Related papers: Mesoscopic modelling of epithelial tissues
This study integrates pedestrian flow characteristics to formulate a mesoscopic cellular automata model tailored for simulating evacuations in large-scale scenarios. Departing from the conventional planar grid cell division, the model…
A powerful experimental approach for investigating computation in networks of biological neurons is the use of cultured dissociated cortical cells grown into networks on a multi-electrode array. Such preparations allow investigation of…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
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.…
During morphogenesis, the shape of a tissue emerges from collective cellular behaviors, which are in part regulated by mechanical and biochemical interactions between cells. Quantification of force and stress is therefore necessary to…
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on…
Model biomembrane systems play a crucial role in advancing biomedical research by providing simplified yet effective platforms for exploring complex biological mechanisms. These systems span a wide range of scales, from…
One of the most important issue in soft tissue modeling is to assess the quality of the simulations. A validation protocol is presented based on two CT scans of the patient acquired before and after cranio-maxillofacial surgery. The actual…
We discuss the role coarse-grained models play in the investigation of the structure and thermodynamics of bilayer membranes, and we place them in the context of alternative approaches. Because they reduce the degrees of freedom and employ…
Most biological tissues grow by the synthesis of new material close to the tissue's interface, where spatial interactions can exert strong geometric influences on the local rate of growth. These geometric influences may be mechanistic, or…
The simulation of morphogenetic problems requires the simultaneous and coupled simulation of signalling and tissue dynamics. A cellular resolution of the tissue domain is important to adequately describe the impact of cell-based events,…
In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing…
Understanding cell fate patterning and morphogenesis in the mammalian embryo remains a formidable challenge. Recently, in vivo models based on embryonic stem cells (ESCs) have emerged as complementary methods to quantitatively dissect the…
Recent advances in electron microscopy have enabled the imaging of single cells in 3D at nanometer length scale resolutions. An uncharted frontier for in silico biology is the ability to simulate cellular processes using these observed…
Simulation models are an absolute necessity in the human and social sciences, which can only very exceptionally use experimental science methods to construct their knowledge. Models enable the simulation of social processes by replacing the…
We introduce an Active Vertex Model (AVM) for cell-resolution studies of the mechanics of confluent epithelial tissues consisting of tens of thousands of cells, with a level of detail inaccessible to similar methods. The AVM combines the…
Tissue homeostasis, the biological process of maintaining a steady state in tissue via control of cell proliferation, death, and metabolic function, is essential for the development, growth, maintenance, and proper function of living…
Cross-sections of cell shapes in a tissue monolayer typically resemble a tiling of convex polygons. Yet, examples exist where the polygons are not convex with curved cell-cell interfaces, as seen in the adaxial epidermis. To date,…
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…