| Year |
Citation |
Score |
| 2023 |
Calonaci N, Bernetti M, Jones A, Sattler M, Bussi G. Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments. Journal of Chemical Theory and Computation. 19: 3672-3685. PMID 37288967 DOI: 10.1021/acs.jctc.3c00084 |
0.373 |
|
| 2023 |
Fröhlking T, Bernetti M, Bussi G. Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data. The Journal of Chemical Physics. 158. PMID 37272569 DOI: 10.1063/5.0151163 |
0.367 |
|
| 2023 |
Zhang Z, Šponer J, Bussi G, Mlýnský V, Šulc P, Simmons CR, Stephanopoulos N, Krepl M. Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of Chemical Information and Modeling. 63: 2794-2809. PMID 37126365 DOI: 10.1021/acs.jcim.3c00358 |
0.306 |
|
| 2022 |
Bernetti M, Bussi G. Integrating experimental data with molecular simulations to investigate RNA structural dynamics. Current Opinion in Structural Biology. 78: 102503. PMID 36463773 DOI: 10.1016/j.sbi.2022.102503 |
0.447 |
|
| 2022 |
Rolband L, Beasock D, Wang Y, Shu YG, Dinman JD, Schlick T, Zhou Y, Kieft JS, Chen SJ, Bussi G, Oukhaled A, Gao X, Šulc P, Binzel D, Bhullar AS, et al. Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions. Computational and Structural Biotechnology Journal. 20: 6120-6137. PMID 36420155 DOI: 10.1016/j.csbj.2022.11.007 |
0.325 |
|
| 2022 |
Grothaus IL, Bussi G, Colombi Ciacchi L. Exploration, Representation, and Rationalization of the Conformational Phase Space of N-Glycans. Journal of Chemical Information and Modeling. 62: 4992-5008. PMID 36179122 DOI: 10.1021/acs.jcim.2c01049 |
0.343 |
|
| 2022 |
Piomponi V, Fröhlking T, Bernetti M, Bussi G. Molecular Simulations Matching Denaturation Experiments for N-Methyladenosine. Acs Central Science. 8: 1218-1228. PMID 36032773 DOI: 10.1021/acscentsci.2c00565 |
0.428 |
|
| 2022 |
Fröhlking T, Mlýnský V, Janeček M, Kührová P, Krepl M, Banáš P, Šponer J, Bussi G. Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field. Journal of Chemical Theory and Computation. PMID 35699952 DOI: 10.1021/acs.jctc.2c00200 |
0.351 |
|
| 2022 |
Mlýnský V, Janeček M, Kührová P, Fröhlking T, Otyepka M, Bussi G, Banáš P, Šponer J. 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: 2642-2656. PMID 35363478 DOI: 10.1021/acs.jctc.1c01222 |
0.434 |
|
| 2021 |
Bernetti M, Hall KB, Bussi G. Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles. Nucleic Acids Research. PMID 34107023 DOI: 10.1093/nar/gkab459 |
0.429 |
|
| 2021 |
Bottaro S, Bussi G, Lindorff-Larsen K. Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations. Journal of the American Chemical Society. 143: 8333-8343. PMID 34039006 DOI: 10.1021/jacs.1c01094 |
0.817 |
|
| 2021 |
Paloni M, Bussi G, Barducci A. Arginine multivalency stabilizes protein/RNA condensates. Protein Science : a Publication of the Protein Society. 30: 1418-1426. PMID 33982350 DOI: 10.1002/pro.4109 |
0.342 |
|
| 2020 |
Calonaci N, Jones A, Cuturello F, Sattler M, Bussi G. Machine learning a model for RNA structure prediction. Nar Genomics and Bioinformatics. 2: lqaa090. PMID 33575634 DOI: 10.1093/nargab/lqaa090 |
0.319 |
|
| 2020 |
Bernetti M, Bussi G. Pressure control using stochastic cell rescaling. The Journal of Chemical Physics. 153: 114107. PMID 32962386 DOI: 10.1063/5.0020514 |
0.336 |
|
| 2020 |
Fröhlking T, Bernetti M, Calonaci N, Bussi G. Toward empirical force fields that match experimental observables. The Journal of Chemical Physics. 152: 230902. PMID 32571067 DOI: 10.1063/5.0011346 |
