{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T18:26:44Z","timestamp":1787164004765,"version":"build-2736575974"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013698","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:00:00Z","timestamp":1787097600000}}],"reference-count":79,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["492009575"],"award-info":[{"award-number":["492009575"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"\n In vitro<\/jats:italic>\n colonies of the unicellular parasite\n Trypanosoma brucei<\/jats:italic>\n expand radially and establish fingering instabilities, a collective behavior known as social motility. The underlying mechanisms are thought to involve single-cell motility, chemical communication among cells, and mechanical interactions with the liquid boundary, but their relative contributions remain unclear. We aimed to determine which of the mechanisms are necessary to quantitatively reproduce the morphological characteristics of social motility. We developed a two-dimensional agent-based model that simulates colonies of\n \n \n \n \n \n \n 10<\/mml:mn>\n 5<\/mml:mn>\n <\/mml:msup>\n \u2212<\/mml:mo>\n \n 10<\/mml:mn>\n 6<\/mml:mn>\n <\/mml:msup>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n cells at single-cell resolution\u2014two to four orders of magnitude larger than previous models. Cells are represented as point particles executing directional random walks with auto-chemotactic alignment and exponential colony growth. The colony boundary is modelled using a grid-based approach in which interactions with agents can locally weaken and expand it. The model was quantitatively evaluated by applying our previously established morphology metrics. We show quantitative agreement of the simulation results and experimental data in terms of colony morphology. Parameter exploration revealed that finger formation arises within a narrow range of trypanosome motility parameters that balance stochasticity and alignment, while boundary conditions modulate the speed of colony expansion. The diffusion coefficient of the chemotactic signal is the key determinant of pattern formation. Realistic behavior occurs at\n \n \n \n \n \n 2<\/mml:mn>\n \u00d7<\/mml:mo>\n \n 10<\/mml:mn>\n \n \u2212<\/mml:mo>\n 11<\/mml:mn>\n <\/mml:mrow>\n <\/mml:msup>\n <\/mml:mrow>\n <\/mml:math>\n <\/jats:alternatives>\n <\/jats:inline-formula>\n \u2013 10\n -10<\/jats:sup>\n m\n 2<\/jats:sup>\n \/s which corresponds to molecules of 12.1\u20131690 kDa. These results demonstrate that complex colony morphologies can emerge from minimal cell-level rules, suggesting testable hypotheses for the molecular drivers of trypanosome social motility. Furthermore, our approach provides a framework for dissecting the interplay between motility, signaling, and mechanical confinement in other microbial systems exhibiting collective behavior.\n <\/jats:p>","DOI":"10.1371\/journal.pcbi.1013698","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T17:46:21Z","timestamp":1786556781000},"page":"e1013698","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["An agent-based model of Trypanosoma brucei social motility to explore determinants of colony pattern 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Oberholzer","year":"2010","journal-title":"PLoS Pathog"},{"issue":"10","key":"pcbi.1013698.ref002","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004493","article-title":"Social motility of African trypanosomes is a property of a distinct life-cycle stage that occurs early in tsetse fly transmission","volume":"10","author":"S Imhof","year":"2014","journal-title":"PLoS Pathog"},{"issue":"3","key":"pcbi.1013698.ref003","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01954-14","article-title":"Cyclic AMP regulates social behavior in African trypanosomes","volume":"6","author":"M Oberholzer","year":"2015","journal-title":"mBio"},{"issue":"3","key":"pcbi.1013698.ref004","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1140\/epje\/s10189-021-00052-7","article-title":"Single-cell motile behaviour of Trypanosomabrucei in thin-layered fluid collectives","volume":"44","author":"T Kr\u00fcger","year":"2021","journal-title":"Eur Phys J E Soft 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Kozlovsky","year":"1999","journal-title":"Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics"},{"issue":"6","key":"pcbi.1013698.ref022","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1098\/rsif.2005.0089","article-title":"Self-engineering capabilities of bacteria","volume":"3","author":"E Ben-Jacob","year":"2006","journal-title":"J R Soc Interface"},{"key":"pcbi.1013698.ref023","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1142\/S0218202511005428","article-title":"Multiscale modeling of Pseudomonas aeruginosa swarming","author":"H Du","year":"2011","journal-title":"Math