Posani, Janos, Haack, Toor, Bonomi, Magistrato, Bussi All atom molecular dynamics simulations enable ensemble refinement of flexible and mismodelled cryo-EM derived RNA structures biorxiv:10.1101/2024.07.24.604258 #preprint

Di Marco, Aupic, Bussi, Magistrato All-atom simulations elucidate the molecular mechanismunderlying RNA-membrane interactions biorxiv:10.1101/2024.11.01.618995 #preprint

Silva, Bussi Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations arXiv:2410.16064 #preprint

Boccalini, Berezovska, Bussi, Paloni, Barducci Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic Simulations biorxiv:10.1101/2024.09.13.612876 #preprint

Gilardoni, Piomponi, Fröhlking, Bussi MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data arXiv:2411.07798 #preprint

Tribello, Bonomi, Bussi, Camilloni, Armstrong, Arsiccio, Aureli, Ballabio, Bernetti, Bonati, Brookes, Brotzakis, Capelli, Ceriotti, Chan, Cossio, Dasetty, Donadio, Ensing, Ferguson, Fraux, Gale, Gervasio, Giorgino, Herringer, Hocky, Hoff, Invernizzi, Languin-Cattöen, Leone, Limongelli, Lopez-Acevedo, Marinelli, Martinez, Masetti, Mehdi, Michaelides, Murtada, Parrinello, Piaggi, Pietropaolo, Pietrucci, Pipolo, Pritchard, Raiteri, Raniolo, Rapetti, Rizzi, Rydzewski, Salvalaglio, Schran, Seal, Zadeh, Silva, Spiwok, Stirnemann, Sucerquia, Tiwary, Valsson, Vendruscolo, Voth, White, Wu PLUMED Tutorials: a collaborative, community-driven learning ecosystem arXiv:2412.03595 #preprint

Amaro, Åqvist, Bahar, Battistini, Bellaiche, Beltran, Biggin, Bonomi, Bowman, Bryce, Bussi, Carloni, Case, Cavalli, Chang, III, Cheung, Chipot, Chong, Choudhary, Cisneros, Clementi, Collepardo-Guevara, Coveney, Covino, Crawford, Peraro, Groot, Delemotte, Vivo, Essex, Fraternali, Gao, Gelpí, Gervasio, Gonzalez-Nilo, Grubmüller, Guenza, Guzman, Harris, Head-Gordon, Hernandez, Hospital, Huang, Huang, Hummer, Iglesias-Fernández, Jensen, Jha, Jiao, Jorgensen, Kamerlin, Khalid, Laughton, Levitt, Limongelli, Lindahl, Lindorff-Larsen, Loverde, Lundborg, Luo, Luque, Lynch, MacKerell, Magistrato, Marrink, Martin, McCammon, Merz, Moliner, Mulholland, Murad, Naganathan, Nangia, Noe, Noy, Oláh, O'Mara, Ondrechen, Onuchic, Onufriev, Osuna, Panchenko, Pantano, Parish, Parrinello, Perez, Perez-Acle, Perilla, Pettitt, Pietropalo, Piquemal, Poma, Praprotnik, Ramos, Ren, Reuter, Roitberg, Rosta, Rovira, Roux, Röthlisberger, Sanbonmatsu, Schlick, Shaytan, Simmerling, Smith, Sugita, Świderek, Taiji, Tao, Tikhonova, Tirado-Rives, Tunón, Kamp, Spoel, Velankar, Voth, Wade, Warshel, Welborn, Wetmore, Wong, Yang, Zacharias, Orozco The need to implement FAIR principles in biomolecular simulations arXiv:2407.16584 #preprint

Janeček, Kührová, Mlýnský, Stadlbauer, Otyepka, Bussi, Šponer, Banáš Computer Folding of Parallel DNA G‐Quadruplex: Hitchhiker's Guide to the Conformational Space JOURNAL OF COMPUTATIONAL CHEMISTRY e27535 (2025)

Gilardoni, Fröhlking, Bussi Boosting Ensemble Refinement with Transferable Force-Field Corrections: Synergistic Optimization for Molecular Simulations JOURNAL OF PHYSICAL CHEMISTRY LETTERS 15, 1204 (2024)

Mykuliak, Rahikainen, Ball, Bussi, Goult, Hytönen Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force PLOS COMPUTATIONAL BIOLOGY 20, e1012341 (2024)

Pokorná, Mlýnský, Bussi, Šponer, Stadlbauer Molecular dynamics simulations reveal the parallel stranded d(GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES 261, 129712 (2024)

