bonito, R.H. Nochetto, M.S. Pauletti, Parametric FEM for geometric biomembranes. J. Comput. Phys. 229(9), 3171–3188 (2010)
K.A. Brakke, The surface evolver. Exp. Math. 1(2), 141–165 (1992)
P.B. Canham, The minimum energy of bending as a possible explanation of the biconcave shape of the human red blood cell. J. Theor. Biol. 26(1), 61–76 (1970)
J. Chen, S. Grundel, T.P.-Y. Yu, A flexible C 2 subdivision scheme on the sphere: with application to biomembrane modelling. SIAM J. Appl. Algebra Geom. 1(1), 459–483 (2017)
J. Chen, T.P.-Y. Yu, P. Brogan, Y. Yang, A. Zigerelli, Numerical methods for biomembranes: SS versus PL methods (2017, in preparation)
F.E. Curtis, T. Mitchell, M.L. Overton, A BFGS-SQP method for nonsmooth, nonconvex, constrained optimization and its evaluation using relative minimization profiles. Optim. Methods Softw. 32(1), 148–181 (2017)
E.A. Evans, Bending resistance and chemically induced moments in membrane bilayers. Biophys. J. 4(12), 923–931 (1974)
F. Feng, W.S. Klug, Finite element modeling of lipid bilayer membranes. J. Comput. Phys. 220(1), 394–408 (2006)
G. Francis, J.M. Sullivan, R.B. Kusner, K.A. Brakke, C. Hartman, G. Chappell, The minimax sphere eversion, in Visualization and Mathematics (Springer, Berlin, 1997), pp. 3–20
W. Helfich, Elastic properties of lipid bilayers: theory and possible experiments. Z. Naturforsch C 28(11), 693–703 (1973)
L. Hsu, R. Kusner, J. Sullivan, Minimizing the squared mean curvature integral for surfaces in space forms. Exp. Math. 1(3), 191–207 (1992)
J. Jost, Riemannian Geometry and Geometric Analysis, Universitext, 6th edn. (Springer, Berlin, 2011)
F. Jülicher, U. Seifert, R. Lipowsky, Conformal degeneracy and conformal diffusion of vesicles. Phys. Rev. Lett. 71(3), 452–455 (1993).
R. Lipowsky, The conformation of membranes. Nature 349, 475–481 (1991).
M. Meyer, M. Desbrun, P. Schröder, A.H. Barr, Discrete differential-geometry operators for triangulated 2-manifolds, in Visualization and Mathematics III (Springer, Berlin, 2003), pp. 35–57
X. Michalet, D. Bensimon, Observation of stable shapes and conformal diffusion in genus 2 vesicles. Science 269(5224), 666–668 (1995)
U. Seifert, Configurations of fluid membranes and vesicles. Adv. Phys. 46(1), 13–137 (1997)
Acknowledgements
TY thanks Tom Duchamp, Robert Kusner, Shawn Walker and Aaron Yip for extensive discussions. This work is partially supported by NSF grants DMS 1115915 and DMS 1522337. We also thank the support of the Office of the Provost and the Steinbright Career Development Center of Drexel University.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this paper
Cite this paper
Brogan, J.P., Yang, Y., Yu, T.P.Y. (2019). Numerical Methods for Biomembranes Based on Piecewise Linear Surfaces. In: Radu, F., Kumar, K., Berre, I., Nordbotten, J., Pop, I. (eds) Numerical Mathematics and Advanced Applications ENUMATH 2017. ENUMATH 2017. Lecture Notes in Computational Science and Engineering, vol 126. Springer, Cham. https://doi.org/10.1007/978-3-319-96415-7_76
Download citation
DOI: https://doi.org/10.1007/978-3-319-96415-7_76
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-96414-0
Online ISBN: 978-3-319-96415-7
eBook Packages: Mathematics and StatisticsMathematics and Statistics (R0)