Models Methods Appl Sci"},{"issue":"3","key":"pcbi.1013698.ref024","doi-asserted-by":"crossref","first-page":"031305","DOI":"10.1063\/5.0128140","article-title":"Swarming of P. aeruginosa: through the lens of biophysics","volume":"4","author":"J-L Bru","year":"2023","journal-title":"Biophys Rev (Melville)"},{"issue":"14","key":"pcbi.1013698.ref025","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2120508119","article-title":"A new mode of swimming in singly flagellated Pseudomonas aeruginosa","volume":"119","author":"M Tian","year":"2022","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"15","key":"pcbi.1013698.ref026","doi-asserted-by":"crossref","first-page":"4734","DOI":"10.1128\/AEM.01027-13","article-title":"Bacterial tethering analysis reveals a \u201crun-reverse-turn\u201d mechanism for Pseudomonas species motility","volume":"79","author":"C Qian","year":"2013","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"pcbi.1013698.ref027","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003967","article-title":"Simulating the complex cell design of Trypanosoma brucei and its motility","volume":"11","author":"D Alizadehrad","year":"2015","journal-title":"PLoS Comput 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Babu","year":"2012"},{"issue":"5","key":"pcbi.1013698.ref038","doi-asserted-by":"crossref","first-page":"056601","DOI":"10.1088\/0034-4885\/78\/5\/056601","article-title":"Physics of microswimmers - single particle motion and collective behavior","volume":"78","author":"J Elgeti","year":"2015","journal-title":"Rep Prog Phys"},{"issue":"42","key":"pcbi.1013698.ref039","doi-asserted-by":"crossref","first-page":"8590","DOI":"10.1039\/C8SM01390J","article-title":"Clustering of microswimmers: interplay of shape and hydrodynamics","volume":"14","author":"M Theers","year":"2018","journal-title":"Soft Matter"},{"issue":"1","key":"pcbi.1013698.ref040","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s42005-024-01587-9","article-title":"Collective motion in a sheet of microswimmers","volume":"7","author":"D B\u00e1rdfalvy","year":"2024","journal-title":"Commun 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Distributed parallelization of xpu stencil computations in julia; 2022."},{"key":"pcbi.1013698.ref049","article-title":"Computational fluid dynamics","author":"PJ Roache","year":"1976","journal-title":"Comput Fluid Dyn"},{"key":"pcbi.1013698.ref050","volume-title":"Computational fluid mechanics and heat transfer","author":"DA Anderson","year":"1997"},{"key":"pcbi.1013698.ref051","volume-title":"Computational fluid dynamics: principles and applications","author":"J Blazek","year":"2015"},{"key":"pcbi.1013698.ref052","first-page":"154","article-title":"Errors and an analysis of stability.","volume-title":"Computational fluid dynamics: the basics with applications","author":"D John","year":"1995"},{"key":"pcbi.1013698.ref053","volume-title":"Computational fluid dynamics: a practical approach","author":"J Tu","year":"2023"},{"key":"pcbi.1013698.ref054","article-title":"On-lattice Vicsek model in confined geometries","author":"A Kuhn","year":"2022","journal-title":"arXiv"},{"issue":"12","key":"pcbi.1013698.ref055","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0115893","article-title":"Generation of a nanobody targeting the paraflagellar rod protein of trypanosomes","volume":"9","author":"E Obishakin","year":"2014","journal-title":"PLoS One"},{"issue":"1","key":"pcbi.1013698.ref056","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1137\/141000671","article-title":"Julia: a fresh approach to numerical computing","volume":"59","author":"J Bezanson","year":"2017","journal-title":"SIAM Rev"},{"issue":"65","key":"pcbi.1013698.ref057","doi-asserted-by":"crossref","first-page":"3349","DOI":"10.21105\/joss.03349","article-title":"Makie.jl: Flexible high-performance data visualization for Julia","volume":"6","author":"S Danisch","year":"2021","journal-title":"JOSS"},{"key":"pcbi.1013698.ref058","doi-asserted-by":"crossref","first-page":"117826","DOI":"10.1016\/j.molliq.2021.117826","article-title":"Diffusion of glucose in water: a molecular dynamics study","volume":"345","author":"RP Koirala","year":"2022","journal-title":"J Mol Liq"},{"key":"pcbi.1013698.ref059","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/0003-9861(64)90265-6","article-title":"The diffusion of adenosine triphosphate through aqueous solutions","volume":"107","author":"WJ Bowen","year":"1964","journal-title":"Arch Biochem Biophys"},{"issue":"5","key":"pcbi.1013698.ref060","doi-asserted-by":"crossref","first-page":"2861","DOI":"10.1016\/S0006-3495(99)77440-0","article-title":"Cyclic AMP diffusion coefficient in frog olfactory cilia","volume":"76","author":"C Chen","year":"1999","journal-title":"Biophys J"},{"issue":"3","key":"pcbi.1013698.ref061","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1038\/s41556-018-0040-4","article-title":"Identification