Department of Theoretical Physics

[Biophysics seminar] Robert Vácha: "How Non-Enveloped Viruses Can Infect Cells"
2022-05-10 13:00 - 14:00 (Europe/Ljubljana) | 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
The meeting will take place online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[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

[Biophysics seminar] Matej Kanduč: "Lipids’ dilemma: a monolayer or a bilayer?"
2021-11-23 13:00 - 14:00 | Zoom
Lipids are amphiphilic molecules and tend to self-assemble into various supramolecular formations. The most eminent among them is the lipid bilayer – also a continuous barrier around all cells. Some surfaces have the ability to unfold the bilayer and “coat” themselves with a single layer of lipids – the monolayer. In the talk, I will discuss what kinds of surfaces can do this. Lipid coatings are namely of viable importance in many biomedical applications owing to their biocompatibility.

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

[Biophysics seminar] Fabio Staniscia: "Surfactant-induced apparent line tension"
2021-11-16 13:00 - 14:00 | Zoom
Line tension is the tension generated at the three-phase contact line by the interaction between the phases, and is usually negligible at large sizes while becoming important at smaller scales. In this talk I will introduce the concept and show how the addition of a surfactant in water can have the effect of generating an effective line tension. I will discuss its effects on the properties of the system, as for instance on the contact angle of droplets on a substrate.

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

[Biophysics seminar] Julija Zavadlav: "Neural network potentials trained top-down"
2021-11-09 13:00 - 14:00 | Zoom
Molecular modeling has become a cornerstone of many disciplines, including soft matter physics. However, the quality of predictions critically depends on the employed model that defines particle interactions. A class of models with tremendous success in recent years are neural network (NN) potentials due to their flexibility and capacity of learning many-body interactions. Traditionally, these models are trained bottom-up on quantum mechanical data. Top-down approaches that learn NN potentials directly from experimental data have received less attention, typically facing numerical and computational challenges when backpropagating through molecular dynamics (MD) simulations. We recently developed the Differentiable Trajectory Reweighting (DiffTRe) method, which bypasses differentiation through the MD simulation for time-independent observables. Leveraging thermodynamic perturbation theory, we avoid exploding gradients and achieve around 2 orders of magnitude speed-up in gradient computation for top-down learning. The effectiveness of DiffTRe is showcased on atomistic and coarse-grained models using diverse experimental observables including thermodynamic, structural, and mechanical properties. Our approach opens the way to high fidelity molecular models, particularly when bottom-up data is unavailable or insufficiently accurate.

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

[Biophysics seminar] Boris Rogelj: "Molecular and cellular basis of neurodegeneration"
2021-10-26 13:00 - 14:00 | Seminarska soba fizike (106), Jozef Stefan Institute (Jamova 39), Ljubljana
I will describe the basic molecular processes associated with disruption of homeostasis in a nerve cell and leading to neurodegeneration. We are mainly engaged in research into the causes of amyotrophic lateral sclerosis and frontotemporal dementia. We look at the mechanisms associated with mutations and with the altered behavior of certain genes, RNAs, and proteins. In particular, we study the interactions of these molecules, and their roles in processes such as nuclear transport, cellular stress response, and liquid-liquid phase separations characteristic of the formation of nonmembrane organelles.

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

[Biophysics seminar] Andraž Gnidovec: "Simulating the packing of spherical ellipses"
2021-10-19 13:00 - 14:00 | F1 tearoom
Packing problems are abundant in nature and are thoroughly researched both experimentally and in numerical models. In particular, packings of anisotropic, elliptical particles emerge in models of liquid crystals, colloids, as well as granular and jammed matter. While most of these studies deal with packings in Euclidean geometries, there are many experimental systems where anisotropically shaped particles are confined to a curved surface, such systems of colloidal rods trapped at the interface of emulsion droplets, and protein adsorbates on vesicles.
In this talk, I will first present an algorithm we developed to determine overlaps between two spherical ellipses. More generally, the proposed method allows us to define a continuous contact function that could also be applied to long-range interactions, however, the use case as a distance metric must be considered with care. Returning to the main objective of the algorithm, I will demonstrate its efficiency in packing simulations. I will show the random close packing results for a monodispersed system of hard ellipses and present some challenges in the analysis of the configurations in comparison to the ellipse packings in Euclidean space.

