Department of Theoretical Physics

Jan Rozman, "Multi-Phase Field Tissue Modelling: Fluidisation, Internal Dissipation, and Hole Formation"
2025-12-04 14:00 - 15:00 (Europe/Ljubljana) | C/2-X – F1 čajnica (Jamova)
https://indico.ijs.si/event/3288/

Anders Eller Thomsen: Functional EFT Methods: New Developments and the Matchete Tool
2025-12-11 11:00 - 12:00 | A/1-106 – Seminarska soba fizike (F5)
With the absence of new resonance discoveries at the LHC, the role of Effective Field Theories (EFTs) in Beyond the Standard Model (BSM) physics has become increasingly crucial. EFTs serve as indispensable tools in precision physics, offering the potential to reveal indirect evidence of new phenomena. Matching calculations can bridge the gap between underlying theories and EFTs and should ideally be performed at the loop level to include all relevant effects. In this talk, I will discuss functional methods as an avenue to perform cutting-edge matching and RG calculations. From a practical perspective these methods form the foundation of the public automated matching tool Matchete, and I will outline some of its core functionality.
https://indico.ijs.si/event/3080/

Kristjan Muursepp: Baryogenesis from bubble collisions
2025-12-12 11:00 - 12:00 | F1 tea room
In this talk I will consider models connecting baryogenesis with first order phase transition. In particular, I will elaborate on scenarios where the required amount of CP-violation originates from the production of heavy particles after scalar shells interpolating between true and false vacuum collide. I will focus on the case when both heavy particles are produced on-shell as well as the opposite regime when one of the heavy particles is produced off-shell, subsequently decaying to light Standard Model states. I will elaborate on the phenomenological implications of both scenarios.
https://indico.ijs.si/event/3291/

Dominik Haslehner: Running Field-Space Curvature from Quantum Corrections
2025-12-18 10:45 - 11:45 | F1 tea room
We present a systematic study of one-loop quantum corrections in scalar effective field theories from a geometric viewpoint, emphasizing the role of field-space curvature and its renormalisation. By treating the scalar fields as coordinates on a Riemannian manifold, we exploit field redefinition invariance to maintain manifest coordinate independence of physical observables. Focusing on the non-linear sigma model (NLSM) and (phi^4) theory, we demonstrate how loop corrections induce momentum- and scale-dependent shifts in the curvature of the field-space manifold. These corrections can be elegantly captured through the recently proposed geometry-kinematics duality, which generalizes the colour-kinematics duality in gauge theories to curved field-space backgrounds. Our results highlight a universal structure emerging in the contractions of Riemann tensors that contribute to renormalisation of the field-space curvature. In particular, we find explicit expressions and a universal structure for the running curvature and Ricci scalar in simple models, illustrating how quantum effects reshape the underlying geometry. This geometric formulation unifies a broad class of scalar EFTs, providing insight into the interplay of curvature, scattering amplitudes, and renormalisation.
https://indico.ijs.si/event/3439/

Anže Božič, "Some electrostatics of proteins and capsids"
2026-01-15 14:00 - 15:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/3107/

Sofie Martins: Computing cross-sections from the lattice — A recent shift in lattice thinking paradigms?
2026-01-22 11:00 - 12:00 | A/1-106 – Seminarska soba fizike (F5)
Extracting scattering amplitudes — and consequently cross-sections — from non-perturbative lattice techniques has seen significant advances in recent years. People have so far relied on Luescher’s method, which relates Euclidean finite-volume effects of lattice correlators to infinite-volume Minkowskian Scattering Amplitudes. While this method has achieved enormous success, its limitations are somewhat discouraging: the invalidity beyond the inelastic threshold limits predictions to lower-point exclusive particle-scattering processes. New lattice methods by Hansen/Bulava and Tantalo/Patella have addressed this by rethinking the computation of scattering amplitudes on the lattice in terms of spectral densities, which we can extract from large lattices with increasing precision. These methods allow the examination of exclusive processes even above the inelastic threshold and are consequently an invaluable tool for comparing and complementing perturbative computations with lattice results.I will present preliminary results for the Hansen/Bulava method in a particularly tractable theory that models a gauge-invariant implementation of the electroweak sector.
https://indico.ijs.si/event/3407/

Leah Rank, "Hollow microgels: From single particle characterisation to bulk behaviour"
2026-01-22 13:00 - 14:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
Hollow microgels are elastic polymer shells easily realisable in experiments. Recent works have shown the emergence of buckling events in dilute hollow microgels under the effect of an added osmotic pressure. Here, we perform large-scale simulations to show that these microgels at high enough packing fractions undergo spontaneous symmetry-breaking deformations ranging from single large dents to multiple indentations, even in the absence of any externally applied stress. This self-induced buckling phenomenon is thus solely driven by interparticle crowding. We construct a phase diagram inspired by vesicle shape theories, mapping local curvature metrics as a function of the reduced volume, to quantify these findings, and we also propose ways to observe the occurrence of buckling in experiments. The present results thus rationalize the deformations occurring in suspensions of micro- and nano-scale elastic shells, offering a synthetic analogue to biological ones and allowing direct control on buckling instabilities for potential applications. Beyond materials design, these insights may also help to describe shape regulation in natural systems such as cells and vesicles, where similar deformations are observed.
https://indico.ijs.si/event/3442/

