Department of Theoretical Physics

[Biophysics seminar] Fabio Staniscia: "Adsorption at a curved interface"
2022-10-13 14:00 - 15:00 (Europe/Ljubljana) | Seminar room of physics (106)
We study the effect of curvature of the interface on the adsorption properties of water droplets. Using a computational approach we show a decrease in the adsorption strength with the droplet curvature, which is accompanied by a decrease of surface tension. We investigate theoretically the causes and implications of this phenomenon.

The meeting will take place in the seminar room of physics (106).

[Biophysics seminar] Horacio Guzman: "RNA-substrate interactions"
2022-10-06 11:00 - 12:00 | Zoom
The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] María Pedrosa Bustos: "Biophysics approach in anticancer therapies: Studying anticancer drug interactions with extracted and model cell membranes by Langmuir films and computer simulations"
2022-08-18 15:00 - 16:00 | F1 tearoom
María Pedrosa Bustos, a visiting PhD student from the Biocoloids and Fluid Physics Group of the University of Granada, will give a talk on “Biophysics approach in anticancer therapies: Studying anticancer drug interactions with extracted and model cell membranes by Langmuir films and computer simulations” in preparation for her talk at the next week’s regional biophysics conference.

[Biophysics seminar] Haim Taitelbaum: "Spreading of Metal on Metal-on-glass at Room Temperature"
2022-07-19 12:30 - 13:30 | F1 tearoom
We study the spreading of mercury droplets on thin metal (silver or gold) films on glass at room temperature, which is the only known system of reactive-wetting at room temperature. We show that there exist two main regimes, the bulk propagation regime and the interface kinetic roughening regime. In both regimes, rich spatio-temporal patterns are observed. We characterize these patterns using statistical physics tools, such as the growth, roughness and persistence exponents, and show some recent exotic DLA-like patterns obtained in experiments.

The meeting will take place in the tea room of the F1 department.

Philipp Schicho: Gauge-invariant bubble nucleation rate in finite temperature effective field theory
2022-07-07 11:00 - 12:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
A gauge-invariant framework for computing bubble nucleation rates at finite temperature in the presence of radiative barriers was presented and advocated for model-building and phenomenological studies in an accompanying article arXiv:2112.05472. Here, we detail this computation using the Abelian Higgs Model as an illustrative example. Subsequently, we recast this approach in the dimensionally-reduced high-temperature effective field theory for nucleation. This allows one to include several higher order thermal resummations and furthermore delineate clearly the approach’s limits of validity. This approach provides for robust perturbative treatments of bubble nucleation during possible first order cosmic phase transitions, with implications for electroweak baryogenesis and production of a stochastic gravitational wave background. Furthermore, it yields a sound comparison between results of perturbative and non-perturbative computations.
https://indico.ijs.si/event/1443/

5th Trilateral meeting (tentative) at ICTP/IFPU
2022-06-30 10:00 - 16:00 | TBD (ICTP/IFPU)
The trilateral meetings are a series of one day events designed to strengthen the scientific relations in particle, astroparticle physics and cosmology between Trieste, Nova Gorica and Ljubljana.
The venue will be posted soon.
Organizing committee:
Miha Nemevšek (IJS)
Andrea Romanino (SISSA)
Lorenzo Ubaldi (INFN)
Gabrijela Zaharijas (UNG)
Past meetings
Ljubljana meeting, 16 December 2021 at IJS
Nova Gorica meeting, 15 September 2021 at Vipava
Trieste meeting, 5 February 2020 at IFPU
Ljubljana meeting, 17 October 2019 at IJS

https://indico.ijs.si/event/1419/

Barry Dillon: What's Anomalous in LHC Jets?
2022-06-23 11:00 - 12:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
Searches for anomalies are the main motivation for the LHC and define key analysis steps, including triggers. We discuss how LHC anomalies can be defined through probability density estimates, evaluated in a physics space or in an appropriate neural network latent space. We illustrate this for classical k-means clustering, a Dirichlet variational autoencoder, and invertible neural networks. For two especially challenging scenarios of jets from a dark sector we evaluate the strengths and limitations of each method.
https://indico.ijs.si/event/1425/

Joe Davighi: TBA
2022-06-09 11:00 - 12:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1429/

Francesco D'Eramo: TBA
2022-06-02 11:00 - 12:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1423/

