Related papers: LBIBCell: A Cell-Based Simulation Environment for …
Microfluidics provides a powerful and versatile technology to accurately control spatial and temporal conditions for cell culturing and can therefore be used to study cellular responses to gradients. Here we use Lattice Boltzmann methods…
Cell-based, mathematical modeling of collective cell behavior has become a prominent tool in developmental biology. Cell-based models represent individual cells as single particles or as sets of interconnected particles, and predict the…
This paper presents an improved immersed moving boundary model (IBM) for solving complex fluid-particle interactions in a coupled lattice Boltzmann method (LBM) and an adhesive discrete element method (DEM), using the "partially saturated…
In this paper we present an individual-based mechanical model that describes the dynamics of two contiguous cell populations with different proliferative and mechanical characteristics. An off-lattice modelling approach is considered…
In this study we present a kinematic approach to modeling needle insertion into soft tissues. The kinematic approach allows the presentation of the problem as Dirichlet-type (i.e. driven by enforced motion of boundaries) and therefore…
We propose a description for transient penetration simulations of miscible and immiscible fluid mixtures into anisotropic porous media, using the lattice Boltzmann (LB) method. Our model incorporates hydrodynamic flow, diffusion, surface…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…
In this paper, phase field models are developed for multi-component vesicle membranes with different lipid compositions and membranes with free boundary. These models are used to simulate the deformation of membranes under the elastic…
A method is described for embedding a deformable, elastic, membrane within a lattice Boltzmann fluid. The membrane is represented by a set of massless points which advect with the fluid and which impose forces on the fluid which are derived…
A numerical method for simulating three-phase flows with moving contact lines on arbitrarily complex surfaces is developed in the framework of lattice Boltzmann method. In this method, the immiscible three-phase flow is modeled through a…
An immersed interface-lattice Boltzmann method (II-LBM) is developed for modelling fluid-structure systems. The key element of this approach is the determination of the jump conditions that are satisfied by the distribution functions within…
Organogenesis is a tightly regulated process that has been studied experimentally for decades. Computational models can help to integrate available knowledge and to better understand the underlying regulatory logic. We are currently…
Various experiments have found a boundary slip in hydrophobic microchannel flows, but a consistent understanding of the results is still lacking. While Molecular Dynamics (MD) simulations cannot reach the low shear rates and large system…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
Quantum computing holds great promise to accelerate scientific computations in fluid dynamics and other classical physical systems. While various quantum algorithms have been proposed for linear flows, developing quantum algorithms for…
Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
Mathematical Modelling has a long history in developmental biology. Advances in experimental techniques and computational algorithms now permit the development of increasingly more realistic models of organogenesis. In particular, 3D…
In this paper homogenization of a mathematical model for biomechanics of a plant tissue with randomly distributed cells is considered. Mechanical properties of a plant tissue are modelled by a strongly coupled system of…