The talk will be in the tea room at the F1 department. It will be simultaneously transmitted online via Zoom:
Meeting ID: 833 0750 1179
Passcode: bio

[Biophysics seminar] Antonio Šiber: "Mechanics of inactive swelling and bursting of porate pollen grains"
2021-10-05 13:00 - 14:00 | Zoom
The structure of pollen grains, which is typically characterized by soft apertures in an otherwise stiff exine shell, guides their response to changes in the humidity of the environment. These changes can lead to the desiccation of the grain and its infolding but also to excessive swelling of the grain and even its bursting. Here, we use an elastic model to explore the mechanics of pollen grain swelling and the role that soft, circular apertures (pores) play in this process. Small, circular apertures typically occur in airborne and allergenic pollen grains so that the bursting of such grains is important in the context of human health. We identify and quantify a mechanical weakness of the pores, which are prone to a rapid inflation once the grain swells to a critical extent. The inflation occurs as a sudden transition and may induce the bursting of the grain and the release of its content. This process crucially depends on the size of the pores and their softness. Our results provide insight in the inactive part of the mechanical response of pollen grains to hydration once they land on a stigma as well as on bursting of airborne pollen grains during changes in air humidity.

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

3rd trilateral meeting
2021-09-15 10:00 - 16:00 | Lanthieri mansion
This is an informal series of one day events meant to strengthen the scientific relations in astroparticle physics between Trieste, Nova Gorica and Ljubljana.
Organizing committee:
Andrea Romanino (SISSA)
Lorenzo Ubaldi (SISSA)
Gabrijela Zaharijas (UNG)
Miha Nemevšek (IJS)
Next meeting (host UNG)
Venue: Lanthieri Mansion, Vipava
Date: Sept 15, 2021
Note: the plan is to have a meeting in presence if allowed by the pandemic conditions at that time.
Current rules require that all UNG visitors meet the ‘PCT’ requirement (equivalent to the Green pass in Italy), i.e. to be either vaccinated, have a negative test (quick-antigen test not older than 48h) or a proof that they had COVID within past 6 months. It is likely that this proof will need to be shown within the government mobile app (more details soon).

Preliminary program:

entrance hall of the Lanthieri mansion or the park in front of the building (if weather allows)
9.45 – 10.15 coffee break (+Green pass/PCT control)
Aula Magna, Lanthieri (first floor)
10.15 – 11.15 Pasquale Serpico (LAPTh, Annecy): high-energy photon probes of ‘unusual’ dark matter candidates” (will cover PBHvia X-ray probes and the potential of ground-based instruments like HAWC, Tibet, LHAASO too look for heavy DM decay).
11.30 – 12.15 Tanja Petrushevska (UNG), how to use multimessenger astrophysics to constrain Axion-Like-Particles (Paper and follow-up study ) and in general about Vera Rubin Observatory (LSST) activities at UNG
restaurant Theodosius
12.30 Lunch
Aula Magna, Lanthieri (first floor)
14.00 – 14.45 Miha Petac (LUPM, Montpellier), Using machine learning with Gaia data to constrain dark matter Galactic substructures
14.45 – 15.30 Gabrijela Zaharijas (UNG), using machine-learning to discover faint Fermi LAT point sources and determine the nature of the GCE and/or the CTA sensitivity to multi-TeV DM
http://www.ung.si/en/research/cac/Events/Trilateral
https://indico.ijs.si/event/1296/

Jure Zupan: Muonic Force Behind Flavor Anomalies
2021-07-22 11:00 - 11:45 | Seminarska soba fizike, Jamova 39, Ljubljana, Slovenia
Muonic Force Behind Flavor Anomalies
https://indico.ijs.si/event/1307/

Olcyr Sumensari: TBA
2021-06-22 10:15 - 11:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1300/

[Biophysics seminar] Primož Ziherl and Matej Krajnc: "Biophysics of membranes, cells, and tissues"
2021-06-04 13:00 - 15:30 | Zoom
Meeting ID: 990 5563 4981
Passcode: bio

Shaikh Saad: New Physics Solutions to Lepton Anomalous Magnetic Moments
2021-05-27 10:15 - 11:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
Recent precise measurement of the electron anomalous magnetic moment (AMM) adds to the longstanding tension of the muon AMM and together strongly point towards physics beyond the Standard Model. In this talk, I present an overview of simultaneous solutions to lepton AMMs; both possibilities of new physics states appearing below and above the electroweak scale are discussed.
https://indico.ijs.si/event/1295/

[Biophysics seminar] Matjaž Humar: "Microlasers and microcavities for sensing, barcoding and imaging"
2021-05-14 13:00 - 14:00 | Zoom
Zoom meeting ID: 990 5563 4981
Passcode: bio
