Novel methods for mixed-mode modeling of soft and active matter in confined geometries

We demonstrate innovations in mixed-mode modeling techniques for coarse-grained simulation studies of soft and active matter. For a model of an active nematic in a confined geometry, we study a 3D thin layer of polar flexible filaments, where activity is introduced via filament-filament shear forces. As a novel approach for hydrodynamic interactions, we couple the filaments to an underlying 2D coarse-grained liquid [1]. Results are compared with experimental studies of an active nematic in a cardioid geometry [2]. To study mechanics of squishy, deformable colloids under compression, we demonstrate use of a Hamiltonian-based Finite Element Method (FEM) elastodynamics model with internal dissipation, optimized for GPU execution. To develop mixed-mode simulation studies combining particle-based models (e.g. coarse grained fluids or filaments) with deformable elastic solid bodies of any shape, we demonstrate interoperability of our fast FEM algorithm with coarse-grained molecular dynamics (MD), coupled via handshake particles. This approach bridges scales for mixed-mode modeling and can be adapted to work with many available MD codes.We discuss strategies to bring these methods together to model squishy active matter, e.g. to model how cell contraction induces nematic order in a cross-linked fiber network representing extra-cellular matrix. Further development of mixed-mode simulation methods will enable more realistic models of both living and non-living soft and active matter. [1] Klein et al https://arxiv.org/abs/2503.10880 [2] Memarian et al Phys Rev Lett 132, 228301 (2024)