RNA-like Polyelectrolyte in a Viral Capsid: Molecular Dynamics with Explicit Electrostatic Interactions

[2608.27825] RNA-like Polyelectrolyte in a Viral Capsid: Molecular Dynamics with Explicit Electrostatic Interactions Skip to main content Search Submit Donate Log in Physics > Biological Physics arXiv:2608.27825 (physics) [Submitted on 28 Aug 2026] Title: RNA-like Polyelectrolyte in a Viral Capsid: Molecular Dynamics with Explicit Electrostatic Interactions Authors: Xintong Jiang , Colin Denniston , Gonca Erdemci-Tandogan View PDF HTML (experimental) Abstract: The organization of RNA genomes within viral capsids is primarily controlled by electrostatic interactions between the negatively charged genome and positively charged N-terminal domains of coat proteins. In theoretical approaches, these interactions are commonly captured by mean-field models that smooth capsid charge over the inner surface and treat ionic screening as a continuum. However, charges are localized at discrete N-terminal binding sites and ionic screening arises from correlated ion distributions. Here we use molecular dynamics simulations with explicit ions, explicit water, and full Coulomb electrostatics to simulate a linear polyelectrolyte confined within a model capsid bearing discrete N-terminal-like charge sites. We first validate our approach by simulating a polyelectrolyte in bulk solution and demonstrating that persistence length decreases with increasing salt, matching experimental measurements for single-stranded RNA. When confined within a capsid, radial density profiles shift systematically inward from the capsid wall with increasing salt concentration, in agreement with mean-field predictions. By independently varying charge magnitude, binding-site density, and N-terminal protrusion length, we show that total electrostatic coupling governs global organization while geometric details modulate local genome-wall contact and angular genome organization near N-terminals (within the T=3 architecture, linear genome topology, and monovalent salt range studied here). Across all simulations, equilibration times increase sevenfold with salt, revealing kinetic effects inaccessible to equilibrium theory. These results validate continuum approximations for radial organization while revealing deviations arising from discrete molecular details and establishing a framework for future investigations of genome secondary structure, capsid geometry, and assembly kinetics. Subjects: Biological Physics (physics.bio-ph) Cite as: arXiv:2608.27825 [physics.bio-ph] (or arXiv:2608.27825v1 [physics.bio-ph] for this version) https://doi.org/10.48550/arXiv.2608.27825 Focus to learn more arXiv-issued DOI via DataCite Submission history From: Gonca Erdemci-Tandogan [ view email ] [v1] Fri, 28 Aug 2026 01:47:55 UTC (4,301 KB) Full-text links: Access Paper: View PDF HTML (experimental) TeX Source view license Current browse context: physics.bio-ph < prev | next > new | recent | 2026-08 Change to browse by: physics References & Citations SciX Google Scholar Semantic Scholar export BibTeX citation Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer ( What is the Explorer? ) Connected Papers Toggle Connected Papers ( What is Connected Papers? ) Litmaps Toggle Litmaps ( What is Litmaps? ) scite.ai Toggle scite Smart Citations ( What are Smart Citations? ) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv ( What is alphaXiv? ) Links to Code Toggle CatalyzeX Code Finder for Papers ( What is CatalyzeX? ) DagsHub Toggle DagsHub ( What is DagsHub? ) GotitPub Toggle Gotit.pub ( What is GotitPub? ) Huggingface Toggle Hugging Face ( What is Huggingface? ) ScienceCast Toggle ScienceCast ( What is ScienceCast? ) Demos Demos Replicate Toggle Replicate ( What is Replicate? ) Spaces Toggle Hugging Face Spaces ( What is Spaces? ) Spaces Toggle TXYZ.AI ( What is TXYZ.AI? ) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower ( What are Influence Flowers? ) Core recommender toggle CORE Recommender ( What is CORE? ) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs . Which authors of this paper are endorsers? | Disable MathJax ( What is MathJax? ) We gratefully acknowledge support from our major funders , member institutions , and all contributors. About · Help · Contact · Subscribe · Copyright · Privacy · Accessibility · Operational Status (opens in new tab)

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