Related papers: LBIBCell: A Cell-Based Simulation Environment for …
The birth of the lattice Boltzmann method (LBM) fulfils a dream that simple arithmetic calculations can simulate complex fluid flows without solving complicated partial differential flow equations. Its power and potential of resolving more…
Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…
We develop a modeling and simulation framework capable of massively parallel simulation of multicellular systems with spatially resolved stochastic kinetics in individual cells. By the use of operator-splitting we decouple the simulation of…
Physics-based simulation is essential for developing and evaluating robot manipulation policies, particularly in scenarios involving deformable objects and complex contact interactions. However, existing simulators often struggle to balance…
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing…
We develop a numerical method for simulating the dynamics of a droplet immersed in a generic time-dependent velocity gradient field. This approach is grounded on the hybrid coupling between the lattice Boltzmann (LB) method, employed for…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
Morphogenesis involves complex shape changes of biological tissues. Yet, tissue shape changes depend on tissue rheology, which in turn arises from the interplay of large numbers of cells. Here, we link cell- and tissue-scale mechanics by…
In this paper we develop a methodology for the mesoscale simulation of strong electrolytes. The methodology is an extension of the Fluctuating Immersed Boundary (FIB) approach that treats a solute as discrete Lagrangian particles that…
Biological cells sense and respond to mechanical forces, but how such a mechanosensing proccess takes place in a nonlinear inhomogeneous fibrous matrix remains unknown. We show that cells in a fibrous matrix induce deformation fields that…
An accurate modelling of bio-electrochemical processes that govern Microbial Fuel Cells (MFCs) and mapping their behaviour according to several parameters will enhance the development of MFC technology and enable their successful…
Current GPU-accelerated supercomputers promise to enable large-scale simulations of turbulent flows. Lattice Boltzmann Methods (LBM) are particularly well-suited to fulfilling this promise due to their intrinsic compatibility with highly…
In this work we consider how surface-adherent bacterial biofilm communities respond in flowing systems. We simulate the fluid-structure interaction and separation process using the immersed boundary method. In these simulations we model and…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Many complex multiphysics systems in fluid dynamics involve using solvers with varied levels of approximations in different regions of the computational domain to resolve multiple spatiotemporal scales present in the flow. The accuracy of…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. We are developing mechanistic models for the morphogenesis of limbs, lungs, and kidneys with a view to integrate available knowledge and to…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
The fluid dynamics video presented here outlines recent advances in the simulation of multiphase cellular blood flow through the direct numerical simulations of deformable red blood cells (RBCs) demonstrated through several numerical…
During organogenesis tissue grows and deforms. The growth processes are controlled by diffusible proteins, so-called morphogens. Many different patterning mechanisms have been proposed. The stereotypic branching program during lung…
There exists an increasing interest for using immersed boundary methods (IBMs) (Peskin 2000) to model moving objects in computational fluid dynamics. Indeed, this approach is particularly efficient, because the fluid mesh does not require…