Department of Theoretical Physics

Innes Bigaran: Leveraging intermediate resonances to probe CP-violation at colliders
2024-05-28 13:45 - 14:45 (Europe/Ljubljana) | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
We study the phenomenological implications of interference between tree-level contributions to decays to three-body final states. CP-violation in these decays arise via different virtualities of intermediate resonances, and the presence of SM and/or new CP phases in a model Lagrangian. We highlight the manifestation of this CP-violating observable in the interference between SM charged-current decays and new-physics contributions to effective vector interactions in the EFT and in a UV-complete model featuring a scalar leptoquark, $S_1$. We present a novel method for searching for CP-violating new physics effects utilising the differential cross sections of $ppto d_i ell u_ell$ decays, with a detailed study of $ppto b tau u_tau$ simulating signal and background.
https://indico.ijs.si/event/2146/

Gašper Lipnik, "Force inference in epithelial tissues"
2024-05-23 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
In this work, we explore the ways of determining the mechanical properties of epithelial tissues. Knowledge of the mechanical parameters like forces between and pressures within cells leads to a deeper understanding of the processes in these tissues. To determine these parameters, one can perform in vivo measurements using lasers, optical tweezers, micropipettes etc. However, in vivo measurements are invasive, technically challenging and local. Thus, it is best to use noninvasive and global methods. One theoretical approach is force inference from cell shapes and connectivity as seen in microscope images, and here we introduce three force inference methods.
https://indico.ijs.si/event/2091/

Nudžeim Selimović
2024-05-23 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
https://indico.ijs.si/event/2089/

Diego Redigolo: Dark sectors at flavor factories
2024-05-21 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
I will discuss new ideas for reporpusing current flavor experiments to hunt for dark sectors particles.
https://indico.ijs.si/event/2134/

Lorenzo Ubaldi: False Vacuum Decay From Thin to Thick Walls
2024-05-16 14:00 - 15:00 | https://uu-se.zoom.us/j/64706033081 Passcode: [REDACTED] (Zoom)
The computation of the false vacuum decay rate in the situation with nearly degenerate vacua can be performed analytically in the well known thin wall approximation. If we depart from the near degeneracy of the vacua, the approximation quickly ceases to work. This statement is known to practitioners of the field, but it has a caveat: it is true only if one works at the leading order of the thin wall approximation. In this talk I will describe how to organize the calculation to systematically include higher order corrections in the thin wall parameter expansion. The first few orders can be computed analytically. It is enough to include them to improve the approximation and get a very accurate estimate of the bounce action also deep into thick wall regimes, where the vacua are far apart. I plan to also briefly discuss how to deal in these cases with the calculation of the functional determinant, also known as the prefactor, in order to have the full proper understanding of the vacuum decay rate. In the whole talk I will only consider flat spacetime, without gravity.
https://indico.ijs.si/event/2133/

Maciej Kierkla: EFT of supercooled phase transition
2024-05-09 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
We present an analysis of the first-order supercooled phase transition associated with symmetry breaking in the early Universe in a classically scale-invariant model. We analyze the role of higher order thermal corrections for these transitions, and to what extent they can be computed using dimensionally reduced effective field theory (3D EFT). This framework requires high temperature (HT) expansion to be valid, which seems challenging due to the presence of supercooling. We show how to reliably use the HT expansion in dimensionally reduced theory for the calculation of bubble nucleation rate. We compare the obtained results to the results of the most common scheme based on the so-called daisy resummation. We further compute all of phase transition characteristics, discuss various scenarios of completing the transition and predict resulting gravitational-wave spectra and their observational prospects in future experiments such as LISA.
https://indico.ijs.si/event/2070/

Labrini Athanasopoulou (TBA)
2024-04-18 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/2076/