Svjetlana Fajfer: Triple-leptoquark interactions for tree- and loop-level proton decays
2022-05-26 11:00 - 12:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
We study the impact of triple-leptoquark interactions on matter stability for two specific proton decay topologies that arise at the tree- and one-loop level. We demonstrate that the one-loop level topology is much more relevant than the tree-level one when it comes to the proton decay signatures despite the usual loop-suppression factor. Since the two proton decay topologies necessarily coexist, our study renders any phenomenological limits inferred from the tree-level topology redundant for all practical purposes. We subsequently present detailed analysis of the triple-leptoquark interaction effects on the proton stability within one representative scenario to support our claim, where the scenario in question simultaneously features a tree-level topology that yields three-body proton decay p→e+e+e− and a one-loop level topology that induces two-body proton decays p→π0e+ and p→π+ν¯. We also provide a comprehensive classification of all non-trivial cubic and quartic contractions involving three scalar leptoquark multiplets that generate triple-leptoquark interactions of our interest, where in the latter case one of the scalar multiplets is the Standard Model Higgs doublet.
https://indico.ijs.si/event/1417/

Miguel Vanvlasselaer: Dark Matter production from relativistic bubble walls
2022-05-19 11:00 - 12:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
In this paper we present a novel mechanism for producing the observed Dark Matter (DM) relic abundance during the First Order Phase Transition (FOPT) in the early universe. We show that the bubble expansion with ultra-relativistic velocities can lead to the abundance of DM particles with masses much larger than the scale of the transition. We study this non-thermal production mechanism in the context of a generic phase transition and the electroweak phase transition. The application of the mechanism to the Higgs portal DM as well as the signal in the Stochastic Gravitational Background are discussed.
https://indico.ijs.si/event/1421/

Saša Prelovšek: Evidence for a doubly charm tetraquark pole from lattice QCD
2022-05-12 11:00 - 12:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
Recently LHCb collaboration discovered a doubly charmed tetraquark (Tcc) with exotic flavor content ccud slightly below DD* threshold. I’ll present the first lattice QCD determination of DD* scattering amplitude which is needed to theoretically establish Tcc. The resulting scattering amplitude provides a signature for a pole related to Tcc for the first time with ab-initio methods.
https://indico.ijs.si/event/1424/

[Biophysics seminar] Robert Vácha: "How Non-Enveloped Viruses Can Infect Cells"
2022-05-10 13:00 - 14:00 | Zoom
Non-enveloped RNA viruses are composed of a genome protected by a protein shell called a capsid. At the beginning of infection, these viruses get inside the cell and release their genome from the capsid, so the genome can start to be replicated, leading to the production of new copies of the virus. We developed a phenomenological model of an icosahedral virus capsid with a genome and used it to investigate how the virus can get inside the cell. We have shown that virus or virus-like nanoparticles with the right properties can enter the cell spontaneously, i.e., without ATP. Moreover, we demonstrated that the subsequent release of genome/cargo could occur via a rapid or slow pathway, which is mainly determined by the interaction range between capsid subunits. These findings could aid in the development of anti-viral drugs or assist in the design of virus-like nanoparticles for drug delivery.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

Kaladi Babu: TBA
2022-05-05 16:00 - 17:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1422/

[Biophysics seminar] Veronika Bukina (TBA)
2022-05-03 13:00 - 14:00 | Zoom

Nejc Košnik: LFU and CP violation with S3
2022-04-14 11:00 - 12:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
We introduce the CP violating scalar leptoquark S3 to explain the measured values of the lepton universality ratios RK(∗). We derive constraints on the CP-even and CP-odd components of the leptoquark Yukawa couplings stemming from effects in b → sμμ and Bs mixing. For the b → sμμ processes we impose RK(∗), B(Bs → μ+μ−), as well as CP-sensitive angular asymmetries A7,8,9, whereas in the Bs mixing sector ∆Ms and Sψφ are considered. Combining the constraints within the S3 model reveals that a large CP phase with a definite sign is perfectly viable for a leptoquark of mass below a few TeV. For larger mass of the S3 leptoquark the CP phase is suppressed due to the observables pertaining to the Bs system. We provide predictions of direct and mixing-induced CP asymmetries in B → Kμμ that could reveal the presence of the novel CP phase.
https://indico.ijs.si/event/1420/

