New #preprint alert! Fast sampling of #RNA–Mg²⁺ binding. @ollyfutur.bsky.social, Elisa Posani and @bussigio.bsky.social present an enhanced-sampling method, extending our top-performing #CASP16 approach, and validate it with #cryoEM. arxiv.org/abs/2607.07186 Summary in thread👇

New #preprint alert! How should we count molecular ensembles in #Bayesian ensemble refinement? Ivan Gilardoni and @bussigio.bsky.social show that this choice affects posterior estimates, and propose an invariant solution based on the Jeffreys measure. arxiv.org/abs/2606.18495 Summary in thread 👇

Excited to announce our pre-print on the detection of PPI interfaces using ESM3!!! Big thanks to the very young and talented authors www.biorxiv.org/content/10.6...

Our work presented today at an internal seminar at Sanofi, Paris, hosted by Evi Gkeka. @bussigio.bsky.social presented our applications integrating #MD simulations and RNA secondary structure prediction with #NMR, #SAXS, #cryoEM, and #DMS data, to reconstruct #RNA dynamics and RNA-Mg interaction

Our work presented today at the @cecamevents.bsky.social meeting Decoding Allostery in Protein-Nucleic Acid Complexes: The AI Revolution ! www.cecam.org/workshop-det... Maurizio Gilioli discussed our study of Influenza A Virus nucleoproteins using #MD simulations and #cryoEM data

Our work presented today at the @cecamevents.bsky.social meeting Decoding Allostery in Protein-Nucleic Acid Complexes: The AI Revolution www.cecam.org/workshop-det...! @bussigio.bsky.social will show how we integrate #DMS probing and #cryoEM with computational models for #RNA dynamics

Our work presented at the @rnasociety.bsky.social meeting in Montreal! @ollyfutur.bsky.social and @sdimarco.bsky.social are presenting posters showing how we use enhanced molecular simulations to sample #Mg ion binding and #RNA conformational changes

New #openreview from our group at prereview.org/reviews/1973...! @bussigio.bsky.social reviewed a #preprint by @jgreener64.bsky.social and coworkers on the training of a new force field from scratch using quantum mechanical and experimental data. Also available at doi.org/10.5281/zeno...

📢 Apply for the #PhD 🎓 in Molecular and Statistical Biophysics at SISSA in lovely Trieste! 3 fully funded fellowships starting Oct 2026. ~8 months of classes, then choose your project. Remote entrance exam. Application deadline: 11.5.2026. Please repost! 👉 msb.sissa.it/join-us/ #joinus

New #preprint alert! @bussigio.bsky.social contributed to a mixed experimental-simulation paper from the groups of Ali Hassanali and Paul Cremer investigating the microscopic origins of partial molar volumes in LiCl solutions arxiv.org/abs/2604.19622

Want to contribute to a major #opensource project for molecular simulations? We’re opening a research technologist position at SISSA (Trieste) to work on @plumed.org (scientific coding / #HPC) within the #RNAScale project. Fill the expression of interest form: www.bussilab.org/rnascale #joinus

New paper published! @bussigio.bsky.social contributed to a work led by Zhengyue Zhang @astrazeneca.com where #RNA secondary-structure prediction methods were benchmarked in the context of #RNA-targeted #drugdiscovery. doi.org/10.1021/acs....

New #preprint alert! @bussigio.bsky.social contributed to a work led by Vojtech Mlysnky, Pavel Banas et al, where hydrogen bond fixes for #RNA force field (ghbfix19) were reformulated as more portable Lennard-Jones fixes doi.org/10.64898/202...

Undergraduate student interested in molecular dynamics, quantum chemistry, or ML for materials? Join the @cecamevents.bsky.social Summer School at SISSA (Trieste), June 22–July 3, 2026. Designed specifically for beginners. Details & apply: www.cecam.org/workshop-det...

Our review on atomistic simulations of #RNA systems has been published in the Annual Reviews of Physical Chemistry! doi.org/10.1146/annu... Preprint and summary in previous thread: bsky.app/profile/buss...

