Related papers: MorphoSim: An efficient and scalable phase-field f…
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.…
Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
Phase-field methods offer a versatile computational framework for simulating large-scale morphological evolution. However, the applicability and predictability of phase-field models are inherently limited by their ad hoc nature, and there…
Engineering alloys generally exhibit multi-phase microstructures. For simulating their microstructure evolution during solid-state phase transformation, CALPHAD-guided multi-phase-field models coupled with micro-mechanics have proven to be…
The phase-field method has become a useful tool for the simulation of classical metallurgical phase transformations as well as other phenomena related to materials science. The thermodynamic consistency that forms the basis of these…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
Phase-field modeling is an elegant and versatile computation tool to predict microstructure evolution in materials in the mesoscale regime. However, these simulations require rigorous numerical solutions of differential equations, which are…
In silico, cell based approaches for modeling biological morphogenesis are used to test and validate our understanding of the biological and mechanical process that are at work during the growth and the organization of multi-cell tissues.…
This paper presents a phase-field model for simulating the three-dimensional deformation of vesicle membranes, incorporating area-difference elasticity, with constraints on bulk volume and surface area. We develop efficient numerical…
The process of programmed cell death, namely apoptosis, is a natural mechanism that regulates healthy tissue, multicellular structures, and homeostasis. An improved understanding of apoptosis can significantly enhance our knowledge of…
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…
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications…
The morphogenesis of cells and tissues involves an interplay between chemical signals and active forces on their surrounding surface layers. The complex interaction of hydrodynamics and material flows on such active surfaces leads to…
Multiphase field models have emerged as an important computational tool for understanding biological tissue while resolving single-cell properties. While they have successfully reproduced many experimentally observed behaviors of living…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
In this work we propose an efficient and accurate multi-scale optical simulation algorithm by applying a numerical version of slowly varying envelope approximation in FEM. Specifically, we employ the fast iterative method to quickly compute…
Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to…
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…
Phase field modelling offers an extremely general framework to predict microstructural evolutions in complex systems. However, its computational implementation requires a discretisation scheme with a grid spacing small enough to preserve…
Multiplex tissue immunostaining is a technology of growing relevance as it can capture in situ the complex interactions existing between the elements of the tumor microenvironment. The existence and availability of large, annotated image…