Giovanni Bussi
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Physics
Giovanni Bussi's Degrees
- PhD Physics Consorzio ICoN
- Masters Physics Consorzio ICoN
- Bachelors Physics Consorzio ICoN
Why Is Giovanni Bussi Influential?
(Suggest an Edit or Addition)Giovanni Bussi's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Canonical sampling through velocity rescaling. (2007) (10313)
- PLUMED 2: New feathers for an old bird (2013) (1931)
- Well-tempered metadynamics: a smoothly converging and tunable free-energy method. (2008) (1675)
- PLUMED: A portable plugin for free-energy calculations with molecular dynamics (2009) (1266)
- Promoting transparency and reproducibility in enhanced molecular simulations (2019) (437)
- Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. (2006) (413)
- Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration (2013) (348)
- Equilibrium free energies from nonequilibrium metadynamics. (2006) (340)
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview (2018) (322)
- Isothermal-isobaric molecular dynamics using stochastic velocity rescaling. (2009) (270)
- Accurate sampling using Langevin dynamics. (2007) (247)
- Excitons in carbon nanotubes: an ab initio symmetry-based approach. (2004) (242)
- Using metadynamics to explore complex free-energy landscapes (2020) (195)
- Metadynamics with Adaptive Gaussians. (2012) (192)
- Colored-Noise Thermostats à la Carte (2010) (188)
- Hamiltonian replica exchange in GROMACS: a flexible implementation (2013) (160)
- Nuclear quantum effects in solids using a colored-noise thermostat. (2009) (156)
- Langevin equation with colored noise for constant-temperature molecular dynamics simulations. (2008) (141)
- Stochastic thermostats: comparison of local and global schemes (2008) (122)
- Solid state effects on exciton states and optical properties of PPV. (2002) (121)
- The role of nucleobase interactions in RNA structure and dynamics (2014) (104)
- Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. (2016) (102)
- Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments (2018) (89)
- Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations (2018) (88)
- Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement. (2016) (86)
- Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. (2016) (81)
- Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering (2015) (77)
- Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. (2019) (74)
- Free Energy Landscape of GAGA and UUCG RNA Tetraloops. (2016) (63)
- Unraveling Mg2+-RNA binding with atomistic molecular dynamics. (2016) (53)
- Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. (2008) (51)
- Empirical Corrections to the Amber RNA Force Field with Target Metadynamics (2016) (50)
- RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations. (2013) (49)
- Determination of Structural Ensembles of Proteins: Restraining vs Reweighting. (2018) (48)
- Free‐Energy Calculations with Metadynamics: Theory and Practice (2015) (47)
- Trans−cis Switching Mechanisms in Proline Analogues and Their Relevance for the Gating of the 5-HT3 Receptor (2009) (44)
- Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments (2015) (44)
- Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations (2015) (44)
- Reactive force field simulation of proton diffusion in BaZrO3 using an empirical valence bond approach (2011) (43)
- Barnaba: software for analysis of nucleic acid structures and trajectories. (2018) (42)
- Interchain interaction and Davydov splitting in polythiophene crystals: An ab initio approach (2002) (42)
- Fitting Corrections to an RNA Force Field Using Experimental Data. (2019) (41)
- Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations. (2008) (40)
- Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch (2013) (39)
- Pressure control using stochastic cell rescaling. (2020) (38)
- RNA unwinding from reweighted pulling simulations. (2012) (38)
- RNA folding pathways in stop motion (2016) (37)
- Bowl inversion of surface-adsorbed sumanene. (2014) (35)
- First-principles approach for the calculation of optical properties of one-dimensional systems with helical symmetry: The case of carbon nanotubes (2005) (34)
- Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations (2017) (34)
- Exploring RNA structure and dynamics through enhanced sampling simulations. (2017) (33)
- SaX: An open source package for electronic-structure and optical-properties calculations in the GW approximation (2009) (32)
- Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility (2017) (30)
- A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs (2017) (29)
- Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1 (2018) (28)
