Related papers: LBIBCell: A Cell-Based Simulation Environment for …
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
We propose numerical simulations of viscoelastic fluids based on a hybrid algorithm combining Lattice-Boltzmann models (LBM) and Finite Differences (FD) schemes, the former used to model the macroscopic hydrodynamic equations, and the…
This paper presents a generic framework for the numerical simulation of transformation-diffusion processes in complex volume geometric shapes. This work follows a previous one devoted to the simulation of microbial degradation of organic…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
We have developed a simulation technique of multiscale Lagrangian fluid dynamics to tackle hierarchical problems relating to historical dependency of polymeric fluid. We investigate flow dynamics of dilute polymeric fluid by using the…
Coordinated cellular movements are key processes in tissue morphogenesis. Using a cell-based modeling approach we study the dynamics of epithelial layers lining surfaces with constant and varying curvature. We demonstrate that extrinsic…
The present work presents a density-functional microscopic model of soft biological tissue. The model was based on a prototype molecular structure from experimentally resolved collagen peptide residues and water clusters and has the…
We consider a coupled bulk-surface system of partial differential equations with nonlinear coupling modelling receptor-ligand dynamics. The model arises as a simplification of a mathematical model for the reaction between cell surface…
It is proposed a dimensional Lattice Boltzmann Method (LBM) of wide application for simulating fluid flow and heat transfer problems. The proposed LBM consists in the numerical solution of the discrete lattice Boltzmann equation (LBE) using…
We introduce an Active Vertex Model (AVM) for cell-resolution studies of the mechanics of confluent epithelial tissues consisting of tens of thousands of cells, with a level of detail inaccessible to similar methods. The AVM combines the…
We simulate the electrical response of multiple disjoint biological 3D cells undergoing an electropermeabilization process. Instead of solving the boundary value problem in the unbounded volume, we reduce it to a system of boundary…
In this paper, a new progressive mesh algorithm is introduced in order to perform fast physical simulations by the use of a lattice Boltzmann method (LBM) on a single-node multi-GPU architecture. This algorithm is able to mesh automatically…
The wetting dynamics of liquid particles, from coated droplets to soft capsules, holds significant technological interest. Motivated by the need to simulate liquid metal droplet with an oxidize surface layer, in this work we introduce a…
Recently, Murthy et al. [2017] and Escande et al. [2020] adopted the Lattice Boltzmann Method (LBM) to model the linear elastodynamic behaviour of isotropic solids. The LBM is attractive as an elastodynamic solver because it can be…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
We consider a multiscale approach based on immersed methods for the efficient computational modeling of tissues composed of an elastic matrix (in two or three-dimensions) and a thin vascular structure (treated as a co-dimension two…
The current work presents a novel COllaborative Open-source Lattice Boltzmann Method framework, so-called CooLBM. The computational framework is developed for the simulation of single and multi-component multi-phase problems, along with a…
The study of the underlying physics of soft flowing materials depends heavily on numerical simulations, due to the complex structure of the governing equations reflecting the competition of concurrent mechanisms acting at widely disparate…
The performance of a single or the collection of microswimmers strongly depends on the hydrodynamic coupling among their constituents and themselves. We present a numerical study for a single and a pair of microswimmers based on lattice…
Polymer dynamics in a turbulent flow is a problem spanning several orders of magnitude of length and time scales. A microscopic simulation covering all those scales from the polymer segment to the inertial scale of turbulence seems…