Giovanni Bussi

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

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...

MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing The function of RNA molecules is deeply related to their secondary structure, which determines which nucleobases are accessible for pairing. Most RNA molecules however function through dynamic and het...

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

I’m very excited to start this project — it brings together ideas that matured over many years and opens a long-term path for innovation in RNA modelling. 🍾 🧬

🎉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.

Looking back on an inspiring and stimulating two days at the Ultra-Highfield NMR and 4D Structural Biology Symposium. Huge thanks to all speakers, participants, and organizers for making this such an insightful and engaging event! 🧲🧬

Tomorrow we celebrate! 🎉
CECAM is looking forward to honoring Prof. Giulia Galli, recipient of the 2025 Berni J. Alder CECAM Prize, for her pioneering contributions to computational molecular science.
📅 Tomorrow, Nov 12 | 🕒 15:00–19:00
Info & full program: www.cecam.org/award-detail...

R1260 CASP target, water and ions around RNA. Ground truth on left, blind prediction from SoutheRNA MD simulations on right.

#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...

#BNMRZ Symposium 2025
Ultra-Highfield NMR and 4D Structural Biology – From Mechanisms to Therapies

💻 Online attendance is still possible: t1p.de/zdr8j

👉 Further information: t1p.de/rjuz4

@tum.de
#StructuralBiology #CryoEM #AI #TherapeuticInnovations

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

Machine Learning for RNA Secondary Structure Prediction: a review of current methods and challenges Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foun...

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

Making PLUMED fly: a tutorial on optimizing performance PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. Whi...

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

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent bio...

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...

Elisa also contributed to the joint analysis of submissions and cryo-EM maps with @rachael-kretsch.bsky.social — a great example of collaboration across labs. 🤝 Congratulations to all participants!

YouTube video by CASP RNA SIG Giovanni Bussi: RNA molecules are not alone

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

CASP RNA SIG Welcome nucleic acid enthusiasts to the Special Interest Group (SIG) focused different aspects of nucleic acid 3D structure prediction, including but not limited to obtaining experimental data, buildi...

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

And thanks to the opponents @jmbujnicki.bsky.social and @giuliapalermo.bsky.social for evaluating Elisa's work, and sharing their recent research at SISSA

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

And thanks to the opponents Jürgen Köfinger and Julija Zavadlav for evaluating Ivan's work, and sharing their recent research at SISSA

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

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