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To design a method to solve the issues of handling 'dirty' and highly complex geometries, the topology-free method combined with the immersed boundary method is presented for viscous and incompressible flows at a high Reynolds number. The…
We present a practical cell-centred volume-of-fluid method developed within a pure Eulerian setting for the simulation of compressible solid-fluid problems. The method builds on a previously published diffuse-interface Godunov-type scheme…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
This work outlines a new multi-physics-compatible immersed rigid body method for Eulerian finite-volume simulations. To achieve this, rigid bodies are represented as a diffuse scalar field and an interface seeding method is employed to…
Microorganisms develop coordinated beating patterns on surfaces lined with cilia known as metachronal waves. For a chain of cilia attached to a flat ciliate, it has been shown that hydrodynamic interactions alone can lead the system to…
We propose unified data structures and algorithms for free-surface fluid simulations based on partial optimal transport, such as the Power Particles method or Gallou\"et-M\'erigot's scheme. Such methods previously relied on a discretization…
The interaction of fibers in a viscous (Stokes) fluid plays a crucial role in industrial and biological processes, such as sedimentation, rheology, transport, cell division, and locomotion. Numerical simulations generally rely on slender…
Lipid vesicles appear ubiquitously in biological systems. Understanding how the mechanical and intermolecular interations deform vesicle membrane is a fundamental question in biophysics. In this article we developed a fast algorithm to…
Two methods for solid body representation in flow simulations available in the Pencil Code are the immersed boundary method and overset grids. These methods are quite different in terms of computational cost, flexibility and numerical…
The conventional no-slip boundary condition leads to a non-integrable stress singularity at a moving contact line. This makes numerical simulations challenging, especially when capillary effects are essential for the dynamics of the flow.…
Escherichia coli and other bacteria use rotating helical filaments to swim. Each cell typically has about four filaments, which bundle or disperse depending on the sense of motor rotation. To study the bundling process, we built a…
The hydrodynamics of a flagellated microorganism is investigated when swimming close to a planar free-slip surface by means of numerical solu- tions of the Stokes equations obtained via a Boundary Element Method. Depending on the initial…
Cartesian-grid methods in combination with immersed-body and volume-of-fluid methods are ideally suited for simulating breaking waves around ships. A surface panelization of the ship hull is used as input to impose body-boundary conditions…
Cartesian-grid methods in combination with immersed-body and volume-of-fluid methods are ideally suited for simulating breaking waves around ships. A surface panelization of the ship hull is used as input to impose body-boundary conditions…
Recent advances in microscopy techniques has uncovered unique aspects of flagella-driven motility in bacteria. A remarkable example is the discovery of flagellar wrapping, a phenomenon whereby a bacterium wraps its flagellum (or flagellar…
The hybrid method combining particle-in-cell and magnetohydrodynamics can be used to study the interaction between energetic particles and global plasma modes. In this paper we introduce the M3D-C1-K code, which is developed based on the…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
We consider numerical algorithms for the simulation of the rheology of two-dimensional vesicles suspended in a viscous Stokesian fluid. The vesicle evolution dynamics is governed by hydrodynamic and elastic forces. The elastic forces are…
This paper introduces a sharp interface method to simulate fluid-structure interaction (FSI) involving rigid bodies immersed in viscous incompressible fluids. The capabilities of this methodology are demonstrated for a range of benchmark…