0.423 |
|
| 2020 |
Mlýnský V, Kührová P, Kühr T, Otyepka M, Bussi G, Banáš P, Šponer J. Fine-Tuning of the AMBER RNA Force Field with a New Term Adjusting Interactions of Terminal Nucleotides. Journal of Chemical Theory and Computation. PMID 32384244 DOI: 10.1021/Acs.Jctc.0C00228 |
0.52 |
|
| 2020 |
Cuturello F, Tiana G, Bussi G. Assessing the accuracy of direct-coupling analysis for RNA contact prediction. Rna (New York, N.Y.). PMID 32115426 DOI: 10.1261/Rna.074179.119 |
0.41 |
|
| 2019 |
Reißer S, Zucchelli S, Gustincich S, Bussi G. Conformational ensembles of an RNA hairpin using molecular dynamics and sparse NMR data. Nucleic Acids Research. PMID 31889193 DOI: 10.1093/Nar/Gkz1184 |
0.501 |
|
| 2019 |
Kührová P, Mlýnský V, Zgarbová M, Krepl M, Bussi G, Best RB, Otyepka M, Šponer J, Banáš P. Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions". Journal of Chemical Theory and Computation. PMID 31854986 DOI: 10.1021/Acs.Jctc.9B01189 |
0.377 |
|
| 2019 |
Colizzi F, Perez-Gonzalez C, Fritzen R, Levy Y, White MF, Penedo JC, Bussi G. Asymmetric base-pair opening drives helicase unwinding dynamics. Proceedings of the National Academy of Sciences of the United States of America. PMID 31628254 DOI: 10.1073/Pnas.1901086116 |
0.403 |
|
| 2019 |
Bussi G, Tribello GA. Analyzing and Biasing Simulations with PLUMED. Methods in Molecular Biology (Clifton, N.J.). 2022: 529-578. PMID 31396917 DOI: 10.1007/978-1-4939-9608-7_21 |
0.317 |
|
| 2019 |
Bonomi M, Bussi G, Camilloni C, Tribello GA, Banáš P, Barducci A, Bernetti M, Bolhuis PG, Bottaro S, Branduardi D, Capelli R, Carloni P, Ceriotti M, Cesari A, Chen H, et al. Promoting transparency and reproducibility in enhanced molecular simulations Nature Methods. 16: 670-673. PMID 31363226 DOI: 10.1038/S41592-019-0506-8 |
0.765 |
|
| 2019 |
Cesari A, Bottaro S, Lindorff-Larsen K, Banáš P, Sponer J, Bussi G. Fitting corrections to an RNA force field using experimental data. Journal of Chemical Theory and Computation. PMID 31050905 DOI: 10.1021/Acs.Jctc.9B00206 |
0.803 |
|
| 2019 |
Pinamonti G, Paul F, Noé F, Rodriguez A, Bussi G. The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. The Journal of Chemical Physics. 150: 154123. PMID 31005065 DOI: 10.1063/1.5083227 |
0.506 |
|
| 2019 |
Kührová P, Mlynsky V, Zgarbova M, Krepl M, Bussi G, Best RB, Otyepka M, Sponer J, Banáš P. IMPROVING THE PERFORMANCE OF THE AMBER RNA FORCE FIELD BY TUNING THE HYDROGEN-BONDING INTERACTIONS. Journal of Chemical Theory and Computation. PMID 30896943 DOI: 10.1021/Acs.Jctc.8B00955 |
0.508 |
|
| 2018 |
Rangan R, Bonomi M, Heller GT, Cesari A, Bussi G, Vendruscolo M. Determination of Structural Ensembles of Proteins: Restraining vs Reweighting. Journal of Chemical Theory and Computation. PMID 30428663 DOI: 10.1021/Acs.Jctc.8B00738 |
0.432 |
|
| 2018 |
Bottaro S, Bussi G, Pinamonti G, Reißer S, Boomsma W, Lindorff-Larsen K. Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories. Rna (New York, N.Y.). PMID 30420522 DOI: 10.1261/Rna.067678.118 |
0.802 |
|
| 2018 |
Bottaro S, Bussi G, Kennedy SD, Turner DH, Lindorff-Larsen K. Conformational ensembles of RNA oligonucleotides from integrating NMR and molecular simulations. Science Advances. 4: eaar8521. PMID 29795785 DOI: 10.1126/Sciadv.Aar8521 |
0.829 |
|
| 2018 |
Bottaro S, Banáš P, Šponer J, Bussi G. Correction to "Free Energy Landscape of GAGA and UUCG RNA Tetraloops". The Journal of Physical Chemistry Letters. 1674-1675. PMID 29553740 DOI: 10.1021/Acs.Jpclett.8B00754 |
0.798 |
|
| 2018 |
Podbevšek P, Fasolo F, Bon C, Cimatti L, Reißer S, Carninci P, Bussi G, Zucchelli S, Plavec J, Gustincich S. Structural determinants of the SINE B2 element embedded in the long non-coding RNA activator of translation AS Uchl1. Scientific Reports. 8: 3189. PMID 29453387 DOI: 10.1038/S41598-017-14908-6 |
0.375 |
|
| 2018 |
Mlýnský V, Bussi G. Exploring RNA structure and dynamics through enhanced sampling simulations. Current Opinion in Structural Biology. 49: 63-71. PMID 29414513 DOI: 10.1016/J.Sbi.2018.01.004 |
0.54 |
|
| 2018 |
Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chemical Reviews. PMID 29297679 DOI: 10.1021/Acs.Chemrev.7B00427 |
0.831 |
|
| 2018 |
Mlýnský V, Bussi G. Molecular Dynamics Simulations Reveal an Interplay between SHAPE Reagent Binding and RNA Flexibility. The Journal of Physical Chemistry Letters. 313-318. PMID 29265824 DOI: 10.1021/Acs.Jpclett.7B02921 |
0.508 |
|
| 2018 |
Cesari A, Reißer S, Bussi G. Using the Maximum Entropy Principle to Combine Simulations and Solution Experiments Computation. 6: 15. DOI: 10.3390/Computation6010015 |
0.463 |
|
| 2018 |
Hildebrand N, Michaelis M, Wurzler N, Li Z, Hirst JD, Micsonai A, Kardos J, Gil-Ley A, Bussi G, Köppen S, Delle Piane M, Ciacchi LC. Atomistic Details of Chymotrypsin Conformational Changes upon Adsorption on Silica Acs Biomaterials Science & Engineering. 4: 4036-4050. DOI: 10.1021/Acsbiomaterials.8B00819 |
0.333 |
|
| 2018 |
Cesari A, Bottaro S, Bussi G. Automated Force-Field Parametrization Guided by Multisystem Ensemble Averages Biophysical Journal. 114: 437a. DOI: 10.1016/J.Bpj.2017.11.2417 |
0.768 |
|
| 2017 |
Poblete S, Bottaro S, Bussi G. A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs. Nucleic Acids Research. PMID 29272539 DOI: 10.1093/Nar/Gkx1269 |
0.802 |
|
| 2017 |
Poblete S, Bottaro S, Bussi G. Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered molecular dynamics. Biochemical and Biophysical Research Communications. PMID 29248728 DOI: 10.1016/J.Bbrc.2017.12.057 |
0.813 |
|
| 2017 |
Islam B, Stadlbauer P, Gil Ley A, Pérez-Hernández G, Haider S, Neidle S, Bussi G, Banáš P, Otyepka M, Sponer J. Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations. Journal of Chemical Theory and Computation. PMID 28475322 DOI: 10.1021/Acs.Jctc.7B00226 |
0.451 |
|
| 2017 |
Mlynsky V, Bussi G. Understanding In-line Probing Experiments by Modeling Cleavage of Non-reactive RNA Nucleotides. Rna (New York, N.Y.). PMID 28202709 DOI: 10.1261/Rna.060442.116 |
0.516 |
|
| 2017 |
Cunha RA, Bussi G. Unraveling Mg2+-RNA binding with atomistic molecular dynamics. Rna (New York, N.Y.). 23: 628-638. PMID 28148825 DOI: 10.1261/Rna.060079.116 |
0.478 |
|
| 2017 |
Bellucci L, Bussi G, Di Felice R, Corni S. Fibrillation-prone conformations of the amyloid-β-42 peptide at the gold/water interface. Nanoscale. 9: 2279-2290. PMID 28124697 DOI: 10.1039/C6Nr06010B |
0.318 |
|
| 2016 |
Pinamonti G, Zhao J, Condon DE, Paul F, Noé F, Turner DH, Bussi G. Predicting the kinetics of RNA oligonucleotides using Markov state models. Journal of Chemical Theory and Computation. PMID 28001394 DOI: 10.1021/Acs.Jctc.6B00982 |
