Related papers: Modeling mammalian gastrulation with embryonic ste…
Extracting accurate cosmological information from galaxy-galaxy and galaxy-matter correlation functions on non-linear scales ($\lesssim 10 h^{-1} \mathrm{Mpc}$) requires cosmological simulations. Additionally, one has to marginalise over…
We investigate morphologies of proliferating cellular tissue using a newly developed numerical simulation model for mechanical cell division. The model reproduces structures of simple multi-cellular organisms via simple rules for selective…
This paper describes an Artificial Embryology method (called ``Epigenetic Tracking'') to generate predefined arbitrarily shaped 2-dimensional arrays of cells by means of evolutionary techniques. It is based on a model of development, whose…
We present a novel method for identification of the boundary of embryonic cells (blastomeres) in Hoffman Modulation Contrast (HMC) microscopic images that are taken between day one to day three. Identification of boundaries of blastomeres…
Many biological tissues are viscoelastic, behaving as elastic solids on short timescales and fluids on long timescales. This collective mechanical behavior enables and helps to guide pattern formation and tissue layering. Here we…
During embryonic development tissue morphogenesis and signaling are tightly coupled. It is therefore important to simulate both tissue morphogenesis and signaling simultaneously in in silico models of developmental processes. The resolution…
This chapter provides a brief introduction to the theory and practice of spatial stochastic simulations. It begins with an overview of different methods available for biochemical simulations highlighting their strengths and limitations.…
As an injury heals, an embryo develops, or a carcinoma spreads, epithelial cells systematically change their shape. In each of these processes cell shape is studied extensively, whereas variation of shape from cell-to-cell is dismissed most…
The question of what guides lineage segregation is central to development, where cellular differentiation leads to segregated cell populations destined for specialized functions. Here, using optical tweezers measurements of mouse embryonic…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
Collective cell migration is a key driver of embryonic development, wound healing, and some types of cancer invasion. Here we provide a physical perspective of the mechanisms underlying collective cell migration. We begin with a catalogue…
Many of the intriguing properties of blood originate from its cellular nature. Bulk effects, such as viscosity, depend on the local shear rates and on the size of the vessels. While empirical descriptions of bulk rheology are available for…
During epithelial wound healing, cell morphology near the healed wound and the healing rate vary strongly among different developmental stages even for a single species like \textit{Drosophila}. We develop deformable particle (DP) model…
In preimplantation mammalian embryos, the second cell fate decision introduces spatial patterns of embryonic and extra-embryonic precursor cells. The transcription factors NANOG and GATA6 are the earliest markers for the two cell types and…
Spatial models where growth is limited to the edge of the expansions have been instrumental to understand the population dynamics and the clone size distribution in growing cellular populations, such as microbial colonies and avascular…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
Visual observation of Cumulus Oocyte Complexes provides only limited information about its functional competence, whereas the molecular evaluations methods are cumbersome or costly. Image analysis of mammalian oocytes can provide attractive…
The fundamental understanding of how cells physically interact with each other and their environment is key to understanding their organisation in living tissues. Over the past decades several computational methods have been developed to…