Bussi Lab

Bussi Lab

@bussilab.org

Research group lead by @bussigio.bsky.social at SISSA | #RNA, #moleculardynamics, and more | web: http://bussilab.org

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Bussi Lab
@bussilab.org

Our work presented at the Erice School on Exploring and Quantifying Rough Free Energy Landscapes! @bussigio.bsky.social will talk about our recent methodological developments on the optimization of replica exchange methods and on Bayesian integrative modeling

Bussi Lab
@bussilab.org

Our work presented at the poster session of the Erice School on Exploring and Quantifying Rough Free Energy Landscapes! @ollyfutur.bsky.social showed how we sample Mg2+-RNA binding in #MD, and Maurizio Gilioli shared our models of Influenza A virus nucleoproteins using #MD and #cryoEM data

Bussi Lab
@bussilab.org

Congratulations to Giuseppe Sacco for successfully defending his PhD thesis "Data-driven models for RNA: physical and statistical approaches to secondary structure, RNA–protein interactions, and siRNA potency"! Cosupervision with Guido Sanguinetti

Bussi Lab
@bussilab.org

Our study on the investigation of the microscopic origins of partial molar volumes in LiCl solutions, in collaboration with Ali Hassanali and Paul Cremer groups, has been published in @acsjacs.bsky.social ! doi.org/10.1021/jacs...

doi.orgBeyond the Virial Expansion: Microscopic Origins of Partial Molar Volumes in LiCl SolutionsAbstract. Although electrolyte density measurements have been reported for over a century, employing them to determine accurate partial molar volume (PMV)
Bussi Lab
@bussilab.org

Our study of the pH-dependent Mn²⁺-sensing alx riboswitch, in collaboration with @nilswalterlab.bsky.social and Tatiana Mishanina’s lab, has been published in @narjournal.bsky.social doi.org/10.1093/nar/... Summary in preprint thread 👉 bsky.app/profile/buss...

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Bussi Lab@bussilab.org

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...

doi.orgdoi.org
Bussi Lab
@bussilab.org

Our MERGE-RNA manuscript, led by Giuseppe Sacco, in collaboration with Guido Sanguinetti and Redmond Smyth's lab, has been published in @narjournal.bsky.social doi.org/10.1093/nar/... Summary in preprint thread 👉 bsky.app/profile/buss...

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Bussi Lab@bussilab.org

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

arxiv.orgMERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probingThe 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...
Bussi Lab
@bussilab.org

Work by Vojtech Mlynksy, Pavel Banas, et al, with contributions from @bussigio.bsky.social, showing the reformulation of gHBfix19 using Lennard Jones potential has been published in JCTC! doi.org/10.1021/acs....

doi.orgFrom gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force FieldsAbstract. Understanding RNA structural dynamics is essential for elucidating its biological functions, and molecular dynamics (MD) simulations provide an i
Bussi Lab
@bussilab.org

Combining simulations with #cryoEM, we validate individual Mg²⁺ binding motifs and identify sampling as a key ingredient for quantitative agreement with experiment. The remaining discrepancies highlight opportunities for further improvements in #RNA ion modelling.

Bussi Lab
@bussilab.org

We provide @plumed.org plugins implementing the method, compatible with any MD engine supporting multiple communicating replicas (e.g., #GROMACS, #AMBER, etc). No coordinate replica exchange required.

Bussi Lab
@bussilab.org

Mg²⁺ binds RNA on timescales far beyond conventional MD. We use a carefully crafter replica exchange scheme to accelerate inner-shell binding by orders of magnitude, making it possible to sample complex binding motifs while preserving equilibrium statistics.

Bussi Lab
@bussilab.org

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 👇

arxiv.orgBayesian Sampling of Structural Ensembles: The Role of Ensemble-Counting MeasuresStructural ensemble refinement is widely used to integrate molecular simulations with experimental measurements. While most applications focus on the maximum-a-posteriori (MAP) ensemble, Bayesian samp...
Bussi Lab
@bussilab.org

Most ensemble-refinement studies focus on a single optimal (MAP) ensemble. Bayesian posterior sampling also provides uncertainty estimates and posterior averages for arbitrary observables. However, it requires an explicit ensemble-counting measure, whose consequences have received little attention.

Bussi Lab
@bussilab.org

Using both an analytically tractable model and #RNA ensemble refinement, we compare different measures. The choice can substantially affect Bayesian estimates. The Jeffreys measure proves particularly robust to trajectory decimation while providing an invariant definition of posterior averages.

Bussi Lab
@bussilab.org

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

Bussi Lab
@bussilab.org

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

arxiv.orgBeyond the Virial Expansion: Microscopic Origins of Partial Molar Volumes in LiCl SolutionsAlthough electrolyte density measurements have been reported for over a century, employing them to obtain accurate partial molar volume (PMV) profiles as a function of salt concentration has remained ...
Bussi Lab
@bussilab.org

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....

doi.orgExploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and ChallengesRNAs are increasingly recognized as promising drug targets, as both coding and noncoding RNAs act as key regulators in disease-related biological processes. However, a significant gap persists between...
Bussi Lab
@bussilab.org

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...

doi.orgRNA Dynamics and Interactions Revealed Through Atomistic SimulationsRNA 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...
Bussi Lab@bussilab.org

📢 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

arxiv.orgRNA Dynamics and Interactions Revealed through Atomistic SimulationsRNA 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...
Bussi Lab
@bussilab.org

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...

doi.orgMaking PLUMED Fly: A Tutorial on Optimizing PerformancePLUMED 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...
Bussi Lab@bussilab.org

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

arxiv.orgMaking PLUMED fly: a tutorial on optimizing performancePLUMED 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...
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Bussi Lab
@bussilab.org

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.

Bussi Lab
@bussilab.org

Together, the work defines how an RNA #aptamer integrates metal and proton cues for combinatorial environmental sensing.

Bussi Lab
@bussilab.org

The alx aptamer uniquely integrates two orthogonal signals — Mn²⁺ and cytoplasmic pH — to control gene expression.

Bussi Lab
@bussilab.org

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.

Bussi Lab
@bussilab.org

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...

doi.orgPREreview of "Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking"This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/18475062. Preprint Toward Accurate RNA Folding Thermodynamics...
Bussi Lab
@bussilab.org

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...

dx.doi.orgMachine Learning for RNA Secondary Structure Prediction: a review of current methods and challenges A monthly journal publishing high-quality, peer-reviewed research on all topics related to RNA and its metabolism in all organisms
Bussi Lab@bussilab.org

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

arxiv.orgMachine Learning for RNA Secondary Structure Prediction: a review of current methods and challengesPredicting 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...
Bussi Lab
@bussilab.org

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

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Molecular Ocean Lab
@molecularocean.bsky.social

📣 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

biorxiv.orgEnergetic Constraints in the Enzymatic Depolymerization of Crystalline PETPolyethylene terephthalate (PET) is a widely used thermoplastic whose high crystallinity poses a major barrier to upscaling enzymatic recycling. While PETases with high activity and stability have bee...
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Bussi Lab
@bussilab.org

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.

Bussi Lab
@bussilab.org

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.

Bussi Lab
@bussilab.org

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.