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X-WR-CALNAME:Department of Theoretical Physics
X-ORIGINAL-URL:https://web-f1.ijs.si
X-WR-CALDESC:Events for Department of Theoretical Physics
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BEGIN:VTIMEZONE
TZID:Europe/Ljubljana
BEGIN:DAYLIGHT
TZOFFSETFROM:+0100
TZOFFSETTO:+0200
TZNAME:CEST
DTSTART:20210328T010000
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TZOFFSETFROM:+0200
TZOFFSETTO:+0100
TZNAME:CET
DTSTART:20211031T010000
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TZOFFSETFROM:+0100
TZOFFSETTO:+0200
TZNAME:CEST
DTSTART:20220327T010000
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TZOFFSETTO:+0100
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DTSTART:20221030T010000
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BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220707T110000
DTEND;TZID=Europe/Ljubljana:20220707T120000
DTSTAMP:20260403T231216
CREATED:20220414T084239Z
LAST-MODIFIED:20220414T101238Z
UID:5100-1657191600-1657195200@web-f1.ijs.si
SUMMARY:Philipp Schicho: Gauge-invariant bubble nucleation rate in finite temperature effective field theory
DESCRIPTION: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.\nhttps://indico.ijs.si/event/1443/
URL:https://web-f1.ijs.si/event/philipp-schicho-gauge-invariant-bubble-nucleation-rate-in-finite-temperature-effective-field-theory/
LOCATION:https://zoom.us/j/3601731049?pwd=bVNQRjUxU2ExZ0cveWcxYXNUUGdjZz09 (Zoom)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220630T100000
DTEND;TZID=Europe/Ljubljana:20220630T160000
DTSTAMP:20260403T231216
CREATED:20220414T084238Z
LAST-MODIFIED:20220414T101238Z
UID:5099-1656583200-1656604800@web-f1.ijs.si
SUMMARY:5th Trilateral meeting (tentative) at ICTP/IFPU
DESCRIPTION: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.\nThe venue will be posted soon.\nOrganizing committee:\n	Miha Nemevšek (IJS)\n	Andrea Romanino (SISSA)\n	Lorenzo Ubaldi (INFN)\n	Gabrijela Zaharijas (UNG)\nPast meetings\n	Ljubljana meeting\, 16 December 2021 at IJS\n	Nova Gorica meeting\, 15 September 2021 at Vipava\n	Trieste meeting\, 5 February 2020 at IFPU\n	Ljubljana meeting\, 17 October 2019 at IJS\n \nhttps://indico.ijs.si/event/1419/
URL:https://web-f1.ijs.si/event/5th-trilateral-meeting-tentative-at-ictp-ifpu/
LOCATION:TBD (ICTP/IFPU)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220623T110000
DTEND;TZID=Europe/Ljubljana:20220623T120000
DTSTAMP:20260403T231216
CREATED:20220414T084238Z
LAST-MODIFIED:20220414T101237Z
UID:5097-1655982000-1655985600@web-f1.ijs.si
SUMMARY:Barry Dillon: What's Anomalous in LHC Jets?
