Related papers: LBIBCell: A Cell-Based Simulation Environment for …
Morphogenetic dynamics of tissue sheets require coordinated cell shape changes regulated by global patterning of mechanical forces. Inspired by such biological phenomena, we propose a minimal mechanochemical model based on the notion that…
Cells exhibit a wide variety of different shapes. This diversity poses a challenge for computational approaches that attempt to shed light on the role cell geometry plays in regulating cell physiology and behavior. The simulation platform…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Within the MNPBEM toolbox, developed for the simulation of plasmonic nanoparticles using a boundary element method approach, we show how to include substrate and layer structure effects. We develop the methodology for solving Maxwell's…
Computational Fluid Dynamics (CFD) is currently used to design and improve the hydraulic properties of biomedical devices, wherein the large scale blood circulation needs to be simulated by accounting for the mechanical response of red…
This study explores the emergence of life through a simulation model approach. The model "Multi-set chemical lattice model" is a model that allows virtual molecules of multiple types to be placed in each lattice cell on a two-dimensional…
The Immersed Boundary Method (IBM) is one of the popular one-fluid mixed Eulerian-Lagrangian methods to simulate motion of droplets. While the treatment of a moving complex boundary is an extremely time consuming and formidable task in a…
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…
The development of fluid-structure interaction (FSI) software involves trade-offs between ease of use, generality, performance, and cost. Typically there are large learning curves when using low-level software to model the interaction of an…
We report an implementation of the lattice Boltzmann method (LBM) to integrate the Bloch-Torrey equation, which describes the evolution of the transverse magnetization vector and the fate of the signal of diffusion magnetic resonance…
We present numerical simulations of active fluid droplets immersed in an external fluid in 2-dimensions { using} an Immersed Boundary method to simulate the fluid droplet interface as a Lagrangian mesh. We present results from two example…
The complexity of the interactions between the constituent granular and liquid phases of a suspension requires an adequate treatment of the constituents themselves. A promising way for numerical simulations of such systems is given by…
Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of…
We investigate the convergence of solutions of a recently proposed diffuse interface/phase field model for cell blebbing by means of matched asymptotic expansions. It is a biological phenomenon that increasingly attracts attention by both…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…
The deformability of soft condensed matter often requires modelling of hydrodynamical aspects to gain quantitative understanding. This, however, requires specialised methods that can resolve the multiscale nature of soft matter systems. We…
Imbibition is a commonly encountered multiphase problem in various fields, and exact prediction of imbibition processes is a key issue for better understanding capillary flow in heterogeneous porous media. In this work, a numerical…
Complex colloidal fluids, such as emulsions stabilized by complex shaped particles, play an important role in many industrial applications. However, understanding their physics requires a study at sufficiently large length scales while…
We propose a two-scale model to resolve essential features of developmental tissue deformations. The model couples individual cellular behavior to the mechanics at tissue scale. This is realized by a multiphase-field model addressing the…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…