BEGIN:VCALENDAR VERSION:2.0 PRODID:-//CERN//INDICO//EN BEGIN:VEVENT SUMMARY:Boosted continuous Wang-Landau Algorithm: A Novel Approach for Sof t Matter Sampling DTSTART;VALUE=DATE-TIME:20250612T104500Z DTEND;VALUE=DATE-TIME:20250612T105000Z DTSTAMP;VALUE=DATE-TIME:20260410T200856Z UID:indico-contribution-322-1649@cern.ch DESCRIPTION:Speakers: Camilla Spreti (UNITN - TIFPA)\nhttps://indico.unina .it/event/91/contributions/1649/ LOCATION:Hotel Palazzo Alabardieri Sala Caracciolo URL:https://indico.unina.it/event/91/contributions/1649/ END:VEVENT BEGIN:VEVENT SUMMARY:Inference of Chromatin Architecture in Sleep-Deprived Neurons DTSTART;VALUE=DATE-TIME:20250612T104000Z DTEND;VALUE=DATE-TIME:20250612T104500Z DTSTAMP;VALUE=DATE-TIME:20260410T200856Z UID:indico-contribution-322-1648@cern.ch DESCRIPTION:Speakers: FLORINDA DI PIERNO (INFN)\nhttps://indico.unina.it/e vent/91/contributions/1648/ LOCATION:Hotel Palazzo Alabardieri Sala Caracciolo URL:https://indico.unina.it/event/91/contributions/1648/ END:VEVENT BEGIN:VEVENT SUMMARY:Cross-feeding dynamics in microbial communities under different en vironmental DTSTART;VALUE=DATE-TIME:20250612T102000Z DTEND;VALUE=DATE-TIME:20250612T104000Z DTSTAMP;VALUE=DATE-TIME:20260410T200856Z UID:indico-contribution-322-1630@cern.ch DESCRIPTION:Speakers: Gabriele Micali (IRCCS Humanitas Research Hospital)\ nhttps://indico.unina.it/event/91/contributions/1630/ LOCATION:Hotel Palazzo Alabardieri Sala Caracciolo URL:https://indico.unina.it/event/91/contributions/1630/ END:VEVENT BEGIN:VEVENT SUMMARY:Calorimetric cooperativity revisited and generalized: the role of intermediate states DTSTART;VALUE=DATE-TIME:20250612T100000Z DTEND;VALUE=DATE-TIME:20250612T102000Z DTSTAMP;VALUE=DATE-TIME:20260410T200856Z UID:indico-contribution-322-1629@cern.ch DESCRIPTION:Speakers: Antonio Trovato (University of Padova)\nhttps://indi co.unina.it/event/91/contributions/1629/ LOCATION:Hotel Palazzo Alabardieri Sala Caracciolo URL:https://indico.unina.it/event/91/contributions/1629/ END:VEVENT BEGIN:VEVENT SUMMARY:Microbial billiards DTSTART;VALUE=DATE-TIME:20250612T093000Z DTEND;VALUE=DATE-TIME:20250612T100000Z DTSTAMP;VALUE=DATE-TIME:20260410T200856Z UID:indico-contribution-322-1543@cern.ch DESCRIPTION:Speakers: Roberto Di Leonardo (DIPARTIMENTO DI FISICA SAPIENZ A Università di Roma)\nUnlike gas molecules at equilibrium\, the spatial organization of self-propelled particles can be very sensitive to what ha ppens at the boundaries of their container. Understanding the link between boundary phenomena and bulk stationary distributions could enable the des ign of optimized con- tainer shapes for the geometric control of confined active particles. Here we propose a boundary method based on the flux tran sfer formalism typical of radiometry problems\, where surface ele- ments t ransmit and receive “rays” of active particles with infinite persisten ce length. We demon- strate the power of this boundary method in the case of the swimming microalgae Euglena gracilis trapped in light-defined billi ard geometries. Leveraging our boundary method\, we were able to design a stacked multi-stage billiard geometry\, with a connection scheme between s ubunits that breaks spatial symmetry and achieves an exponential amplifica tion of cell concentration between its two ends. Surprisingly\, the sensit ive dependence on boundary geometry observed in closed microbial billiards stands in marked contrast to the robust invariance of mean path lengths t raced by E.coli bacteria swimming in microfabricated open billiards with f rozen internal disorder.\n\nhttps://indico.unina.it/event/91/contributions /1543/ LOCATION:Hotel Palazzo Alabardieri Sala Caracciolo URL:https://indico.unina.it/event/91/contributions/1543/ END:VEVENT BEGIN:VEVENT SUMMARY:Reinforcement Learning and animal behavior DTSTART;VALUE=DATE-TIME:20250612T090000Z DTEND;VALUE=DATE-TIME:20250612T093000Z DTSTAMP;VALUE=DATE-TIME:20260410T200856Z UID:indico-contribution-322-1542@cern.ch DESCRIPTION:Speakers: Antonio Celani (ICTP)\nI will review some concepts a nd applications of Reinforcement Learning to modeling of animal behavior\n \nhttps://indico.unina.it/event/91/contributions/1542/ LOCATION:Hotel Palazzo Alabardieri Sala Caracciolo URL:https://indico.unina.it/event/91/contributions/1542/ END:VEVENT BEGIN:VEVENT SUMMARY:Reconceiving microRNAs as post-transcriptional frequency decoders DTSTART;VALUE=DATE-TIME:20250612T080000Z DTEND;VALUE=DATE-TIME:20250612T083000Z DTSTAMP;VALUE=DATE-TIME:20260410T200856Z UID:indico-contribution-322-1541@cern.ch DESCRIPTION:Speakers: Carla Bosia (Politecnico di Torino)\nGene regulation is a complex web across biological levels\, and its intricacy often compl icates pre- cise interventions\, with off-target effects being a major hur dle. To transform this\, we here propose a photoactivatable microRNA-based circuit that enables unmatched accuracy in gene targeting\, po- tentially reducing off-target effects. Our approach leverages the concept of microR NAs (miRNAs) as frequency decoders\, interpreting signal frequencies—suc h as oscillatory pulses—to regulate vi- tal cellular processes. We’ve recently shown that periodically expressed miRNAs can selectively repress targets within specific frequency ranges\, creating bell-shaped response c urves typical of true frequency decoders. Our model highlights the importa nce of miRNA-target interaction dy- namics in frequency-dependent repressi on\, adding an orthogonal layer of specificity beyond mere sequence pairin g. After introducing our theoretical results\, we present a simple yet pow erful cir- cuit in which a photoactivatable miRNA\, whose expression can b e periodically controlled by light\, enables dynamic gene expression modul ation in single cells.