Jure Zupan: TBA
2022-12-22 11:15 - 12:15 (Europe/Ljubljana) | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
https://indico.ijs.si/event/1549/

[Biophysics journal club] Domen Vaupotič: "Elastic properties and shape of the Piezo dome underlying its mechanosensory function"
2023-01-05 14:00 - 15:00 | Seminar room of physics (106)
We will be discussing the following paper: https://www.pnas.org/doi/full/10.1073/pnas.2208034119 (“Elastic properties and shape of the Piezo dome underlying its mechanosensory function”).

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

[Biophysics seminar] Jan Rozman: "Shape-tension coupling produces nematic order in an epithelium vertex model"
2023-01-10 14:00 | F1 tearoom
We study the vertex model for epithelial tissue mechanics extended to include coupling between the cell shapes and tensions in cell-cell junctions. This coupling represents an active force which drives the system out of equilibrium and leads to the formation of nematic order interspersed with prominent, long-lived +1 defects. The defects in the nematic ordering are coupled to the shape of the cell tiling, affecting cell areas and coordinations. This intricate interplay between cell shape, size, and coordination provides a possible mechanism by which tissues could spontaneously develop long-range polarity through local mechanical forces without resorting to long-range chemical patterning.

The seminar will take place in the tearoom of the F1 department.

Maciej Kierkla: Conformal model for gravitational waves and dark matter. A status update
2023-01-12 11:15 - 12:15 | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
We present an updated analysis of the first-order phase transition associated with symmetry breaking in the early Universe in a classically scale-invariant model extended with a new SU(2) gauge group.
Including recent developments in understanding supercooled phase transitions, we compute all of its characteristics and significantly constrain the parameter space. We then predict gravitational-wave spectra generated during this phase transition and by computing the signal-to-noise ratio we conclude that this model is well testable (and falsifiable) with LISA. We also provide predictions for the relic dark matter abundance. It is consistent with observations in a rather narrow part of the parameter space, as we exclude the so-called supercool dark matter scenario based on an improved description of percolation and reheating after the phase transition as well as inclusion of the running of couplings.
Finally, we pay special attention to renormalisation-scale dependence of the results and even though our main results are obtained with the use of renormalisation-group improved effective potential, we also present the outcome of a fixed-scale analysis. It proves that the dependence on the scale is not only qualitative but also quantitative.
https://indico.ijs.si/event/1555/

[Biophysics journal club] Urška Andrenšek: "Muscular hydraulics drive larva-polyp morphogenesis"
2023-01-12 14:00 - 15:00 | Seminar room of physics (106)
The meeting will take place in the seminar room of physics (room 106).

Luka Leskovec: A lattice QCD study of B → π π l 𝜈
2023-01-19 11:15 - 12:15 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
$V_{ub}$ is the smallest and least known of all CKM matrix elements; it’s currently determined primarily through the exclusive process B → π l 𝜈. I will present progress toward a lattice QCD determination of the $V_{ub}$​ matrix element from a novel transition — the B → π π l 𝜈 process, where the π π system is in a P-wave and features the ρ(770) resonance as an enhancement. The calculation is performed an ensemble with $N_f​=2+1$ isotropic clover fermions wiht $L≈3.6$ fm and a pion mass of 320 MeV; for the b-quark we use the anisotropic clover action. After a brief overview of the theoretical framework, I will discuss some preliminary results.
https://indico.ijs.si/event/1548/

[DBS lunch seminar]: Marko Gosak, "Quantifying Calcium Activity Patterns in Normal and Diabetic Pancreatic Islets of Langerhans with Network Analyses"
2023-01-19 14:00 - 15:30 | Lecture hall of IPS (MPŠ)
Islets of Langerhans consist of a large functional syncytium of beta cells that produce pulses of insulin, a key component for controlling metabolic homeostasis. In response to stimulation, the islet cells display rather well-coordinated intercellular activity patterns, which was found crucial for ensuring normal secretory patterns. However, it is not clear how coordinated cellular rhythmicity emerges within the heterogeneous cellular collectives and how it is altered in diabetes. To address these questions, we combined multicellular calcium imaging in mouse pancreatic tissue slices as well as in isolated human islets with advanced network analyses. Describing the intercellular activity patterns by means of network language has not only revealed that intercellular networks in islets share many architectural similarities with several other real-life networks, such as small-worldness, heterogeneity, and modularity, but also leads to important new insights into the relationship between cellular metabolic activity and the orchestration of collective behaviour [1,2]. Importantly, analyses of islets from diabetic donors have revealed that the intercellular activity in these islets is characterized by a lower fraction of global calcium waves and more segregated network structures [3]. However, there was a rather large variability in responses in islets from donors with diabetes, with some exhibited striking pathophysiological changes, whilst others behaved rather normally. This great heterogeneity in susceptibility of different islets towards diabetogenic insults should be considered as an important aspect by conducting further research on the pancreatic islets.

