Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 1904.13009

Collective dynamics and self-organization of active particles on random networks

Hanqing Nan·Yu Zheng·Shaohua Chen·Christopher Eddy·Jianxiang Tian·Wenxiang Xu·Bo Sun·Yang Jiao
View original source ↗Read source document ↗Export metadata ↓

Abstract

Collective cell migration in 3D extracellular matrix (ECM) is crucial to many physiological and pathological processes. Migrating cells can generate active pulling forces via actin filament contraction, which are transmitted to the ECM fibers and lead to a dynamically evolving force network in the system. Here, we elucidate the role of such force network in regulating collective cell behaviors using a minimal active-particle-on-network (APN) model, in which active particles can pull the fibers and hop between neighboring nodes of the network following local durotaxis. Our model reveals a dynamic transition as the particle number density approaches a critical value, from an "absorbing" state containing isolated stationary small particle clusters, to a "active" state containing a single large cluster undergone constant dynamic reorganization. This reorganization is dominated by a subset of highly dynamic "radical" particles in the cluster, whose number also exhibits a transition at the same critical density. The transition is underlaid by the percolation of "influence spheres" due to the particle pulling forces. Our results suggest a robust mechanism based on ECM-mediated mechanical coupling for collective cell behaviors in 3D ECM.

Explore related subjects

physics.bio-phcond-mat.softq-bio.CB

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Hanqing Nan, Yu Zheng, Shaohua Chen, Christopher Eddy, Jianxiang Tian, Wenxiang Xu, Bo Sun, Yang Jiao. 2019-04-26. Collective dynamics and self-organization of active particles on random networks. https://arxiv.org/abs/1904.13009

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Signature of mechanically induced cell extrusions in cell size distribution

How a growing tissue organizes its own homeostatic state is a central question in the physics of living matter. We show that when a growing epithelial sheet counteracts increasing cell density by mechanically squeezing cells out of its plane, a homeostatic in-plane pressure emerges as a generalization of a yield stress. We find that in the quasistatic growth limit the homeostatic state is marginally stable, with a pseudogap in the distribution of local distances to the extrusion threshold pressure. Because such mechanically induced extrusions arise from an instability of individual cells, the pseudogap is imprinted in the distribution of cell areas. This provides an image-based way to test for presence of mechanically induced extrusions and we identify this signature in the developing wing epithelium of \textit{D.~melanogaster}. We expect the same principles to apply to confined three-dimensional tissues.

physics.bio-ph↗
arXiv2026

Towards Accurate Prediction of Mutation-Induced Changes in Protein Structure

Proteins can possess numerous mutations relative to their wild-type amino acid sequences with minimal impact to their structure and function. However, in other cases, even a single amino acid mutation relative to the wild-type sequence can lead to a large change in structure or even a disease phenotype. While the accuracy of wild-type protein structure prediction has improved significantly in recent years, it remains difficult to accurately predict the structure of mutant proteins. Here, we characterize the local mutation-induced structural changes in proteins for a dataset of wildtype and the corresponding single-amino acid mutant x-ray crystal structures from the Protein Data Bank (PDB). We find that mutation-induced structural changes in these proteins are localized at the site of the mutation, decaying rapidly with increasing spatial distance from the mutation site. In addition, we evaluate how well AlphaFold3 can recapitulate the observed mutation-induced structural deformations in the x-ray crystal structures. We find that the accuracy of the AlphaFold3 predictions decreases strongly with increasing mutation-induced deformation. In contrast to the results for AlphaFold3, the Pearson correlation between a single physical feature, i.e. the change in solvent accessibility, and the mutation-induced deformation does not depend on the magnitude of the deformation. Our results and analyses provide a framework for further studies aimed at predicting the structural changes in proteins caused by single amino acid mutations.

physics.bio-ph↗
arXiv2026

Biology and Physics

This article frames the relation between biology and physics by characterizing the former as a subdiscipline rather than a special case of the latter. To do this, we posit biological physics as the science of living matter in contrast to classic biophysics, the study of organismal properties by physical techniques. At the scale of the individual cell, living matter is nonunitary, i.e., not composed of aggregated subunits, and has features (e.g., intracellular organizational arrangements and biomolecular condensates) that are unlike any materials of the nonliving world. In transiently or constitutively multicellular forms (social microorganisms, animals, plants), living matter sustains physical processes that are generic (shared with nonliving matter, e.g., subunit communication by molecular diffusion in cellular slime molds), biogeneric (analogous to nonliving matter but realized through cellular activities, e.g., subunit demixing in animal embryos) or nongeneric (pertaining to sui generis materials, e.g., budding of active solids in plants). This "forms of matter" perspective is philosophically situated in the dialectical materialism of Engels and Hessen and the multilevel physicalism of Neurath and the logical empiricists. We counterpose this view to informationism and to genetic and other hierarchically reductionist physical theories of biological systems and highlight open questions regarding incompletely characterized and enigmatic forms of living matter.

physics.bio-ph↗