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BP: Fachverband Biologische Physik
BP 2: Computational Biophysics I
BP 2.4: Talk
Monday, March 9, 2026, 10:15–10:30, BAR/0106
A coarse-grained model for investigating the ejection of dsDNA from a viral capsid — •Adrian John Pinto1, Klara Strobl2, Carmen San Martin3, Mar Alcazar Hutardo2, Paul van der Schoot4, Pedro J. de Pablo2, Horacio V. Guzman5, and Peter Virnau1 — 1Institute of Physics, JGU, Mainz, Germany — 2Autonomous University of Madrid, Madrid, Spain — 3Spanish National Center for Biotechnology, Madrid, Spain — 4Eindhoven University of Technology, Eindhoven, Netherlands — 5Institute of Material Science of Barcelona, Barcelona, Spain
Viruses are microscopic infectious agents that hijack the metabolic machinery of their hosts to replicate. They consist of genetic material, DNA for adenovirus, enclosed within a protein shell called a capsid. Adenoviruses are associated with respiratory diseases, gastroenteritis, conjunctivitis, and urinary tract infections. In this work, we investigate the denaturation of the viral capsid in the presence of urea as a chemical denaturant and analyze how increasing urea concentration affects capsid stability. To model the experimental system in simulations, we propose a coarse-grained representation of viral DNA based on a Kratky-Porod chain, which allows us to incorporate solvent conditions and obtain realistic length scales. Additionally, we model the capsid as a spherical confinement composed of discrete beads and introduce openings of various sizes to map changes in urea concentration to the simulation environment. Our findings indicate that the lag time observed in intensity curves can be explained by differences between partial and complete capsid opening.
Keywords: Coarse-grained DNA model; Viral Capsid; Denaturation of Capsid; Adenovirus