- Analyzing and Biasing Simulations with PLUMED. (2018) (28)
- Ab initio complex band structure of conjugated polymers: Effects of hydrid density functional theory and GW schemes (2012) (28)
- Accurate multiple time step in biased molecular simulations. (2014) (27)
- Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models. (2016) (27)
- Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations (2015) (26)
- Toward empirical force fields that match experimental observables. (2020) (26)
- Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide. (2009) (24)
- ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations (2015) (23)
- Role of the subunit interactions in the conformational transitions in adult human hemoglobin: an explicit solvent molecular dynamics study. (2012) (22)
- Ab initio study of transport parameters in polymer crystals (2004) (21)
- DFT: B3LYP/6-311G (d, p) vibrational analysis of bis-(diethyldithiocarbamate)zinc(II) and natural bond orbitals. (2013) (20)
- Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles (2021) (18)
- Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. (2020) (18)
- Effects of the Electron–Hole Interaction on the Optical Properties of Materials: the Bethe–Salpeter Equation (2004) (18)
- Assessing the accuracy of direct-coupling analysis for RNA contact prediction (2018) (18)
- Metadynamics: A Unified Framework for Accelerating Rare Events and Sampling Thermodynamics and Kinetics (2020) (18)
- The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. (2018) (17)
- Machine learning a model for RNA structure prediction (2020) (17)
- SiO2 in density functional theory and beyond (2011) (16)
- Ab‐initio study of excitonic effects in conventional and organic semiconductors (2005) (15)
- Unraveling effects of disorder on the electronic structure of SiO2 from first principles (2010) (15)
- Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface. (2017) (13)
- Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data (2019) (13)
- Quantum interferences in the Raman cross section for the radial breathing mode in metallic carbon nanotubes (2004) (13)
- Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions". (2019) (12)
- Directional translocation resistance of Zika xrRNA (2020) (12)
- Asymmetric base-pair opening drives helicase unwinding dynamics (2019) (11)
- Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica. (2018) (11)
- Fine-tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides (2020) (10)
- Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications. (2022) (10)
- Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides. (2017) (10)
- Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations (2021) (9)
- Nonkinetic modeling of the mechanical unfolding of multimodular proteins: theory and experiments. (2011) (9)
- Arginine multivalency stabilizes protein/RNA condensates (2021) (8)
- Analysis of air-turborocket performance (1995) (8)
- Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations (2021) (8)
- Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field (2022) (8)
- Improving the Performance of the RNA Amber Force Field by Tuning the Hydrogen-Bonding Interactions (2018) (7)
- Charge transport and radiative recombination in polythiophene crystals: a first-principles study (2003) (7)
- Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics. (2017) (6)
- Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolution (2019) (6)
- Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine (2022) (5)
- A simple asynchronous replica-exchange implementation (2008) (5)
- Using reweighted pulling simulations to characterize conformational changes in riboswitches. (2015) (5)
- Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays. (2014) (5)
- Correction to "Free Energy Landscape of GAGA and UUCG RNA Tetraloops". (2018) (5)
- Optics and transport in conjugated polymer crystals: Interchain interaction effects (2003) (4)
- Relationship between structural and optoelectronic properties in semiconducting polymers (2004) (4)
- Adding alchemical variables to metadynamics to enhance sampling in free energy calculations (2022) (3)
- An analysis of air-turborocket performance (1993) (3)
- Analyze Nucleic Acids Structures and Trajectories with Barnaba. (2018) (3)
- Structural Role of Uracil DNA Glycosylase for the Recognition of Uracil in DNA Duplexes. Clues from Atomistic Simulations (2013) (3)
- ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations (2015) (3)
- Surface enhanced Raman scattering, electronic spectrum and Mulliken charge distribution in the normal modes of bis(diethyldithiocarbamate)zinc(II) complex. (2013) (3)
