scholarly journals Large-scale simulations of biological cell sorting driven by differential adhesion follow diffusion-limited domain coalescence regime

2021 ◽  
Vol 17 (8) ◽  
pp. e1008576
Author(s):  
Marc Durand
Keyword(s):  
Cell Sorting ◽  
Large Scale ◽  
Domain Size ◽  
Cellular Potts Model ◽  
Mixture Ratio ◽  
Cell Behaviors ◽  
Differential Adhesion ◽  
Interfacial Energies ◽  
Diffusion Limited ◽  
Medium Increase

Cell sorting, whereby a heterogeneous cell mixture segregates and forms distinct homogeneous tissues, is one of the main collective cell behaviors at work during development. Although differences in interfacial energies are recognized to be a possible driving source for cell sorting, no clear consensus has emerged on the kinetic law of cell sorting driven by differential adhesion. Using a modified Cellular Potts Model algorithm that allows for efficient simulations while preserving the connectivity of cells, we numerically explore cell-sorting dynamics over very large scales in space and time. For a binary mixture of cells surrounded by a medium, increase of domain size follows a power-law with exponent n = 1/4 independently of the mixture ratio, revealing that the kinetics is dominated by the diffusion and coalescence of rounded domains. We compare these results with recent numerical studies on cell sorting, and discuss the importance of algorithmic differences as well as boundary conditions on the observed scaling.

scholarly journals Large-scale simulations of biological cell sorting driven by differential adhesion follow diffusion-limited domain coalescence regime

2020 ◽  
Author(s):  
Marc Durand
Keyword(s):  
Cell Sorting ◽  
Large Scale ◽  
Experimental Studies ◽  
Finite Size ◽  
Domain Size ◽  
Cellular Potts Model ◽  
Mixture Ratio ◽  
Cell Behaviors ◽  
Differential Adhesion ◽  
Initial Cluster

Cell sorting, whereby a heterogeneous cell mixture segregates and forms distinct homogeneous tissues, is one of the main collective cell behaviors at work during development. Although differences in interfacial energies are recognized to be a possible driving source for cell sorting, no clear consensus has emerged on the kinetic law of cell sorting driven by differential adhesion. Using a modified Cellular Potts Model algorithm that allows for efficient simulations while preserving the connectivity of cells, we numerically explore cell-sorting dynamics over unprecedentedly large scales in space and time. For a binary mixture of cells surrounded by a medium, increase of domain size follows a power-law with exponent n = 1/4 independently of the mixture ratio, revealing that the kinetics is dominated by the diffusion and coalescence of rounded domains. We compare these results with recent numerical and experimental studies on cell sorting, and discuss the importance of boundary conditions, space dimension, initial cluster geometry, and finite size effects on the observed scaling.

scholarly journals Self-* properties through gossiping

2008 ◽  
Vol 366 (1881) ◽  
pp. 3747-3757 ◽  
Author(s):  
Ozalp Babaoglu ◽  
Márk Jelasity
Keyword(s):  
Cell Sorting ◽  
Mobile Agents ◽  
Large Scale ◽  
Overlay Networks ◽  
Biological Mechanism ◽  
Human Intervention ◽  
Differential Adhesion ◽  
Novel Approach ◽  
Large Numbers ◽  
Ubiquitous Systems

As computer systems have become more complex, numerous competing approaches have been proposed for these systems to self-configure, self-manage, self-repair, etc. such that human intervention in their operation can be minimized. In ubiquitous systems, this has always been a central issue as well. In this paper, we overview techniques to implement self-* properties in large-scale, decentralized networks through bio-inspired techniques in general, and gossip-based algorithms in particular. We believe that gossip-based algorithms could be an important inspiration for solving problems in ubiquitous computing as well. As an example, we outline a novel approach to arrange large numbers of mobile agents (e.g. vehicles, rescue teams carrying mobile devices) into different formations in a totally decentralized manner. The approach is inspired by the biological mechanism of cell sorting via differential adhesion, as well as by our earlier work in self-organizing peer-to-peer overlay networks.

