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...
Together, the work defines how an RNA #aptamer integrates metal and proton cues for combinatorial environmental sensing.
These models complement single-molecule #FRET experiments revealing pH-tuned conformational sampling, as well as functional in vivo assays showing that both the Mn²⁺-binding core and the pH-sensitive loop are required for maximal activation.
Using conventional and constant-pH #MD simulations, we identified a pH-dependent alternative base-pairing interaction in a loop that allosterically perturbs the Mn²⁺-binding site and remodels the conformational ensemble.
The alx aptamer uniquely integrates two orthogonal signals — Mn²⁺ and cytoplasmic pH — to control gene expression.
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...
Anyone looking for a Christmas reading? We plan to submit in January, feedback welcome 🎄🎅
We develop a method to reconstruct RNA 2D ensembles based on nano-DMS-MaP data! Correlation as not measured from data, but rather inferred via a physics based model, which describes also RNA-probe interaction and can be straightforwardly extended to multiple reagents
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
If you are interested in joining the project as a postdoctoral researcher in computational RNA biophysics, integrative modelling, molecular dynamics, HPC, software development, or related areas, #joinus at www.bussilab.org/fis3
A key component will be the further development and benchmarking of methods within @plumed.org , our community-driven platform for enhanced sampling and integrative molecular simulations, providing efficient high-performance workflows.
The project includes a strong link with Redmond Smyth (CNRS), whose expertise in virology and chemical probing will be central to integrating modelling with experimental virology.
This is a large, ERC-scale initiative aimed at developing new methodologies for RNA modelling by integrating chemical probing data with state-of-the-art simulations.
The applied focus will be on understanding the genome architecture of Influenza A, in close connection with experiment.
🎉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.
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...
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
We also discuss key challenges, such as the generalization crisis, data scarcity, and the rise of RNA #foundationmodels, and outline future directions toward predicting dynamic structural ensembles.