Michele Parrinello - Publications

Affiliations: 
Chemistry and Applied Biosciences ETH Zürich, Zürich, ZH, Switzerland 
Website:
http://www.rgp.ethz.ch/

276 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Ponte F, Piccini G, Sicilia E, Parrinello M. A metadynamics perspective on the reduction mechanism of the Pt(IV) asplatin prodrug. Journal of Computational Chemistry. PMID 31691997 DOI: 10.1002/jcc.26100  1
2019 Bonati L, Zhang YY, Parrinello M. Neural networks-based variationally enhanced sampling. Proceedings of the National Academy of Sciences of the United States of America. PMID 31416918 DOI: 10.1073/pnas.1907975116  0.8
2019 Niu H, Yang YI, Parrinello M. Temperature Dependence of Homogeneous Nucleation in Ice. Physical Review Letters. 122: 245501. PMID 31322390 DOI: 10.1103/PhysRevLett.122.245501  0.88
2019 Rizzi V, Mendels D, Sicilia E, Parrinello M. Blind search for complex chemical pathways using Harmonic Linear Discriminant Analysis. Journal of Chemical Theory and Computation. PMID 31314521 DOI: 10.1021/acs.jctc.9b00358  0.8
2019 Polino D, Parrinello M. Kinetics of Aqueous Media Reactions via Ab Initio Enhanced Molecular Dynamics: The Case of Urea Decomposition. The Journal of Physical Chemistry. B. PMID 31286763 DOI: 10.1021/acs.jpcb.9b05271  0.56
2019 Piccini G, Parrinello M. Accurate Quantum Chemical Free Energies at Affordable Cost. The Journal of Physical Chemistry Letters. 3727-3731. PMID 31244270 DOI: 10.1021/acs.jpclett.9b01301  1
2019 Capelli R, Carloni P, Parrinello M. Exhaustive Search of Ligand Binding Pathways via Volume-Based Metadynamics. The Journal of Physical Chemistry Letters. 3495-3499. PMID 31188006 DOI: 10.1021/acs.jpclett.9b01183  0.44
2019 Capelli R, Bochicchio A, Piccini G, Casasnovas R, Carloni P, Parrinello M. Chasing the full free energy landscape of neuroreceptor/ligand unbinding by metadynamics simulations. Journal of Chemical Theory and Computation. PMID 30913388 DOI: 10.1021/acs.jctc.9b00118  1
2019 Zhang YY, Niu H, Piccini G, Mendels D, Parrinello M. Improving collective variables: The case of crystallization. The Journal of Chemical Physics. 150: 094509. PMID 30849916 DOI: 10.1063/1.5081040  1
2019 Grifoni E, Piccini G, Parrinello M. Microscopic description of acid-base equilibrium. Proceedings of the National Academy of Sciences of the United States of America. PMID 30765522 DOI: 10.1073/pnas.1819771116  1
2019 Rizzi V, Polino D, Sicilia E, Russo N, Parrinello M. The onset of dehydrogenation in solid Ammonia Borane, an ab-initio metadynamics study. Angewandte Chemie (International Ed. in English). PMID 30689299 DOI: 10.1002/anie.201900134  0.56
2018 Bonati L, Parrinello M. Silicon Liquid Structure and Crystal Nucleation from Ab Initio Deep Metadynamics. Physical Review Letters. 121: 265701. PMID 30636123 DOI: 10.1103/PhysRevLett.121.265701  0.52
2018 Brotzakis ZF, Parrinello M. Enhanced Sampling of Protein Conformational Transitions via Dynamically Optimized Collective Variables. Journal of Chemical Theory and Computation. PMID 30557019 DOI: 10.1021/acs.jctc.8b00827  0.64
2018 Brotzakis ZF, Limongelli V, Parrinello M. Accelerating the Calculation of Protein-Ligand Binding Free Energy and Residence Times using Dynamically Optimized Collective Variables. Journal of Chemical Theory and Computation. PMID 30537822 DOI: 10.1021/acs.jctc.8b00934  0.64
2018 Mendels D, Piccini G, Brotzakis ZF, Yang YI, Parrinello M. Folding a small protein using harmonic linear discriminant analysis. The Journal of Chemical Physics. 149: 194113. PMID 30466286 DOI: 10.1063/1.5053566  1
