Giovanni Bussi

This study shows how pH modulates Mn2+ sensing in the alx riboswitch through conformational changes and allosteric interactions.

This paper reparameterizes RNA force fields by replacing hydrogen-bond corrections with Lennard-Jones modifications, improving simulation accuracy without external potentials.

This paper evaluates blind predictions of dynamic water and ion ensembles around RNA using cryo-EM densities from CASP16, finding that molecular dynamics approaches perform best.

The paper refines cryo-EM RNA structures using all-atom simulations and metainference to account for structural flexibility, revealing inaccuracies in single-structure approaches.

This study uses atomistic simulations to show that RNA structure is destabilized in biomolecular condensates due to interactions with peptides, with amino acid composition affecting RNA conformation.

This study uses all-atom simulations to reveal that guanine in RNA has the strongest interaction with membranes, while base pairing reduces membrane binding.

The paper introduces a multiscale pipeline using SAXS data and computational models to determine RNA 3D structures from low-resolution to atomistic precision.

This study uses molecular dynamics simulations to explore the folding pathways of a parallel G-quadruplex DNA structure, revealing multiple folding paths and limitations of current force fields.

Barnaba is a Python library for analyzing nucleic acids structures and molecular trajectories, offering tools for distance calculation, cluster analysis, motif search, and elastic network modeling.