[Biophysics seminar] Aljaž Godec: "From the kinetic Ising model to specific cell adhesion, and back"
2022-03-29 13:00 - 14:00 | Zoom
By exploiting a mapping onto a kinetic Ising-like model we will illuminate the many-body effects underlying the structure, formation, and dissolution of cellular adhesion domains in the presence and absence of external forces. We will present analytical results on the pair-correlation level for the complete thermodynamics and kinetics of adhesion clusters of any size, including the thermodynamic limit. A new kind of dynamical phase transition will be demonstrated: the mean formation and dissolution times per adhesion bond change discontinuously with respect to the bond-coupling parameter that in turn is controlled by the membrane rigidity. At the dynamical critical point, adhesion cluster formation and dissolution are the fastest, while the statistically dominant transition path undergoes a qualitative change. In the context of the classical Ising model the dynamical phase transition reflects a first order discontinuity in the magnetization-reversal time. Will will conclude by briefly discussing the relevance of these results for the mechanical regulation of cell adhesion, and argue that it is biologically favorable if cell adhesion is poised at criticality.
[1] K. Blom & A. Godec, Phys. Rev. X 11, 031067 (2021).

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Simon Čopar: "Hyperuniformity and spherical structure factor"
2022-03-24 13:00 - 14:00 | Zoom
Hyperuniformity is an interesting measure of order which detects and quantifies long range positional correlations without requiring local crystalline order. This measure can be defined in real space, through scaling of fluctuations of the number of building blocks in asymptotically large volumes, or in frequency space, where hyperuniformity manifests as a gap in the structure factor.
I will review the hyperuniformity concepts and highlight the main obstacles and solutions that arise when dealing with a spherical geometry. I will present it on a few model spherical lattices.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Mauricio Comas-García: "Understanding selective packaging in Alphaviruses"
2022-03-17 15:00 - 16:00 | Zoom
Alphaviruses are a genus of positive-sense single-stranded RNA viruses that infect mammals and are transmitted by mosquitos. These viruses can cause a wide range of diseases, from dengue-like symptoms (e.g., Chikungunya virus) to encephalitis (e.g., Venezuelan Equine Encephalitis virus). While during the ’80 and ’90s, there was a great deal of interest in studying these viruses, with time, other pathogens became more attractive for research purposes. However, the spread of the Chikungunya virus during the beginning of the XXI century to Asia, Oceania, and the Americas has brought new attention to these viruses.
These viruses have been widely studied from several aspects; structural biology, epidemiology, and immunology. For example, we know the 3D structure of most of these viruses with almost an atomic detail. Furthermore, a series of in vitro assembly experiments have shed light on some of the key RNA-protein interactions that are needed for core-like-practice assembly. Nonetheless, there is very little information on how these viruses select their genome during infection.
Our group has been working on creating a series of plasmids for expression in mammalian cells that contain a series of viral elements from the Chikungunya virus. The goal of these constructs is to generate a system that allows us to carry out competition experiments between mutant and wild-type viral RNAs in infected cells to find the packaging signal in the genomic RNAs that allows for its selective packaging. In this seminar, we will present some preliminary results and the strategy we are following to understand how RNA structure and sequence determine selective packaging in an infected cell.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Horacio Guzman: "Polymer swelling model based on dynamic AFM experiments"
2022-03-08 13:00 - 14:00 | Zoom

[Biophysics seminar] Gregor Posnjak: "From DNA origami to photonic crystals"
2022-03-01 13:00 - 14:00 | Zoom
The idea of using the predictable base pairing of DNA nucleobases for programmable assembly on the nanoscale dates back to the 1980s when the recently deceased Ned Seeman had the idea of using it to crystalize proteins on a DNA-based lattice for their structure determination with x-ray crystallography. After the first successful DNA nanostructures in the 1990s, the real boom came after 2006 when the concept of DNA origami was introduced. The use of a long DNA scaffold strand in combination with short staple strands eliminated many of the short-comings of the earlier approaches and enabled robust programmable assembly with resolution on the order of nanometers.
In the first part of the talk I will introduce the concept of DNA origami and give a short review of the various structures and super-structures that were developed and their applications in drug delivery, biophysics, super-resolution microscopy, sensing and plasmonics. In the second part I will shortly introduce photonic crystals as motivation for my work and then present a DNA-origami based self-assembled diamond lattice, which we will use as a template for realization of visible spectrum photonic crystals.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Jaffar Hasnain: "Spontaneous emulsification induced by nanoparticle surfactants"
2022-02-22 13:00 - 14:00 | Zoom
Microemulsions, mixtures of oil, water, and surfactant, are thermodynamically stable. Unlike conventional emulsions, microemulsions form spontaneously, have a monodisperse droplet size that can be controlled by adjusting the surfactant concentration, and do not degrade with time. To make microemulsions, a judicious choice of surfactant molecules must be made, which significantly limits their potential use. Nanoparticle surfactants, on the other hand, are a promising alternative because the surface chemistry needed to make them bind to a liquid-liquid interface is both well flexible and understood. Here, we derive a thermodynamic model predicting the conditions in which nanoparticle surfactants drive spontaneous emulsification that agrees quantitatively with experiments using Noria nanoparticles. This new class of microemulsions inherits the mechanical, chemical, and optical properties of the nanoparticles used to form them, leading to novel applications.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Matej Krajnc
2022-02-15 13:00 - 14:00 | Zoom