Piomponi, Krepl, Sponer, Bussi Molecular Simulations to Investigate the Impact of N6-Methylation in RNA Recognition: Improving Accuracy and Precision of Binding Free Energy Prediction JOURNAL OF PHYSICAL CHEMISTRY B 128, 8896 (2024)

Bussi, Bonomi, Gkeka, Sattler, Al-Hashimi, Auffinger, Duca, Foricher, Incarnato, Jones, Kirmizialtin, Krepl, Orozco, Palermo, Pasquali, Salmon, Schwalbe, Westhof, Zacharias RNA dynamics from experimental and computational approaches STRUCTURE 32, 1281 (2024) #review

Thiel, Bussi, Poblete, Hofacker Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data NUCLEIC ACIDS RESEARCH 52, e73 (2024)

Hsu, Piomponi, Merz, Bussi, Shirts Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations JOURNAL OF CHEMICAL THEORY AND COMPUTATION 19, 1805 (2023)

Zhang, Šponer, Bussi, Mlýnský, Šulc, Simmons, Stephanopoulos, Krepl Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations JOURNAL OF CHEMICAL INFORMATION AND MODELING 63, 2794 (2023)

Bernetti, Bussi Integrating experimental data with molecular simulations to investigate RNA structural dynamics CURRENT OPINION IN STRUCTURAL BIOLOGY 78, 102503 (2023) #review

Piomponi, Bernetti, Bussi Molecular Dynamics Simulations of Chemically Modified Ribonucleotides RNA Structure and Function. RNA Technologies 14, 595 (2023) #bookchapter

Calonaci, Bernetti, Jones, Sattler, Bussi Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments JOURNAL OF CHEMICAL THEORY AND COMPUTATION 19, 3672 (2023)

Fröhlking, Bernetti, Bussi Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data JOURNAL OF CHEMICAL PHYSICS 158, 214120 (2023)

Fröhlking, Mlýnský, Janeček, Kührová, Krepl, Banáš, Šponer, Bussi Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field JOURNAL OF CHEMICAL THEORY AND COMPUTATION 18, 4490 (2022)

Rolband, Beasock, Wang, Shu, Dinman, Schlick, Zhou, Kieft, Chen, Bussi, Oukhaled, Gao, Šulc, Binzel, Bhullar, Liang, Guo, Afonin Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 20, 6120 (2022) #review

Grothaus, Bussi, Colombi Ciacchi Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans JOURNAL OF CHEMICAL INFORMATION AND MODELING 62, 4992 (2022)

Del Tatto, Raiteri, Bernetti, Bussi Molecular Dynamics of Solids at Constant Pressure and Stress Using Anisotropic Stochastic Cell Rescaling APPLIED SCIENCES-BASEL 12, 1139 (2022)

Piomponi, Fröhlking, Bernetti, Bussi Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine ACS CENTRAL SCIENCE 8, 1218 (2022)

Dutta, Tapio, Suma, Mostafa, Kanehira, Carnevale, Bussi, Bald Molecular states and spin crossover of hemin studied by DNA origami enabled single-molecule surface-enhanced Raman scattering NANOSCALE 14, 16467 (2022)

Mlýnský, Janeček, Kührová, Fröhlking, Otyepka, Bussi, Banáš, Šponer Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications JOURNAL OF CHEMICAL THEORY AND COMPUTATION 18, 2642 (2022)

Paloni, Bussi, Barducci Arginine multivalency stabilizes protein/RNA condensates PROTEIN SCIENCE 30, 1418 (2021)

Bernetti, Bussi Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations EUROPEAN PHYSICAL JOURNAL B 94, 180 (2021)

Bottaro, Bussi, Lindorff-Larsen Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 143, 8333 (2021)

Bernetti, Hall, Bussi Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles NUCLEIC ACIDS RESEARCH 49, e84 (2021)

Cuturello, Tiana, Bussi Assessing the accuracy of direct-coupling analysis for RNA contact prediction RNA 26, 637 (2020)

Reißer, Zucchelli, Gustincich, Bussi Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data NUCLEIC ACIDS RESEARCH 48, 1164 (2020)

Suma, Coronel, Bussi, Micheletti Directional translocation resistance of Zika xrRNA NATURE COMMUNICATIONS 11, 3749 (2020)

Mlynsky, Kührová, Kühr, Otyepka, Bussi, Banáš, Šponer Fine-tuning of the AMBER RNA force field with a new term adjusting interactions of terminal nucleotides JOURNAL OF CHEMICAL THEORY AND COMPUTATION 16, 3936 (2020)

