The Cellular Potts Model on Disordered Lattices DOI Creative Commons
Hossein Nemati, Joost de Graaf

Soft Matter, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

The cellular Potts model, also known as the Glazier-Graner-Hogeweg is a lattice-based approach by which biological tissues at level of individual cells can be numerically studied. Traditionally, square or hexagonal underlying lattice structure assumed for two-dimensional systems, and this to introduce artifacts in dynamics model tissues. That is, on regular lattices, assume shapes that are dictated symmetries lattice. Here, we developed variant method applied broad class (ir)regular lattices. We show an irregular deriving from fluid-like configuration, two types removed. further report transition between disordered solid-like hexagonally ordered phase present monodisperse confluent function their surface tension. This shows hallmarks first-order different glass/jamming transitions commonly reported vertex active Voronoi models. emphasize analyzing distribution shape parameters found our state space. Our analysis provides useful reference future study epithelia using model.

Language: Английский

Biochemical and Biophysical Cues of The Extracellular Matrix Modulates Stem Cell Fate: Progress and Prospect in Extracellular Matrix Mimicking Biomaterials DOI Creative Commons
Anil K. Mishra, Unnati Modi, Rahul Sharma

et al.

Biomedical Engineering Advances, Journal Year: 2025, Volume and Issue: unknown, P. 100143 - 100143

Published: Jan. 1, 2025

Language: Английский

Citations

3
Mechanical signatures in cancer metastasis DOI Creative Commons
Ayushi Agrawal,

Yousef Javanmardi,

Sara A. Watson

et al.

npj Biological Physics and Mechanics., Journal Year: 2025, Volume and Issue: 2(1)

Published: Feb. 4, 2025

Abstract The cancer metastatic cascade includes a series of mechanical barrier-crossing events, involving the physical movement cells from their primary location to distant organ. This review describes changes that influence tumour proliferation, progression, and metastasis. We identify potential signatures at every step discuss some latest mechanobiology-based therapeutic interventions highlight importance interdisciplinary approaches in diagnosis treatment.

Language: Английский

Citations

3
A Simple Framework for Agent-Based Modeling with Extracellular Matrix DOI Creative Commons
John Metzcar, Ben Duggan,

Brandon Fischer

et al.

Bulletin of Mathematical Biology, Journal Year: 2025, Volume and Issue: 87(3)

Published: Feb. 12, 2025

Abstract Extracellular matrix (ECM) is a key component of the cellular microenvironment and critical in multiple disease developmental processes. Representing ECM cell-ECM interactions challenging multiscale problem as they span molecular-level details to tissue-level dynamics. While several computational frameworks exist for modeling, often focus on very detailed modeling individual fibers or represent only single aspect ECM. Using PhysiCell agent-based platform, we developed framework intermediate detail with ability capture bidirectional interactions. We small region ECM, an element, three variables describing its local microstructure: anisotropy, density, overall fiber orientation. To spatially model use array elements. Cells remodel microstructure turn, impacts motility. demonstrate utility this reusability core interaction through examples invasion, wound healing, basement membrane degradation, leader-follower collective migration. Despite relative simplicity framework, it able broad range interest community. Furthermore, representing are accessible simple programming interfaces. This allows them impact cell behaviors, such proliferation death, without requiring custom code each interaction, particularly PhysiCell’s grammar, enabling rapid diverse cell-matrix biology. make available free open source software package at https://github.com/PhysiCell-Models/collective-invasion .

Language: Английский

Citations

1
The next revolution in computational simulations: Harnessing AI and quantum computing in molecular dynamics DOI
Anna Lappala

Current Opinion in Structural Biology, Journal Year: 2024, Volume and Issue: 89, P. 102919 - 102919

Published: Sept. 21, 2024

Language: Английский

Citations

8
How cells align to structured collagen fibrils: a hybrid cellular Potts and molecular dynamics model with dynamic mechanosensitive focal adhesions DOI Creative Commons
Koen A.E. Keijzer, Erika Tsingos, Roeland M. H. Merks

et al.

Frontiers in Cell and Developmental Biology, Journal Year: 2025, Volume and Issue: 12

Published: Jan. 6, 2025

Many mammalian cells, including endothelial cells and fibroblasts, align elongate along the orientation of extracellular matrix (ECM) fibers in a gel when cultured vitro. During cell elongation, clusters focal adhesions (FAs) form near poles elongating cells. FAs are mechanosensitive that grow under mechanical tension exerted by cells' pulling on ECM shrink is released. In this study, we use mathematical modeling to study hypothesis reciprocity between sufficient for directing shape changes orientation. We show preferentially stabilized fibers, where can generate higher than directions perpendicular fibers. present hybrid computational model coupling three approaches: first, cellular Potts (CPM) describes an individual contractile cell; second, molecular dynamics (MD) represent as network cross-linked, deformable fibers; third, set ordinary differential equations (ODEs) cell's FAs, terms balance assembly mechanoresponsive disassembly. The resulting shows suffices stiffness-dependent spreading, local remodeling, ECM-alignment-dependent elongation. These combined effects explain how morphology influenced structure mechanics.