2018 Yang YI, Niu H, Parrinello M. Combining Metadynamics and Integrated Tempering Sampling. The Journal of Physical Chemistry Letters. 6426-6430. PMID 30354148 DOI: 10.1021/acs.jpclett.8b03005  0.88
2018 Piccini G, Mendels D, Parrinello M. Metadynamics with Discriminants: a Tool for Understanding Chemistry. Journal of Chemical Theory and Computation. PMID 30222350 DOI: 10.1021/acs.jctc.8b00634  1
2018 Wang Y, Valsson O, Tiwary P, Parrinello M, Lindorff-Larsen K. Frequency adaptive metadynamics for the calculation of rare-event kinetics. The Journal of Chemical Physics. 149: 072309. PMID 30134721 DOI: 10.1063/1.5024679  0.8
2018 Perego C, Valsson O, Parrinello M. Chemical potential calculations in non-homogeneous liquids. The Journal of Chemical Physics. 149: 072305. PMID 30134712 DOI: 10.1063/1.5024631  0.68
2018 Niu H, Piaggi PM, Invernizzi M, Parrinello M. Molecular dynamics simulations of liquid silica crystallization. Proceedings of the National Academy of Sciences of the United States of America. PMID 29735667 DOI: 10.1073/pnas.1803919115  0.88
2018 Mendels D, Piccini G, Parrinello M. Collective Variables from Local Fluctuations. The Journal of Physical Chemistry Letters. 2776-2781. PMID 29733652 DOI: 10.1021/acs.jpclett.8b00733  1
2018 Yang YI, Parrinello M. Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling. Journal of Chemical Theory and Computation. PMID 29715017 DOI: 10.1021/acs.jctc.8b00231  0.88
2017 McCarty J, Parrinello M. A variational conformational dynamics approach to the selection of collective variables in metadynamics. The Journal of Chemical Physics. 147: 204109. PMID 29195289 DOI: 10.1063/1.4998598  0.6
2017 Jagannath V, Brotzakis ZF, Parrinello M, Walitza S, Grünblatt E. Controversial Effects of D-Amino Acid Oxidase Activator (DAOA)/G72 on D-Amino Acid Oxidase (DAO) Activity in Human Neuronal, Astrocyte and Kidney Cell Lines: The N-methyl D-aspartate (NMDA) Receptor Hypofunction Point of View. Frontiers in Molecular Neuroscience. 10: 342. PMID 29114206 DOI: 10.3389/fnmol.2017.00342  0.64
2017 Ozcan A, Perego C, Salvalaglio M, Parrinello M, Yazaydin O. Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation. Chemical Science. 8: 3858-3865. PMID 28966778 DOI: 10.1039/c6sc04978h  0.44
2017 Palazzesi F, Valsson O, Parrinello M. Conformational Entropy as Collective Variable for Proteins. The Journal of Physical Chemistry Letters. PMID 28906117 DOI: 10.1021/acs.jpclett.7b01770  0.68
2017 Piccini G, Polino D, Parrinello M. Identifying Slow Molecular Motions in Complex Chemical Reactions. The Journal of Physical Chemistry Letters. 4197-4200. PMID 28829135 DOI: 10.1021/acs.jpclett.7b01889  1
2017 Caldarulo E, Barducci A, Wüthrich K, Parrinello M. Prion protein β2-α2 loop conformational landscape. Proceedings of the National Academy of Sciences of the United States of America. PMID 28827331 DOI: 10.1073/pnas.1712155114  0.56
2017 Piaggi PM, Valsson O, Parrinello M. Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations. Physical Review Letters. 119: 015701. PMID 28731736 DOI: 10.1103/PhysRevLett.119.015701  0.68
2017 Bartl J, Palazzesi F, Parrinello M, Leif H, Riederer P, Walitza S, Grünblatt E. The impact of methylphenidate and its enantiomers on dopamine synthesis and metabolism in vitro. Progress in Neuro-Psychopharmacology & Biological Psychiatry. PMID 28690202 DOI: 10.1016/j.pnpbp.2017.07.002  0.52