Calonaci, Jones, Cuturello, Sattler, Bussi Machine learning a model for RNA structure prediction NAR GENOMICS AND BIOINFORMATICS 2, lqaa090 (2020)

Bussi, Laio, Tiwary Metadynamics: A Unified Framework for Accelerating Rare Events and Sampling Thermodynamics and Kinetics Handbook of Materials Modeling 565 (2020) #bookchapter

Bernetti, Bussi Pressure control using stochastic cell rescaling JOURNAL OF CHEMICAL PHYSICS 153, 114107 (2020)

Fröhlking, Bernetti, Calonaci, Bussi Toward empirical force fields that match experimental observables JOURNAL OF CHEMICAL PHYSICS 152, 230902 (2020)

Bussi, Laio Using metadynamics to explore complex free-energy landscapes NATURE REVIEWS PHYSICS 2, 200 (2020) #review

Bussi, Tribello Analyzing and Biasing Simulations with PLUMED BIOMOLECULAR SIMULATIONS: METHODS AND PROTOCOLS 2022, 529 (2019) #bookchapter

Colizzi, Perez-Gonzalez, Fritzen, Levy, White, Carlos Penedo, Bussi Asymmetric base-pair opening drives helicase unwinding dynamics PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 116, 22471 (2019)

Bottaro, Bussi, Pinamonti, Reiber, Boomsma, Lindorff-Larsen Barnaba: software for analysis of nucleic acid structures and trajectories RNA 25, 219 (2019)

Cesari, Bottaro, Lindorff-Larsen, Banáš, Šponer, Bussi Fitting Corrections to an RNA Force Field Using Experimental Data JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15, 3425 (2019)

Kührová, Mlýnský, Zgarbová, Krepl, Bussi, Best, Otyepka, Šponer, Banáš Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15, 3288 (2019)

Bonomi, Bussi, Camilloni, Tribello, Banas, Barducci, Bernetti, Bolhuis, Bottaro, Branduardi, Capelli, Carloni, Ceriotti, Cesari, Chen, Chen, Colizzi, De, De, Donadio, Drobot, Ensing, Ferguson, Filizola, Fraser, Fu, Gasparotto, Gervasio, Giberti, Gil-Ley, Giorgino, Heller, Hocky, Iannuzzi, Invernizzi, Jelfs, Jussupow, Kirilin, Laio, Limongelli, Lindorff-Larsen, Lohr, Marinelli, Martin-Samos, Masetti, Meyer, Michaelides, Molteni, Morishita, Nava, Paissoni, Papaleo, Parrinello, Pfaendtner, Piaggi, Piccini, Pietropaolo, Pietrucci, Pipolo, Provasi, Quigley, Raiteri, Raniolo, Rydzewski, Salvalaglio, Sosso, Spiwok, Sponer, Swenson, Tiwary, Valsson, Vendruscolo, Voth, White Promoting transparency and reproducibility in enhanced molecular simulations NATURE METHODS 16, 670 (2019)

Franco, Cagiada, Bussi, Tiana Statistical mechanical properties of sequence space determine the efficiency of the various algorithms to predict interaction energies and native contacts from protein coevolution PHYSICAL BIOLOGY 16, 046007 (2019)

Pinamonti, Paul, Noe, Rodriguez, Bussi The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models JOURNAL OF CHEMICAL PHYSICS 150, 154123 (2019)

Poblete, Bottaro, Bussi A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs NUCLEIC ACIDS RESEARCH 46, 1674 (2018)

Hildebrand, Michaelis, Wurzler, Li, Hirst, Micsonai, Kardos, Gil-Ley, Bussi, Köppen, Piane, Ciacchi Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica ACS BIOMATERIALS SCIENCE & ENGINEERING 4, 4036 (2018)

Bottaro, Bussi, Kennedy, Turner, Lindorff-Larsen Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations SCIENCE ADVANCES 4, eaar8521 (2018)

Rangan, Bonomi, Heller, Cesari, Bussi, Vendruscolo Determination of Structural Ensembles of Proteins: Restraining vs Reweighting JOURNAL OF CHEMICAL THEORY AND COMPUTATION 14, 6632 (2018)

Poblete, Bottaro, Bussi Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 498, 352 (2018)

Mlýnský, Bussi Exploring RNA structure and dynamics through enhanced sampling simulations CURRENT OPINION IN STRUCTURAL BIOLOGY 49, 63 (2018) #review