DESCRIPTION: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.\nhttps://indico.ijs.si/event/1425/
URL:https://web-f1.ijs.si/event/barry-dillon-whats-anomalous-in-lhc-jets/
LOCATION:https://zoom.us/j/3601731049?pwd=bVNQRjUxU2ExZ0cveWcxYXNUUGdjZz09 (Zoom)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220609T110000
DTEND;TZID=Europe/Ljubljana:20220609T120000
DTSTAMP:20260403T231216
CREATED:20220414T084236Z
LAST-MODIFIED:20220414T101236Z
UID:5095-1654772400-1654776000@web-f1.ijs.si
SUMMARY:Joe Davighi: TBA
DESCRIPTION:https://indico.ijs.si/event/1429/
URL:https://web-f1.ijs.si/event/joe-davighi-tba/
LOCATION:https://zoom.us/j/3601731049?pwd=bVNQRjUxU2ExZ0cveWcxYXNUUGdjZz09 (Zoom)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220602T110000
DTEND;TZID=Europe/Ljubljana:20220602T120000
DTSTAMP:20260403T231216
CREATED:20220414T084236Z
LAST-MODIFIED:20220414T101236Z
UID:5094-1654167600-1654171200@web-f1.ijs.si
SUMMARY:Francesco D'Eramo: TBA
DESCRIPTION:https://indico.ijs.si/event/1423/
URL:https://web-f1.ijs.si/event/francesco-deramo-tba/
LOCATION:https://zoom.us/j/3601731049?pwd=bVNQRjUxU2ExZ0cveWcxYXNUUGdjZz09 (Zoom)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220526T110000
DTEND;TZID=Europe/Ljubljana:20220526T120000
DTSTAMP:20260403T231216
CREATED:20220414T084235Z
LAST-MODIFIED:20220414T101236Z
UID:5093-1653562800-1653566400@web-f1.ijs.si
SUMMARY:Svjetlana Fajfer: Triple-leptoquark interactions for tree- and loop-level proton decays
DESCRIPTION: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.\nhttps://indico.ijs.si/event/1417/
URL:https://web-f1.ijs.si/event/svjetlana-fajfer-triple-leptoquark-interactions-for-tree-and-loop-level-proton-decays/
LOCATION:https://zoom.us/j/3601731049?pwd=bVNQRjUxU2ExZ0cveWcxYXNUUGdjZz09 (Zoom)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220519T110000
DTEND;TZID=Europe/Ljubljana:20220519T120000
DTSTAMP:20260403T231216
CREATED:20220414T084234Z
LAST-MODIFIED:20220414T101235Z
UID:5092-1652958000-1652961600@web-f1.ijs.si
SUMMARY:Miguel Vanvlasselaer: Dark Matter production from relativistic bubble walls
DESCRIPTION: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.\nhttps://indico.ijs.si/event/1421/
URL:https://web-f1.ijs.si/event/miguel-vanvlasselaer-dark-matter-production-from-relativistic-bubble-walls/
LOCATION:https://zoom.us/j/3601731049?pwd=bVNQRjUxU2ExZ0cveWcxYXNUUGdjZz09 (Zoom)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220512T110000
DTEND;TZID=Europe/Ljubljana:20220512T120000
DTSTAMP:20260403T231216
CREATED:20220414T084234Z
LAST-MODIFIED:20220414T101235Z
UID:5091-1652353200-1652356800@web-f1.ijs.si
SUMMARY:Saša Prelovšek: Evidence for a doubly charm tetraquark pole from lattice QCD
DESCRIPTION: 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. \nhttps://indico.ijs.si/event/1424/
URL:https://web-f1.ijs.si/event/sasa-prelovsek-evidence-for-a-doubly-charm-tetraquark-pole-from-lattice-qcd/
LOCATION:https://zoom.us/j/3601731049?pwd=bVNQRjUxU2ExZ0cveWcxYXNUUGdjZz09 (Zoom)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220510T130000
DTEND;TZID=Europe/Ljubljana:20220510T140000
DTSTAMP:20260403T231216
CREATED:20220325T141719Z
LAST-MODIFIED:20220506T073630Z
UID:5076-1652187600-1652191200@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Robert Vácha: "How Non-Enveloped Viruses Can Infect Cells"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-robert-vacha-viruses-cell-infection/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220505T160000
DTEND;TZID=Europe/Ljubljana:20220505T170000
DTSTAMP:20260403T231216
CREATED:20220414T084233Z
LAST-MODIFIED:20220414T101234Z
UID:5090-1651766400-1651770000@web-f1.ijs.si
SUMMARY:Kaladi Babu: TBA
DESCRIPTION:https://indico.ijs.si/event/1422/
URL:https://web-f1.ijs.si/event/kaladi-babu-tba/
LOCATION:https://zoom.us/j/3601731049?pwd=bVNQRjUxU2ExZ0cveWcxYXNUUGdjZz09 (Zoom)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220503T130000
DTEND;TZID=Europe/Ljubljana:20220503T140000
DTSTAMP:20260403T231216
CREATED:20220111T115947Z
LAST-MODIFIED:20220111T115947Z
UID:5001-1651582800-1651586400@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Veronika Bukina (TBA)
DESCRIPTION:
URL:https://web-f1.ijs.si/event/biophysics-seminar-veronika-bukina-tba/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220414T110000
DTEND;TZID=Europe/Ljubljana:20220414T120000
DTSTAMP:20260403T231216
CREATED:20220414T084233Z
LAST-MODIFIED:20220414T101234Z
UID:5089-1649934000-1649937600@web-f1.ijs.si
SUMMARY:Nejc Košnik: LFU and CP violation with S3