Language: Английский

Citations

0
Outside influences: The impact of extracellular matrix mechanics on cell migration DOI
Ronen Zaidel‐Bar, Priti Agarwal

Current topics in developmental biology/Current Topics in Developmental Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

Citations

0
A hybrid computational model of cancer spheroid growth with ribose-induced collagen stiffening DOI Creative Commons

Margherita Botticelli,

John Metzcar,

Thomas Phillips

et al.

Frontiers in Bioengineering and Biotechnology, Journal Year: 2025, Volume and Issue: 13

Published: April 9, 2025

Metastasis, the leading cause of death in cancer patients, arises when cells disseminate from a primary solid tumour to distant organs. Growth and invasion often involve collective cell migration, which is profoundly influenced by cell-cell interactions extracellular matrix (ECM). The ECM's biochemical composition mechanical properties, such as stiffness, regulate behaviour migration dynamics. Mathematical modelling serves pivotal tool for studying predicting these complex dynamics, with hybrid discrete-continuous models offering powerful approach combining agent-based representations continuum descriptions surrounding microenvironment. In this study, we investigate impact ECM modulated via ribose-induced collagen cross-linking, on spheroid growth invasion. We employed model implemented PhysiCell simulate successfully replicating three-dimensional vitro experiments. incorporates detailed cell-ECM interactions, remodelling, proliferation. Our simulations align experimental observations two breast lines, non-invasive MCF7 invasive HCC 1954, under varying stiffness conditions. results demonstrate that increased due cross-linking inhibits cells, whereas remain largely unaffected. Furthermore, our show higher degradation not only enables but also facilitates formation multicellular protrusions. Conversely, increasing maximum speed can reach enhances while promoting single-cell This understanding interplay between proliferation, paving way future studies incorporating additional characteristics microenvironmental

Language: Английский

Citations

0
PhysiMeSS - a new physiCell addon for extracellular matrix modelling DOI Creative Commons
Vincent Noël, Marco Ruscone, Robyn Shuttleworth

et al.

Gigabyte, Journal Year: 2024, Volume and Issue: 2024

Published: Oct. 16, 2024

The extracellular matrix, composed of macromolecules like collagen fibres, provides structural support to cells and acts as a barrier that metastatic degrade spread beyond the primary tumour. While agent-based frameworks, such PhysiCell, can simulate spatial dynamics tumour evolution, they only implement circles (2D) or spheres (3D). To model matrix network we require new type agent represented by line segments cylinders Here, present PhysiMeSS, an addon introducing describe fibres their physical interactions with other fibres. PhysiMeSS implementation is available at https://github.com/PhysiMeSS/PhysiMeSS in official PhysiCell repository. We provide examples describing possibilities this framework. This tool may help tackle important biological questions, diseases linked dysregulation processes leading cancer metastasis.

Language: Английский

Citations

3
Collective Transitions from Orbiting to Matrix Invasion in 3D Multicellular Spheroids DOI Creative Commons
Jiwon Kim, Hee-Won Jeong, Carles Falcó

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 11, 2025

Coordinated cell rotation along a curved matrix interface can sculpt epithelial tissues into spherical morphologies. Subsequently, radially-oriented invasion of multicellular strands or branches occur by local remodeling the confining matrix. These symmetry-breaking transitions emerge from dynamic reciprocity between cells and matrix, but remain poorly understood. Here, we show that spheroids collectively transition circumferential orbiting to radial via bi-directional interactions with surrounding curvature. Initially, exhibit an ellipsoidal shape become rounded as occurs. However, gradually reorient coordinated towards outward strand due accumulation contractile tractions at discrete sites. Remarkably, initial ellipsoid morphology predicts subsequent 2-4 roughly aligned major axis. We then perturb collective migration using osmotic pressure, showing be arrested reversed. also investigate in "mosaic" spheroids, small fraction "leader" weakened cell-cell adhesions impede still invade Finally, establish minimal self-propelled particle model elucidate how is mediated crosstalk cell-matrix adhesion boundary. Altogether, this work elucidates tissue morphogenesis governed interplay behaviors curvature cell-matrix, relevance for embryonic development tumor progression.

Language: Английский

Citations

0
Existence of weak solutions for a volume-filling model of cell invasion into extracellular matrix DOI Creative Commons
Rebecca M. Crossley, Jan‐Frederik Pietschmann, Markus Schmidtchen

et al.

Journal of Differential Equations, Journal Year: 2025, Volume and Issue: 428, P. 721 - 746

Published: Feb. 14, 2025

Language: Английский

Citations

0