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Arbitrary Lagrangian–Eulerian finite element method for lipid membranes

Published online by Cambridge University Press:  15 October 2025

Amaresh Sahu*
Affiliation:
McKetta Department of Chemical Engineering, University of Texas, Austin, TX 78712, USA
*
Corresponding author: Amaresh Sahu, asahu@che.utexas.edu

Abstract

An arbitrary Lagrangian–Eulerian finite element method and numerical implementation for curved and deforming lipid membranes is presented here. The membrane surface is endowed with a mesh whose in-plane motion need not depend on the in-plane flow of lipids. Instead, in-plane mesh dynamics can be specified arbitrarily. A new class of mesh motions is introduced, where the mesh velocity satisfies the dynamical equations of a user-specified two-dimensional material. A Lagrange multiplier constrains the out-of-plane membrane and mesh velocities to be equal, such that the mesh and material always overlap. An associated numerical inf–sup instability ensues, and is removed by adapting established techniques in the finite element analysis of fluids. In our implementation, the aforementioned Lagrange multiplier is projected onto a discontinuous space of piecewise linear functions. The new mesh motion is compared to established Lagrangian and Eulerian formulations by investigating a pre-eminent numerical benchmark of biological significance: the pulling of a membrane tether from a flat patch and its subsequent lateral translation.

Information

Type
JFM Papers
Creative Commons
Creative Common License - CCCreative Common License - BY
This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited.
Copyright
© The Author(s), 2025. Published by Cambridge University Press
Figure 0

Figure 1. Surface geometry. A schematic of the mapping $ \boldsymbol{x} = \boldsymbol{x} (\zeta ^{\check {\alpha }}, t)$, at a single instant in time, between the parametric domain $ \varOmega$ and the membrane patch $ \mathcal{P}$. The in-plane basis vectors $ \boldsymbol{a}_{\check {\alpha }}$ and unit normal vector $ \boldsymbol{n}$ are shown at a point $ \boldsymbol{x}$ on the patch, as are the in-plane unit normal $ \boldsymbol{\nu }$ and unit tangent $ \boldsymbol{\tau }$ at a point $ \boldsymbol{x}^{}_{{{b}}}$ at the patch boundary $ \partial \mkern -1mu \mathcal{P}$.

Figure 1

Figure 2. Pure bending scenario. (a) Boundary moments are applied to an initially flat patch in the $x$$y$ plane (top). The right edge is free to move in the $x$ and $y$ directions, but is constrained in the $z$ direction. At equilibrium, the membrane forms a portion of a cylinder (bottom). (b) Time dependence of the prescribed boundary moment, according to (4.4). Errors are calculated at the final time $ t_{{\kern-1.5pt f}}$, as indicated by the blue arrow and circle. (c) Result of a numerical simulation on a $ 128 \times 128$ mesh. The calculated surface tension differs from the analytical solution by less than three parts in 10 000, as shown by the colour bar.

Figure 2

Table 1. Moments and forces on the boundary of a portion of a cylindrical membrane with radius $ r_{\mkern -1mu {{c}}}$, as shown in figure 2 and calculated in Appendix B. The constant surface tension $ \lambda _0$ is set by the net body force per area in the normal direction, $ f := \boldsymbol{f} \boldsymbol{\cdot } \boldsymbol{n}$. In figure 2(a) the cylindrical basis vector $ \boldsymbol{e}^{}_\theta$ is tangent to the black curve and points to the left.

Figure 3

Table 2. Boundary conditions prescribed in the numerical implementation. We choose to set $ k_{{g}} = - k_{{b}} / 2$ and $ \boldsymbol{f} = \boldsymbol{0}$; the latter yields $ \lambda _0 = k_{{b}} / (4 \mkern 1mu r_{\mkern -1mu {{c}}}^{\, 2})$. The prescribed moment $ \mkern 4.5mu\overline {\mkern -4.5mu M \mkern -1.5mu}\mkern 1.5mu(t)$ is given by (4.4). The first three rows are repeated for $ \bar {v}^{{{m}}}_{\mkern -1mu j}$ and $ \mkern 4.5mu\overline {\mkern -4.5mu F \mkern -0.5mu}\mkern 0.5mu^{{m}}_{\! j}$ in the case of a viscous ALE mesh motion.