scholarly journals Computer Simulations of Cell Sorting Due to Differential Adhesion

PLoS ONE ◽  
2011 ◽  
Vol 6 (10) ◽  
pp. e24999 ◽  
Author(s):  
Ying Zhang ◽  
Gilberto L. Thomas ◽  
Maciej Swat ◽  
Abbas Shirinifard ◽  
James A. Glazier
Keyword(s):  
Computer Simulations ◽  
Cell Sorting ◽  
Differential Adhesion

scholarly journals Large-scale immuno-magnetic cell sorting of T cells based on a self-designed high-throughput system for potential clinical application

Nanoscale ◽  
2017 ◽  
Vol 9 (36) ◽  
pp. 13592-13599 ◽  
Author(s):  
Qian Zhang ◽  
Ting Yin ◽  
Rongrong Xu ◽  
Wenjun Gao ◽  
Hui Zhao ◽  
...  
Keyword(s):  
T Cells ◽  
Clinical Application ◽  
High Throughput ◽  
Cell Sorting ◽  
Large Scale ◽  
Magnetic Cell Sorting ◽  
Potential Clinical Application

A self-designed high-throughput system has been developed for large-scale immuno-magnetic cell sorting of different T cells.

scholarly journals Hypoxia triggers collective aerotactic migration in Dictyostelium discoideum

2020 ◽  
Author(s):  
O. Cochet-Escartin ◽  
M. Demircigil ◽  
S. Hirose ◽  
B. Allais ◽  
P. Gonzalo ◽  
...  
Keyword(s):  
Dictyostelium Discoideum ◽  
Cell Communication ◽  
Quantitative Agreement ◽  
Cellular Potts Model ◽  
Detection Mechanism ◽  
Cell Behaviors ◽  
Dense Ring ◽  
Efficient Detection ◽  
Technological Developments ◽  
A Cell

AbstractIt is well known that eukaryotic cells can sense oxygen (O2) and adapt their metabolism accordingly. It is less known that they can also move towards regions of higher oxygen level (aerotaxis). Using a self-generated hypoxic assay, we show that the social amoeba Dictyostelium discoideum displays a spectacular aerotactic behavior. When a cell colony is covered by a coverglass, cells quickly consume the available O2 and the ones close to the periphery move directionally outward forming a dense ring keeping a constant speed and density. To confirm that O2 is the main molecular player in this seemingly collective process, we combined two technological developments, porphyrin based O2 sensing films and microfluidic O2 gradient generators. We showed that Dictyostelium cells exhibit aerotactic and aerokinetic (increased speed at low O2) response in an extremely low range of O2 concentration (0-1.5%) indicative of a very efficient detection mechanism. The various cell behaviors under self-generated or imposed O2 gradients were modeled with a very satisfactory quantitative agreement using an in silico cellular Potts model built on experimental observations. This computational model was complemented with a parsimonious ‘Go or Grow’ partial differential equation (PDE) model. In both models, we found that the collective migration of a dense ring can be explained by the interplay between cell division and the modulation of aerotaxis, without the need for cell-cell communication.

scholarly journals Deconstructing Gastrulation at the Single Cell Level

2021 ◽  
Author(s):  
Tomer Stern ◽  
Sebastian J Streichan ◽  
Stanislav Y Shvartsman ◽  
Eric F Wieschaus
Keyword(s):  
Large Scale ◽  
Drosophila Embryo ◽  
Cell Segmentation ◽  
Model Organisms ◽  
Specific Cell ◽  
Cell Behaviors ◽  
Animal Development ◽  
Wide Range ◽  
Cell Groups ◽  
Epithelial Sheets

Gastrulation movements in all animal embryos start with regulated deformations of patterned epithelial sheets. Current studies of gastrulation use a wide range of model organisms and emphasize either large-scale tissue processes or dynamics of individual cells and cell groups. Here we take a step towards bridging these complementary strategies and deconstruct early stages of gastrulation in the entire Drosophila embryo, where transcriptional patterns in the blastoderm give rise to region-specific cell behaviors. Our approach relies on an integrated computational framework for cell segmentation and tracking and on efficient algorithms for event detection. Our results reveal how thousands of cell shape changes, divisions, and intercalations drive large-scale deformations of the patterned blastoderm, setting the stage for systems-level dissection of a pivotal step in animal development.

