Department of Theoretical Physics

Ana Crnković, "Engineering protein nanopores with genetically encoded noncanonical amino acids"
2026-03-26 14:15 - 15:15 (Europe/Ljubljana) | Seminar room of physics (106) (IJS)
Genetic code expansion enables site-specific incorporation of noncanonical amino acids (ncAAs) into proteins, facilitating the introduction of spectroscopic probes, fluorescent labels, photoreactive groups, enhanced stability, and novel chemical reactivity. Despite the successful incorporation of over 150 ncAAs, the broader application of ncAAs has largely remained limited to proof-of-principle studies. In this lecture, I will discuss key factors that govern the efficient incorporation of ncAAs to achieve high yields of target proteins, with particular emphasis on challenging systems such as phosphoproteins and selenoproteins. In the second part, I will highlight how selected ncAAs are utilized in our group to engineer protein nanopores for biosensing applications – a technique that detects analytes by monitoring changes in ionic current as molecules translocate through a nanopore under an applied voltage. Overall, this lecture aims to highlight the potential of ncAAs to unlock new functionalities in various protein targets and to inspire their broader use in emerging techniques.
https://indico.ijs.si/event/3701/

Jure Dobnikar, "DNA packing in viral capsids"
2026-04-09 14:15 - 15:15 | 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, "From Ca²⁺ Waves to Insulin Pulses: Experimental and Theoretical Perspectives on β-Cell Network Dynamics"
2026-05-14 14:15 - 15:15 | Seminar room of physics (106) (IJS)
Pancreatic β-cells within the islets of Langerhans coordinate their activity to generate pulsatile insulin secretion, a process essential for glucose homeostasis and disrupted during the development of diabetes. This seminar will combine experimental physiology and mathematical modelling to examine how multicellular β-cell networks encode, propagate, and translate Ca²⁺ signals into insulin release. In the experimental part, we will present insights from high-frequency confocal Ca²⁺ imaging, showing how β-cells respond heterogeneously to stimulation, how fast Ca²⁺ oscillations and intercellular waves emerge within islets, and how specific cellular subpopulations may contribute to signal initiation and propagation. We will also discuss conserved and altered features of these dynamics in human islets and during diabetes progression. Building on these findings, the modelling part will address why mathematical abstraction is needed to disentangle the mechanisms underlying such complex multiscale behaviour. We will present a phenomenological multicellular model that links structural gap-junction coupling, timescale-specific functional connectivity, and secretion. The model reproduces experimentally observed slow metabolic oscillations, fast bursts, and ultrafast spikes, and shows how interactions between these temporal domains shape pulsatile insulin output. By integrating high-resolution Ca²⁺ imaging with phenomenological modelling, the seminar highlights how interdisciplinary approaches can reveal the principles governing β-cell network function and its disruption in diabetes.
https://indico.ijs.si/event/3643/

Ezequiel Alvarez: Leveraging Biased Simulations with Bayesian inference
2026-06-02 11:00 - 12:00 | F1 tea room
Scientific measurements often yield data that are mixtures of signal and one or more background components. When class templates (e.g., simulation-based priors) are biased or imprecise, they are typically treated as nuisance systematics. We take a different route: by embedding imprecise priors in a hierarchical Bayesian mixture model and combining them with observed mixed data via Bayesian machine learning, we adapt class shapes toward the true distributions and obtain an unbiased posterior estimate of the signal fraction with calibrated uncertainties. In practice this lets us exploit simulation even when it is imperfect—improving template fidelity during inference. We demonstrate the approach on a collider-physics example (di-Higgs → 4b at the LHC), and show how the same framework can enhance and unbias the ABCD background-estimation method. The framework, Template-Adapted Mixture Model (TAMM, arXiv:2604.022219), is straightforward to implement, scales to high-dimensional and complex distributions, and is broadly applicable across HEP, astrophysics, cosmology, and any domain with mixed data and imperfect priors.
https://indico.ijs.si/event/3833/

Ekaterina Poliukhina, "Direct measurement of protein-protein interaction potentials by cryo-electron tomography"
2026-06-18 14:00 - 15:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
Protein-protein interactions control how proteins behave in solution, dictating aggregation, crystallization, phase separation, and the colloidal stability of formulations central to pharmacology, food science, and biotechnology. Predicting this behavior has long been difficult: theories borrowed from classical colloid science fail for proteins, which are irregularly shaped and chemically heterogeneous, and no direct experimental route to the underlying interaction potential has been available. Cryo-electron tomography now provides such a route. By reconstructing three-dimensional tomograms containing thousands of individual proteins, the spatial distribution of every particle can be recovered and converted, without any assumed functional form, into a measured interaction potential. Validated against analytical ultracentrifugation and small-angle X-ray scattering, the approach spans globular proteins from lysozyme to apoferritin and reveals how ionic strength, pH, temperature, and additives reshape their interactions.
https://indico.ijs.si/event/3599/

