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

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

4
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
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

9
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

1
A Review of Advances in Molecular Imaging of Rheumatoid Arthritis: From In Vitro to Clinic Applications Using Radiolabeled Targeting Vectors with Technetium-99m DOI Creative Commons
Muhammad Ali, Viviana Benfante, Domenico Di Raimondo

et al.

Life, Journal Year: 2024, Volume and Issue: 14(6), P. 751 - 751

Published: June 12, 2024

Rheumatoid arthritis (RA) is a systemic autoimmune disorder caused by inflammation of cartilaginous diarthrodial joints that destroys and cartilage, resulting in synovitis pannus formation. Timely detection effective management RA are pivotal for mitigating inflammatory consequences, potentially influencing disease progression. Nuclear medicine using radiolabeled targeted vectors presents promising avenue diagnosis response to treatment assessment. Radiopharmaceutical such as technetium-99m (

Language: Английский

Citations

4
Two Decades of Advances and Limitations in Organ Recellularization DOI Creative Commons
Alina Stoian,

Aisha Adil,

Felor Biniazan

et al.

Current Issues in Molecular Biology, Journal Year: 2024, Volume and Issue: 46(8), P. 9179 - 9214

Published: Aug. 22, 2024

The recellularization of tissues after decellularization is a relatively new technology in the field tissue engineering (TE). Decellularization involves removing cells from or organ, leaving only extracellular matrix (ECM). This can then be recellularized with to create functional organs. first significant mention decellularized traced research conducted early 2000s. One landmark studies this was published 2008 by Ott, where researchers demonstrated rat heart cardiac cells, resulting organ capable contraction. Since then, other important have been published. These paved way for widespread application TE, demonstrating potential ECM serve as scaffold regenerating tissues. Thus, although concept initially explored previous decades, these 2000s marked major turning point development and practical article reviews historical advances limitations TE over last two decades.

Language: Английский

Citations

3
Spatial interactions modulate tumor growth and immune infiltration DOI Creative Commons
Sadegh Marzban, Sonal Srivastava,

Sharon Kartika

et al.

npj Systems Biology and Applications, Journal Year: 2024, Volume and Issue: 10(1)

Published: Sept. 30, 2024

Language: Английский

Citations

3
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
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