Related papers: LBIBCell: A Cell-Based Simulation Environment for …
LibBi is a software package for state-space modelling and Bayesian inference on modern computer hardware, including multi-core central processing units (CPUs), many-core graphics processing units (GPUs) and distributed-memory clusters of…
A systematic study is carried out on a fully resolved fluid-particle model which couples the Lattice Boltzmann Method (LBM) and the Discrete Element Method (DEM) using an immersed moving boundary technique. Similar algorithms have been…
Simulating the irreversible quantum dynamics of exciton and electron transfer problems poses a nontrivial challenge. Because the irreversibility of the system dynamics is a result of quantum thermal activation and dissipation caused by the…
A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…
The vertex model is widely used to describe the dynamics of epithelial tissues, because of its simplicity and versatility and the direct inclusion of biophysical parameters. Here, it is shown that quite generally, when cells modify their…
The lattice Boltzmann method has become a standard technique for simulating a wide range of fluid flows. However, the intrinsic coupling of momentum and space discretization restricts the traditional lattice Boltzmann method to regular…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
We consider a continuum mechanical model of cell invasion through thin membranes. The model consists of a transmission problem for cell volume fraction complemented with continuity of stresses and mass flux across the surfaces of the…
We present the IAMReX, an adaptive and parallel solver for particle-resolved simulations on the multi-level grid. The fluid equations are solved using a finite-volume scheme on the block-structured semi-staggered grids with both subcycling…
The immersed isogeometric Boundary Element Method is presented and applied to the simulation of underground excavations. Nonuniform rational B-splines (NURBS) are used for the accurate definition of complex geometries with few parameters.…
This paper presents the principal challenges and opportunities associated with computational biomechanics research. The underlying cognitive control involved in the process of human motion is inherently complex, dynamic, multidimensional,…
This paper describes a work in progress about software and hardware architecture to steer and control an ongoing fluid simulation in a context of a serious game application. We propose to use the Lattice Boltzmann Method as the simulation…
We present a computational framework for the simulation of blood flow with fully resolved red blood cells (RBCs) using a modular approach that consists of a lattice Boltzmann solver for the blood plasma, a novel finite element based solver…
In the field of biomedicine magnetic beads are used for drug delivery and to treat hyperthermia. Here we propose to use self-organized bead structures to isolate circulating tumor cells using lab-on-chip technologies. Typically blood flows…
We introduce a non-reflecting boundary condition for the simulation of thermal flows with the lattice Boltzmann Method (LBM). We base the derivation on the locally one-dimensional inviscid analysis, and define target macroscopic values at…
We present a new hybrid lattice-Boltzmann and Langevin molecular dynamics scheme for simulating the dynamics of suspensions of spherical colloidal particles. The solvent is modeled on the level of the lattice-Boltzmann method while the…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
The lattice Boltzmann method, after close to thirty years of presence in computational fluid dynamics has turned into a versatile, efficient and quite popular numerical tool for fluid flow simulations. The lattice Boltzmann method owes its…
The pseudopotential lattice Boltzmann method (LBM) is a prominent approach for simulating multiphase flows, valued for its physical intuitiveness and computational tractability. However, existing immiscible pseudopotential methods for…
We present a two-way coupled fluid-structure interaction scheme for rigid bodies using a two-population lattice Boltzmann formulation for compressible flows. Arbitrary Lagrangian-Eulerian formulation of the discrete Boltzmann equation on…