Figure 4

Figure 3. Errors in the (a) surface tension and (b) mean curvature at the final time $ t_{{\kern-1.5pt f}}$, according to (4.1), when the membrane patch is subjected to pure bending boundary conditions. The mesh consists of $ \textit {nel} = 1 / h^2$ parametric area elements, each of which is a square with side length $ h$. Here, $ 1 / h$ ranges from $ 2^1$ to $ 2^7$ in powers of two. The labels ‘E’, ‘Av’ and ‘L’ refer to Eulerian, ALE-viscous and Lagrangian mesh motions. In all cases, the convergence of the error confirms our numerical implementation is working as expected. Relevant parameters are specified in § 4.1.3; we also choose $ \zeta = 1.0$, $ k_{{b}} = 1.0$ and $ \ell = 1.0$.

Figure 5

Table 3. Boundary conditions prescribed in our numerical implementation to pull a tether, with Lagrangian (LAG), Eulerian (EUL) and ALE-viscous-bending (ALE-vb) mesh motions. Here, ‘Bdry’ refers to nodes on the boundary, ‘Inner’ refers to inner nodes adjacent to the boundary, ‘Pull’ corresponds to nodes associated with the central element $ \varOmega ^e_{{p}}$ and ‘Pin’ refers to nodes at the centre of each edge. The latter conditions are required to prevent rigid body rotations and translations. The ‘Inner’ column enforces zero-slope boundary conditions.

Figure 6

Table 4. Number of degrees of freedom (DOFs) and wall clock run time for the three different mesh motions, corresponding to the results presented in figure 4. All computations were carried out on a single node of the Perlmutter system at the National Energy Research Scientific Computing Center, with area element calculations distributed across 32 cores.

Figure 7

Figure 4. Snapshots from tether pulling simulations with a $ 65 \times 65$ mesh, in which three different mesh motions are employed. The colour bar indicates the surface tension, in units of $ k_{{b}} / r_{\mkern -1mu {{c}}}^2$, for all snapshots. Times are measured in units of $ \zeta r_{\mkern -1mu {{c}}}^2 / k_{{b}}$. (Left) Lagrangian simulations (LAG) successfully generate a tether. The morphological shape change from a tent to a tube occurs around time $ t = 120$. Since the membrane is area incompressible, the patch boundary must be pulled inwards to accommodate the tether surface area. (Centre) The Eulerian mesh motion (EUL) is not able to form a tube. Rather, the tent morphology persists and bulges outward until the method fails around time $ t = 143$. The material velocity degrees of freedom of the central element are constrained to move upwards; no such constraint is placed on the mesh velocity degrees of freedom. (Right) An ALE mesh motion that is viscous and resists bending (ALE-vb) successfully forms a tether. Both material and mesh velocities of the central element are constrained to move upwards. Since the mesh is area compressible, the patch boundary can be constrained to remain stationary as the tether develops. For all three mesh motions, $ \Delta t = 0.5$, $ {{S\scriptstyle {L}}} = 0.1$ and $ {\varGamma } = 1024$, for which $ \ell = 64 \, r_{\mkern -1mu {{c}}}$ and $ v^{}_{\!{p}} = 0.1 \, k_{{b}} / (\zeta r_{\mkern -1mu {{c}}} )$ according to (4.14) and (4.15). See also supplementary movies 13.

Figure 8

Figure 5. Zoomed-in views of the $ t = 240 \, \zeta r_{\mkern -1mu {{c}}}^2 / k_{{b}}$ snapshots from figure 4, with the underlying mesh shown (top) and hidden (bottom). In the Lagrangian simulations (left), the mesh is drawn into the tube along with the lipids due to the areal incompressibility of the membrane. Mesh elements close to the diagonal of the square patch, where $ y = \pm \mkern 1mu x$, become highly distorted – which leads to an artificially low surface tension in the transition region between the tether and surrounding membrane. Numerical artefacts are visible in the striation of the tension. The ALE-viscous-bending result (right), in contrast, shows a less distorted mesh because the choice of mesh constitution resists both shear and dilatation. No surface tension artefacts are visible, and a smooth tension gradient is observed from the flat patch into the tether.

Figure 9

Figure 6. The $ z$ component of the pull force ($ \mathcal{F}_{\! {{p}}, \mkern 1mu z}$) as a function of the $ z$ displacement. The dashed cyan line is the result from the linear theory, as presented in (4.20). The Eulerian simulation (blue circles, dotted line) is unable to form a tether, and is unphysical. The Lagrangian (red triangles, dashed line) and ALE (black squares, solid line) simulations capture the tent-to-tube transition, after which the Lagrangian steady-state pull force $ \mathcal{F}_{\! {\textit{ss}}}$ is slightly larger. Both overshoot the equilibrium pull force $ \mathcal{F}_{\! {eq}}$ (4.17) due to dynamical effects from tether pulling (see § 4.2.4). Numerical parameters are those specified in figure 4.