Maximilian Bachmaier: The slingshot effect and its cosmological implications
2026-07-16 11:00 - 12:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
In my talk, I will present the so-called slingshot effect. It represents a general phenomenon that occurs when a localized source, such as a magnetic monopole, quark, or a D-brane, crosses a wall separating the confined (Higgsed) and unconfined (Coulomb) phases. The crossover is accompanied by a stretched string that confines the source to the wall. The string tension accelerates the source towards the wall as sort of a slingshot. The effect can take place in different setups, such as phase transitions leading to both electric and magnetic confinement, as well as in string cosmology involving D-branes. I will discuss the role of this phenomenon in sourcing gravitational waves.
https://indico.ijs.si/event/3895/

Gerd Schroeder-Turk, "Universal hidden order in amorphous cellular geometries"
2026-07-23 14:00 - 15:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
Partitioning space into cells with certain extreme geometrical properties is a central problem in many fields of science and technology. Here we investigate the Quantizer problem, defined as the optimisation of the moment of inertia of Voronoi cells, i.e., similarly-sized ‘sphere-like’ polyhedra that tile space are preferred. We employ Lloyd’s centroidal Voronoi diagram algorithm to solve this problem and find that it converges to disordered states associated with deep local minima. These states are universal in the sense that their structure factors are characterised by a complete independence of a wide class of initial conditions they evolved from. They moreover exhibit an anomalous suppression of long-wavelength density fluctuations and quickly become effectively hyperuniform. Our findings warrant the search for novel amorphous hyperuniform phases and cellular materials with unique physical properties.
https://indico.ijs.si/event/4003/

Michael Dimitriyev, "Transformations and defect structures in liquid networks"
2026-07-28 14:00 - 15:00 | C/2-X – F1 čajnica (Jamova)
The lyotropic liquid crystals formed by amphiphiles include lamellar and cylindrical phases with smectic A and columnar order, respectively, representing both 2D and 1D layered liquids. Bicontinuous networks form at intermediate compositions and consist of liquid-like interfaces, combining both layer and cylindrical geometries, that percolate all three dimensions. Of the bicontinuous networks, the predominant structures are based on gyroid, diamond, and primitive minimal surfaces, all of which have cubic crystal symmetries. While possessing a rigidity and 3D elasticity description of conventional solids, mass transport along interfaces lead to complex, non-affine relaxation modes. We consider a liquid network model that is able to capture the non-affine deformations observed in bicontinuous networks formed by block copolymers. We additionally identify topology-preserving transformation pathways between different network phases enabled by mass transport along interfaces, uncovering conditions under which the bicontinuous double diamond is a transition state between stable double gyroid and a metastable tetragonal network phase. Finally, we consider a new model of the general structure and free energy of inhomogeneous deformations and defects in bicontinuous networks.
https://indico.ijs.si/event/4010/

Sascha Hilgenfeldt, "Tissue modeling: Insight from continuum mechanics"
2026-07-30 14:00 - 15:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
Two-dimensional vertex models have been used extensively to study and simulate the mechanical behavior of monolayer tissues, a simplified approach that allows for detailed study of structure and disorder in large systems. Morphological indicators from the structure are then taken as indicators for mechanical behavior and even biological fitness. The most common 2D vertex models use generic elasticity terms whose validity has not been closely scrutinized. Starting from experimental data from MDCK epithelial cells, we question (i) the appropriateness of a 2D model in the light of severe breaking of mechanical symmetry along the apical-basal axis, and (ii) the accuracy of the functional form of the standard modeling terms. To make progress in both cases, we describe cells as continuum materials and use the equations of continuum elasticity to derive correlations between elastic deformation energy and shape parameters. Representing the cortex of a three-dimensional cell as a cylindrical shell, we find that agreement with experimental data requires proper modeling of the 3D deformation, i.e., the non-uniformity along the apical-basal axis caused primarily by anisotropic actin contractility at the basal side. The relationship between elastic energy and perimeter is then found to be non-harmonic, even in the limit of vanishing actin content. Therefore, we construct a 2D model modeling cytoplasm and cortex as different materials, but uniform in the apical-basal direction. Here, we can analytically compute the deformation shape and energy for arbitrary outlines of the deformed cell. We find that the non-harmonic relationship between energy and perimeter persists, pointing towards a revised vertex model that retains the simplicity of the standard vertex model, but is informed by and consistent with continuum mechanics.
https://indico.ijs.si/event/4011/

Sheng Fong
2026-10-01 11:00 - 12:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/4007/

Urška Andrenšek, "Elasto-capilary vertex model of epithelia"
2026-10-01 14:00 - 15:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/3732/

Seminars for Theoretical and Computational Biophysics
2026-10-29 14:00 - 15:30 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/3161/

Seminars for Theoretical and Computational Biophysics
2026-11-05 14:00 - 15:30 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/3214/