Boštjan Vihar, "Developing in vitro models of human tissues"
2024-04-11 14:15 - 15:15 | Seminar room of physics (106) (IJS)
Speakers: Boštjan Vihar (IBV MF UM)
The presentation will establish basic concepts of tissue engineering, 3D biofabrication and the development of microphysiological systems, and provide insight into some of the work in progress at the Institute of Biomedical Sciences, Faculty of Medicine, University of Maribor (IBV).The development of advanced in vitro models of human tissues stands at the forefront of advancing medical sciences by developing innovative solutions to complex health issues and requires an interdisciplinary approach combining different fields such as cell and molecular biology, biochemistry, materials science, additive technologies. The development process can vary substantially depending on the target tissue/application and the expected functional characteristics.At IBV different aspects of in vitro tissue model development are explored in parallel and in synergy in the hopes of obtaining new insights into the (patho)physiology of human tissues and organs and creating new ways for the treatment of complex diseases and personalized medicine.Our research activities include the cell culture of immortalized and primary cell lines, which are also isolated and characterization in-house. In parallel, polymer-based hydrogel formulations are developed to mimic the physico-chemical properties of native tissues and are combined with cells to form bioinks. Using extrusion-based, microfluidics and lithographic 3D printing techniques, tissue scaffolds and custom-made microfluidic devices are developed and integrated into microphysiological systems (organ-on-a-chip devices) which allow prolonged maturation, continuous monitoring and functional analysis.
https://indico.ijs.si/event/1866/

Fabio Staniscia, "Line adsorption in sessile droplets"
2024-04-04 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/2075/

"Dynamics of Ribonucleoprotein Assembly in Time and Space"
2024-03-28 14:00 - 15:00 | Seminar room of physics (106) (IJS)
Speakers: Miha Modic (National Institute of Chemistry)
Successful embryo implantation induces rapid morphological progression from rosette to lumen and then to gastrulation, which is closely coordinated with cell fate transition. By integrating machine learning, metabolic RNA sequencing, iCLIP, and proteomics of the protein-RNA interactome with embryology, I will present a blueprint for understanding how multilayered molecular networks coordinate developmental transitions. I will highlight three studies that demonstrate how cross-regulatory molecular logic ensures the robustness of developmental signalling pathways to rewire ribonucleoprotein assembly to drive cell fate transitions (Modic et al., 2023), important for the onset of gastrulation (Modic et al., 2019) and embryonic morphogenesis (Modic & van Genderen et al, in resubmission; Modic et al., Biorxiv 2021).
https://indico.ijs.si/event/1799/

Marco Gorghetto: Early vs late string networks from a minimal QCD Axion
2024-03-19 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
We propose a new regime of minimal QCD axion dark matter that lies between the pre- and post-inflationary scenarios, such that the Peccei-Quinn (PQ) symmetry is restored only on sufficiently large spatial scales. This leads to a novel cosmological evolution, in which strings and domain walls re-enter the horizon and annihilate later than in the ordinary post-inflationary regime, possibly even after the QCD crossover. Such dynamics can occur if the PQ symmetry is restored by inflationary fluctuations, i.e. the Hubble parameter during inflation $H_I$ is larger than the PQ breaking scale $f_a$, but it is not thermally restored afterwards. Solving the Fokker-Planck equation, we estimate the number of inflationary e-folds required for the PQ symmetry to be, on average, restored. Moreover, we show that, in the large parts of parameter space where the radial mode is displaced from the minimum by de Sitter fluctuations, a string network forms due to the radial mode oscillating over the top of its potential after inflation. In both cases we identify order one ranges in $H_I/f_a$ and in the quartic coupling $lambda$ of the PQ potential that lead to the late-string dynamics. In this regime the cosmological dark matter abundance can be reproduced for axion decay constants as low as the astrophysical constraint 𝒪$(10^8)$ GeV, corresponding to axion masses up to $10^{-2}$ eV, and with miniclusters with masses as large as 𝒪(10) solar masses.
https://indico.ijs.si/event/1997/