2017 Invernizzi M, Valsson O, Parrinello M. Coarse graining from variationally enhanced sampling applied to the Ginzburg-Landau model. Proceedings of the National Academy of Sciences of the United States of America. PMID 28292890 DOI: 10.1073/pnas.1618455114  0.68
2017 Casasnovas R, Limongelli V, Tiwary P, Carloni P, Parrinello M. Unbinding kinetics of a p38 MAP kinase type II inhibitor from metadynamics simulations. Journal of the American Chemical Society. PMID 28290199 DOI: 10.1021/jacs.6b12950  0.8
2017 Moraca F, Amato J, Ortuso F, Artese A, Pagano B, Novellino E, Alcaro S, Parrinello M, Limongelli V. Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. PMID 28232513 DOI: 10.1073/pnas.1612627114  0.4
2017 Tribello GA, Giberti F, Sosso GC, Salvalaglio M, Parrinello M. Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. PMID 28121147 DOI: 10.1021/acs.jctc.6b01073  0.84
2017 Piccini G, McCarty J, Valsson O, Parrinello M. Variational Flooding Study of a SN2 Reaction. The Journal of Physical Chemistry Letters. PMID 28071915 DOI: 10.1021/acs.jpclett.6b02852  1
2016 Salvalaglio M, Tiwary P, Maggioni GM, Mazzotti M, Parrinello M. Overcoming time scale and finite size limitations to compute nucleation rates from small scale well tempered metadynamics simulations. The Journal of Chemical Physics. 145: 211925. PMID 28799374 DOI: 10.1063/1.4966265  0.8
2016 Nava M, Palazzesi F, Perego C, Parrinello M. Dimer Metadynamics. Journal of Chemical Theory and Computation. PMID 28005387 DOI: 10.1021/acs.jctc.6b00691  0.72
2016 Angulo G, Astumian RD, Beniwal V, Bolhuis PG, Dellago C, Ellis J, Ensing B, Glowacki DR, Hammes-Schiffer S, Kästner J, Lelièvre T, Makri N, Manolopoulos D, Menzl G, Miller TF, ... ... Parrinello M, et al. New methods: general discussion. Faraday Discussions. PMID 27929586 DOI: 10.1039/C6FD90075E  0.88
2016 Shaffer P, Valsson O, Parrinello M. Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling. Journal of Chemical Theory and Computation. PMID 27813415 DOI: 10.1021/acs.jctc.6b00786  0.68
2016 Palazzesi F, Salvalaglio M, Barducci A, Parrinello M. Communication: Role of explicit water models in the helix folding/unfolding processes. The Journal of Chemical Physics. 145: 121101. PMID 27782670 DOI: 10.1063/1.4963340  0.56
2016 Piaggi PM, Valsson O, Parrinello M. A variational approach to nucleation simulation. Faraday Discussions. PMID 27752683 DOI: 10.1039/c6fd00127k  0.68
2016 Bellucci L, Ardèvol A, Parrinello M, Lutz H, Lu H, Weidner T, Corni S. The interaction with gold suppresses fiber-like conformations of the amyloid β (16-22) peptide. Nanoscale. PMID 27064268 DOI: 10.1039/c6nr01539e  0.36
2016 McCarty J, Valsson O, Parrinello M. Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling. Journal of Chemical Theory and Computation. PMID 27057791 DOI: 10.1021/acs.jctc.6b00125  0.68
2016 Valsson O, Tiwary P, Parrinello M. Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint. Annual Review of Physical Chemistry. PMID 26980304 DOI: 10.1146/annurev-physchem-040215-112229  0.8
2016 Shaffer P, Valsson O, Parrinello M. Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin. Proceedings of the National Academy of Sciences of the United States of America. PMID 26787868 DOI: 10.1073/pnas.1519712113  1
2015 Tiwary P, Dama JF, Parrinello M. A perturbative solution to metadynamics ordinary differential equation. The Journal of Chemical Physics. 143: 234112. PMID 26696051 DOI: 10.1063/1.4937945  1
2015 Ardevol A, Palazzesi F, Tribello GA, Parrinello M. General, PDB-based collective variables for protein folding. Journal of Chemical Theory and Computation. PMID 26632859 DOI: 10.1021/acs.jctc.5b00714  1
2015 Ardevol A, Tribello GA, Ceriotti M, Parrinello M. Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map. Journal of Chemical Theory and Computation. 11: 1086-1093. PMID 26579758 DOI: 10.1021/ct500950z  1
2015 Valsson O, Parrinello M. Well-Tempered Variational Approach to Enhanced Sampling. Journal of Chemical Theory and Computation. 11: 1996-2002. PMID 26574405 DOI: 10.1021/acs.jctc.5b00076  0.68
2015 Quhe R, Nava M, Tiwary P, Parrinello M. Path Integral Metadynamics. Journal of Chemical Theory and Computation. 11: 1383-8. PMID 26574350 DOI: 10.1021/ct501002a  0.8
2015 Nava M, Quhe R, Palazzesi F, Tiwary P, Parrinello M. de Broglie Swapping Metadynamics for Quantum and Classical Sampling. Journal of Chemical Theory and Computation. 11: 5114-9. PMID 26574309 DOI: 10.1021/acs.jctc.5b00818  1
2015 McCarty J, Valsson O, Tiwary P, Parrinello M. Variationally Optimized Free-Energy Flooding for Rate Calculation. Physical Review Letters. 115: 070601. PMID 26317704 DOI: 10.1103/PhysRevLett.115.070601  0.8
2015 Perego C, Salvalaglio M, Parrinello M. Molecular dynamics simulations of solutions at constant chemical potential. The Journal of Chemical Physics. 142: 144113. PMID 25877568 DOI: 10.1063/1.4917200  0.44
2015 Giberti F, Salvalaglio M, Parrinello M. Metadynamics studies of crystal nucleation. Iucrj. 2: 256-66. PMID 25866662 DOI: 10.1107/S2052252514027626  1
2015 Salvalaglio M, Mazzotti M, Parrinello M. Urea homogeneous nucleation mechanism is solvent dependent. Faraday Discussions. 179: 291-307. PMID 25865566 DOI: 10.1039/c4fd00235k  0.44
2015 Formoso E, Limongelli V, Parrinello M. Energetics and structural characterization of the large-scale functional motion of adenylate kinase. Scientific Reports. 5: 8425. PMID 25672826 DOI: 10.1038/srep08425  0.4
2015 Tiwary P, Limongelli V, Salvalaglio M, Parrinello M. Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps. Proceedings of the National Academy of Sciences of the United States of America. 112: E386-91. PMID 25605901 DOI: 10.1073/pnas.1424461112  0.8
2015 Polino D, Parrinello M. Combustion chemistry via metadynamics: benzyl decomposition revisited. The Journal of Physical Chemistry. A. 119: 978-89. PMID 25587630 DOI: 10.1021/jp5118807  0.56
2015 Salvalaglio M, Perego C, Giberti F, Mazzotti M, Parrinello M. Molecular-dynamics simulations of urea nucleation from aqueous solution. Proceedings of the National Academy of Sciences of the United States of America. 112: E6-14. PMID 25492932 DOI: 10.1073/pnas.1421192111  0.68
2015 Tiwary P, Parrinello M. A time-independent free energy estimator for metadynamics. The Journal of Physical Chemistry. B. 119: 736-42. PMID 25046020 DOI: 10.1021/jp504920s  0.8
2015 McCarty J, Valsson O, Tiwary P, Parrinello M. Variationally Optimized Free-Energy Flooding for Rate Calculation Physical Review Letters. 115. DOI: 10.1103/PhysRevLett.115.070601  1
2015 Tiwary P, Limongelli V, Salvalaglio M, Parrinello M. Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps Proceedings of the National Academy of Sciences of the United States of America. 112: E386-E391. DOI: 10.1073/pnas.1424461112  1
2015 Salvalaglio M, Perego C, Giberti F, Mazzotti M, Parrinello M. Molecular-dynamics simulations of urea nucleation from aqueous solution Proceedings of the National Academy of Sciences of the United States of America. 112: E6-E14. DOI: 10.1073/pnas.1421192111  1
2015 Perego C, Salvalaglio M, Parrinello M. Molecular dynamics simulations of solutions at constant chemical potential Journal of Chemical Physics. 142. DOI: 10.1063/1.4917200  1
2015 Salvalaglio M, Mazzotti M, Parrinello M. Urea homogeneous nucleation mechanism is solvent dependent Faraday Discussions. 179: 291-307. DOI: 10.1039/c4fd00235k  1
2015 Formoso E, Limongelli V, Parrinello M. Energetics and structural characterization of the large-scale functional motion of Adenylate Kinase Scientific Reports. 5: 8425. DOI: 10.1038/srep08425  1
2015 Polino D, Parrinello M. Combustion chemistry via metadynamics: Benzyl decomposition revisited Journal of Physical Chemistry A. 119: 978-989. DOI: 10.1021/jp5118807  1
2015 Tiwary P, Parrinello M. A time-independent free energy estimator for metadynamics Journal of Physical Chemistry B. 119: 736-742. DOI: 10.1021/jp504920s  1
2015 Quhe R, Nava M, Tiwary P, Parrinello M. Path integral metadynamics Journal of Chemical Theory and Computation. 11: 1383-1388. DOI: 10.1021/ct501002a  1
2015 Ardevol A, Tribello GA, Ceriotti M, Parrinello M. Probing the unfolded configurations of a β-hairpin using sketch-map Journal of Chemical Theory and Computation. 11: 1086-1093. DOI: 10.1021/ct500950z  1
2015 Sosso GC, Salvalaglio M, Behler J, Bernasconi M, Parrinello M. Heterogeneous crystallization of the phase change material GeTe via atomistic simulations Journal of Physical Chemistry C. 119: 6428-6434. DOI: 10.1021/acs.jpcc.5b00296  1
2015 Valsson O, Parrinello M. Well-tempered variational approach to enhanced sampling Journal of Chemical Theory and Computation. 11: 1996-2002. DOI: 10.1021/acs.jctc.5b00076  1
2015 Giberti F, Salvalaglio M, Mazzotti M, Parrinello M. Insight into the nucleation of urea crystals from the melt Chemical Engineering Science. 121: 51-59. DOI: 10.1016/j.ces.2014.08.032  1
2014 Dama JF, Rotskoff G, Parrinello M, Voth GA. Transition-Tempered Metadynamics: Robust, Convergent Metadynamics via On-the-Fly Transition Barrier Estimation. Journal of Chemical Theory and Computation. 10: 3626-33. PMID 26588507 DOI: 10.1021/ct500441q  0.52
2014 Salvalaglio M, Tiwary P, Parrinello M. Assessing the Reliability of the Dynamics Reconstructed from Metadynamics. Journal of Chemical Theory and Computation. 10: 1420-5. PMID 26580360 DOI: 10.1021/ct500040r  0.8
2014 Cerofolini L, Amato J, Giachetti A, Limongelli V, Novellino E, Parrinello M, Fragai M, Randazzo A, Luchinat C. G-triplex structure and formation propensity. Nucleic Acids Research. 42: 13393-404. PMID 25378342 DOI: 10.1093/nar/gku1084  0.4
2014 Nava M, Ceriotti M, Dryzun C, Parrinello M. Evaluating functions of positive-definite matrices using colored-noise thermostats. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 89: 023302. PMID 25353600  1
2014 Giberti F, Hassanali AA, Ceriotti M, Parrinello M. The role of quantum effects on structural and electronic fluctuations in neat and charged water. The Journal of Physical Chemistry. B. 118: 13226-35. PMID 25286281 DOI: 10.1021/jp507752e  1
2014 Valsson O, Parrinello M. Variational approach to enhanced sampling and free energy calculations. Physical Review Letters. 113: 090601. PMID 25215968 DOI: 10.1103/PhysRevLett.113.090601  0.68
2014 Dama JF, Parrinello M, Voth GA. Well-tempered metadynamics converges asymptotically. Physical Review Letters. 112: 240602. PMID 24996077 DOI: 10.1103/PhysRevLett.112.240602  1
2014 Di Leva FS, Novellino E, Cavalli A, Parrinello M, Limongelli V. Mechanistic insight into ligand binding to G-quadruplex DNA Nucleic Acids Research. 42: 5447-5455. PMID 24753420 DOI: 10.1093/nar/gku247  1
2014 Ding Y, Hassanali AA, Parrinello M. Anomalous water diffusion in salt solutions. Proceedings of the National Academy of Sciences of the United States of America. 111: 3310-5. PMID 24522111 DOI: 10.1073/pnas.1400675111  1
2014 Hassanali AA, Cuny J, Verdolino V, Parrinello M. Aqueous solutions: state of the art in ab initio molecular dynamics. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 372: 20120482. PMID 24516179 DOI: 10.1098/rsta.2012.0482  0.8
2014 Salvalaglio M, Giberti F, Parrinello M. 1,3,5-Tris(4-bromophenyl)benzene prenucleation clusters from metadynamics. Acta Crystallographica. Section C, Structural Chemistry. 70: 132-6. PMID 24508958 DOI: 10.1107/S2053229613026946  0.68
2014 Salvalaglio M, Giberti F, Parrinello M. 1,3,5-Tris(4-bromophenyl)benzene prenucleation clusters from meta-dynamics Acta Crystallographica Section C: Structural Chemistry. 70: 132-136. DOI: 10.1107/S2053229613026946  1
2014 Valsson O, Parrinello M. Variational approach to enhanced sampling and free energy calculations Physical Review Letters. 113. DOI: 10.1103/PhysRevLett.113.090601  1
2014 Nava M, Ceriotti M, Dryzun C, Parrinello M. Evaluating functions of positive-definite matrices using colored-noise thermostats Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 89. DOI: 10.1103/PhysRevE.89.023302  1
2014 Hassanali AA, Cuny J, Verdolino V, Parrinello M. Aqueous solutions: State of the art in ab initio molecular dynamics Philosophical Transactions of the Royal Society a: Mathematical, Physical and Engineering Sciences. 372. DOI: 10.1098/rsta.2012.0482  1
2014 Cerofolini L, Amato J, Giachetti A, Limongelli V, Novellino E, Parrinello M, Fragai M, Randazzo A, Luchinat C. G-triplex structure and formation propensity Nucleic Acids Research. 42: 13393-13404. DOI: 10.1093/nar/gku1084  1
2014 Giberti F, Hassanali AA, Ceriotti M, Parrinello M. The role of quantum effects on structural and electronic fluctuations in neat and charged water Journal of Physical Chemistry B. 118: 13226-13235. DOI: 10.1021/jp507752e  1
2014 Dama JF, Rotskoff G, Parrinello M, Voth GA. Transition-tempered metadynamics: Robust, convergent metadynamics via on-the-fly transition barrier estimation Journal of Chemical Theory and Computation. 10: 3626-3633. DOI: 10.1021/ct500441q  1
2014 Salvalaglio M, Tiwary P, Parrinello M. Assessing the reliability of the dynamics reconstructed from metadynamics Journal of Chemical Theory and Computation. 10: 1420-1425. DOI: 10.1021/ct500040r  1
2014 Hassanali AA, Giberti F, Sosso GC, Parrinello M. The role of the umbrella inversion mode in proton diffusion Chemical Physics Letters. 599: 133-138. DOI: 10.1016/j.cplett.2014.03.034  1
2013 Valsson O, Parrinello M. Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble. Journal of Chemical Theory and Computation. 9: 5267-76. PMID 26592265 DOI: 10.1021/ct400859f  0.68
2013 Ceriotti M, Tribello GA, Parrinello M. Demonstrating the Transferability and the Descriptive Power of Sketch-Map. Journal of Chemical Theory and Computation. 9: 1521-32. PMID 26587614 DOI: 10.1021/ct3010563  1
2013 Giberti F, Tribello GA, Parrinello M. Transient Polymorphism in NaCl. Journal of Chemical Theory and Computation. 9: 2526-30. PMID 26583849 DOI: 10.1021/ct4002027  0.84