Mlýnský, Bussi Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility JOURNAL OF PHYSICAL CHEMISTRY LETTERS 9, 313 (2018)

Sponer, Bussi, Krepl, Banas, Bottaro, Cunha, Gil-Ley, Pinamonti, Poblete, Jurečka, Walter, Otyepka RNA structural dynamics as captured by molecular simulations: A comprehensive overview CHEMICAL REVIEWS 118, 4177 (2018) #review

Podbevšek, Fasolo, Bon, Cimatti, Reißer, Carninci, Bussi, Zucchelli, Plavec, Gustincich Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1 SCIENTIFIC REPORTS 8, 3189 (2018)

Cesari, Reißer, Bussi Using the maximum entropy principle to combine simulations and solution experiments COMPUTATION 6, 15 (2018) #review

Islam, Stadlbauer, Gil-Ley, Pérez-Hernández, Haider, Neidle, Bussi, Banas, Otyepka, Sponer Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13, 2458 (2017)

Bellucci, Bussi, Di Felice, Corni Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface NANOSCALE 9, 2279 (2017)

Šponer, Bussi, Stadlbauer, Kührová, Banáš, Islam, Haider, Neidle, Otyepka Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS 1861, 1246 (2017)

Pinamonti, Zhao, Condon, Paul, Noè, Turner, Bussi Predicting the Kinetics of RNA Oligonucleotides Using Markov State Models JOURNAL OF CHEMICAL THEORY AND COMPUTATION 13, 926 (2017)

Mlýnský, Bussi Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides RNA 23, 712 (2017)

Cunha, Bussi Unraveling Mg2+-RNA binding with atomistic molecular dynamics RNA 23, 628 (2017)

Cesari, Gil-Ley, Bussi Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12, 6192 (2016)

Kührová, Best, Bottaro, Bussi, Šponer, Otyepka, Banáš Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12, 4534 (2016)

Gil-Ley, Bottaro, Bussi Empirical Corrections to the Amber RNA Force Field with Target Metadynamics JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12, 2790 (2016)

Bottaro, Banáš, Šponer, Bussi Free Energy Landscape of GAGA and UUCG RNA Tetraloops JOURNAL OF PHYSICAL CHEMISTRY LETTERS 7, 4032 (2016)

Bottaro, Gil-Ley, Bussi RNA folding pathways in stop motion NUCLEIC ACIDS RESEARCH 44, 5883 (2016)

Ferrarotti, Bottaro, Pérez-Villa, Bussi Accurate multiple time step in biased molecular simulations JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11, 139 (2015)

Pérez-Villa, Darvas, Bussi ATP dependent NS3 helicase interaction with RNA: Insights from molecular simulations NUCLEIC ACIDS RESEARCH 43, 8725 (2015)

Pinamonti, Bottaro, Micheletti, Bussi Elastic network models for RNA: A comparative assessment with molecular dynamics and SHAPE experiments NUCLEIC ACIDS RESEARCH 43, 7260 (2015)

Gil-Ley, Bussi Enhanced conformational sampling using replica exchange with collective-variable tempering JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11, 1077 (2015)

Bussi, Branduardi Free-energy calculations with metadynamics: Theory and practice REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28 28, 1 (2015) #bookchapter

Stadlbauer, Kührová, Banáš, Koča, Bussi, Trantírek, Otyepka, Šponer Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations NUCLEIC ACIDS RESEARCH 43, 9626 (2015)

Di Palma, Bottaro, Bussi Kissing loop interaction in adenine riboswitch: Insights from umbrella sampling simulations BMC BIOINFORMATICS 16, S6 (2015)

Bottaro, Di, Bussi Towards de novo RNA 3D Structure Prediction RNA & DISEASE 1 (2015)

Di Palma, Colizzi, Bussi Using reweighted pulling simulations to characterize conformational changes in riboswitches COMPUTATIONAL METHODS FOR UNDERSTANDING RIBOSWITCHES 553, 139 (2015) #bookchapter

Jaafar, Pignedoli, Bussi, Aït-Mansour, Groening, Amaya, Hirao, Fasel, Ruffieux Bowl inversion of surface-adsorbed sumanene JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 136, 13666 (2014)

Abrams, Bussi Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration ENTROPY 16, 163 (2014)

Bussi Hamiltonian replica exchange in GROMACS: A flexible implementation MOLECULAR PHYSICS 112, 379 (2014)

Tribello, Bonomi, Branduardi, Camilloni, Bussi PLUMED 2: New feathers for an old bird COMPUTER PHYSICS COMMUNICATIONS 185, 604 (2014)