Mojca Krajnc (TBA)
2024-03-14 14:00 - 15:30 | Seminar room of physics (106) (IJS)
Speakers: Mojca Krajnc (Biotechnical Faculty)
https://indico.ijs.si/event/1778/

Urška Andrenšek, "Thickness modulation in supported epithelial sheets"
2024-02-29 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
Surface patterns in epithelial tissues often arise due to effects of differential surface tension and elastic properties of supporting structures, such as basal membrane and bulk elastic substrate. While we cannot clearly distinguish between surface-tension and elastic contributions only from measurement of wave-length of surface patterns, thickness modulation of the tissue might give a better insight into the origins of specific pattern formation. Depending on magnitude of surface-tension and elastic energy contributions, the thickness modulation can change its amplitude and phase. I will present the theoretical predictions of effects that differential surface tension, basal membrane and elastic substrate have on surface-pattern formation and thickness modulation in mono-layered epithelial sheets.
https://indico.ijs.si/event/1875/

Veronika Bukina (TBA)
2024-02-22 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/1874/

"One, two, three, four: simple additions of nucleic acid strands for complex functional outcomes"
2024-02-15 14:15 - 15:15 | Seminar room of physics (106) (IJS)
Speakers: Maja Marušič (National Institute of Chemistry)
Nucleic acids display a range of structural variations beyond the basic helical shape and Watson-Crick hydrogen bond pairing. Some of these structural variations are nuanced, while others result in a vastly different spatial conformation. We will discuss the structural details of single-, double-, triple- and quadruple-stranded nucleic acids and how structural variation translates into functional diversity. What can in vitro biophysical methods reveal about the nucleic acid structure, how can we correlate findings from diverse methods, and when is this approach suitable and when not? Insights into these and related questions will be provided using adenine-rich DNA systems, AT/GC repeat regions, PNA-RNA complexes and 3′ untranslated regions of mRNA.
https://indico.ijs.si/event/1769/

Marin Šako, "Physics of bubble oscillations"
2024-02-07 14:00 - 15:00 | C/2-X – F1 čajnica (Jamova)
Bubbles in liquids, soft and squeezy objects made of gas and vapour, yet so strong as to destroy any material. At first glance bubbles in water might seem like trivial objects with simple physics describing them. However, upon further investigation one finds many interesting phenomena. In this talk I will present Rayleigh–Plesset equation, a mathematical framework for describing bubble oscillations, as well as an overview of some notable solutions.
https://indico.ijs.si/event/1844/

Fran Ivan Vrban, "Many-body effects in microgel suspensions"
2024-02-01 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
Even though there are clear indications of many-body interactions in the dense microgel suspensions, there is still no adequate general description of the phenomena. One possible avenue for exploration of many-body effects is the coarse-grained liquid-drop model, where the soft matter constituents are regarded as compressible drops with a well-defined surface. The interplay between particle’s bulk and surface energy plays the key role in the system characterization, along with the geometry constraints. In this seminar, the general overview of the many-body interactions in field will be presented, as well as the relevant techniques and results of the liquid-drop model.
https://indico.ijs.si/event/1956/

Jules Morand, "Emergent circulation patterns from anonymized mobility data: Clustering Italy in the time of Covid"
2024-01-25 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
Speakers: Jules Morand (Department of Physics, University of Trento)
https://indico.ijs.si/event/1873/

"Studies of bees with smart sensors: at the crossroads of biology, physics, and AI"
2024-01-11 14:15 - 15:15 | Seminar room of physics (106) (IJS)
Speakers: Anton Gradišek (Jožef Stefan Institute)
Honeybees and bumblebees are social insects and are among the most important pollinators in their ecosystems. They are fascinating creatures and even if we think that we know them well, there is still much to discover about their lives. In the seminar, I will present an overview of the studies we carried out especially in the field of bumblebee research. We used several sensors, especially microphones and thermometers, to investigate the daily dynamics of the colony. At the end, I will outline the current project we are working on, we will be using smart sensors to monitor stress on honeybee colonies in the presence of external stressors.
https://indico.ijs.si/event/1770/

