{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:56:37Z","timestamp":1782280597038,"version":"3.54.5"},"posted":{"date-parts":[[2025,8,14]]},"group-title":"Systems Biology","reference-count":102,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T00:00:00Z","timestamp":1755129600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,8,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>Purpose<\/jats:title>\n                  <jats:p>To develop a computational model that addresses limitations in current ocular irritation assessment methods, particularly regarding long-term effects, and recovery patterns following chemical exposure or trauma to the cornea.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>\n                    V-Cornea is an agent-based computer simulation implemented in CompuCell3D that models corneal epithelial homeostasis and injury response. The model incorporates biologically-inspired rules governing cell behaviors (proliferation, differentiation, death) and key signaling pathways including Epidermal Growth Factor (EGF), translating cell-level behaviors to tissue-level outcomes (\n                    <jats:italic>in vitro<\/jats:italic>\n                    to\n                    <jats:italic>in vivo<\/jats:italic>\n                    extrapolation, IVIVE).\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>V-Cornea successfully reproduces corneal epithelial architecture and maintains tissue homeostasis over extended simulated periods. Following simulated trauma or toxicant exposure, the model accurately predicts healing timeframes of 3-5 days for slight and mild injuries. For moderate injuries with basement membrane disruption, the model demonstrates longer recovery times and emergent dynamic structural disorganization that mimics recurrent corneal erosions, providing mechanistic insights into these pathological conditions.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>V-Cornea\u2019s modular CompuCell3D implementation is easily extensible to incorporate additional recovery and injury mechanisms. Future versions will include more realistic basement membrane dynamics and explicit representation of stromal tissue and immune response to improve predictivity for moderate injuries. This virtual-tissue approach shows potential not only for toxicological assessments but also for drug discovery and therapy optimization by providing a platform to test interventions and predict outcomes across various injury scenarios.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.08.11.669602","type":"posted-content","created":{"date-parts":[[2025,8,14]],"date-time":"2025-08-14T18:05:14Z","timestamp":1755194714000},"source":"Crossref","is-referenced-by-count":1,"title":["V-Cornea: A computational model of corneal epithelium homeostasis, injury, and recovery"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9227-9667","authenticated-orcid":false,"given":"Joel","family":"Vanin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Getz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Mahony","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas B.","family":"Knudsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3634-190X","authenticated-orcid":false,"given":"James A.","family":"Glazier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"issue":"2","key":"2025081805000496000_2025.08.11.669602v1.1","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1080\/15569527.2021.1910291","article-title":"Human-relevant approaches to assess eye corrosion\/irritation potential of agrochemical formulations","volume":"40","year":"2021","journal-title":"Cutan Ocul Toxicol"},{"issue":"1","key":"2025081805000496000_2025.08.11.669602v1.2","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1006\/rtph.2002.1551","article-title":"Extent of Initial Corneal Injury as the Mechanistic Basis for Ocular Irritation: Key Findings and Recommendations for the Development of Alternative Assays","volume":"36","year":"2002","journal-title":"Regul Toxicol Pharmacol"},{"key":"2025081805000496000_2025.08.11.669602v1.3","doi-asserted-by":"publisher","DOI":"10.1016\/j.tiv.2009.05.019"},{"issue":"2","key":"2025081805000496000_2025.08.11.669602v1.4","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1097\/00003226-198706020-00017","article-title":"Growth Factors and Corneal Epithelium","volume":"6","year":"1987","journal-title":"Cornea"},{"key":"2025081805000496000_2025.08.11.669602v1.5","unstructured":"Kirazowa T , Kinoshira S , Fujira j K , Araki K , Waranabe H , Ohashi Y , et al. 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