of distinct nanoparticles and subsets of extracellular vesicles by asymmetric flow field-flow fractionation","volume":"20","author":"H Zhang","year":"2018","journal-title":"Nat Cell Biol"},{"issue":"151","key":"pcbi.1013698.ref062","doi-asserted-by":"crossref","DOI":"10.3791\/59254","article-title":"Imaging of extracellular vesicles by atomic force microscopy","author":"M Skliar","year":"2019","journal-title":"J Vis Exp"},{"issue":"43","key":"pcbi.1013698.ref063","doi-asserted-by":"crossref","first-page":"12760","DOI":"10.1039\/D2SC05191E","article-title":"Label-free imaging and biomarker analysis of exosomes with plasmonic scattering microscopy","volume":"13","author":"P Zhang","year":"2022","journal-title":"Chem Sci"},{"issue":"9","key":"pcbi.1013698.ref064","doi-asserted-by":"crossref","first-page":"2840","DOI":"10.1021\/j100881a020","article-title":"The obstruction effect in the self-diffusion coefficients of sodium and cesium in agar gels","volume":"70","author":"AL Slade","year":"1966","journal-title":"J Phys Chem"},{"issue":"6","key":"pcbi.1013698.ref065","doi-asserted-by":"crossref","first-page":"4259","DOI":"10.1529\/biophysj.104.047746","article-title":"The hydrodynamic radii of macromolecules and their effect on red blood cell aggregation","volume":"87","author":"JK Armstrong","year":"2004","journal-title":"Biophys J"},{"key":"pcbi.1013698.ref066","doi-asserted-by":"crossref","first-page":"021901","DOI":"10.1103\/PhysRevE.83.021901","article-title":"Models of collective cell spreading with variable cell aspect ratio: a motivation for degenerate diffusion models","volume":"83","author":"MJ Simpson","year":"2011","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"key":"pcbi.1013698.ref067","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1140\/epjb\/e2008-00275-9","article-title":"Modeling collective motion: variations on the Vicsek model","volume":"64","author":"H Chat\u00e9","year":"2008","journal-title":"Eur Phys J B"},{"key":"pcbi.1013698.ref068","doi-asserted-by":"crossref","first-page":"100084","DOI":"10.1016\/j.bioflm.2022.100084","article-title":"Intra-colony channel morphology in Escherichia coli biofilms is governed by nutrient availability and substrate stiffness","volume":"4","author":"B Bottura","year":"2022","journal-title":"Biofilm"},{"key":"pcbi.1013698.ref069","doi-asserted-by":"crossref","unstructured":"Khameneh NJ, Kr\u00fcger T, Nienaltowski P, Emery Y, Fedosov DA, Polin M, et al. Trypanosomes modulation of rotational motility from swimming to network-threading propulsion in confined environments; 2025. Available from: https:\/\/www.biorxiv.org\/content\/10.1101\/2025.11.03.686241v1","DOI":"10.1101\/2025.11.03.686241"},{"issue":"4","key":"pcbi.1013698.ref070","first-page":"10","article-title":"A framework for megascale agent based model simulations on graphics processing units","volume":"11","author":"M Lysenko","year":"2008","journal-title":"JASSS"},{"key":"pcbi.1013698.ref071","doi-asserted-by":"crossref","unstructured":"Aaby BG, Perumalla KS, Seal SK. Efficient simulation of agent-based models on multi-GPU and multi-core clusters. Proceedings of the 3rd International ICST Conference on Simulation Tools and Techniques. SIMUTools \u201910. Brussels, Belgium: ICST (Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering); 2010. p. 1\u201310.","DOI":"10.4108\/ICST.SIMUTOOLS2010.8822"},{"issue":"48","key":"pcbi.1013698.ref072","doi-asserted-by":"crossref","first-page":"30055","DOI":"10.1073\/pnas.1912789117","article-title":"The frontier of simulation-based inference","volume":"117","author":"K Cranmer","year":"2020","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi.1013698.ref073","doi-asserted-by":"crossref","unstructured":"Tejero-Cantero A, Boelts J, Deistler M, Lueckmann JM, Durkan C, Gon\u00e7alves PJ, et al. SBI \u2013 A toolkit for simulation-based inference; 2020. Available from: http:\/\/arxiv.org\/abs\/2007.09114","DOI":"10.21105\/joss.02505"},{"issue":"6","key":"pcbi.1013698.ref074","doi-asserted-by":"crossref","first-page":"1167","DOI":"10.1007\/s11222-011-9288-2","article-title":"Approximate Bayesian computational methods","volume":"22","author":"J-M Marin","year":"2011","journal-title":"Stat Comput"},{"issue":"1","key":"pcbi.1013698.ref075","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1002803","article-title":"Approximate Bayesian computation","volume":"9","author":"M Sunn\u00e5ker","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"pcbi.1013698.ref076","unstructured":"Papamakarios G, Sterratt D, Murray I. Sequential neural likelihood: fast likelihood-free inference with autoregressive flows. Proceedings of the Twenty-Second International Conference on Artificial Intelligence and Statistics. PMLR; 2019. p. 837\u201348. 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