Biophysics Journal Club: Tanmoy Sarkar, "Inclusion of adaptive tension and strain in vertex model"
2023-12-21 14:00 - 15:00 | C/2-X – F1 čajnica (Jamova)
https://indico.ijs.si/event/1834/

"Understanding bacterial inactivation with cavitation at the single cell level"
2023-12-14 14:00 - 15:30 | Seminar room of physics (106) (IJS)
Speakers: Žiga Pandur (Faculty of Mechanical Engineering)
Cavitation, a sudden decrease in pressure that triggers the formation of vapor and gas bubbles in a liquid medium, can cause many important industrial problems, such as material loss, noise and vibrations in hydraulic machinery. On the other hand, due to the extreme conditions during growth and collapse of vapor bubbles, cavitation can be a potentially useful phenomenon. for surface cleaning, chemical enhancement and wastewater treatment (i.e. bacterial eradication and virus inactivation). Despite extensive research in recent years, there is still a large gap between understanding the mechanisms that contribute to the effects of cavitation and its application. Although engineers have already commercialized devices that use cavitation, we are still not able to answer the fundamental questions, such as how bubbles increase chemical activity disinfect, clean, and how they affect bacterial cells.In this work we have investigated the effects of cavitation on simple cell model systems–and compared it with other known chemical, physical and mechanical stress factors. We showed that the fragile but compliant structure of the lipid bilayer is effectively destroyed by acoustic or hydrodynamic cavitation. We have investigated how different modifications of the cell wall of Gram-negative bacteria (Escherichia coli) affect cell stability during sonication and found that peptidoglycan layer modifications significantly increase susceptibility to sonolysis. To investigate the interaction between individual cavitation bubble and bacterial cell, we have developed a new method to generate single micrometer size cavitation bubble. The combination of optical tweezers and high-voltage discharge allowed us to generate cavitation microbubbles precisely in space and time. At the center of the imploding microbubble, the cells get detached, followed by the area of damaged cells. The results indicate that only the cells in the immediate vicinity of the collapsing bubble were affected. The numerical model of bubble collapse allowed us to determine the threshold values of hydrodynamic forces and wall shear stress for cell detachment and cell death.Quantifying mechanical stability response of bacteria to high-frequency perturbations reveals the mechanisms behind the cleaning effects of cavitation, and also provides a unique tool to characterize the high-frequency mechanical stress response of different biological materials. Our work contributes to a better understanding of the effects of cavitation on bacterial cells and promotes further development of cavitation applications to remove or eradicate bacteria.
https://indico.ijs.si/event/1777/

XBW preparation
2023-12-07 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
Vita Movrin, “Active dynamics of wound closure”Urban Zeleznik, “Topological Transformations in Graph Vertex Model”Marin Sako, “Tensile strength of water with organic impurities”
https://indico.ijs.si/event/1872/

Matej Kanduč, "The enigmatic boundary between hydrophilic and hydrophobic"
2023-11-23 14:15 - 15:15 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
Hydrophobic attraction, macromolecule adhesion, and even biofouling occur when the surface contact angle exceeds 65°, known as the “Berg limit.” While this threshold seems widely applicable, the reasons behind its universality remain unclear. In the seminar, I will discuss our current knowledge of this threshold and explore possible underlying mechanisms.
https://indico.ijs.si/event/1833/

Anže Božič, "Towards improved simple models of electrostatic interactions in patchy colloids and proteins"
2023-11-16 14:00 - 15:00 | C/2-X – F1 čajnica (Jamova)
https://indico.ijs.si/event/1832/

Biophysics Journal Club: Marin Šako, "Industrial applications of cavitation"
2023-11-09 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/1807/