0.502 |
|
| 2016 |
Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M. Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochimica Et Biophysica Acta. PMID 27979677 DOI: 10.1016/J.Bbagen.2016.12.008 |
0.359 |
|
| 2016 |
Cesari A, Gil-Ley A, Bussi G. Combining Simulations and Solution Experiments as a Paradigm for RNA Force Field Refinement. Journal of Chemical Theory and Computation. 12: 6192-6200. PMID 27951677 DOI: 10.1021/Acs.Jctc.6B00944 |
0.526 |
|
| 2016 |
Bottaro S, Banáš P, Šponer J, Bussi G. Free Energy Landscape of GAGA and UUCG RNA Tetraloops. The Journal of Physical Chemistry Letters. 7: 4032-4038. PMID 27661094 DOI: 10.1021/Acs.Jpclett.6B01905 |
0.815 |
|
| 2016 |
Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P. Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. Journal of Chemical Theory and Computation. 12: 4534-48. PMID 27438572 DOI: 10.1021/Acs.Jctc.6B00300 |
0.824 |
|
| 2016 |
Gil-Ley A, Bottaro S, Bussi G. Empirical Corrections to the Amber RNA Force Field with Target Metadynamics. Journal of Chemical Theory and Computation. 12: 2790-8. PMID 27153317 DOI: 10.1021/Acs.Jctc.6B00299 |
0.833 |
|
| 2016 |
Bottaro S, Gil-Ley A, Bussi G. RNA folding pathways in stop motion. Nucleic Acids Research. 44: 5883-91. PMID 27091499 DOI: 10.1093/Nar/Gkw239 |
0.824 |
|
| 2016 |
Gil-Ley A, Bottaro S, Bussi G. RNA Conformational Ensembles: Narrowing the GAP between Experiments and Simulations with Metadynamics Biophysical Journal. 110: 522a-523a. DOI: 10.1016/J.Bpj.2015.11.2796 |
0.834 |
|
| 2016 |
Pinamonti G, Bottaro S, Micheletti C, Bussi G. RNA Conformational Fluctuations from Elastic Network Models: A Comparison with Molecular Dynamics and Shape Experiments Biophysical Journal. 110: 330a. DOI: 10.1016/J.Bpj.2015.11.1772 |
0.83 |
|
| 2015 |
Pérez-Villa A, Darvas M, Bussi G. AATP dependent NS3 helicase interaction with RNA: insights from molecular simulations. Nucleic Acids Research. PMID 26635398 DOI: 10.1093/nar/gkv1378 |
0.368 |
|
| 2015 |
Gil-Ley A, Bussi G. Correction to Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering. Journal of Chemical Theory and Computation. 11: 5554. PMID 26574342 DOI: 10.1021/Acs.Jctc.5B00981 |
0.386 |
|
| 2015 |
Ferrarotti MJ, Bottaro S, Pérez-Villa A, Bussi G. Accurate multiple time step in biased molecular simulations. Journal of Chemical Theory and Computation. 11: 139-46. PMID 26574212 DOI: 10.1021/Ct5007086 |
0.804 |
|
| 2015 |
Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Research. PMID 26433223 DOI: 10.1093/Nar/Gkv994 |
0.383 |
|
| 2015 |
Pérez-Villa A, Darvas M, Bussi G. ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations. Nucleic Acids Research. 43: 8725-34. PMID 26358809 DOI: 10.1093/Nar/Gkv872 |
0.496 |
|
| 2015 |
Pinamonti G, Bottaro S, Micheletti C, Bussi G. Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments. Nucleic Acids Research. 43: 7260-9. PMID 26187990 DOI: 10.1093/Nar/Gkv708 |
0.824 |
|
| 2015 |
Di Palma F, Bottaro S, Bussi G. Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations. Bmc Bioinformatics. 16: S6. PMID 26051557 DOI: 10.1186/1471-2105-16-S9-S6 |
0.808 |
|
| 2015 |
Gil-Ley A, Bussi G. Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering. Journal of Chemical Theory and Computation. 11: 1077-85. PMID 25838811 DOI: 10.1021/Ct5009087 |
0.454 |
|
| 2015 |