Colizzi, Lamontagne, Lafontaine, Bussi Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays Therapeutic applications of ribozymes and riboswitches : methods and protocols 1103, 141 (2014) #bookchapter

Bottaro, Di Palma, Bussi The role of nucleobase interactions in RNA structure and dynamics NUCLEIC ACIDS RESEARCH 42, 13306 (2014)

Di Palma, Colizzi, Bussi Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch RNA 19, 1517 (2013)

Do, Carloni, Varani, Bussi RNA/peptide binding driven by electrostatics - Insight from bidirectional pulling simulations JOURNAL OF CHEMICAL THEORY AND COMPUTATION 9, 1720 (2013)

Franco, Sgrignani, Bussi, Magistrato Structural role of uracil DNA glycosylase for the recognition of uracil in DNA duplexes. Clues from atomistic simulations JOURNAL OF CHEMICAL INFORMATION AND MODELING 53, 1371 (2013)

Ferretti, Mallia, Martin-Samos, Bussi, Ruini, Montanari, Harrison Ab initio complex band structure of conjugated polymers: Effects of hydrid density functional theory and GW schemes PHYSICAL REVIEW B 85, 235105 (2012)

Branduardi, Bussi, Parrinello Metadynamics with adaptive gaussians JOURNAL OF CHEMICAL THEORY AND COMPUTATION 8, 2247 (2012)

Colizzi, Bussi RNA unwinding from reweighted pulling simulations JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134, 5173 (2012)

Yusuff, Babalola, Bussi, Raugei Role of the subunit interactions in the conformational transitions in adult human hemoglobin: An explicit solvent molecular dynamics study JOURNAL OF PHYSICAL CHEMISTRY B 116, 11004 (2012)

Benedetti, Micheletti, Bussi, Sekatskii, Dietler Nonkinetic modeling of the mechanical unfolding of multimodular proteins: Theory and experiments BIOPHYSICAL JOURNAL 101, 1504 (2011)

Raiteri, Gale, Bussi Reactive force field simulation of proton diffusion in BaZrO3 using an empirical valence bond approach JOURNAL OF PHYSICS-CONDENSED MATTER 23, 334213 (2011)

Martin-Samos, Bussi, Ruini, Molinari, Caldas SiO2 in density functional theory and beyond PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS 248, 1061 (2011)

Ceriotti, Bussi, Parrinello Colored-noise thermostats àla Carte JOURNAL OF CHEMICAL THEORY AND COMPUTATION 6, 1170 (2010)

Martin-Samos, Bussi, Ruini, Molinari, Caldas Unraveling effects of disorder on the electronic structure of SiO2 from first principles PHYSICAL REVIEW B 81, 081202 (2010)

Bussi A simple asynchronous replica-exchange implementation NUOVO CIMENTO DELLA SOCIETA ITALIANA DI FISICA C-COLLOQUIA ON PHYSICS 32, 61 (2009)

Mantz, Branduardi, Bussi, Parrinello Ensemble of Transition State Structures for the Cis-Trans Isomerization of N-Methylacetamide JOURNAL OF PHYSICAL CHEMISTRY B 113, 12521 (2009)

Bussi, Zykova-Timan, Parrinello Isothermal-isobaric molecular dynamics using stochastic velocity rescaling JOURNAL OF CHEMICAL PHYSICS 130, 074101 (2009)

Ceriotti, Bussi, Parrinello Langevin equation with colored noise for constant-temperature molecular dynamics simulations PHYSICAL REVIEW LETTERS 102, 020601 (2009)

Ceriotti, Bussi, Parrinello Nuclear quantum effects in solids using a colored-noise thermostat PHYSICAL REVIEW LETTERS 103, 030603 (2009)

Bonomi, Branduardi, Bussi, Camilloni, Provasi, Raiteri, Donadio, Marinelli, Pietrucci, Broglia, Parrinello PLUMED: A portable plugin for free-energy calculations with molecular dynamics COMPUTER PHYSICS COMMUNICATIONS 180, 1961 (2009)

Martin-Samos, Bussi SaX: An open source package for electronic-structure and optical-properties calculations in the GW approximation COMPUTER PHYSICS COMMUNICATIONS 180, 1416 (2009)

Melis, Bussi, Lummis, Molteni Trans-cis switching mechanisms in proline analogues and their relevance for the gating of the 5-HT3 receptor JOURNAL OF PHYSICAL CHEMISTRY B 113, 12148 (2009)

