998 citations · 1.2k across the 9 of their papers we have counts for
9 papers
PLUMED Tutorials: a collaborative, community-driven learning ecosystem
Gareth A. Tribello, Massimiliano Bonomi, Giovanni Bussi +60
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific p…
Refinement of molecular dynamics ensembles using experimental data and flexible forward models
Thorben Fröhlking, Mattia Bernetti, Giovanni Bussi
A novel method combining maximum entropy principle, the Bayesian-inference of ensembles approach, and the optimization of empirical forward models is presented. Here we focus on th…
Molecular dynamics simulations of chemically modified ribonucleotides
Valerio Piomponi, Mattia Bernetti, Giovanni Bussi
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions.…
Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments
Nicola Calonaci, Mattia Bernetti, Alisha Jones +2
Chemical probing experiments such as SHAPE are routinely used to probe RNA molecules. In this work, we use atomistic molecular dynamics simulations to test the hypothesis that bind…
Integrating experimental data with molecular simulations to investigate RNA structural dynamics
Mattia Bernetti, Giovanni Bussi
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scatter…
Molecular simulations matching denaturation experiments for N6-Methyladenosine
Valerio Piomponi, Thorben Fröhlking, Mattia Bernetti +1
Post-transcriptional modifications are crucial for RNA function and can affect its structure and dynamics. Force-field based classical molecular dynamics simulations are a fundamen…
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
Mattia Bernetti, Kathleen B. Hall, Giovanni Bussi
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural…
Pressure control using stochastic cell rescaling
Mattia Bernetti, Giovanni Bussi
Molecular dynamics simulations require barostats to be performed at constant pressure. The usual recipe is to employ the Berendsen barostat first, which displays a first-order volu…
Towards empirical force fields that match experimental observables
Thorben Fröhlking, Mattia Bernetti, Nicola Calonaci +1
Biomolecular force fields have been traditionally derived based on a mixture of reference quantum chemistry data and experimental information obtained on small fragments. However,…