Figure 10

Figure 7. Mesh dilatation of the Eulerian simulation shown in figure 4. (a) The relative area change at the patch centre, $ J^{{{m}}}$, is plotted as a function of the displacement $ z^{}_{{p}}$. The dashed vertical line is the displacement at which a tent is expected to transition to a tether, according to Lagrangian and ALE data in figure 6. (Inset) At small displacements, simulation data agrees with an approximate solution to (4.19). Here $ v = \dot {z}_{{{p}}}$; if the mean curvature is linear in $ z^{}_{{p}}$ then $ H \sim - z^{}_{{p}} / r_{\mkern -1mu {{c}}}^{\, 2}$ and integrating (4.19) yields $ \ln J^{{{m}}} \sim (z^{}_{{p}} / r_{\mkern -1mu {{c}}})^2$. The number 16 in the analytical expression is a fitting parameter. (b) The same data in a log–log plot suggests a power-law growth of the dilatation at large displacements, prior to the expected morphological transition (dotted vertical line) – though the data does not span even a single decade.

Figure 11

Figure 8. The $ z$ component of the pull force ($ \mathcal{F}_{\! {{p}}, \mkern 1mu z}$) as a function of $ z^{}_{{p}}$ for different values of $ {\varGamma }$ and $ {{S\scriptstyle {L}}}$. (a) When $ {{S\scriptstyle {L}}} = 0.1$ and $ {\varGamma }$ is varied, the initial slope of the force vs displacement curve is altered according to the linear theory (see (4.20)). (b) By scaling the $ z$ displacement appropriately, the data collapses – with the steady-state pull force independent of $ {\varGamma }$ after tether formation. The cyan line has slope one. (c) When $ {\varGamma } = 1024$ and $ {{S\scriptstyle {L}}}$ is varied, the initial slope of the force vs displacement curve is unchanged. The tent-to-tube transition occurs at larger displacements, and the long-time pull force increases with $ {{S\scriptstyle {L}}}$. (d) Long-time pull force, $ \mathcal{F}_{\! {\textit{ss}}}$, as a function of $ {{S\scriptstyle {L}}}$ for $ {\varGamma } = 1024$. The dotted grey line is the linear prediction from (4.21), which agrees with simulation results when $ {{S\scriptstyle {L}}} \ll 1$ – as highlighted by the zoomed-in inset. The nonlinear dependence of $ \mathcal{F}_{\! {\textit{ss}}}$ on $ {{S\scriptstyle {L}}}$ arises from the coupling between in-plane flows and out-of-plane shape deformations.

Figure 12

Figure 9. Tether translation in the $ + \boldsymbol{e}_x$ (left column) and then $ - \boldsymbol{e}_x$ (right column) directions. Times are measured in units of $ \zeta \mkern 1mu r_{\mkern -1mu {{c}}}^{\, 2} / k_{{b}}$, the pull velocity is specified in (4.22), and all other parameters are identical to those in figure 4. The vertical red lines are a visual aid to highlight the lateral translation of the tether. For a video of the simulation results, see supplementary movie 4.

Figure 13

Figure 10. Tether translation in the $ \boldsymbol{e}_x$ direction with a Lagrangian mesh motion. In the left column, simulation boundary conditions are those specified in the first two rows of table 3. Twisting and tilting of the tether, along with further striation of the surface tension, ensue. In the right column, an attempt is made to remove unphysical constraints on the membrane by only pinning the centre of the bottom boundary. Upon lateral pulling, the mesh rotates about the centre of the bottom edge; twisting and tension striation are once again observed. Both simulations fail to capture the expected behaviour shown in the left column of figure 9. As in the main text, times are measured in units of $ \zeta \mkern 1mu r_{\mkern -1mu {{c}}}^{\, 2} / k_{{b}}$, the pull velocity is specified in the first row of (4.22), and all other parameters are identical to those in figure 4. The vertical red lines are a visual aid to highlight the motion of the tether.

Supplementary material: File

Sahu supplementary movie 1

Lagrangian simulation of tether pulling, corresponding to the left columns of Figs.
Download Sahu supplementary movie 1(File)
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Supplementary material: File

Sahu supplementary movie 2

Lagrangian–Eulerian simulation of tether pulling, corresponding to the center column of Fig.
Download Sahu supplementary movie 2(File)
File 611 KB
Supplementary material: File

Sahu supplementary movie 3

Arbitrary Lagrangian–Eulerian simulation of tether pulling, corresponding to the right columns of Figs.
Download Sahu supplementary movie 3(File)
File 730 KB
Supplementary material: File

Sahu supplementary movie 4

Arbitrary Lagrangian–Eulerian simulation of lateral translation of a tether, corresponding to Fig.
Download Sahu supplementary movie 4(File)
File 539 KB