Di Palma F, Colizzi F, Bussi G. Using reweighted pulling simulations to characterize conformational changes in riboswitches. Methods in Enzymology. 553: 139-62. PMID 25726464 DOI: 10.1016/Bs.Mie.2014.10.055 |
0.427 |
|
| 2015 |
Poblete S, Bottaro S, Bussi G. A Nucleobase-Centric Coarse-Grained Model for Structure Prediction of RNA Fragments Biophysical Journal. 108: 235a. DOI: 10.1016/J.Bpj.2014.11.1300 |
0.822 |
|
| 2014 |
Bottaro S, Di Palma F, Bussi G. The role of nucleobase interactions in RNA structure and dynamics. Nucleic Acids Research. 42: 13306-14. PMID 25355509 DOI: 10.1093/Nar/Gku972 |
0.819 |
|
| 2014 |
Jaafar R, Pignedoli CA, Bussi G, Aït-Mansour K, Groening O, Amaya T, Hirao T, Fasel R, Ruffieux P. Bowl inversion of surface-adsorbed sumanene. Journal of the American Chemical Society. 136: 13666-71. PMID 25181621 DOI: 10.1021/Ja504126Z |
0.34 |
|
| 2014 |
Colizzi F, Lamontagne AM, Lafontaine DA, Bussi G. Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays. Methods in Molecular Biology (Clifton, N.J.). 1103: 141-51. PMID 24318892 DOI: 10.1007/978-1-62703-730-3_11 |
0.354 |
|
| 2014 |
Abrams C, Bussi G. Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperature-acceleration Entropy. 16: 163-199. DOI: 10.3390/E16010163 |
0.388 |
|
| 2014 |
Tribello GA, Bonomi M, Branduardi D, Camilloni C, Bussi G. PLUMED 2: New feathers for an old bird Computer Physics Communications. 185: 604-613. DOI: 10.1016/J.Cpc.2013.09.018 |
0.35 |
|
| 2014 |
Di Palma F, Colizzi F, Bussi G. Role of Magnesium Ions and Ligand Stacking in the Adenine Riboswitch Folding Biophysical Journal. 106: 285a. DOI: 10.1016/J.Bpj.2013.11.1665 |
0.448 |
|
| 2013 |
Do TN, Carloni P, Varani G, Bussi G. RNA/Peptide Binding Driven by Electrostatics-Insight from Bidirectional Pulling Simulations. Journal of Chemical Theory and Computation. 9: 1720-30. PMID 26587630 DOI: 10.1021/Ct3009914 |
0.605 |
|
| 2013 |
Di Palma F, Colizzi F, Bussi G. Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch. Rna (New York, N.Y.). 19: 1517-24. PMID 24051105 DOI: 10.1261/Rna.040493.113 |
0.371 |
|
| 2013 |
Franco D, Sgrignani J, Bussi G, Magistrato A. 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: 1371-87. PMID 23705837 DOI: 10.1021/Ci4001647 |
0.339 |
|
| 2013 |
Bussi G. Hamiltonian replica exchange in GROMACS: a flexible implementation Molecular Physics. 112: 379-384. DOI: 10.1080/00268976.2013.824126 |
0.44 |
|
| 2013 |
Do TN, Carloni P, Varani G, Bussi G. RNA/peptide binding driven by electrostatics - Insight from bidirectional pulling simulations Journal of Chemical Theory and Computation. 9: 1720-1730. DOI: 10.1021/ct3009914 |
0.52 |
|
| 2012 |
Branduardi D, Bussi G, Parrinello M. Metadynamics with Adaptive Gaussians. Journal of Chemical Theory and Computation. 8: 2247-54. PMID 26588957 DOI: 10.1021/Ct3002464 |
0.57 |
|
| 2012 |
Yusuff OK, Babalola JO, Bussi G, Raugei S. Role of the subunit interactions in the conformational transitions in adult human hemoglobin: an explicit solvent molecular dynamics study. The Journal of Physical Chemistry. B. 116: 11004-9. PMID 22838506 DOI: 10.1021/Jp3022908 |
0.648 |
|
| 2012 |
Colizzi F, Bussi G. RNA unwinding from reweighted pulling simulations. Journal of the American Chemical Society. 134: 5173-9. PMID 22313354 DOI: 10.1021/Ja210531Q |
0.52 |
|
| 2012 |