[Biophysics seminar] Tomer Stern: "Deconstructing Gastrulation at Single-Cell Resolution"
2022-01-25 13:00 - 14:00 | Zoom
Gastrulation movements in all animal embryos start with regulated deformations of patterned epithelial sheets. Current studies of gastrulation use a wide range of model organisms and emphasize either large-scale tissue processes or dynamics of individual cells and cell groups. In this work I take a step towards bridging these complementary strategies and deconstruct early stages of gastrulation in the entire Drosophila embryo, where transcriptional patterns in the blastoderm give rise to region-specific cell behaviors. This approach relies on an integrated computational framework for cell segmentation and tracking and on efficient algorithms for event detection. Our results reveal how thousands of cell shape changes, divisions, and intercalations drive large-scale deformations of the patterned blastoderm, setting the stage for systems-level dissection of a pivotal step in animal development.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Urška Andrenšek: "The continuum approximation of the vertex model"
2022-01-18 13:40 - 14:20 | Zoom
The continuum-mechanics approach to the vertex model is useful to understand the phenomenology of tissue deformations during morphogenesis. I will review the past attempzs to derive the continuum theory and compare the theoretical results to the results of numerical simulation. Finally, I will discuss a more general approach to derivation of the continuum approximation of the vertex model.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Domen Vaupotič: "Viral RNA as a randomly branching polymer"
2022-01-18 13:00 - 13:40 | Zoom

[Biophysics seminar] Marin Šako: "Soft matter under tension and cavitation"
2022-01-11 13:00 - 14:00 | Zoom

[Biophysics seminar] Toshikaze Chiba: "Deformation and rearrangement of membranes in adhering vesicles"
2022-01-04 13:00 - 14:00 | Zoom
Vesicle is a molecular assembly configuring lipid bilayer shell, and investigated as a model system of biological cell. Using both experimental observation and minimising the total energy, we study the morphology of lipid vesicle doublet and triplet. We demonstrate that non-uniform tension in contact and non-contact zone can control a variety of different shape, which is reminiscent of the four-cell stage in embryogenesis. Our results can be extended to the multiple adhering vesicles, we briefly introduce our recent work in microfluidics experiment as a next step.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Clement Zankoc: "Active Instability and Nonlinear Dynamics of Cell-Cell Junctions"
2021-12-07 15:00 - 16:00 | Zoom
Active cell-junction remodeling is important for tissue morphogenesis, yet its underlying physics is not understood. We study a mechanical model that describes junctions as dynamic active force dipoles. Their instability can trigger cell intercalations by a critical collapse. Nonlinearities in tissue’s elastic response can stabilize the collapse either by a limit cycle or condensation of junction lengths at cusps of the energy landscape. Furthermore, active junction networks undergo collective instability to drive active in-plane ordering or develop a limit cycle of collective oscillations, which extends over regions of the energy landscape corresponding to distinct network topologies.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Tanmoy Sarkar: "A minimal lattice model of lipid membranes with liquid-ordered domains"
2021-11-30 13:00 - 14:00 | Zoom
Binary or ternary mixtures of lipids and cholesterol featuring liquid-ordered (Lo) domains serve as model systems for studying the formation of lipid rafts in complex biological membranes. In the talk, I will present a new lattice model of a binary mixture of saturated DPPC lipids and cholesterol, which is the simplest model system exhibiting Lo domains in the sea of liquid-disordered (Ld) matrix. Simulations of mixtures of thousands of lipids and cholesterol molecules on time scales of hundreds of microseconds reveal a phase diagram that is in complete agreement with the well-established phase diagram of this mixture. The simulations provide important information on the morphologies and lifetime of the Lo domains which are not available by more detailed computational approaches. Strikingly, the lattice simulation also reproduces local structures that have been observed in atomistic simulations. Specifically, we find that the Lo domains are highly heterogeneous and consist of gel-like hexagonally packed clusters of ordered DPPC chains, surrounded by cholesterol-rich regions at the domain boundaries. The simulation results are explained by a new thermodynamic mechanism that considers the disparity between the packing interactions of ordered lipid chains with cholesterol and each other.

The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio
