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Gilardoni, Bussi Bayesian Sampling of Structural Ensembles: The Role of Ensemble-Counting Measures arXiv:2606.18495 #preprint
Lin, Dasgupta, Yang, Malosso, Sormani, Egan, Bussi, Hassanali, Cremer Beyond the Virial Expansion: Microscopic Origins of Partial Molar Volumes in LiCl Solutions arXiv:2604.19622 #preprint
Colizzi, Blázquez-Sánchez, Bussi, André, Ballabio, Bayer, Bertocchini, Butenschön, Carosati, Piero, Pede-Mattatelli, Faggian, Favaro, Fernandes, Ferretti, Fojan, Gagsteiger, García-Ruiz, Gardossi, Giorgino, Graefe, Gunkel, Jiménez, Keller, Künze, Lim, Lippens, Maria-Solano, Mitusińska, Moliner, Molla, Myburgh, Panel, Ramírez-Sarmiento, Rocher, Strodel, Ruiz, Turak, Varrone, Vezzini, Westh, Zimmermann Computations Meet Experiments to Advance the Enzymatic Depolymerization of Plastics One Atom at a Time arXiv:2507.14413 #preprint
Languin-Cattoën, Posani, Bussi Enhanced sampling and cryo-EM data resolve magnesium binding to RNA arXiv:2607.07186 #preprint
Sacco, Li, Smyth, Sanguinetti, Bussi MERGE-RNA: a physics-based model to predict RNA secondary structure ensembles with chemical probing arXiv:2512.20581 #preprint
Palmer, Chauvier, Silva, Ontiveros, Bussi, Walter, Mishanina pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing biorxiv:10.64898/2026.02.18.706685 #preprint
Mlynsky, Kuhrova, Bussi, Otyepka, Sponer, Banas* From gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields JOURNAL OF CHEMICAL THEORY AND COMPUTATION 1 (2026) #pnrr2022
Languin-Cattoën, Bussi* RNA Dynamics and Interactions Revealed Through Atomistic Simulations ANNUAL REVIEW OF PHYSICAL CHEMISTRY 77, 489 (2026) #review #msca2023
Zhang*, Dolcetti, Tyrchan, De Maria, Bussi, Czechtizky Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges JOURNAL OF CHEMICAL INFORMATION AND MODELING 66, 4215 (2026)
Sacco, Bussi, Sanguinetti* Machine learning for RNA secondary structure prediction: a review of current methods and challenges RNA 32, 443 (2026) #review
Rapetti, Bonomi*, Camilloni*, Bussi*, Tribello* Making PLUMED Fly: A Tutorial on Optimizing Performance JOURNAL OF PHYSICAL CHEMISTRY B 130, 2504 (2026) #pnrr2022
Kretsch, Posani, Baulin, Bujnicki, Bussi, Cheatham, Chen, Elofsson, Farsani, Fisher, Gromiha, Gupta, Hamada, Harini, Hu, Huang, Iwakiri, Jain, Kagaya, Kihara, Kmiecik, Krishnan, Kurisaki, Languin‐Cattoen, Li, Li, Malekzadeh, Nakamura, Ni, Nithin, Palo, Park, Pilla, Poblete, Pucci, Punuru, Saha, Sato, Srivastava, Terashi, Tugolukova, Verburgt, Wuyun, Zerze, Zhang, Zhang, Zheng, Zhou, Chiu*, Case*, Das* Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16 PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 94, 381 (2026) #prin2022 #pnrr2022 #msca2023 #eurohpc2024
Posani Ensemble Refinement of Cryo-Electron Microscopy-Derived RNA Structures Using Molecular Dynamics Simulations PHD THESIS (2025)
Gilardoni Development and application of methods to integrate molecular simulations with experimental measurements PHD THESIS (2025)
Mizrahi, Corley, Feldman, Fröhlking, Sun, Ziesel, Antczak, Bernetti, Elhajjajy, Huang, Nguyen, Park, Perez Martell, Trinity, Xu, Zok, Bussi, Jabbari, Orenstein, Aviran*, Meyer*, Yeo* Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data RNA 31, 1103 (2025)
Müller-Hermes, Piomponi, Hilber, Asami, Kreutz, Bussi, Sattler* Unique conformational dynamics and protein recognition of A-to-I hyper-edited dsRNA NUCLEIC ACIDS RESEARCH 53, gkaf550 (2025) #pnrr2022
Posani, Janoš, Haack, Toor, Bonomi, Magistrato*, Bussi* Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations NATURE COMMUNICATIONS 16, 4549 (2025) #prin2022 #pnrr2022 #eurohpc2024