Figure: Analysis of calcium activity in the pancreatic cells in the islets of Langerhans and the generation of functional intercellular networks.

[1] Gosak M, et al., Network science of biological systems at different scales: A review, Physics of Life Reviews 2018, 24.
[2] Stožer A, et al., From isles of Königsberg to islets of Langerhans: Examining the function of the endocrine pancreas through network science, Frontiers in Endocrinology 2022, 922640.
[3] Gosak M, et al., Ca2+ oscillations, waves, and networks in islets from human donors with and without type 2 diabetes, Diabetes 2022, 71.

The seminar will take place in the lecture hall of the International Postgraduate School (MPŠ, https://www.mps.si/en/o-nas/lokacija/) at the Jožef Stefan Institute. It will be followed by discussion and snacks.

[Biophysics seminar] Tanmoy Sarkar
2023-01-26 14:00 - 15:00 | Seminar room of physics (106)
I will present a new approach to studying epithelial mechanics, which is based on representing the tissue structure by a graph. As a proof of concept, I will study a tissue with random cell rearrangements and compare the results with an alternative approach, based on a Markov chain.

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

Oliver Gould: Effective field theory for cosmological phase transitions
2023-02-02 11:15 - 12:15 | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
A cosmological first-order phase transition would have given rise to a stochastic gravitational wave background which may be observable today. Phase transitions are driven by thermal loop fluctuations, which modify background fields at leading order. This breaks the usual loop expansion and leads to large theoretical uncertainties in typical calculations, especially for gravitational wave predictions. I will give an overview of our present understanding of these uncertainties, and of the tools that have been developed to overcome them. Effective field theory has been at the forefront of this development, and I will outline how it solves a number of long-standing theoretical problems.

https://indico.ijs.si/event/1551/

[Biophysics seminar] Fabio Staniscia: "Heat release effect in domain relaxation of long-range interacting systems"
2023-02-02 14:00 - 15:00 | Seminar room of physics (106)
The meeting will take place in the seminar room of physics (106).

Robert Harlander: TBA
2023-02-16 11:15 - 12:15 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1547/

[DBS lunch seminar] Denis Kutnjak: "Environmental virology and virus ecology: from plant virus diversity to monitoring SARS-CoV-2 in wastewater"
2023-02-16 14:00 - 15:30 | Seminar room of physics (106)
Abstract
Viruses likely represent the most diverse part of the biosphere; nevertheless, a large part of their diversity is still unknown. Viromics approaches, based on high-throughput sequencing, enable the studies of virus diversity inside and outside of their hosts, in different environments, where some viruses can persist for long periods of time. In the past few years, we have addressed the diversity of viruses in crop and wild plants, invertebrates, and different water types. We discovered several previously unknown viruses, mostly in wild plants and in surface water samples. Using viromics, we have also discovered a diverse set of nucleic acids of viruses infecting plants in wastewater and demonstrated their infectivity even after wastewater treatment using classical virology approaches. During the SARS-CoV-2 pandemic, we have extended wastewater analyses to measurements of the concentrations and detection of variants of this virus in wastewater from different Slovenian wastewater treatment plants. This resulted in a very early establishment of such monitoring on a national scale, which now helps us to better understand the epidemiological trends of SARS-CoV-2. In this lecture, different cases of research from the fields of virus discovery, environmental virology, virus ecology, and wastewater epidemiology will be presented.

Event information
The seminar will take place at 14h in the seminar room of physics (106) in the main building of Jožef Stefan Institute. The seminar will start with a snack (pizza) and will be followed by an informal discussion.

Ilja Doršner: Fully Testable Axion Dark Matter within a Minimal SU(5) Unification Model
2023-02-23 11:15 - 12:15 | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
I will present a minimal Grand Unified Theory model, based on an SU(5) gauge symmetry and a global U(1) Peccei-Quinn symmetry, that predicts the existence of an ultralight axion dark matter within a narrow mass range between 0.1 neV and 4.7 neV. This mass window is determined through an interplay between gauge coupling unification constraints, partial proton decay lifetime limits, and the need to reproduce the experimentally observed fermion mass spectrum. The entire parameter space of the proposed model will be probed through a synergy between several low-energy experiments that look for proton decay (Hyper-Kamiokande), axion dark matter through axion-photon coupling (ABRACADABRA and DMRadio-GUT) and nucleon electric dipole moments (CASPEr Electric).
https://indico.ijs.si/event/1541/

[Biophysics journal club] Marin Šako: "Bicelle-to-Vesicle Transition"
2023-02-23 14:00 - 15:00 | Seminar room of physics (106)
Vesicles are of great research interest as they not only form naturally but are also artificially produced as liposomes, primarily used as a drug (including vaccines) delivery mechanism, owning to their biocompatibility with the cell membrane. An essential step of liposome formation is the transition from a bicelle to a vesicle. In this seminar, I will talk about the aforementioned transition, under what conditions it occurs, and how temperature and lipid composition affect the transition process.

