Arbitrary Lagrangian–Eulerian finite element method for curved and deforming surfaces: I. General theory and application to fluid interfaces

An arbitrary Lagrangian–Eulerian (ALE) finite element method for arbitrarily curved and deforming two-dimensional materials and interfaces is presented here. An ALE theory is developed by endowing the surface with a mesh whose in-plane velocity need not depend on the in-plane material velocity, and can be specified arbitrarily. A finite element implementation of the theory is formulated and applied to curved and deforming surfaces with in-plane incompressible flows. Numerical inf–sup instabilities associated with in-plane incompressibility are removed by locally projecting the surface tension onto a discontinuous space of piecewise linear functions. The general isoparametric finite element method, based on an arbitrary surface parametrization with curvilinear coordinates, is tested and validated against several numerical benchmarks. A new physical insight is obtained by applying the ALE developments to cylindrical fluid films, which are computationally and analytically found to be stable to non-axisymmetric perturbations, and unstable with respect to long-wavelength axisymmetric perturbations when their length exceeds their circumference. A Lagrangian scheme is attained as a special case of the ALE formulation. Though unable to model fluid films with sustained shear flows, the Lagrangian scheme is validated by reproducing the cylindrical instability. However, relative to the ALE results, the Lagrangian simulations are found to have spatially unresolved regions with few nodes, and thus larger errors

On Approximations of the Curve Shortening Flow and of the Mean Curvature Flow based on the DeTurck trick

In this paper we discuss novel numerical schemes for the computation of the curve shortening and mean curvature flows that are based on special reparametrizations. The main idea is to use special solutions to the harmonic map heat flow in order to reparametrize the equations of motion. This idea is widely known from the Ricci flow as the DeTurck trick. By introducing a variable time scale for the harmonic map heat flow, we obtain families of numerical schemes for the reparametrized flows. For the curve shortening flow this family unveils a surprising geometric connection between the numerical schemes in [5] and [9]. For the mean curvature flow we obtain families of schemes with good mesh properties similar to those in [3]. We prove error estimates for the semi-discrete scheme of the curve shortening flow. The behaviour of the fully-discrete schemes with respect to the redistribution of mesh points is studied in numerical experiments. We also discuss possible generalizations of our ideas to other extrinsic flows

Approximation of tensor fields on surfaces of arbitrary topology based on local Monge parametrizations

We introduce a new method, the Local Monge Parametrizations (LMP) method, to approximate tensor fields on general surfaces given by a collection of local parametrizations, e.g.~as in finite element or NURBS surface representations. Our goal is to use this method to solve numerically tensor-valued partial differential equations (PDE) on surfaces. Previous methods use scalar potentials to numerically describe vector fields on surfaces, at the expense of requiring higher-order derivatives of the approximated fields and limited to simply connected surfaces, or represent tangential tensor fields as tensor fields in 3D subjected to constraints, thus increasing the essential number of degrees of freedom. In contrast, the LMP method uses an optimal number of degrees of freedom to represent a tensor, is general with regards to the topology of the surface, and does not increase the order of the PDEs governing the tensor fields. The main idea is to construct maps between the element parametrizations and a local Monge parametrization around each node. We test the LMP method by approximating in a least-squares sense different vector and tensor fields on simply connected and genus-1 surfaces. Furthermore, we apply the LMP method to two physical models on surfaces, involving a tension-driven flow (vector-valued PDE) and nematic ordering (tensor-valued PDE). The LMP method thus solves the long-standing problem of the interpolation of tensors on general surfaces with an optimal number of degrees of freedom.Comment: 16 pages, 6 figure

Variational Methods for Biomolecular Modeling

Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrostatics and solvation that includes the curvature energy of the molecular surface, the formation of microdomains on lipid membrane due to the geometric and molecular mechanics at the lipid interface, and the mean curvature driven protein localization on membrane surfaces. By further implicitly representing the interface using a phase field function over the entire domain, one can simulate the dynamics of the interface and the corresponding energy variation by evolving the phase field function, achieving significant reduction of the number of degrees of freedom and computational complexity. Strategies for improving the efficiency of computational implementations and for extending applications to coarse-graining or multiscale molecular simulations are outlined.Comment: 36 page

Modeling Shallow Water Flows on General Terrains

A formulation of the shallow water equations adapted to general complex terrains is proposed. Its derivation starts from the observation that the typical approach of depth integrating the Navier-Stokes equations along the direction of gravity forces is not exact in the general case of a tilted curved bottom. We claim that an integration path that better adapts to the shallow water hypotheses follows the "cross-flow" surface, i.e., a surface that is normal to the velocity field at any point of the domain. Because of the implicitness of this definition, we approximate this "cross-flow" path by performing depth integration along a local direction normal to the bottom surface, and propose a rigorous derivation of this approximation and its numerical solution as an essential step for the future development of the full "cross-flow" integration procedure. We start by defining a local coordinate system, anchored on the bottom surface to derive a covariant form of the Navier-Stokes equations. Depth integration along the local normals yields a covariant version of the shallow water equations, which is characterized by flux functions and source terms that vary in space because of the surface metric coefficients and related derivatives. The proposed model is discretized with a first order FORCE-type Godunov Finite Volume scheme that allows implementation of spatially variable fluxes. We investigate the validity of our SW model and the effects of the bottom geometry by means of three synthetic test cases that exhibit non negligible slopes and surface curvatures. The results show the importance of taking into consideration bottom geometry even for relatively mild and slowly varying curvatures

An adaptive octree finite element method for PDEs posed on surfaces

The paper develops a finite element method for partial differential equations posed on hypersurfaces in $\mathbb{R}^N$, $N=2,3$. The method uses traces of bulk finite element functions on a surface embedded in a volumetric domain. The bulk finite element space is defined on an octree grid which is locally refined or coarsened depending on error indicators and estimated values of the surface curvatures. The cartesian structure of the bulk mesh leads to easy and efficient adaptation process, while the trace finite element method makes fitting the mesh to the surface unnecessary. The number of degrees of freedom involved in computations is consistent with the two-dimension nature of surface PDEs. No parametrization of the surface is required; it can be given implicitly by a level set function. In practice, a variant of the marching cubes method is used to recover the surface with the second order accuracy. We prove the optimal order of accuracy for the trace finite element method in $H^1$ and $L^2$ surface norms for a problem with smooth solution and quasi-uniform mesh refinement. Experiments with less regular problems demonstrate optimal convergence with respect to the number of degrees of freedom, if grid adaptation is based on an appropriate error indicator. The paper shows results of numerical experiments for a variety of geometries and problems, including advection-diffusion equations on surfaces. Analysis and numerical results of the paper suggest that combination of cartesian adaptive meshes and the unfitted (trace) finite elements provide simple, efficient, and reliable tool for numerical treatment of PDEs posed on surfaces