Jure Dobnikar, "DNA packing in viral capsids"
2026-04-09 14:15 - 15:15 (Europe/Ljubljana) | Seminar room of physics (106) (IJS)
Assembly of viral capsids containing genetic material, is a key process in viral reproduction cycle. The bacteriophages and double stranded DNA viruses assemble their capsids prior to genome packaging and actively push DNA inside by ATP-driven packaging motors. The genome is typically densely packed in the capsid and understanding its spatial configuration presents a challenging problem, which is not completely understood despite its obvious importance.
To elucidate the mechanism of DNA packing, we first explored a simple model of elastic filament confined to a sphere with three competing interactions . The simple phenomenological theory supported by extensive parallel tempering MD simulations of the wormlike chain (WLC) model show that the optimal ground state packing is not an inverse spool configuration as previously assumed; it is a more complex structure where the filament is compartmentalized into multiple domains, resembling nested tori or topological links. While this suggests that DNA will also form multidomain structures in a viral capsid, it is important to realize that DNA cannot be completely described by the linear elastic model. Under sufficient local torsion, the base pairs of the double helix can locally melt creating regions with large flexibility that can easily form kinks. We incorporated this effect into a meltable WLC model and explored nonequilibrium process of pushing such kinkable chains into a capsid by molecular motors . It turns out that the kink formation crucially affects the structure: for sufficiently slow packing process we observe a coexistence of outer spool domain and a twisted nematic core – in a perfect agreement with available cryo-EM experimental observations. Our findings suggest that the nonlinear elasticity of biological molecules plays an important role in their spatial structuring in confined biological systems.
References
T. Curk, J.D. Farrell, J. Dobnikar, R. Podgornik, Spontaneous Domain Formation in Spherically Confined Elastic Filaments, Phys. Rev. Lett. 123 047801 (2019)
J.D. Farrell, J. Dobnikar, R. Podgornik, T. Curk: Spool-nematic ordering of dsDNA and dsRNA under confinement, Phys. Rev. Lett. 133 148101 (2024)
https://indico.ijs.si/event/3601/

Marin Šako, PhD presentation
2026-04-13 13:00 - 14:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/3734/

Rishav Roshan: Gravitational wave production during reheating: From the inflaton to primordial black holes
2026-04-16 11:00 - 12:00 | A/1-106 – Seminarska soba fizike (F5)
We calculate the gravitational waves (GWs) produced by primordial black holes (PBHs) in the presence of the inflaton condensate in the early Universe. Combining the GW production from the evaporation process, the gravitational scattering of the inflaton itself, and the density fluctuations due to the inhomogeneous distribution of PBHs, we propose for the first time a complete, coherent analysis of the spectrum, revealing three peaks, one for each source. Three frequency ranges (~kHz, GHz, and PHz, respectively) are expected, each giving rise to a similar GW peak amplitude Ω_GW. We also compare our predictions with current and future GW detection experiments.
https://indico.ijs.si/event/3730/

Markus Miettinen, "High-fidelity biomolecular modelling"
2026-04-20 13:00 - 14:00 | MPŠ Lecture Hall (Jamova)
https://indico.ijs.si/event/3733/

Elie Hammou: Tailored PDFs for new physics searches
2026-05-07 11:00 - 12:00 | A/1-106 – Seminarska soba fizike (F5)
https://indico.ijs.si/event/3731/

Andraž Stožer & Marko Gosak (TBA)
2026-05-14 14:15 - 15:15 | Seminar room of physics (106) (IJS)
https://indico.ijs.si/event/3643/

Urška Andrenšek, "Elasto-capilary vertex model of epithelia"
2026-05-28 14:00 - 15:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/3732/