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

Sašo Grozdanov: TBA
2023-03-02 11:15 - 12:15 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1485/

[Biophysics seminar] Marc Cabases: "Interaction of SARS-CoV-2 with surfaces and surfactants: Molecular dynamics simulations"
2023-03-02 14:00 - 15:00 | Seminar room of physics (106)
I will talk about the work accomplished for two years of my PhD. First, I will explain the simulations of the interaction between the spike protein and human skin. Using all-atom (AA) simulations we showed which are the relevant residues of the S protein interacting with the skin. I will also talk about surfactants-SARS-CoV-2 interaction. Surfactants are typycally used as disinfection agents in personal care products against bacteria and viruses, including SARS-CoV-2. However, there is a lack of understanding of the molecular mechanisms of the inactivation of viruses by surfactants. We employed coarse grain (CG) and AA molecular dynamics simulations to investigate the interaction between surfactants and the SARS-CoV-2 virus.

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

[Biophysics seminar] Horacio Guzman, "Adsorption patterns of the WT, delta and omicron RBDs onto polarized model surfaces"
2023-03-07 14:00 - 15:00 | F1 tearoom
Respiratory viruses are airborne and commonly form microdroplets which can be easily adsorbed onto surfaces of different materials, like plastics, metals or skin. Although these situations occur on a daily basis, less is known about the mechanisms and effectiveness of the virus-materials interaction. In particular, when spike proteins mutate in the binding regions, as is the case of SARS-CoV-2 where several residues mutated in the Receptor-Binding-Domain (RBD) and correspond to different Variants of Concern (VoC). Potentially, simplified modeled surfaces with manifold polarities and characterized by a contact-angle can serve as sensors to assess the adsorption mechanisms of virus proteins. Here, we perform extensive molecular dynamics simulations of three RBDs interacting with hydrophobic and hydrophilic substrates. Overall, the simulations show a higher amount of contacts with the hydrophobic surface, in spite of the H-bonds formed at the hydrophilic substrate. Considering two regions of adsorption at the RBD-surface interface with the same total amount of residues, we show how the regions balances out (hops) during adsorption and favors contact formation.

The seminar will take place in the tearoom of the F1 department.

[Biophysics seminar] Anže Božič: "Changes in number of dissociable amino acids on spike proteins and nucleoproteins of SARS-CoV-2 variants and other coronaviruses"
2023-03-16 14:00 - 15:00 | Seminar room of physics (106)
The seminar will take place in the seminar room of physics (106).

Patrick Bolton: Probing the Nature of Heavy Neutral Leptons in Direct Searches and Neutrinoless Double Beta Decay
2023-03-23 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
In this seminar, I will discuss recent efforts to assess the complementarity of direct searches at fixed target experiments and searches for neutrinoless double beta (0νββ) decay in probing the Majorana vs. pseudo-Dirac nature of a Heavy Neutral Lepton (HNL) pair. Firstly, I will outline a phenomenological parametrisation relating the active-sterile mixing strengths to the neutrino oscillation data, assuming that the HNL pair generates masses for two light neutrinos. I will then summarise the possible constructive or destructive interference of the HNL pair with the light neutrino contribution in 0νββ decay and the production and decay of HNLs in fixed target experiments, which depend on the active-sterile mixing strengths and CP phases in the HNL sector. Finally, I will show what signals at LEGEND-1000 and DUNE (or a signal at one or neither of the experiments) imply about the HNL parameter space; in particular, the mass splitting between the HNL pair.
https://indico.ijs.si/event/1561/

Benjamin Fuks: Composite dark matter: simplified models, non-minimality and overlooked channels
2023-03-30 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
Studies of dark matter lie at the interface of collider physics, astrophysics and cosmology, and they entail comparisons with a wide spectrum of data. We consider an effective top-philic t-channel model of dark matter, which finds some motivation in composite theories. We make use of a general framework allowing for precision predictions from the sole knowledge of the model’s Lagrangian to investigate the resulting phenomenology both at colliders and in cosmology. We then explore some of the non-minimal features of the model, and we additionally highlight overlooked search channels that are relevant for generalised version of the models.
https://indico.ijs.si/event/1430/

