Lightnews — Scholar-powered news

Bussi Lab @bussilab.org · 2h

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

1 1

Bussi Lab @bussilab.org · 16d

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

1 2

Bussi Lab @bussilab.org · 16d

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

1 1 6

Bussi Lab @bussilab.org · 16d

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

1 2

Bussi Lab @bussilab.org · 16d

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

1 1 2

Bussi Lab @bussilab.org · 23d

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! 🥳

Bussi Lab @bussilab.org · Sep 10

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

1 5

Bussi Lab @bussilab.org · Aug 21

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

1 3

Bussi Lab @bussilab.org · Aug 2

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...

PREreview of “Molecular Drivers of RNA Phase Separation”

Authored by Giovanni Bussi and 1 other author

prereview.org

2 4

Bussi Lab @bussilab.org · Jul 22

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

4

Bussi Lab @bussilab.org · Jul 22

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

Molecular Ocean Lab @molecularocean.bsky.social · Jul 22

The paper highlighting key insights, future challenges, and research priorities identified during our recent CECAM workshop in Trieste is now available online. Take a look to see what’s coming next in the field of enzymatic plastic degradation:

arxiv.org/abs/2507.14413

Many thanks, everyone!

Computations Meet Experiments to Advance the Enzymatic Depolymerization of Plastics One Atom at a Time

Plastics are essential to modern life, yet poor disposal practices contribute to low recycling rates and environmental accumulation-biological degradation and by-product reuse offer a path to mitigate...

arxiv.org

1 3

Bussi Lab @bussilab.org · Jul 16

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...

Cambridge Ellis Unit Summer School on Probabilistic Machine Learning 2025 – ELLIS Cambridge Unit

www.ellis.eng.cam.ac.uk

1 4

Bussi Lab @bussilab.org · Jul 14

The review has been already submitted to a journal — but we’re committed to improving it. Comments, suggestions, and discussions are very welcome! 🙏

1 2

Bussi Lab @bussilab.org · Jul 14

We cover recent advances in atomistic simulations of #RNA: from #folding and #ion binding to interactions with #proteins and #ligands. A broad overview, with many references and open questions.

1 1 1

Bussi Lab @bussilab.org · Jul 14

📢 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

RNA Dynamics and Interactions Revealed through Atomistic Simulations

RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in di...

arxiv.org

1 5 7

Bussi Lab @bussilab.org · Jul 14

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

StatPhys29 – 2025 Florence, Italy – The 29th International Conference on Statistical Physics

statphys29.org

1 2

Bussi Lab @bussilab.org · Jun 26

📢 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

Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA

Abstract. Adenosine-to-inosine (A-to-I) editing is a highly abundant modification of double-stranded RNA (dsRNA) and plays an important role in posttranscr

doi.org

6 13

Bussi Lab @bussilab.org · Jun 26

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!

www.reprohack.org

3

Bussi Lab @bussilab.org · Jun 25

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...

PREreview of “Minimum-Excess-Work Guidance”

Authored by Giovanni Bussi and Olivier Languin-Cattoën

prereview.org

1 5

Bussi Lab @bussilab.org · Jun 23

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!

Protein Electrostatics 2025, Lisbon

proteinelectrostatics.org

1 4

Bussi Lab @bussilab.org · Jun 18

Our research presented at the meeting of the Division of Chemistry of Biological Systems of the @socchimita.bsky.social! Elisa Posani will show our integrative modelling of #RNA using #cryoEM data and @sdimarco.bsky.social will share our simulations of #RNA membrane interactions

1 1

Bussi Lab @bussilab.org · Jun 4

Our research presented at the GRC on computational #NMR organized by @katjapetzold.bsky.social in Les Diablerets! @bussigio.bsky.social will share our integrative approach to reconstruct the impact of A-to-I modifications on dynamics and our protocol to predict Mg2+ binding sites in #RNA molecules

2 6

Bussi Lab @bussilab.org · May 27

📢 Paper on the RBP Footprint Grand Challenge—launched at RNA2021 — is out in @rnajournal.bsky.social doi.org/10.1261/rna....! A community-driven benchmark of methods for predicting RBP binding sites, with contributions from @tfroehlking.bsky.social, Mattia Bernetti, and @bussigio.bsky.social

Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data

A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms

doi.org

2 10

Bussi Lab @bussilab.org · May 21

Congratulations to @tf-silva.bsky.social for winning the best poster prize at the #RNA modelling across scales @cecamevents.bsky.social workshop, describing our constant pH simulations of RNA systems 👏

Bussi Lab @bussilab.org · May 21

Our research was featured at the @cecamevents.bsky.social meeting #RNA modelling across scales at SISSA, Trieste! @ollyfutur.bsky.social gave a talk on our enhanced sampling strategy for exploring RNA-Mg2+ binding, and all other group members presented posters on their research

binding.group

1 5

Bussi Lab @bussilab.org · May 21

Our research was featured at the @cecamevents.bsky.social meeting #RNA modelling across scales at SISSA, Trieste! @ollyfutur.bsky.social gave a talk on our enhanced sampling strategy for exploring RNA-Mg2+ binding, and all other group members presented posters on their research

binding.group

1 6