Study of Wake Profiles of a Simplified Model of High Speed Train Using RANS and LES Turbulent Models

2014 ◽  
Vol 629 ◽  
pp. 426-430
Author(s):  
Sufiah Mohd Salleh ◽  
Mohamed Sukri Mat Ali ◽  
Sheikh Ahmad Zaki Shaikh Salim ◽  
Sallehuddin Muhamad ◽  
Muhammad Iyas Mahzan
Keyword(s):  
High Speed ◽  
Large Scale ◽  
Sudden Change ◽  
Domain Size ◽  
Recirculation Region ◽  
Bluff Bodies ◽  
Computational Domain ◽  
High Speed Train ◽  
Free Shear Layer ◽  
Turbulent Models

Flow structure over bluff bodies is more complex in wake. The wake is characterized by the unsteady behavior of the flow, large scale turbulent structure and strong recirculation region. For the case of high speed train, wake can be observed at the gap between the coaches and also on the rear coach. Wakes formation of high speed train are generated by free shear layer that is originated from the flow separation due to the sudden change in geometry. RANS and LES turbulent models are used in this paper to stimulate the formation of wakes and behavior of the flow over a simplified high speed train model. This model consists of two coaches with the gap between them is 0.5D. A total of four simulations have been made to study the effect of computational domain size and grid resolution on wake profiles of a simplified high speed train. The result shows that the computational domain can be reduced by decreasing the ground distance to 1.5D without affecting the magnitude of the wake profile. Both RANS and LES can capture the formation of the wake, but LES requires further grid refinement as the results between the two grid resolutions are grid dependent.

scholarly journals Model-Based Prediction of an Effective Adhesion Parameter Guiding Multi-Type Cell Segregation

Entropy ◽  
2021 ◽  
Vol 23 (11) ◽  
pp. 1378
Author(s):  
Philipp Rossbach ◽  
Hans-Joachim Böhme ◽  
Steffen Lange ◽  
Anja Voss-Böhme
Keyword(s):  
Cell Sorting ◽  
Cell Types ◽  
Series Data ◽  
Analytical Prediction ◽  
Differential Migration ◽  
Migration Model ◽  
Differential Adhesion ◽  
Cell Segregation ◽  
Differential Adhesion Hypothesis ◽  
The Impact

The process of cell-sorting is essential for development and maintenance of tissues. Mathematical modeling can provide the means to analyze the consequences of different hypotheses about the underlying mechanisms. With the Differential Adhesion Hypothesis, Steinberg proposed that cell-sorting is determined by quantitative differences in cell-type-specific intercellular adhesion strengths. An implementation of the Differential Adhesion Hypothesis is the Differential Migration Model by Voss-Böhme and Deutsch. There, an effective adhesion parameter was derived analytically for systems with two cell types, which predicts the asymptotic sorting pattern. However, the existence and form of such a parameter for more than two cell types is unclear. Here, we generalize analytically the concept of an effective adhesion parameter to three and more cell types and demonstrate its existence numerically for three cell types based on in silico time-series data that is produced by a cellular-automaton implementation of the Differential Migration Model. Additionally, we classify the segregation behavior using statistical learning methods and show that the estimated effective adhesion parameter for three cell types matches our analytical prediction. Finally, we demonstrate that the effective adhesion parameter can resolve a recent dispute about the impact of interfacial adhesion, cortical tension and heterotypic repulsion on cell segregation.

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