[DBS lunch seminar] Uroš Tkalec: "From microcargo transport at liquid crystal/water interfaces to volumetric microscopy of anisotropic fluids"
2023-03-30 14:00 - 15:30 | Seminar room of physics (106)
Abstract
Microcargo transport between immiscible fluids, usually water and unstructured oils, is a physical process essential in adsorption and separation, emulsification, liquid-liquid extraction, and drug delivery. However, in conventional water-oil systems, it is difficult to manipulate the direction of cargo transport from one liquid to another. To address these issues, we have designed a series of drop impact experiments with liquid crystal interfaces where we can selectively trigger mass transport by tuning the mesophases and post-impact dynamics. To study such phenomena in more detail, we aim to explore the potential of quantitative volumetric microscopy based on the principle of holography. Recently, numerous advances have been made in optical imaging of anisotropic fluids, including stimulated emission depletion, and light sheet microscopy. However, these modalities are not label-free and are generaly not fast enough to follow dynamic processes. Therefore, we will develop an experimental setup for digital holographic microscopy to quantify the morphology and spatial refractive index distribution of anisotropic fluids at microscale interfaces.

Event information
The seminar will take place at 14h in the seminar room of physics (106) in the main building of Jožef Stefan Institute. The seminar will start with a snack (pizza) and will be followed by an informal discussion.

Ana M. Teixeira: TBA
2023-04-06 11:15 - 12:15 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1569/

Florian Goertz: TBA
2023-04-06 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (F1 tea room)
https://indico.ijs.si/event/1613/

[Biophysics journal club] Matej Kanduč, "The mystery of nanobubbles: How come they exist?"
2023-04-13 14:00 - 15:00 | Seminar room of physics (106)
The industry of nanoscopic bubbles is booming. Nanobubbles are used in various industries, from agriculture and water treatment to humane medicine. Yet, in the academic world, the existence of nanobubbles has attracted both skepticism and intrigue since classical theory predicts that gas bubbles cannot achieve stable equilibrium. Can we prove these gaseous domains exist, and if they do, how do they survive? I will review contemporary theoretical perspectives on the stability of nanobubbles and explain how experiments either vindicate or disprove them.

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

Yutaro Shoji: TBA
2023-04-20 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1600/

[Biophysics seminar] Domen Vaupotič, "Analiza razvejenosti genomov virusov RNA"
2023-04-20 14:00 - 15:00 | Seminar room of physics (106)

Paolo Benincasa
2023-04-27 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1608/

Ben Stefanek
2023-05-04 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
https://indico.ijs.si/event/1609/

Elena Santopinto: TBA
2023-05-11 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
TBA
https://indico.ijs.si/event/1595/

Jonathan Kriewald: Heavy Neutrino effects on leptonic Higgs, $W$ and $Z$ decays in the inverse seesaw
2023-05-18 14:00 - 15:00 | https://zoom.us/j/3601731049?pwd=[REDACTED] (Zoom)
In addition to their role in well-motivated mechanisms of neutrino mass generation, heavy neutral leptons (HNL) can be at the source of an extensive array of new phenomena, which are forbidden (or strongly suppressed) in the Standard Model (SM), several manifesting the possible Majorana nature of the extended neutral lepton sector.
These phenomena include lepton number violating (LNV) processes such as (semi) leptonic tau and meson decays, charged lepton flavour violating (cLFV) transitions (including radiative and three-body decays, $Z$ and Higgs bosons decays, as well as rare phenomena in the presence of matter).
Such heavy Majorana fermions are also expected to have a significant
impact concerning electroweak (EW) precision observables, and also lead to striking signatures at colliders (be it the LHC, or future lepton colliders). All the above new phenomena are rooted in the non-negligible mixings of the heavy Majorana states with the light active neutrinos, which in turn is responsible for modifying the flavour mixings in the lepton sector.
Within the framework of the inverse seesaw mechanism, we calculate the electroweak corrections to leptonic Higgs, $W$ and $Z$ decays, which are modified due to the presence of HNL in the loop diagrams.
In certain regions of the currently viable parameter space significant deviations from the SM predictions can be observed.
In view of the anticipated increased precision of experimental measurements of these decay modes at future $Z$ factories (such as FCC-ee), precision measurements of leptonic Higgs, $W$ and $Z$ decays can lead to complementary constraints on seesaw-like neutrino mass models.
https://indico.ijs.si/event/1597/
