Cell shape and forces in elastic and structured environments: from single cells to organoids

R Link, K Weißenbruch, M Tanaka… - Advanced Functional …, 2024 - Wiley Online Library
With the advent of mechanobiology, cell shape and forces have emerged as essential
elements of cell behavior and fate, in addition to biochemical factors such as growth factors …

Shaping the organ: a biologist guide to quantitative models of plant morphogenesis

M Marconi, K Wabnik - Frontiers in plant science, 2021 - frontiersin.org
Organ morphogenesis is the process of shape acquisition initiated with a small reservoir of
undifferentiated cells. In plants, morphogenesis is a complex endeavor that comprises a …

Tissue forge: interactive biological and biophysics simulation environment

TJ Sego, JP Sluka, HM Sauro… - PLOS Computational …, 2023 - journals.plos.org
Tissue Forge is an open-source interactive environment for particle-based physics,
chemistry and biology modeling and simulation. Tissue Forge allows users to create …

[HTML][HTML] Digitize your Biology! Modeling multicellular systems through interpretable cell behavior

JAI Johnson, GL Stein-O'Brien, M Booth, R Heiland… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Cells are fundamental units of life, constantly interacting and evolving as dynamical systems.
While recent spatial multi-omics can quantitate individual cells' characteristics and …

Computational approaches for simulating luminogenesis

K Fuji, S Tanida, M Sano, M Nonomura… - Seminars in Cell & …, 2022 - Elsevier
Lumens, liquid-filled cavities surrounded by polarized tissue cells, are elementary units
involved in the morphogenesis of organs. Theoretical modeling and computations, which …

Matrix obstructions cause multiscale disruption in collective epithelial migration by suppressing leader cell function

YL Lee, J Mathur, C Walter, H Zmuda… - Molecular biology of the …, 2023 - Am Soc Cell Biol
During disease and development, physical changes in extracellular matrix cause jamming,
unjamming, and scattering in epithelial migration. However, whether disruptions in matrix …

Long-term adherent cell dynamics emerging from energetic and frictional interactions at the interface

S Okuda, T Hiraiwa - Physical Review E, 2023 - APS
Cell adhesion plays an important role in a wide range of biological situations, including
embryonic development, cancer invasion, and wound healing. Although several …

Biological multiscale computational modeling: A promising tool for 3D bioprinting and tissue engineering

BC dos Santos, PY Noritomi, JVL da Silva, IA Maia… - Bioprinting, 2022 - Elsevier
The progress of three-dimensional (3D) bioprinting techniques has driven several advances
in tissue engineering (TE), which allow the obtention of biological constructs analogous to …

Stochastic pursuit-evasion curves for foraging dynamics

K Toman, NK Voulgarakis - Physica A: Statistical mechanics and its …, 2022 - Elsevier
Many predator species attempt to locate prey by following seemingly random paths.
Although the underlying physical mechanism of the search remains largely unknown, such …

PI3K inhibition reverses migratory direction of single cells but not cell groups in electric field

Y Sun, H Yue, C Copos, K Zhu, Y Zhang, Y Sun, X Gao… - Biorxiv, 2020 - biorxiv.org
Motile cells migrate directionally in the electric field in a process known as galvanotaxis.
Galvanotaxis is important in wound healing, development, cell division, and nerve growth …