DESCRIPTION: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.\nhttps://indico.ijs.si/event/1420/
URL:https://web-f1.ijs.si/event/nejc-kosnik-lfu-and-cp-violation-with-s3/
LOCATION:https://zoom.us/j/3601731049?pwd=bVNQRjUxU2ExZ0cveWcxYXNUUGdjZz09 (Zoom)
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220329T130000
DTEND;TZID=Europe/Ljubljana:20220329T140000
DTSTAMP:20260403T231216
CREATED:20220316T090207Z
LAST-MODIFIED:20220318T110115Z
UID:5061-1648558800-1648562400@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Aljaž Godec: "From the kinetic Ising model to specific cell adhesion\, and back"
DESCRIPTION: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.  \n[1] K. Blom & A. Godec\, Phys. Rev. X 11\, 031067 (2021).\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-aljaz-godec-kinetic-ising-cell-adhesion/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220324T130000
DTEND;TZID=Europe/Ljubljana:20220324T140000
DTSTAMP:20260403T231216
CREATED:20220308T094513Z
LAST-MODIFIED:20220319T195149Z
UID:5054-1648126800-1648130400@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Simon Čopar: "Hyperuniformity and spherical structure factor"
DESCRIPTION: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. \nI 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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-simon-copar-hyperuniformity/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220317T150000
DTEND;TZID=Europe/Ljubljana:20220317T160000
DTSTAMP:20260403T231216
CREATED:20220311T162205Z
LAST-MODIFIED:20220311T162252Z
UID:5056-1647529200-1647532800@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Mauricio Comas-García: "Understanding selective packaging in Alphaviruses"
DESCRIPTION: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. \nThese 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. \nOur 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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-mauricio-comas-garcia-selective-packaging-alphaviruses/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220308T130000
DTEND;TZID=Europe/Ljubljana:20220308T140000
DTSTAMP:20260403T231216
CREATED:20220119T113425Z
LAST-MODIFIED:20220119T113425Z
UID:5019-1646744400-1646748000@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Horacio Guzman: "Polymer swelling model based on dynamic AFM experiments"
DESCRIPTION:
URL:https://web-f1.ijs.si/event/biophysics-seminar-horacio-guzman-polymer-swelling-afm/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220301T130000
DTEND;TZID=Europe/Ljubljana:20220301T140000
DTSTAMP:20260403T231216
CREATED:20211203T175329Z
LAST-MODIFIED:20220223T094306Z
UID:4972-1646139600-1646143200@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Gregor Posnjak: "From DNA origami to photonic crystals"
DESCRIPTION: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. \nIn 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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-gregor-posnjak-dna-origami/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220222T130000
DTEND;TZID=Europe/Ljubljana:20220222T140000
DTSTAMP:20260403T231216
CREATED:20220203T110553Z
LAST-MODIFIED:20220204T114534Z
UID:5044-1645534800-1645538400@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Jaffar Hasnain: "Spontaneous emulsification induced by nanoparticle surfactants"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-jaffar-hasnain-emulsification-nanoparticle-surfactants/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220215T130000
DTEND;TZID=Europe/Ljubljana:20220215T140000
DTSTAMP:20260403T231216
CREATED:20211025T102254Z
LAST-MODIFIED:20220203T110500Z
UID:4888-1644930000-1644933600@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Matej Krajnc
DESCRIPTION:
URL:https://web-f1.ijs.si/event/biophysics-seminar-matej-krajnc-wip/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220125T130000
DTEND;TZID=Europe/Ljubljana:20220125T140000
DTSTAMP:20260403T231216
CREATED:20211112T124951Z
LAST-MODIFIED:20220119T200341Z
UID:4939-1643115600-1643119200@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Tomer Stern: "Deconstructing Gastrulation at Single-Cell Resolution"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-tomer-stern-deconstructing-gastrulation/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220118T134000
DTEND;TZID=Europe/Ljubljana:20220118T142000
DTSTAMP:20260403T231216
CREATED:20211214T095540Z
LAST-MODIFIED:20220115T110445Z