Urban Bren, "Biomolecular Simulations as a Useful Tool in a Fight against Cancer"
2026-01-29 14:15 - 15:15 | Seminar room of physics (106) (IJS)
The lecture focuses on food safety in the context of chemical carcinogens, which are often present in raw or thermally processed foods and, after initial activation, alkylate DNA, usually guanine at position N7. Recently, important biochemical phenomena have been discovered, such as DNA catalysis of genetic damage, biomolecular cooperativity, in-vivo persistence of DNA adducts and the mutational propensity of DNA polymerases, which still lack an adequate mechanistic explanation. To elucidate their molecular basis, we used a range of state-of-the-art computer simulation techniques in conjunction with free energy calculations and the corresponding thermodynamic cycles. Since microwaves have been shown to catalyze numerous chemical reactions, we are concerned about the possibility of increased reactivity of chemical carcinogens, which also offers an explanation for why microwaves were recently classified as potentially carcinogenic by the World Health Organization. Therefore, we considered the reactions between chemical carcinogens and DNA in the context of our recently proposed physical mechanism of microwave catalysis, based on rotationally excited polar reaction species. Moreover, microwave irradiation has been shown to accelerate peptide misfolding and aggregation, processes that are generally associated with the occurrence of certain cancer types, e.g. amyloidosis. The microwave-irradiated solution thus through rotationally excited water molecules presents a less polar and less protic medium, thereby accelerating the harmful misfolding of peptides and their aggregation. We tested this hypothesis using molecular dynamics simulations in combination with a dedicated integrator, which is capable of efficiently decoupling individual degrees of freedom of water molecules and connecting them with the corresponding thermostats. Furthermore, we have used quantum chemical approaches to study the reactions between chemical carcinogens and polyphenols, secondary metabolites from fruits and vegetables. As a general rule for preventing DNA damage, a chemical carcinogen should react faster with a polyphenol scavenger than with DNA. Since the activation free energy represents a direct measure of reactivity, the reaction of a chemical carcinogen with a scavenger should have a lower activation barrier than the competitive alkylation of DNA. The long-term goal is to discover natural compounds or their mixtures with high antigenotoxic activities that could, after optimization, serve as functional dietary supplements and thus significantly contribute to cancer prevention.
https://indico.ijs.si/event/3605/

Aleks Smolkovič - Fast and differentiable EFT likelihoods
2026-01-30 10:30 - 11:30 | F1 tea room
The Standard Model Effective Field Theory (SMEFT) has proven to be a valuable framework for studying a broad class of models beyond the SM containing heavy degrees of freedom. The phenomenology of SMEFT can be developed systematically, incorporating essential effects such as Renormalization Group evolution and matching onto subsequent low-energy Weak Effective Field Theories (WET), enabling predictions for a wide range of observables. A likelihood function for the SMEFT that compares theory predictions to experimental data can be employed to identify patterns of deviation from SM predictions, but also to study the phenomenology of any specific model that can be matched onto SMEFT. In this talk, we present a new open source Python package jelli – JAX-based EFT likelihoods, which provides fast and analytically differentiable generic likelihood functions for EFT studies. We discuss a major new version of smelli – a SMEFT likelihood, which incorporates a large number of observables, ranging from quark and lepton flavor physics, to Higgs physics, electroweak precision observables, beta decays, and high-mass Drell-Yan tails. Running on the jelli backend, it provides a global flavorful likelihood function for the SMEFT, WET, and for new physics models, with no assumptions on the flavor structure. Thanks to its numerical efficiency and differentiability, it opens up new avenues in exploring BSM parameter spaces.
https://indico.ijs.si/event/3638/

Toshikaze Chiba, "Deep Learning and Large Language Models for scRNA-seq Data Analysis"
2026-02-12 14:00 - 15:00 | MPŠ Lecture Hall (Jamova)
https://indico.ijs.si/event/3637/

Fabrizio Nesti: A ghost story
2026-03-05 11:00 - 12:00 | F1 tea room
https://indico.ijs.si/event/3697/

Fabian Esser: Higher-dimensional SMEFT operators and UV models for neutrinoless double beta decay
2026-03-12 11:00 - 12:00 | A/1-106 – Seminarska soba fizike (F5)
The observation of lepton number violation (LNV) would be clear evidence for physics beyond the Standard Model, and non-zero neutrino masses particularly motivate a study of processes that violate lepton number by two units, like e.g. neutrinoless double beta decay. In the Standard Model Effective Field Theory (SMEFT), a ubiquitous framework used for indirect new physics searches, $Delta L =2$ operators appear at dimension-5 and higher odd dimensions. Focusing on dimension-9 operators, I will present a diagram-based classification of tree-level UV models and isolate minimal two-particle models that avoid generating the dimension-5 operator or dimension-7 LNV operators at tree level. I then chart how these minimal models populate the operator landscape and organise them by the loop order at which they radiatively induce lower-dimensional LNV operators, highlighting sce- narios in which the tree-level dimension-9 contribution can compete with or dominate loop-suppressed neutrino-mass (dimension-5) effects. Finally, I will show representative one-loop and two- loop models, their matching onto the SMEFT, and their implications for neutrino masses, charged-lepton flavour violation, and the relative size of dimension-9 versus dimension-5 contributions to 0νββ.
https://indico.ijs.si/event/3692/

Ana Crnković, "Engineering protein nanopores with genetically encoded noncanonical amino acids"
2026-03-26 14:15 - 15:15 | 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/

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/

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 (TBA)
2026-06-18 14:00 - 15:00 | A/1-106 – Seminarska soba fizike (F5) (Jamova)
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/
