Related papers: LBIBCell: A Cell-Based Simulation Environment for …
Many biological examples of fluid-structure interaction, including the transit of red blood cells through the narrow slits in the spleen and the intracellular trafficking of vesicles into dendritic spines, involve the near-contact of…
Cell motility is one of the most fundamental phenomena underlying biological processes that maintain living organisms alive. Here we introduce a simple model to describe the motility of cells which include not only time-correlated internal…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
How morphogenesis depends on cell properties is an active direction of research. Here, we focus on mechanical models of growing plant tissues, where microscopic (sub)cellular structure is taken into account. In order to establish links…
We carry out the homogenization of a fluid-structure interaction problem consisting in the periodic inclusions of a viscous fluid in an elastic body. We get a macrostructure model where the body behaves as a viscoelastic material with a…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
The Immersed Boundary (IB) method is a mathematical framework for constructing robust numerical methods to study fluid-structure interaction in problems involving an elastic structure immersed in a viscous fluid. The IB formulation uses an…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
We describe in detail a recently proposed lattice-Boltzmann model for simulating flows with multiple phases and components. In particular, the focus is on the modeling of one-component fluid systems which obey non-ideal gas equations of…
The deformation of an initially spherical capsule, freely suspended in simple shear flow, can be computed analytically in the limit of small deformations [D. Barthes-Biesel, J. M. Rallison, The Time-Dependent Deformation of a Capsule Freely…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…
The article describes parallel multiphysics simulations of charged particles in microfluidic flows with the waLBerla framework. To this end, three physical effects are coupled: rigid body dynamics, fluid flow modelled by a lattice Boltzmann…
We present a new method for the geometric reconstruction of elastic surfaces simulated by the immersed boundary method with the goal of simulating the motion and interactions of cells in whole blood. Our method uses parameter-free radial…
Examining individual components of cellular systems has been successful in uncovering molecular reactions and interactions. However, the challenge lies in integrating these components into a comprehensive system-scale map. This difficulty…
Recent work on particle-based models of tissues has suggested that any finite rate of cell division and cell death is sufficient to fluidize an epithelial tissue. At the same time, experimental evidence has indicated the existence of glassy…
Navigating topological transitions in cellular mechanical systems is a significant challenge for existing simulation methods. While abstract models lack predictive capabilities at the cellular level, explicit network representations…
Lattice-Boltzmann (LB) simulations are a common tool to numerically estimate the permeability of porous media. For valuable results, the porous structure has to be well resolved resulting in a large computational effort as well as high…
We propose a method of simulating efficiently many-body interacting fermion lattice models in trapped ions, including highly nonlinear interactions in arbitrary spatial dimensions and for arbitrarily distant couplings. We map products of…
Optical networks composed of interconnected waveguides are a versatile platform to simulate bosonic physical phenomena. Significant work in the non-interacting regime has demonstrated the capabilities of this platform to simulate many…
The Lattice Boltzmann Method (LBM) is a computational technique of Computational Fluid Dynamics (CFD) that has gained popularity due to its high parallelism and ability to handle complex geometries with minimal effort. Although LBM…