Our #tutorial on how to make @plumed.org faster is now published in @acs.org #JPCB! doi.org/10.1021/acs.... Preprint and summary in previous thread: bsky.app/profile/buss...

New #preprint alert! @bussigio.bsky.social and @tf-silva.bsky.social from our group contributed to an experimental investigation of the pH-dependent Mn²⁺-sensing alx riboswitch, in collaboration with @nilswalterlab.bsky.social and Tatiana Mishanina’s lab. doi.org/10.64898/202...

Our work presented today at the #PhysicsOfBiomolecules workshop in Bressanone sites.unimi.it/bressanone/! @sdimarco.bsky.social will show our attempts to make replica exchange molecular dynamics simulations more effective for sampling #RNA conformations

Our work presented today at the #PhysicsOfBiomolecules workshop in Bressanone sites.unimi.it/bressanone/! @ollyfutur.bsky.social will show our enhanced sampling MD for #RNA-Mg2+ binding, its application to an intron used as a target for #CASP16, and validation of results against #cryoEM data

Our work presented today at the #PhysicsOfBiomolecules workshop in Bressanone sites.unimi.it/bressanone/! @bussigio.bsky.social will show our recent results on combining #DMS and thermodynamics to get #RNA ensembles. See also our recent #preprint arxiv.org/abs/2512.20581

New #openreview from our group at prereview.org/reviews/1847...! @bussigio.bsky.social and @sdimarco.bsky.social reviewed a #preprint by Pavel Banas and coworkers on the evaluation of enhanced sampling methods for force field benchmarking. Also available at doi.org/10.5281/zeno...

Our review on Machine Learning for #RNA Secondary Structure Prediction is now published in @rnajournal.bsky.social ! dx.doi.org/10.1261/rna.... Summary in this previous thread bsky.app/profile/buss...

New #preprint alert! 🧬 MERGE-RNA: a physics-based model to predict #RNA secondary structure ensembles with chemical probing, lead by Giuseppe Sacco, in collaboration with Guido Sanguinetti and Redmond Smyth's lab arxiv.org/abs/2512.20581

Our work presented today at the XBW2025 workshop homepage.uni-graz.at/de/georg.pab...! Maurizio Gilioli presented our recent #MD simulations of nucleoproteins from influenza A virus

📣 New preprint out! We are zooming in on the molecular determinants and energetics that limit PETase activity on crystalline PET: it requires high energy both to reach reactive configurations and to separate its chains. Feedback is welcome. Submission in two weeks. lnkd.in/d3MCJhEg

🎉Our group has been awarded a prestigious #FIS grant! #RNAScale - Exploring RNA Dynamics across Scales: From Base Pairs to Viral Genomes 👉 www.bussilab.org/fis3 We will soon open postdoctoral positions across several components of the project! An expression-of-interest form is already online.

#MD blind predictions of water/ions around Tetrahymena ribozyme #RNA matched cryo-EM data better than our baselines! Congrats #CASP16 + @rachael-kretsch.bsky.social + 23 brave groups. Still a ways to go — time for #DeepLearning of water? Community paper: doi.org/10.1002/prot...

The work describing the #CASP16 solvation challenge has been published in Proteins journal! doi.org/10.1002/prot...

Our work presented at the Ultra-Highfield NMR and 4D Structural Biology workshop www.bnmrz.org/4dstructbiol organized by @sattler-lab.bsky.social! @bussigio.bsky.social will show our works on #RNA dynamics integrating #MD, #SAXS, and #NMR and validating a #CASP16 target using #cryoEM data

New #preprint alert! 🧬 Machine Learning for #RNA Secondary Structure Prediction: a #review of current methods and challenges, by Giuseppe Sacco, @bussigio.bsky.social, and Guido Sanguinetti arxiv.org/abs/2511.02622

A new tutorial manuscript is out! 🚀 Making @plumed.org fly: a tutorial on optimizing performance, by Daniele Rapetti, @bonomimax.bsky.social @carlocamilloni.bsky.social @bussigio.bsky.social and Gareth Tribello. arxiv.org/abs/2511.02699

A recent manuscript describing our and others’ efforts to predict the solvation shell of a group I intron is now available on bioRxiv! 🔬 doi.org/10.1101/2025...