- Conformational Ensemble of RNA Oligonucleotides from Reweighted Molecular Simulations (2017) (3)
- Optical properties of organic materials: from single molecules to solid state (2002) (3)
- Nozzle Effects on Linear Stability Behaviour of Combustors (1993) (2)
- Conformational Ensembles of Non-Coding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations (2020) (2)
- Conjugate gradient heat bath for ill-conditioned actions. (2007) (2)
- Correction to Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering (2015) (2)
- Combining simulations and experiments to investigate RNA dynamics (2022) (2)
- Barnaba: software for analysis of nucleic acid structures and trajectories (2018) (2)
- Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions (2022) (2)
- Towards Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Corrections (2021) (2)
- On the Performance of the Air-TurboRocket (1990) (1)
- Light‐Emitting Polymers: a First‐Principles Analysis of Singlet‐Exciton Harvesting in PPV (2005) (1)
- A symmetrized‐basis approach to excitons in carbon nanotubes (2005) (1)
- Integrating experimental data with molecular simulations to investigate RNA structural dynamics. (2022) (1)
- Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations (2015) (1)
- Towards de novo RNA 3D structure prediction (2015) (1)
- Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations. (2023) (1)
- Molecular Dynamics of Solids at Constant Pressure and Stress Using Anisotropic Stochastic Cell Rescaling (2022) (1)
- Role of Magnesium Ions and Ligand Stacking in the Adenine Riboswitch Folding (2014) (1)
- Off-design performance of an Oblique Detonation wave Engine (1998) (1)
- Sampling globally and locally correct RNA 3D structures using ERNWIN, SPQR and experimental SAXS data (2022) (1)
- Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering (2022) (0)
- RNA: Reviewers for Volume 21, 2015. (2015) (0)
- RNA Conformational Ensembles: Narrowing the GAP between Experiments and Simulations with Metadynamics (2016) (0)
- Automated Force-Field Parametrization Guided by Multisystem Ensemble Averages (2018) (0)
- Ab initio optical properties of conjugated polymers: the role of interchain interaction (0)
- Theory of Resonance Raman Scattering in Carbon Nanotubes using Excitonic Intermediate States (2005) (0)
- Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1 (2018) (0)
- RNA Conformational Fluctuations from Elastic Network Models: A Comparison with Molecular Dynamics and Shape Experiments (2016) (0)
- M ar 2 00 8 Canonical sampling through velocity-rescaling (2021) (0)
- System for recovering fuel vapors (2001) (0)
- Wall Curvature Effects on External Burning in Supersonic Flow (2000) (0)
- Understanding CNG Channels Gating Process by MD Simulations (2012) (0)
- Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments (2022) (0)
- Excited states in low-dimensional systems (2005) (0)
- Molecular dynamics simulations of chemically modified ribonucleotides (2022) (0)
- Exploration, representation and rationalization of the conformational phase-space of N-glycans (2022) (0)
- 3 1 M ar 2 00 8 Conjugate gradient heatbath for ill-conditioned actions (2021) (0)
- Towards empirical force fields that reproduce experimental observables (2020) (0)
- Heat Transfer Analysis in Pressurizer Tank Under Microgravity (1986) (0)
- Using metadynamics to explore complex free-energy landscapes (2020) (0)
- CHAPTER 1 Free-Energy Calculations with Metadynamics : Theory and Practice (2015) (0)
- 2 8 M ar 2 00 8 Accurate sampling using Langevin dynamics (2021) (0)
- A Nucleobase-Centric Coarse-Grained Model for Structure Prediction of RNA Fragments (2015) (0)
- Drag reduction by external burning in supersonic flows (1999) (0)
- Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. (2023) (0)
- Analysis of Conical Detonation Waves (2001) (0)
- External Combustion in Supersonic Flow - Problems and Limitations (1997) (0)
- Unraveling disease mechanisms using molecular modeling of bio-interfaces. (2023) (0)
- Molecular simulations and SAXS experiments elucidate ion-dependent conformational ensembles in GAC RNA (2021) (0)
- Refinement of molecular dynamics ensembles using experimental data and flexible forward models (2023) (0)
- PHYS 410-Beta-hairpin folding with parallel-tempering and metadynamics (2007) (0)
- COMP 463-Free-energy landscapes from combined parallel-tempering and metadynamics (2007) (0)
- External burning on curved surfaces in supersonic flow - Problems and limitations (1997) (0)
- Introducing atomistic details into a base-centered representation of RNA (2017) (0)
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