High order direct Arbitrary-Lagrangian-Eulerian schemes on moving Voronoi meshes with topology changes

We present a new family of very high order accurate direct Arbitrary-Lagrangian-Eulerian (ALE) Finite Volume (FV) and Discontinuous Galerkin (DG) schemes for the solution of nonlinear hyperbolic PDE systems on moving 2D Voronoi meshes that are regenerated at each time step and which explicitly allow topology changes in time. The Voronoi tessellations are obtained from a set of generator points that move with the local fluid velocity. We employ an AREPO-type approach, which rapidly rebuilds a new high quality mesh rearranging the element shapes and neighbors in order to guarantee a robust mesh evolution even for vortex flows and very long simulation times. The old and new Voronoi elements associated to the same generator are connected to construct closed space--time control volumes, whose bottom and top faces may be polygons with a different number of sides. We also incorporate degenerate space--time sliver elements, needed to fill the space--time holes that arise because of topology changes. The final ALE FV-DG scheme is obtained by a redesign of the fully discrete direct ALE schemes of Boscheri and Dumbser, extended here to moving Voronoi meshes and space--time sliver elements. Our new numerical scheme is based on the integration over arbitrary shaped closed space--time control volumes combined with a fully-discrete space--time conservation formulation of the governing PDE system. In this way the discrete solution is conservative and satisfies the GCL by construction. Numerical convergence studies as well as a large set of benchmarks for hydrodynamics and magnetohydrodynamics (MHD) demonstrate the accuracy and robustness of the proposed method. Our numerical results clearly show that the new combination of very high order schemes with regenerated meshes with topology changes lead to substantial improvements compared to direct ALE methods on conforming meshes

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

The Semi Implicit Gradient Augmented Level Set Method

Here a semi-implicit formulation of the gradient augmented level set method is presented. By tracking both the level set and it's gradient accurate subgrid information is provided,leading to highly accurate descriptions of a moving interface. The result is a hybrid Lagrangian-Eulerian method that may be easily applied in two or three dimensions. The new approach allows for the investigation of interfaces evolving by mean curvature and by the intrinsic Laplacian of the curvature. In this work the algorithm, convergence and accuracy results are presented. Several numerical experiments in both two and three dimensions demonstrate the stability of the scheme.Comment: 19 Pages, 14 Figure

4D topology optimization: Integrated optimization of the structure and self-actuation of soft bodies for dynamic motions

Topology optimization is a powerful tool utilized in various fields for structural design. However, its application has primarily been restricted to static or passively moving objects, mainly focusing on hard materials with limited deformations and contact capabilities. Designing soft and actively moving objects, such as soft robots equipped with actuators, poses challenges due to simulating dynamics problems involving large deformations and intricate contact interactions. Moreover, the optimal structure depends on the object's motion, necessitating a simultaneous design approach. To address these challenges, we propose "4D topology optimization," an extension of density-based topology optimization that incorporates the time dimension. This enables the simultaneous optimization of both the structure and self-actuation of soft bodies for specific dynamic tasks. Our method utilizes multi-indexed and hierarchized density variables distributed over the spatiotemporal design domain, representing the material layout, actuator layout, and time-varying actuation. These variables are efficiently optimized using gradient-based methods. Forward and backward simulations of soft bodies are done using the material point method, a Lagrangian-Eulerian hybrid approach, implemented on a recent automatic differentiation framework. We present several numerical examples of self-actuating soft body designs aimed at achieving locomotion, posture control, and rotation tasks. The results demonstrate the effectiveness of our method in successfully designing soft bodies with complex structures and biomimetic movements, benefiting from its high degree of design freedom.Comment: 36 pages, 27 figures; for supplementary video, see https://youtu.be/sPY2jcAsNY

A Material Point Method for Elastoplasticity with Ductile Fracture and Frictional Contact

Simulating physical materials with dynamic movements to photo-realistic resolution has always been one of the most crucial and challenging topics in Computer Graphics. This dissertation considers large-strain elastoplasticity theory applied to the low-to-medium stiffness regime, with topological changes and codimensional objects incorporated. We introduce improvements to the Material Point Method (MPM) for two particular objectives, simulating fracturing ductile materials and incorporation of MPM and Lagrangian Finite Element Method (FEM).Our first contribution, simulating ductile fracture, utilizes traditional particle-based MPM [SSC13, SCS94] as well as the Lagrangian energy formulation of [JSS15] which uses a tetrahedron mesh, rather than particle-based estimation of the deformation gradient and potential energy. We model failure and fracture via elastoplasticity with damage. The material is elastic until its deformation exceeds a Rankine or von Mises yield condition. At that point, we use a softening model that shrinks the yield surface until it reaches the damage thresh- old. Once damaged, the material Lam ́e coefficients are modified to represent failed material. This approach to simulating ductile fracture with MPM is successful, as MPM naturally captures the topological changes coming from the fracture. However, rendering the crack surfaces can be challenging. We design a novel visualization technique dedicated to rendering the material’s boundary and its intersection with the evolving crack surfaces. Our approach uses a simple and efficient element splitting strategy for tetrahedron meshes to create crack surfaces. It employs an extrapolation technique based on the MPM simulation. For traditional particle-based MPM, we use an initial Delaunay tetrahedralization to connect randomly sampled MPM particles. Our visualization technique is a post-process and can run after the MPM simulation for efficiency. We demonstrate our method with several challenging simulations of ductile failure with considerable and persistent self-contact and applications with thermomechanical models for baking and cooking.Our second contribution, hybrid MPM–Lagrangian-FEM, aims to simulate elastic objects like hair, rubber, and soft tissues. It utilizes a Lagrangian mesh for internal force computation and a Eulerian grid for self-collision, as well as coupling with external materials. While recent MPM techniques allow for natural simulation of hyperelastic materials represented with Lagrangian meshes, they utilize an updated Lagrangian discretization and use the Eulerian grid degrees of freedom to take variations of the potential energy. It often coarsens the degrees of freedom of the Lagrangian mesh and can lead to artifacts. We develop a hybrid approach that retains Lagrangian degrees of freedom while still allowing for natural coupling with other materials simulated with traditional MPM, e.g., sand, snow, etc. Furthermore, while recent MPM advances allow for resolution of frictional contact with codimensional simulation of hyperelasticity, they do not generalize to the case of volumetric materials. We show that our hybrid approach resolves these issues. We demonstrate the efficacy of our technique with examples that involve elastic soft tissues coupled with kinematic skeletons, extreme deformation, and coupling with various elastoplastic materials. Our approach also naturally allows for two-way rigid body coupling