📽️ The recording of @bussigio.bsky.social 's talk at CASP RNA Special Interest Group is now available at www.youtube.com/watch?v=NRCg...

Our work presented today at the www.youtube.com/@CASPRNASIG online seminar! @bussigio.bsky.social will report on the #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data

Our work presented today at the Biophysical Modeling of the Structure and Function of Viruses @cecamevents.bsky.social workshop at the @iescargese.bsky.social! @bussigio.bsky.social will report on the recent #CASP16 solvation challenge and 2D ensemble reconstructions using #DMS data

Congratulations to Elisa Posani for successfully defending her PhD thesis "Ensemble Refinement of Cryo-Electron Microscopy-Derived RNA Structures Using Molecular Dynamics Simulations"! Cosupervision with @magistratolab.bsky.social

Congratulations to Ivan Gilardoni for successfully defending his PhD thesis "Development and application of methods to integrate molecular simulations with experimental measurements"!

Congratulations to Davide Di Vora for successfully defending his master thesis on the "On-the-fly integration of experimental data and molecular simulations" at University of Trieste! 🥳

Our work presented today at the ICTP Conference on Frontiers in Atomistic Simulations: from Physics to Chemistry and Biology! @ollyfutur.bsky.social and Ivan Gilardoni will share posters with our results on enhancing #RNA - Mg binding and on integrating #MD simulations and experiments

Our research presented at the Cargese school on Molecular Evolution and Design! @sdimarco.bsky.social will show our simulations of #RNA #membrane interactions and Elisa Posani will share our approach integrating #MD and #cryoEM to investigate the #dynamics of a group I intron

New #openreview from our group at prereview.org/reviews/1672...! @sdimarco.bsky.social and @bussigio.bsky.social reviewed a #preprint by @potoyan.bsky.social on the Molecular Drivers of #RNA Phase Separation. Also available at doi.org/10.5281/zeno...

Our research presented today at the Telluride meeting on #RNA dynamics! @bussigio.bsky.social will report on some of our ongoing projects: the recent #CASP16 solvation challenge, constant pH #MD simulations on #RNA, and 2D ensemble reconstructions using #DMS data

A review reporting on the discussions held at the recent @cecamevents.bsky.social workshop on enzymatic plastic degradation that we co-organized in Trieste is now available on #arxiv

Our research presented at the Cambridge Ellis Unit Summer School on Probabilistic Machine Learning! Giuseppe Sacco will present a poster reporting our machine-learned model for DMS-guided ensemble prediction of RNA systems www.ellis.eng.cam.ac.uk/summer-schoo...

📢 New #preprint alert! Our review "RNA Dynamics and Interactions Revealed through Atomistic Simulations" is now available on arxiv.org/abs/2507.08474 ! Written by @bussigio.bsky.social and @ollyfutur.bsky.social

Our research presented at #StatPhys29! Ivan Gilardoni will present a poster reporting on our methodological work in integrating molecular simulations and experimental data statphys29.org

📢 Paper with @sattler-lab.bsky.social now published in @narjournal.bsky.social ! doi.org/10.1093/nar/... We combine #NMR, #SAXS, and #MD to construct conformational ensembles, showing that A-to-I hyper-editing leads to significant structural dynamics. MD simulations by @piompons.bsky.social

A paper from our group (doi.org/10.1093/narg...) has been tested and reviewed in ReproHack www.reprohack.org/review/151! We got interesting feedback on how to improve documentation of our notebooks. Very useful initiative!

New #openreview from our group at prereview.org/reviews/1573...! @bussigio.bsky.social and @ollyfutur.bsky.social reviewed a #preprint by Simon Olsson showing their Minimum-Excess-Work Guidance method. Also available at doi.org/10.5281/zeno...

Our research presented at the proteinelectrostatics.org Protein Electrostatics 2025, Lisbon! @tf-silva.bsky.social shared our constant pH simulations on #RNA systems, from oligomers to introns!