\n\nhttps://indico.unina.it/event/91/contributions/1 541/ LOCATION:Hotel Palazzo Alabardieri Sala Caracciolo URL:https://indico.unina.it/event/91/contributions/1541/ END:VEVENT BEGIN:VEVENT SUMMARY:All-atom Simulations unveil Physiological and Pharmacological Role of Protein Folding Intermediates DTSTART;VALUE=DATE-TIME:20250612T073000Z DTEND;VALUE=DATE-TIME:20250612T080000Z DTSTAMP;VALUE=DATE-TIME:20260410T200856Z UID:indico-contribution-322-1540@cern.ch DESCRIPTION:Speakers: Pietro Faccioli (Università Milano-Bicocca and INFN )\nOver the last decade\, the combined development of accurate time- resol ved experimental tech- niques and advanced algorithms for computer simulat ions has opened the possibility of investigat- ing biological mechanisms a t atomic resolution with physics-based models. In particular\, combi- nati on of experimental information and enhanced sampling techniques now allow the reconstruc- tion of the co- translational folding pathways of biologic ally relevant proteins\, at an atomic level of resolution. These innovativ e computational technologies reveals the existence of non-native metastabl e states transiently appearing along the co-transcriptional folding proces s of such pro- teins. The lifetime of these intermediates is set by the am ino- acid synthesis rate\, hence is in the several second time scale. In t his talk\, we review the evidence indicating that these protein fold- ing intermediates play roles in post-translational regulation. We also discuss how the information encoded into protein folding pathways is being exploi ted in an entirely new generation of drugs capable of promoting the select ive degradation of protein targets. \n\n[1] G. Spagnolli et al.\, “Pharm acological inactivation of the prion protein by targeting a folding interm ediate”\, Communications Biology 4 (1)\, 6223–124 (2021). DOI:10.1038/ s42003-020-01585-x. [2] E. Biasini and P. Faccioli “Functional\, pathoge nic\, and pharmacological role of protein folding pathways”. Proteins. 2 023\; 1-9.\n\nhttps://indico.unina.it/event/91/contributions/1540/ LOCATION:Hotel Palazzo Alabardieri Sala Caracciolo URL:https://indico.unina.it/event/91/contributions/1540/ END:VEVENT BEGIN:VEVENT SUMMARY:Predicting the structure of enzymes with metal cofactors: The exam ple of [FeFe] hydrogenases DTSTART;VALUE=DATE-TIME:20250612T070000Z DTEND;VALUE=DATE-TIME:20250612T073000Z DTSTAMP;VALUE=DATE-TIME:20260410T200856Z UID:indico-contribution-322-1539@cern.ch DESCRIPTION:Speakers: Velia Minicozzi (Department of Physics\, University of Roma Tor Vergata and INFN\, Roma\, Italy)\nThe advent of deep learning algorithms for protein folding opened a new era in the ability of pre- dic ting and optimizing the function of proteins once the sequence is known. T he task is more intricate when cofactors like metal ions or small ligands are essential to functioning. In this case\, the combined use of tradition al simulation methods based on interatomic force fields and deep learning predictions is mandatory. We use the example of [FeFe] hydrogenases\, enzy mes of uni- cellular algae promising for biotechnology applications to ill ustrate this situation. [FeFe] hydroge- nase is an iron–sulfur protein t hat catalyses the chemical reduction of protons dissolved in liquid water into molecular hydrogen as a gas. Hydrogen production efficiency and cell sensitivity to dioxygen are important parameters to optimize the industria l applications of biological hydro- gen production. Both parameters are re lated to the organization of iron–sulfur clusters within protein domains . In this work\, we propose possible three- dimensional structures of Chlo rella vulgaris 211/11P [FeFe] hydrogenase\, the sequence of which was extr acted from the recently pub- lished genome of the given strain. Initial st ructural models are built using: (i) the deep learning algorithm AlphaFold \; (ii) the homology modeling server SwissModel\; (iii) a manual construct ion based on the best known bacterial crystal structure. Missing iron–su lfur clusters are included and microsecond-long molecular dynamics of init ial structures embedded into the water solution envi- ronment were perform ed. Multiple- walkers metadynamics was also used to enhance the sampling o f structures encompassing both functional and non-functional organizations of iron–sulfur clus- ters. The resulting structural model provided by d eep learning is consistent with functional [FeFe] hydrogenase characterize d by peculiar interactions between cofactors and the protein matrix.\n\nht tps://indico.unina.it/event/91/contributions/1539/ LOCATION:Hotel Palazzo Alabardieri Sala Caracciolo URL:https://indico.unina.it/event/91/contributions/1539/ END:VEVENT END:VCALENDAR