UID:4990-1642513200-1642515600@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Urška Andrenšek: "The continuum approximation of the vertex model"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-urska-andrensek-continuum-approximation-vertex/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220118T130000
DTEND;TZID=Europe/Ljubljana:20220118T134000
DTSTAMP:20260403T231216
CREATED:20211207T091457Z
LAST-MODIFIED:20220115T110511Z
UID:4974-1642510800-1642513200@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Domen Vaupotič: "Viral RNA as a randomly branching polymer"
DESCRIPTION:The meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-domen-vaupotic-viral-rna-branching/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220111T130000
DTEND;TZID=Europe/Ljubljana:20220111T140000
DTSTAMP:20260403T231216
CREATED:20211120T074701Z
LAST-MODIFIED:20220105T093048Z
UID:4962-1641906000-1641909600@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Marin Šako: "Soft matter under tension and cavitation"
DESCRIPTION:The meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-marin-sako-soft-matter-tension/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20220104T130000
DTEND;TZID=Europe/Ljubljana:20220104T140000
DTSTAMP:20260403T231216
CREATED:20211209T103119Z
LAST-MODIFIED:20211217T092006Z
UID:4977-1641301200-1641304800@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Toshikaze Chiba: "Deformation and rearrangement of membranes in adhering vesicles"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-toshikaze-chiba-deformation-rearrangement-membranes/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20211207T150000
DTEND;TZID=Europe/Ljubljana:20211207T160000
DTSTAMP:20260403T231216
CREATED:20211010T182945Z
LAST-MODIFIED:20211203T131454Z
UID:4863-1638889200-1638892800@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Clement Zankoc: "Active Instability and Nonlinear Dynamics of Cell-Cell Junctions"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-clement-zankoc-active-instability/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20211130T130000
DTEND;TZID=Europe/Ljubljana:20211130T140000
DTSTAMP:20260403T231216
CREATED:20211011T082432Z
LAST-MODIFIED:20211120T205839Z
UID:4868-1638277200-1638280800@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Tanmoy Sarkar: "A minimal lattice model of lipid membranes with liquid-ordered domains"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-tanmoy-sarkar-minimal-model-lipids/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20211123T130000
DTEND;TZID=Europe/Ljubljana:20211123T140000
DTSTAMP:20260403T231216
CREATED:20211011T082357Z
LAST-MODIFIED:20211118T132249Z
UID:4866-1637672400-1637676000@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Matej Kanduč: "Lipids’ dilemma: a monolayer or a bilayer?"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminars-matej-kanduc-lipids-dilemma/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20211116T130000
DTEND;TZID=Europe/Ljubljana:20211116T140000
DTSTAMP:20260403T231216
CREATED:20210928T062323Z
LAST-MODIFIED:20211112T124505Z
UID:4659-1637067600-1637071200@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Fabio Staniscia: "Surfactant-induced apparent line tension"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-fabio-staniscia-induced-tension/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20211109T130000
DTEND;TZID=Europe/Ljubljana:20211109T140000
DTSTAMP:20260403T231216
CREATED:20210924T082053Z
LAST-MODIFIED:20211103T092853Z
UID:4579-1636462800-1636466400@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Julija Zavadlav: "Neural network potentials trained top-down"
DESCRIPTION: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.\n\n\nThe meeting will take place online via Zoom: \nMeeting ID: 833 0750 1179 \nPasscode: bio
URL:https://web-f1.ijs.si/event/biophysics-seminar-julija-zavadlav-nn-potentials/
LOCATION:Zoom
END:VEVENT
BEGIN:VEVENT
DTSTART;TZID=Europe/Ljubljana:20211026T130000
DTEND;TZID=Europe/Ljubljana:20211026T140000
DTSTAMP:20260403T231216
CREATED:20210924T074520Z
LAST-MODIFIED:20211025T102206Z
UID:4576-1635253200-1635256800@web-f1.ijs.si
SUMMARY:[Biophysics seminar] Boris Rogelj: "Molecular and cellular basis of neurodegeneration"
DESCRIPTION: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.\n\n\nThe meeting will take place in the physics seminar room (106) in the main building.\n\n\n\n 
URL:https://web-f1.ijs.si/event/biophysics-seminar-boris-rogelj-basis-of-neurodegeneration/
LOCATION:Seminarska soba fizike (106)\, Jozef Stefan Institute (Jamova 39)\, Ljubljana
END:VEVENT
END:VCALENDAR