Branduardi D, Bussi G, Parrinello M. Metadynamics with adaptive gaussians Journal of Chemical Theory and Computation. 8: 2247-2254. DOI: 10.1021/ct3002464 |
0.452 |
|
| 2011 |
Benedetti F, Micheletti C, Bussi G, Sekatskii SK, Dietler G. Nonkinetic Modeling of the Mechanical Unfolding of Multimodular Proteins: Theory and Experiments Biophysical Journal. 101: 1504-1512. PMID 21943432 DOI: 10.1016/J.Bpj.2011.07.047 |
0.36 |
|
| 2011 |
Raiteri P, Gale JD, Bussi G. Reactive force field simulation of proton diffusion in BaZrO3 using an empirical valence bond approach. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 23: 334213. PMID 21813946 DOI: 10.1088/0953-8984/23/33/334213 |
0.339 |
|
| 2011 |
Martin-Samos L, Bussi G, Ruini A, Molinari E, Caldas MJ. SiO2 in density functional theory and beyond Physica Status Solidi B-Basic Solid State Physics. 248: 1061-1066. DOI: 10.1002/Pssb.201046283 |
0.504 |
|
| 2010 |
Martin-Samos L, Bussi G, Ruini A, Molinari E, Caldas MJ. Unraveling effects of disorder on the electronic structure of SiO2 from first principles Physical Review B. 81: 81202-81202. DOI: 10.1103/Physrevb.81.081202 |
0.478 |
|
| 2010 |
Ceriotti M, Bussi G, Parrinello M. Colored-noise thermostats àla Carte Journal of Chemical Theory and Computation. 6: 1170-1180. DOI: 10.1021/Ct900563S |
0.68 |
|
| 2009 |
Mantz YA, Branduardi D, Bussi G, Parrinello M. Ensemble of transition state structures for the cis-trans isomerization of N-methylacetamide. The Journal of Physical Chemistry. B. 113: 12521-9. PMID 19694484 DOI: 10.1021/Jp8106556 |
0.583 |
|
| 2009 |
Ceriotti M, Bussi G, Parrinello M. Nuclear quantum effects in solids using a colored-noise thermostat. Physical Review Letters. 103: 030603. PMID 19659261 DOI: 10.1103/Physrevlett.103.030603 |
0.656 |
|
| 2009 |
Ceriotti M, Bussi G, Parrinello M. Langevin equation with colored noise for constant-temperature molecular dynamics simulations. Physical Review Letters. 102: 020601. PMID 19257259 DOI: 10.1103/Physrevlett.102.020601 |
0.669 |
|
| 2009 |
Bussi G, Zykova-Timan T, Parrinello M. Isothermal-isobaric molecular dynamics using stochastic velocity rescaling. The Journal of Chemical Physics. 130: 074101. PMID 19239278 DOI: 10.1063/1.3073889 |
0.61 |
|
| 2009 |
Bonomi M, Branduardi D, Bussi G, Camilloni C, Provasi D, Raiteri P, Donadio D, Marinelli F, Pietrucci F, Broglia RA, Parrinello M. PLUMED: A portable plugin for free-energy calculations with molecular dynamics Computer Physics Communications. 180: 1961-1972. DOI: 10.1016/J.Cpc.2009.05.011 |
0.731 |
|
| 2008 |
Micheletti C, Bussi G, Laio A. Optimal Langevin modeling of out-of-equilibrium molecular dynamics simulations. The Journal of Chemical Physics. 129: 074105. PMID 19044758 DOI: 10.1063/1.2969761 |
0.63 |
|
| 2008 |
Raiteri P, Bussi G, Cucinotta CS, Credi A, Stoddart JF, Parrinello M. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane. Angewandte Chemie (International Ed. in English). 47: 3536-9. PMID 18357607 DOI: 10.1002/Anie.200705207 |
0.523 |
|
| 2008 |
Barducci A, Bussi G, Parrinello M. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Physical Review Letters. 100: 020603. PMID 18232845 DOI: 10.1103/Physrevlett.100.020603 |
0.591 |
|
| 2008 |
Bussi G, Parrinello M. Stochastic thermostats: comparison of local and global schemes Computer Physics Communications. 179: 26-29. DOI: 10.1016/J.Cpc.2008.01.006 |
0.562 |