Domen Vaupotič, "Effects of Coarse Graining on Topological Indices of Trees"
2023-10-26 14:00 - 15:00 | C/2-X – F1 čajnica (Jamova)
https://indico.ijs.si/event/1806/

"Importance of variation in cytoplasm viscoelasticity throughout embryonic cell division"
2023-10-05 14:00 - 15:30 | Seminar room of physics (106) (IJS)
Speakers: Urša Uršič (Max Planck Institute of Molecular Cell Biology and Genetics)
The first few cell divisions are crucial for successful embryonic development of multicellular organisms. In order to divide properly, a myriad of biochemical and mechanical events need to be precisely coordinated. Mechanical events, such as positioning of the mitotic spindle, segregation of chromosomes, and cytokinesis, depend on the material properties of the cytoplasm. For more than a century, studies have consistently shown that the cytoplasm behaves as a viscoelastic material, with properties changing throughout the cell cycle stages. Nonetheless, variation of viscoelasticity throughout the cell cycle and its importance for correct embryonic cell division remains poorly understood.We aim to understand how different cytoplasmic components contribute to the viscoelastic properties through different stages of the cell cycle, focusing on the centrosome positioning mechanisms. We approach this question by using textit{Xenopus Laevis} cytoplasmic extract, which recapitulates several mechanical and biochemical processes of embryonic cell divisions. Cytoplasmic extracts are valuable model systems because they combine the complexity of textit{in vivo} systems with a wide possibility to be biochemically and mechanically modified. Using magnetic tweezers and introducing magnetic particles into the cytoplasmic extract, we probe the mechanical properties of the bulk cytoplasm. This reveals drastic increases in the fluidity of the cytoplasm during mitosis.To examine the mechanics of centrosome positioning, we encapsulate cytoplasmic extract with artificial centrosomes in oil. Interestingly, the dynamics of microtubules cause centrosomes to oscillate around the geometric center of the droplet, reaching the center of the droplet consistently at a very precise cell cycle stage of the extract. Linking centrosome positioning and variability of viscoelastic properties of the cytoplasm might offer insight into the mechanics of cell division in large embryonic cells, a subject that continues to be debated. In the future, understanding the mechanical properties of cytoplasm in early embryonic cells could reveal a better understanding of human embryonic development, potentially addressing the challenge of textit{in vitro} fertilization failure.
https://indico.ijs.si/event/1754/

Jan Rozman, "Extensile-Contractile Phase Separation in an Active Nematic Vertex Model"
2023-09-14 14:00 - 15:30 | MPS lecture hall (IJS)
The importance of nematic order and active nematic behaviour to epithelial morphogenesis is becoming increasingly clear. Several approaches have been developed to adapt vertex models, one of the most ubiquitous methods of modelling epithelia, to also include nematic activity. Here, we use one of these modified vertex models to study the dynamics of a mixture of extensile and contractile cells. We find that the two cell population separate over time, with the degree of separation depending on the magnitudes of extensile and contractile activity. This phase separation appears to be driven by two mechanisms. Firstly, only extensile model cells are intrinsically motile on their own. Therefore, the two populations move at different speeds when mixed. Secondly, contractile activity in the vertex model leads to cells of that type ‘sticking’ together, preventing separation.
https://indico.ijs.si/event/1753/

Liam Scarratt: " Probing Aqueous Nanofluids Confined Between an Oil Droplet and a Charged Solid Surface"
2023-09-07 14:00 - 15:00 | C/0-106 – Seminarska soba fizike (F5) (Jamova)
https://indico.ijs.si/event/1718/

Prospecting for new physics using muons
2023-08-10 11:00 - 12:00 | Z9/0-0 – F1 čajnica (Jamova)
Speakers: Jure Zupan (University of Cincinnati)
https://zoom.us/j/3601731049?pwd=[REDACTED]
https://indico.ijs.si/event/1723/