Gilardoni*, Piomponi, Fröhlking, Bussi* MDRefine: A Python package for refining molecular dynamics trajectories with experimental data JOURNAL OF CHEMICAL PHYSICS 162, 192501 (2025) #pnrr2022
Boccalini, Berezovska, Bussi, Paloni*, Barducci* Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic simulations PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 122, e2425261122 (2025) #pnrr2022
Amaro, Åqvist, Bahar, Battistini, Bellaiche, Beltran, Biggin, Bonomi, Bowman, Bryce, Bussi, Carloni, Case, Cavalli, Chang, Cheatham, Cheung, Chipot, Chong, Choudhary, Cisneros, Clementi, Collepardo-Guevara, Coveney, Covino, Crawford, Dal Peraro, de Groot, Delemotte, De Vivo, Essex, Fraternali, Gao, Gelpí, Gervasio, González-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, Palermo, Panchenko, Pantano, Parish, Parrinello, Perez, Perez-Acle, Perilla, Pettitt, Pietropaolo, Piquemal, Poma, Praprotnik, Ramos, Ren, Reuter, Roitberg, Rosta, Rovira, Roux, Rothlisberger, Sanbonmatsu, Schlick, Shaytan, Simmerling, Smith, Sugita, Świderek, Taiji, Tao, Tieleman, Tikhonova, Tirado-Rives, Tuñón, van der Kamp, van der Spoel, Velankar, Voth, Wade, Warshel, Welborn, Wetmore, Wheeler, Wong, Yang, Zacharias, Orozco* The need to implement FAIR principles in biomolecular simulations NATURE METHODS 22, 641 (2025)
Silva*, Bussi Characterizing RNA Oligomers Using Stochastic Titration Constant-pH Metadynamics Simulations JOURNAL OF CHEMICAL INFORMATION AND MODELING 65, 3568 (2025) #pnrr2022 #embo2022
Di Marco, Aupič*, Bussi, Magistrato* All-Atom Simulations Elucidate the Molecular Mechanism Underlying RNA-Membrane Interactions NANO LETTERS 25, 4628 (2025) #pnrr2022
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-Cattoën, Leone, Limongelli, Lopez-Acevedo, Marinelli, Febrer Martinez, Masetti, Mehdi, Michaelides, Murtada, Parrinello, Piaggi, Pietropaolo, Pietrucci, Pipolo, Pritchard, Raiteri, Raniolo, Rapetti, Rizzi, Rydzewski, Salvalaglio, Schran, Seal, Shayesteh Zadeh, Silva, Spiwok, Stirnemann, Sucerquia, Tiwary, Valsson, Vendruscolo, Voth, White, Wu PLUMED Tutorials: A collaborative, community-driven learning ecosystem JOURNAL OF CHEMICAL PHYSICS 162, 092501 (2025) #prin2022 #pnrr2022 #embo2022
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 46, e27535 (2025)
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
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)
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)
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)
Gilardoni, Fröhlking, Bussi* Boosting Ensemble Refinement with Transferable Force-Field Corrections: Synergistic Optimization for Molecular Simulations JOURNAL OF PHYSICAL CHEMISTRY LETTERS 15, 1204 (2024)
Piomponi, Bernetti, Bussi* Molecular Dynamics Simulations of Chemically Modified Ribonucleotides RNA Structure and Function. RNA Technologies 14, 595 (2023) #bookchapter
Piomponi Molecular simulations to investigate the impact of post-transcriptional modifications on RNA structural dynamics PHD THESIS (2023)
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)
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)
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)
Bernetti, Bussi* Integrating experimental data with molecular simulations to investigate RNA structural dynamics CURRENT OPINION IN STRUCTURAL BIOLOGY 78, 102503 (2023) #review
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
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)
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)
Froehlking Machine learning RNA force fields from experimental data PHD THESIS (2022)
Piomponi, Fröhlking, Bernetti, Bussi* Molecular Simulations Matching Denaturation Experiments for N6-Methyladenosine ACS CENTRAL SCIENCE 8, 1218 (2022)
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)
