{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,5,6]],"date-time":"2026-05-06T03:36:26Z","timestamp":1778038586489,"version":"3.51.4"},"posted":{"date-parts":[[2025,10,15]]},"group-title":"Biophysics","reference-count":49,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,10,15]],"date-time":"2025-10-15T00:00:00Z","timestamp":1760486400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"U.S. National Science Foundation","doi-asserted-by":"crossref","award":["CBET-2232718"],"award-info":[{"award-number":["CBET-2232718"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Superradiance (SR) arises when fluorophores radiate collectively rather than independently, producing ultrabright emission bursts. Recent experiments show that dye-labeled virus-like particles (VLPs) can exhibit SR at room temperature, where the VLP scaffold organizes dyes into a macrodipole of coherent emitters under pulsed excitation. To elucidate the biophysical basis of this phenomenon, microsecond-scale all-atom molecular dynamics (MD) simulations were performed on intact Brome mosaic virus (BMV) VLPs, comparing the native scaffold to a capsid decorated with Oregon Green 488 (OG). Results show that OG conjugation at K105 induces only subtle structural changes: a slight expansion of VLP volume and marginally higher inter-subunit flexibility, while overall shell morphology and pore architecture remain intact. However, dianionic OG alters VLP electrostatics, increasing water exchange across the shell and reducing chloride permeability. Dyes bound in pentamers are more closely packed and conformationally restricted than those in hexamers, and their transition dipoles more frequently adopt parallel orientations predicted to favor excitonic coupling and cooperative emission. By examining the role of scaffold architecture in dye interactions and dynamics, this work offers a mechanistic framework and design principles for engineering SR-VLPs as next-generation fluorescent probes and photonic materials.<\/jats:p>","DOI":"10.1101\/2025.10.15.682673","type":"posted-content","created":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T03:05:26Z","timestamp":1760583926000},"source":"Crossref","is-referenced-by-count":1,"title":["Computational biophysical characterization of a superradiant virus-like particle in its ground state"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2387-9970","authenticated-orcid":false,"given":"Anjali","family":"Krishna","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anoushka","family":"Buddhikot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4685-8291","authenticated-orcid":false,"given":"Jodi A.","family":"Hadden-Perilla","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2025101813550438000_2025.10.15.682673v1.1","doi-asserted-by":"publisher","DOI":"10.7150\/thno.103127"},{"key":"2025101813550438000_2025.10.15.682673v1.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41423-022-00897-8"},{"key":"2025101813550438000_2025.10.15.682673v1.3","first-page":"1","article-title":"Virus-like particles: preparation, immunogenicity and their roles as nanovaccines and drug nanocarriers","volume":"19","year":"2021","journal-title":"Journal of Nanobiotechnology"},{"key":"2025101813550438000_2025.10.15.682673v1.4","doi-asserted-by":"crossref","first-page":"3670","DOI":"10.1039\/c2ra01376b","article-title":"Engineering of Brome mosaic virus for biomedical applications","volume":"2","year":"2012","journal-title":"RSC Advances"},{"key":"2025101813550438000_2025.10.15.682673v1.5","doi-asserted-by":"crossref","first-page":"11401","DOI":"10.1021\/acsnano.9b04786","article-title":"Radiation Brightening from Virus-like Particles","volume":"13","year":"2019","journal-title":"ACS Nano"},{"key":"2025101813550438000_2025.10.15.682673v1.6","doi-asserted-by":"crossref","first-page":"10494","DOI":"10.1021\/acs.jpcb.1c06395","article-title":"Subset of Fluorophores Is Responsible for Radiation Brightening in Viromimetic Particles","volume":"125","year":"2021","journal-title":"Journal of Physical Chemistry B"},{"key":"2025101813550438000_2025.10.15.682673v1.7","doi-asserted-by":"crossref","first-page":"3237","DOI":"10.1021\/acs.jpclett.2c00262","article-title":"Ultrafast Collective Excited-State Dynamics of a Virus-Supported Fluorophore Antenna","volume":"13","year":"2022","journal-title":"Journal of Physical Chemistry Letters"},{"key":"2025101813550438000_2025.10.15.682673v1.8","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRev.93.99"},{"key":"2025101813550438000_2025.10.15.682673v1.9","doi-asserted-by":"crossref","unstructured":"Valeur, B. ; Berberan-Santos, M. 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