Micheletti, Bussi, Laio Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations JOURNAL OF CHEMICAL PHYSICS 129, 074105 (2008)

Bussi, Parrinello Stochastic thermostats: comparison of local and global schemes COMPUTER PHYSICS COMMUNICATIONS 179, 26 (2008)

Raiteri, Bussi, Cucinotta, Credi, Stoddart, Parrinello Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane ANGEWANDTE CHEMIE-INTERNATIONAL EDITION 47, 3536 (2008)

Barducci, Bussi, Parrinello Well-tempered metadynamics: A smoothly converging and tunable free-energy method PHYSICAL REVIEW LETTERS 100, 020603 (2008)

Bussi, Parrinello Accurate sampling using Langevin dynamics PHYSICAL REVIEW E 75, 056707 (2007)

Bussi, Donadio, Parrinello Canonical sampling through velocity rescaling JOURNAL OF CHEMICAL PHYSICS 126, 014101 (2007)

Ceriotti, Bussi, Parrinello Conjugate gradient heat bath for ill-conditioned actions PHYSICAL REVIEW E 76, 026707 (2007)

Bussi, Laio, Parrinello Equilibrium free energies from nonequilibrium metadynamics PHYSICAL REVIEW LETTERS 96, 090601 (2006)

Bussi, Gervasio, Laio, Parrinello Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 128, 13435 (2006)

Bussi, Gervasio, Laio, Parrinello Protein folding with combined parallel tempering and metadynamics High Performance Computing in Science and Engineering, 587 (2006) #bookchapter

Bussi, Chang, Ruini, Molinari A symmetrized-basis approach to excitons in carbon nanotubes PHYSICS OF SEMICONDUCTORS, PTS A AND B 772, 1025 (2005) #proceedings

Hummer, Ambrosch-Draxl, Bussi, Ruini, Caldas, Molinari, Laskowski, Christensen Ab-initio study of excitonic effects in conventional and organic semiconductors PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS 242, 1754 (2005)

Chang, Bussi, Ruini, Molinari First-principles approach for the calculation of optical properties of one-dimensional systems with helical symmetry: The case of carbon nanotubes PHYSICAL REVIEW B 72, 195423 (2005)

Caldas, Bussi, Ruini, Molinari Light-emitting polymers: A first-principles analysis of singlet-exciton harvesting in PPV PHYSICS OF SEMICONDUCTORS, PTS A AND B 772, 1085 (2005) #proceedings

Bussi, Menéndez, Ren, Canonico, Molinari Quantum interferences in the Raman cross section for the radial breathing mode in metallic carbon nanotubes PHYSICAL REVIEW B 71, 041404 (2005)

Ferretti, Ruini, Bussi, Molinari, Caldas Ab initio study of transport parameters in polymer crystals PHYSICAL REVIEW B 69, 205205 (2004)

Bussi Effects of the electron-hole interaction on the optical properties of materials: The Bethe-Salpeter equation PHYSICA SCRIPTA T109, 141 (2004)

Chang, Bussi, Ruini, Molinari Excitons in carbon nanotubes: An ab initia symmetry-based approach PHYSICAL REVIEW LETTERS 92, 196401 (2004)

Ruini, Ferretti, Bussi, Molinari, Caldas Relationship between structural and optoelectronic properties in semiconducting polymers SEMICONDUCTOR SCIENCE AND TECHNOLOGY 19, S362 (2004)

Ruini, Bussi, Ferretti, Caldas, Molinari Charge transport and radiative recombination in polythiophene crystals: A first-principles study SYNTHETIC METALS 139, 755 (2003)

Bussi, Ferretti, Ruini, Caldas, Molinari Optics and transport in conjugated polymer crystals: Interchain interaction effects ADVANCES IN SOLID STATE PHYSICS 43 313 (2003) #bookchapter

Bussi, Ruini, Molinari, Caldas, Puschnig, Ambrosch-Draxl Interchain interaction and Davydov splitting in polythiophene crystals: An ab initio approach APPLIED PHYSICS LETTERS 80, 4118 (2002)

Ruini, Caldas, Bussi, Ferretti, Silva, Goldoni, Molinari Optical properties of organic materials: from single molecules to solid state Radiation-Matter interaction in confined systems 155 (2002) #bookchapter

Ruini, Caldas, Bussi, Molinari Solid state effects on exciton states and optical properties of PPV PHYSICAL REVIEW LETTERS 88, 206403 (2002)

Records per page: 10 20 50