Related papers: LBIBCell: A Cell-Based Simulation Environment for …
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
The aim of this paper is to develop suitable models for the phenomenon of cell blebbing, which allow for computational predictions of mechanical effects including the crucial interaction of the cell membrane and the actin cortex. For this…
Over the last decade, the Lattice Boltzmann method has found major scope for the simulation of a large spectrum of problems in soft matter, from multiphase and multi-component microfluidic flows, to foams, emulsions, colloidal flows, to…
Continuum solvation models are becoming increasingly relevant in condensed matter simulations, allowing to characterize materials interfaces in the presence of wet electrified environments at a reduced computational cost with respect to all…
We present a COMSOL Multiphysics implementation of a continuum model for directed cell migration, a key mechanism underlying tissue self-organization and morphogenesis. The model is formulated as a partial integro-differential equation…
The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such…
Computational modeling and simulation of fluid-structure interactions constitute a fundamental cornerstone for advancing aerospace engineering endeavors. This paper addresses the notion and implementation of the immersed boundary method for…
Immersed boundary methods are extensively used for simulations of dynamic solid objects interacting with fluids due to their computational efficiency and modelling flexibility compared to body-fitted grid methods. However, thin geometries,…
The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes…
We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue…
The lattice Boltzmann method (LBM) is routinely employed in the simulation of complex multiphase flows comprising bulk phases separated by non-ideal interfaces. LBM is intrinsically mesoscale with an hydro-dynamic equivalence popularly set…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
Multi-component fluid flow simulations in multi-scale porous structures often involve regions that are under-resolved at practical computational resolutions. Accurately capturing the contributions from these unresolved regions is critical.…
In processes such as embryo shaping, wound healing, and malignant cell invasion, epithelial cells transition between dispersed phases, where the cells move independently, and condensed phases, where they aggregate and deform to close gaps,…
We study the dynamics of elastic interfaces-membranes-immersed in thermally excited fluids. The work contains three components: the development of a numerical method, a purely theoretical approach, and numerical simulation. In developing a…
The topology and form finding of tensegrity structures have been studied extensively since the introduction of the tensegrity concept. However, most of these studies address topology and form separately, where the former represented a…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
We consider an immersed elastic body that is actively driven through a structured fluid by a motor or an external force. The behavior of such a system generally cannot be solved analytically, necessitating the use of numerical methods.…
We present a loosely coupled approach for the solution of fluid-structure interaction problems between a compressible flow and a deformable structure. The method is based on staggered Dirichlet-Neumann partitioning. The interface motion in…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…