|
| 2008 |
Raiteri P, Bussi G, Cucinotta CS, Credi A, Stoddart JF, Parrinello M. Unravelling the shuttling mechanism in a photoswitchable multicomponent bistable rotaxane Angewandte Chemie - International Edition. 47: 3536-3539. DOI: 10.1002/anie.200705207 |
0.471 |
|
| 2007 |
Ceriotti M, Bussi G, Parrinello M. Conjugate gradient heat bath for ill-conditioned actions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 026707. PMID 17930174 DOI: 10.1103/Physreve.76.026707 |
0.644 |
|
| 2007 |
Bussi G, Parrinello M. Accurate sampling using Langevin dynamics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 75: 056707. PMID 17677198 DOI: 10.1103/Physreve.75.056707 |
0.61 |
|
| 2007 |
Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. The Journal of Chemical Physics. 126: 014101. PMID 17212484 DOI: 10.1063/1.2408420 |
0.708 |
|
| 2006 |
Bussi G, Gervasio FL, Laio A, Parrinello M. Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. Journal of the American Chemical Society. 128: 13435-41. PMID 17031956 DOI: 10.1021/Ja062463W |
0.701 |
|
| 2006 |
Bussi G, Laio A, Parrinello M. Equilibrium free energies from nonequilibrium metadynamics. Physical Review Letters. 96: 090601. PMID 16606249 DOI: 10.1103/Physrevlett.96.090601 |
0.717 |
|
| 2005 |
Chang E, Bussi G, Ruini A, Molinari E. 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. DOI: 10.1103/Physrevb.72.195423 |
0.528 |
|
| 2005 |
Bussi G, Menendez J, Ren J, Canonico M, Molinari E. Quantum interferences in the Raman cross section for the radial breathing mode in metallic carbon nanotubes Physical Review B. 71: 41404. DOI: 10.1103/Physrevb.71.041404 |
0.483 |
|
| 2005 |
Hummer K, Ambrosch-Draxl C, Bussi G, Ruini A, Caldas MJ, Molinari E, Laskowski R, Christensen NE. Ab-initio study of excitonic effects in conventional and organic semiconductors Physica Status Solidi B-Basic Solid State Physics. 242: 1754-1758. DOI: 10.1002/Pssb.200461785 |
0.51 |
|
| 2004 |
Chang E, Bussi G, Ruini A, Molinari E. Excitons in carbon nanotubes: an ab initio symmetry-based approach. Physical Review Letters. 92: 196401. PMID 15169423 DOI: 10.1103/Physrevlett.92.196401 |
0.508 |
|
| 2004 |
Ferretti A, Ruini A, Bussi G, Molinari E, Caldas MJ. Ab initio study of transport parameters in polymer crystals Physical Review B. 69: 205205-205205. DOI: 10.1103/Physrevb.69.205205 |
0.512 |
|
| 2004 |
Ruini A, Ferretti A, Bussi G, Molinari E, Caldas MJ. Relationship between structural and optoelectronic properties in semiconducting polymers Semiconductor Science and Technology. 19: 362-364. DOI: 10.1088/0268-1242/19/4/119 |
0.503 |
|
| 2003 |
Ruini A, Bussi G, Ferretti A, Caldas MJ, Molinari E. Charge transport and radiative recombination in polythiophene crystals: a first-principles study Synthetic Metals. 139: 755-757. DOI: 10.1016/S0379-6779(03)00319-9 |
0.488 |
|
| 2002 |
Ruini A, Caldas MJ, Bussi G, Molinari E. Solid state effects on exciton states and optical properties of PPV. Physical Review Letters. 88: 206403. PMID 12005587 DOI: 10.1103/Physrevlett.88.206403 |
0.5 |
|
| 2002 |
Bussi G, Ruini A, Molinari E, Caldas MJ, Puschnig P, Ambrosch-Draxl C. Interchain interaction and Davydov splitting in polythiophene crystals: An ab initio approach Applied Physics Letters. 80: 4118-4120. DOI: 10.1063/1.1483905 |
0.514 |
|
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