Related papers: Simulating cilia-driven mixing and transport in co…

Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh…

We apply the boundary-element method to Stokes flows with helical symmetry, such as the flow driven by an immersed rotating helical flagellum. We show that the two-dimensional boundary integral method can be reduced to one dimension using…

Deformable elastic bodies in viscous and viscoelastic media constitute a large portion of synthetic and biological complex fluids. We present a parallelized 3D-simulation methodology which fully resolves the momentum balance in the solid…

It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…

This work is devoted to analyze the relation between the thermodynamic properties of a confined fluid and the shape of its confining vessel. Recently, new insights in this topic were found through the study of cluster integrals for…

Controlling and suppressing bacterial accumulation at solid surfaces is essential for preventing biofilm formation and biofouling. Whereas various chemical surface treatments are known to reduce cell accumulation and attachment, the role of…

Cilia and flagella are essential building blocks for biological fluid transport and locomotion at the micron scale. They often beat in synchrony and may transition between different synchronization modes in the same cell type. Here, we…

Several micro-organisms, such as bacteria, algae, or spermatozoa, use flagella or cilia to swim in a fluid, while many other micro-organisms instead use ample shape deformation, described as amoeboid, to propel themselves by either crawling…

Microorganism motility often takes place within complex, viscoelastic fluid environments, e.g., sperm in cervicovaginal mucus and bacteria in biofilms. In such complex fluids, strains and stresses generated by the microorganism are stored…

We employ the Partially Saturated Cells Method (PSM) to model the interaction between the fluid flow and solid moving objects as an extension to the conventional lattice Boltzmann method. We introduce an efficient and accurate method for…

We consider a Stokeslet applied to a viscous fluid next to an infinite, flat wall, or in-between two parallel walls. We calculate the forces exerted by the resulting flow on the confining boundaries, and use the results obtained to estimate…

This paper describes the results of our theoretical and numerical studies of hydrodynamic interactions in a suspension of spherical particles confined between two parallel planar walls, under creeping-flow conditions. We propose a novel…

We consider a molecular dynamics method, the so-called flea gas for computing the evolution of entanglement after inhomogeneous quantum quenches in an integrable quantum system. In such systems the evolution of local observables is…

Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…

Most biological tissues grow by the synthesis of new material close to the tissue's interface, where spatial interactions can exert strong geometric influences on the local rate of growth. These geometric influences may be mechanistic, or…

We use coarse-grained molecular-dynamics (MD) simulations to investigate the structural and dynamical properties of micelles under non-equilibrium Poiseuille flow in a nano-confined geometry. The effects of flow, confinement, and the…

A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…

Active particles, including swimming microorganisms, autophoretic colloids and droplets, are known to self-organize into ordered structures at fluid-solid boundaries. The entrainment of particles in the attractive parts of their spontaneous…

We present a novel computational modeling framework to numerically investigate fluid-structure interaction in viscous fluids using the phase field embedding method. Each rigid body or elastic structure immersed in the incompressible viscous…

Cilia and flagella exhibit regular bending waves that perform mechanical work on the surrounding fluid, to propel cellular swimmers and pump fluids inside organisms. Here, we quantify a force-velocity relationship of the beating flagellum,…