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)
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)
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*, Bussi* Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations EUROPEAN PHYSICAL JOURNAL B 94, 180 (2021)
Bernetti*, Hall, Bussi* Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles NUCLEIC ACIDS RESEARCH 49, e84 (2021)
Paloni, Bussi, Barducci* Arginine multivalency stabilizes protein/RNA condensates PROTEIN SCIENCE 30, 1418 (2021)
Suma, Coronel, Bussi, Micheletti* Directional translocation resistance of Zika xrRNA NATURE COMMUNICATIONS 11, 3749 (2020)
Calonaci Computational investigations of structure probing experiments for RNA structure prediction PHD THESIS (2020)
Calonaci, Jones, Cuturello, Sattler, Bussi* Machine learning a model for RNA structure prediction NAR GENOMICS AND BIOINFORMATICS 2, lqaa090 (2020)
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)
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)
Bussi, Laio*, Tiwary Metadynamics: A Unified Framework for Accelerating Rare Events and Sampling Thermodynamics and Kinetics Handbook of Materials Modeling 565 (2020) #bookchapter
Cuturello, Tiana, Bussi* Assessing the accuracy of direct-coupling analysis for RNA contact prediction RNA 26, 637 (2020)
Bussi, Laio* Using metadynamics to explore complex free-energy landscapes NATURE REVIEWS PHYSICS 2, 200 (2020) #review
Reißer*, Zucchelli, Gustincich, Bussi* Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data NUCLEIC ACIDS RESEARCH 48, 1164 (2020) #erc2012
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) #erc2012
Cuturello Covariance models for RNA structure prediction PHD THESIS (2019)
Bussi*, Tribello* Analyzing and Biasing Simulations with PLUMED Biomolecular Simulation 2022, 529 (2019) #bookchapter
Bonomi*, Bussi*, Camilloni*, Tribello*, Banas, Barducci, Bernetti, Bolhuis, Bottaro, Branduardi, Capelli, Carloni, Ceriotti, Cesari, Chen, Chen, Colizzi, De, De La Pierre, 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)
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)
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) #erc2012
Bottaro*, Bussi*, Pinamonti, Reiber, Boomsma, Lindorff-Larsen Barnaba: software for analysis of nucleic acid structures and trajectories RNA 25, 219 (2019) #erc2012
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)
Rangan, Bonomi*, Heller, Cesari, Bussi, Vendruscolo* Determination of Structural Ensembles of Proteins: Restraining vs Reweighting JOURNAL OF CHEMICAL THEORY AND COMPUTATION 14, 6632 (2018)
Bottaro*, Bussi, Kennedy, Turner, Lindorff-Larsen* Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations SCIENCE ADVANCES 4, eaar8521 (2018) #erc2012
Cesari Enforcing ensemble averages in molecular dynamics simulations using the Maximum Entropy principle PHD THESIS (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) #erc2012
Poblete*, Bottaro, Bussi* A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs NUCLEIC ACIDS RESEARCH 46, 1674 (2018) #erc2012
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 #erc2012
Mlýnský, Bussi* Exploring RNA structure and dynamics through enhanced sampling simulations CURRENT OPINION IN STRUCTURAL BIOLOGY 49, 63 (2018) #review #erc2012
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) #erc2012
Cesari, Reißer, Bussi* Using the maximum entropy principle to combine simulations and solution experiments COMPUTATION 6, 15 (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) #erc2012
Andre Cunha Dissecting Mg2+-RNA interactions using atomistic molecular dynamics PHD THESIS (2017)
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) #erc2012
Mlýnský*, Bussi* Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides RNA 23, 712 (2017) #erc2012
