Related papers: Simulation of morphogen and tissue dynamics
Fibrous dysplasia (FD) is a mosaic non-inheritable genetic disorder of the skeleton in which normal bone is replaced by structurally unsound fibro-osseous tissue. There is no curative treatment for FD, partly because its pathophysiology is…
This study presents an internalized morphogenesis model for autonomous systems, such as swarm robotics and micro-nanomachines, that eliminates the need for external spatial computation. Traditional self-organizing models often require…
In this paper I present a first attempt for a possible description of fluids dynamics by mean of a cellular automata technique. With the use of simple and elementary rules, based on random behaviour either, the model permits to obtain the…
A limited mobility nonequilibrium solid-on-solid dynamical model for kinetic surface growth is introduced as a simple description for the morphological evolution of a growing interface under random vapor deposition and surface diffusion…
During the last decades, medical observations and multiscale data concerning tumor growth are mounting. At the same time, contemporary imaging techniques well established in clinical practice, provide a variety of information on real-time,…
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…
This article presents formalistic tool for description of structural and biochemical relations between cells in the course of development of the body of plants. This is flexible formalistic space, based on the Category theory and the Petri…
We propose a modelling framework to analyse the stochastic behaviour of heterogeneous, multi-scale cellular populations. We illustrate our methodology with a particular example in which we study a population with an oxygen-regulated…
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of…
Morphogenesis is the process whereby the body of an organism develops its target shape. The morphogen BMP is known to play a conserved role across bilaterian organisms in determining the dorsoventral (DV) axis. Yet, how BMP governs the…
This paper proposes a single form for statistical models that accommodates a broad range of models, from ordinary least squares to agent-based microsimulations. The definition makes it almost trivial to define morphisms to transform and…
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…
Growth-fragmentation processes describe the evolution of systems of cells which grow continuously and fragment suddenly; they are used in models of cell division and protein polymerisation. Typically, we may expect that in the long run, the…
The orientation of cell division is a major determinant of three-dimensional plant morphogenesis. Whether and how a simple division orientation rule explains the establishment of symmetric body plans is a fundamental question. Testing such…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
We argue that embryological morphogenesis provides a model of how massive swarms of microscopic agents can be coordinated to assemble complex, multiscale hierarchical structures. This is accomplished by understanding natural morphogenetic…
Spatial distributions of morphogens provide positional information in developing systems, but how the distributions are established and maintained remains an open problem. Transport by diffusion has been the traditional mechanism, but…
We use a Convolutional Recurrent Neural Network approach to learn morphological evolution driven by surface diffusion. To this aim we first produce a training set using phase field simulations. Intentionally, we insert in such a set only…
Recent advancements in the ability to construct three-dimensional (3D) tissues and organoids from stem cells and biomaterials have not only opened abundant new research avenues in disease modeling and regenerative medicine but also have…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…