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List of works by Giovanni Bussi

Ab initiocomplex band structure of conjugated polymers: Effects of hydrid density functional theory andGWschemes

scholarly article in Physical Review B, vol. 85 no. 23, June 2012

Ab-initio study of excitonic effects in conventional and organic semiconductors

article

Accurate multiple time step in biased molecular simulations. ⬇️

scientific article published on 23 December 2014

Accurate sampling using Langevin dynamics

scientific article published on 25 May 2007

Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica

scientific article published on 15 November 2018

Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field

scientific article published on 14 June 2022

Barnaba: software for analysis of nucleic acid structures and trajectories

scientific article published on 12 November 2018

Bowl Inversion of Surface-Adsorbed Sumanene

scientific article published on 18 September 2014

Colored-Noise Thermostats à la Carte

scientific article published on 13 April 2010

Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations.

scientific article

Conjugate gradient heat bath for ill-conditioned actions

scientific article published on 29 August 2007

Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions"

scientific article published on 19 December 2019

Correction to “Free Energy Landscape of GAGA and UUCG RNA Tetraloops”

scientific article published on 19 March 2018

Determination of Structural Ensembles of Proteins: Restraining vs Reweighting

scientific article published on 28 November 2018

Directional translocation resistance of Zika xrRNA

scientific article published on 27 July 2020

Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments. ⬇️

scientific article

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering ⬇️

scientific article

Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide

scientific article published in September 2009

Equilibrium Free Energies from Nonequilibrium Metadynamics

scientific article published in Physical Review Letters

Excitons in carbon nanotubes: an ab initio symmetry-based approach.

scientific article published on 12 May 2004

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.

scientific article

First-principles approach for the calculation of optical properties of one-dimensional systems with helical symmetry: The case of carbon nanotubes

article

Fitting Corrections to an RNA Force Field Using Experimental Data

scientific article published on 23 May 2019

Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics

scientific article published in October 2006

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions

scientific article published on 02 April 2019

Interchain interaction and Davydov splitting in polythiophene crystals: An ab initio approach

article

Isothermal-isobaric molecular dynamics using stochastic velocity rescaling

scientific article published in February 2009

Langevin equation with colored noise for constant-temperature molecular dynamics simulations

scientific article published on 14 January 2009

Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch.

scientific article published on 19 September 2013

Metadynamics with Adaptive Gaussians

scientific article published on 4 June 2012

Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility

scientific article published on 21 December 2017

Molecular Simulations Matching Denaturation Experiments for N<sup>6</sup>-Methyladenosine

scientific article published in 2022

Nonkinetic modeling of the mechanical unfolding of multimodular proteins: theory and experiments.

scientific article

Nuclear quantum effects in solids using a colored-noise thermostat

scientific article published on 17 July 2009

Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations

scientific article published in August 2008

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

article

Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models ⬇️

scientific article

Pressure control using stochastic cell rescaling

scientific article published on 01 September 2020

Quantum interferences in the Raman cross section for the radial breathing mode in metallic carbon nanotubes

scientific article published on 13 January 2005

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

scientific article published on 3 January 2018

RNA Unwinding from Reweighted Pulling Simulations

scientific article published on 06 March 2012

RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations

scientific article published on 22 February 2013

Reactive force field simulation of proton diffusion in BaZrO3 using an empirical valence bond approach

scientific article published on 3 August 2011

Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles

scientific article published on 17 May 2021

Role of the subunit interactions in the conformational transitions in adult human hemoglobin: an explicit solvent molecular dynamics study

scientific article published on 30 August 2012

SiO2 in density functional theory and beyond

Solid state effects on exciton states and optical properties of PPV.

scientific article published on 7 May 2002

Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations

scientific article published on 11 June 2013

The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models

scientific article published on 01 April 2019

The role of nucleobase interactions in RNA structure and dynamics. ⬇️

scientific article published on 29 October 2014

Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications

scientific article published on 01 April 2022

Toward empirical force fields that match experimental observables

scientific article published on 01 June 2020

Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor.

scientific article published on September 2009

Unraveling Mg2+-RNA binding with atomistic molecular dynamics ⬇️

scientific article published in February 2017

Unraveling effects of disorder on the electronic structure ofSiO2from first principles

scholarly article in Physical Review B, vol. 81 no. 8, February 2010

Unravelling the Shuttling Mechanism in a Photoswitchable Multicomponent Bistable Rotaxane

scientific article published on 01 January 2008

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

scientific article

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