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) #erc2012
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) #erc2012
Cunha, Bussi* Unraveling Mg2+-RNA binding with atomistic molecular dynamics RNA 23, 628 (2017) #erc2012
Bellucci*, Bussi, Di Felice, Corni* Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface NANOSCALE 9, 2279 (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) #erc2012
Bottaro, Banáš, Šponer, Bussi Free Energy Landscape of GAGA and UUCG RNA Tetraloops JOURNAL OF PHYSICAL CHEMISTRY LETTERS 7, 4032 (2016) #erc2012
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) #erc2012
Gil-Ley, Bottaro, Bussi* Empirical Corrections to the Amber RNA Force Field with Target Metadynamics JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12, 2790 (2016) #erc2012
Bottaro, Gil-Ley, Bussi* RNA folding pathways in stop motion NUCLEIC ACIDS RESEARCH 44, 5883 (2016) #erc2012
Pinamonti Studying the dynamical properties of small RNA molecules with computational techniques PHD THESIS (2016)
Gil Ley Enhanced sampling and force field corrections for RNA oligomers PHD THESIS (2016)
Di Palma, Colizzi, Bussi* Using reweighted pulling simulations to characterize conformational changes in riboswitches COMPUTATIONAL METHODS FOR UNDERSTANDING RIBOSWITCHES 553, 139 (2015) #bookchapter #erc2012 #iscrab2012a
Bussi, Branduardi Free-energy calculations with metadynamics: Theory and practice REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28 28, 1 (2015) #bookchapter
Gil-Ley, Bussi* Enhanced conformational sampling using replica exchange with collective-variable tempering JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11, 1077 (2015) #erc2012
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) #erc2012
Pinamonti, Bottaro, Micheletti, Bussi* Elastic network models for RNA: A comparative assessment with molecular dynamics and SHAPE experiments NUCLEIC ACIDS RESEARCH 43, 7260 (2015) #erc2012
Bottaro, Di Palma, Bussi Towards de novo RNA 3D Structure Prediction RNA & DISEASE 2, e544 (2015) #erc2012
Ferrarotti, Bottaro, Pérez-Villa, Bussi* Accurate multiple time step in biased molecular simulations JOURNAL OF CHEMICAL THEORY AND COMPUTATION 11, 139 (2015) #erc2012
Di Palma*, Bottaro, Bussi* Kissing loop interaction in adenine riboswitch: Insights from umbrella sampling simulations BMC BIOINFORMATICS 16, S6 (2015) #erc2012 #iscrab2013
Pérez-Villa, Darvas, Bussi* ATP dependent NS3 helicase interaction with RNA: Insights from molecular simulations NUCLEIC ACIDS RESEARCH 43, 8725 (2015) #erc2012 #iscrab2012b
Perez Villa Translocation of NS3 from Hepatitis C Virus on RNA: Insights from Atomistic Molecular Simulations PHD THESIS (2015)
Colizzi, Lamontagne, Lafontaine, Bussi Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays METHODS IN MOLECULAR BIOLOGY 1103, 141 (2014) #bookchapter #erc2012
Bottaro, Di Palma, Bussi* The role of nucleobase interactions in RNA structure and dynamics NUCLEIC ACIDS RESEARCH 42, 13306 (2014) #erc2012
Abrams*, Bussi Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration ENTROPY 16, 163 (2014) #erc2012
Bussi* Hamiltonian replica exchange in GROMACS: A flexible implementation MOLECULAR PHYSICS 112, 379 (2014) #erc2012 #iscrab2010
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)
Tribello, Bonomi, Branduardi, Camilloni, Bussi* PLUMED 2: New feathers for an old bird COMPUTER PHYSICS COMMUNICATIONS 185, 604 (2014) #firb2012 #erc2012
Di Palma Conformational changes in the adenine riboswitch PHD THESIS (2014)
Di Palma, Colizzi, Bussi* Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch RNA 19, 1517 (2013) #erc2012 #iscrab2012a
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)
Do, Carloni, Varani, Bussi* RNA/peptide binding driven by electrostatics - Insight from bidirectional pulling simulations JOURNAL OF CHEMICAL THEORY AND COMPUTATION 9, 1720 (2013) #erc2012 #iscraa2011
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)
Colizzi*, Bussi* RNA unwinding from reweighted pulling simulations JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 134, 5173 (2012) #firb2012 #iscrab2011
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) #firb2012
Do Investigating Peptide/RNA binding in Anti-HIV research by molecular simulations: electrostatic recognition and accelerated sampling PHD THESIS (2012)
Martin-Samos*, Bussi, Ruini, Molinari, Caldas* SiO2 in density functional theory and beyond PHYSICA STATUS SOLIDI B-BASIC SOLID STATE PHYSICS 248, 1061 (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)
Benedetti, Micheletti, Bussi, Sekatskii, Dietler* Nonkinetic modeling of the mechanical unfolding of multimodular proteins: Theory and experiments BIOPHYSICAL JOURNAL 101, 1504 (2011)
Martin-Samos, Bussi, Ruini, Molinari, Caldas Unraveling effects of disorder on the electronic structure of SiO2 from first principles PHYSICAL REVIEW B 81, 081202(R) (2010)
Ceriotti*, Bussi, Parrinello Colored-noise thermostats àla Carte JOURNAL OF CHEMICAL THEORY AND COMPUTATION 6, 1170 (2010)
Bussi*, Zykova-Timan, Parrinello Isothermal-isobaric molecular dynamics using stochastic velocity rescaling JOURNAL OF CHEMICAL PHYSICS 130, 074101 (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)
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)
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)
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)
Ceriotti, Bussi*, Parrinello Langevin equation with colored noise for constant-temperature molecular dynamics simulations PHYSICAL REVIEW LETTERS 102, 020601 (2009)
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)
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)
Ceriotti*, Bussi, Parrinello Conjugate gradient heat bath for ill-conditioned actions PHYSICAL REVIEW E 76, 026707 (2007)
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)
Bussi, Gervasio, Laio, Parrinello Protein folding with combined parallel tempering and metadynamics High Performance Computing in Science and Engineering, 587 (2006) #bookchapter
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*, Laio, Parrinello Equilibrium free energies from nonequilibrium metadynamics PHYSICAL REVIEW LETTERS 96, 090601 (2006)
Bussi, Chang, Ruini, Molinari A symmetrized-basis approach to excitons in carbon nanotubes PHYSICS OF SEMICONDUCTORS, PTS A AND B 772, 1025 (2005) #proceedings
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
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)
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(R) (2005)
Bussi* Effects of the electron-hole interaction on the optical properties of materials: The Bethe-Salpeter equation PHYSICA SCRIPTA 2004, 141 (2004)
Ferretti*, Ruini, Bussi, Molinari, Caldas Ab initio study of transport parameters in polymer crystals PHYSICAL REVIEW B 69, 205205 (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)
Bussi, Ferretti, Ruini, Caldas, Molinari Optics and transport in conjugated polymer crystals: Interchain interaction effects ADVANCES IN SOLID STATE PHYSICS 43 43, 313 (2003) #bookchapter
Ruini*, Bussi, Ferretti, Caldas, Molinari Charge transport and radiative recombination in polythiophene crystals: A first-principles study SYNTHETIC METALS 139, 755 (2003)
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
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, Molinari Solid state effects on exciton states and optical properties of PPV PHYSICAL REVIEW LETTERS 88, 206403 (2002)