2013 Tiwary P, Parrinello M. From metadynamics to dynamics. Physical Review Letters. 111: 230602. PMID 24476246 DOI: 10.1103/PhysRevLett.111.230602  0.8
2013 Barducci A, Bonomi M, Prakash MK, Parrinello M. Free-energy landscape of protein oligomerization from atomistic simulations Proceedings of the National Academy of Sciences of the United States of America. 110: E4708-E4713. PMID 24248370 DOI: 10.1073/pnas.1320077110  1
2013 Salvalaglio M, Vetter T, Mazzotti M, Parrinello M. Controlling and predicting crystal shapes: the case of urea. Angewandte Chemie (International Ed. in English). 52: 13369-72. PMID 24166825 DOI: 10.1002/anie.201304562  1
2013 Ceriotti M, Cuny J, Parrinello M, Manolopoulos DE. Nuclear quantum effects and hydrogen bond fluctuations in water. Proceedings of the National Academy of Sciences of the United States of America. 110: 15591-6. PMID 24014589 DOI: 10.1073/pnas.1308560110  1
2013 Palazzesi F, Barducci A, Tollinger M, Parrinello M. The allosteric communication pathways in KIX domain of CBP Proceedings of the National Academy of Sciences of the United States of America. 110: 14237-14242. PMID 23940332 DOI: 10.1073/pnas.1313548110  1
2013 Hassanali A, Giberti F, Cuny J, Kühne TD, Parrinello M. Proton transfer through the water gossamer Proceedings of the National Academy of Sciences of the United States of America. 110: 13723-13728. PMID 23868853 DOI: 10.1073/pnas.1306642110  1
2013 Limongelli V, Bonomi M, Parrinello M. Funnel metadynamics as accurate binding free-energy method Proceedings of the National Academy of Sciences of the United States of America. 110: 6358-6363. PMID 23553839 DOI: 10.1073/pnas.1303186110  1
2013 Limongelli V, De Tito S, Cerofolini L, Fragai M, Pagano B, Trotta R, Cosconati S, Marinelli L, Novellino E, Bertini I, Randazzo A, Luchinat C, Parrinello M. The G-triplex DNA. Angewandte Chemie (International Ed. in English). 52: 2269-73. PMID 23335456 DOI: 10.1002/anie.201206522  1
2013 Tiwary P, Parrinello M. From metadynamics to dynamics Physical Review Letters. 111. DOI: 10.1103/PhysRevLett.111.230602  1
2013 Caravati S, Sosso GC, Bernasconi M, Parrinello M. Density functional simulations of hexagonal Ge2Sb 2Te5 at high pressure Physical Review B - Condensed Matter and Materials Physics. 87. DOI: 10.1103/PhysRevB.87.094117  1
2013 Pavan GM, Barducci A, Albertazzi L, Parrinello M. Combining metadynamics simulation and experiments to characterize dendrimers in solution Soft Matter. 9: 2593-2597. DOI: 10.1039/c3sm27706b  1
2013 Molina-Montes E, Donadio D, Hernández-Laguna A, Parrinello M, Sainz-Díaz CI. Water release from pyrophyllite during the dehydroxylation process explored by quantum mechanical simulations Journal of Physical Chemistry C. 117: 7526-7532. DOI: 10.1021/jp310739y  1
2013 Valsson O, Parrinello M. Thermodynamical description of a quasi-first-order phase transition from the well-tempered ensemble Journal of Chemical Theory and Computation. 9: 5267-5276. DOI: 10.1021/ct400859f  1
2013 Giberti F, Tribello GA, Parrinello M. Transient polymorphism in NaCl Journal of Chemical Theory and Computation. 9: 2526-2530. DOI: 10.1021/ct4002027  1
2013 Ceriotti M, Tribello GA, Parrinello M. Demonstrating the transferability and the descriptive power of sketch-map Journal of Chemical Theory and Computation. 9: 1521-1532. DOI: 10.1021/ct3010563  1
2013 Yeung HHM, Kosa M, Parrinello M, Cheetham AK. Chiral, racemic, and meso-lithium tartrate framework polymorphs: A detailed structural analysis Crystal Growth and Design. 13: 3705-3715. DOI: 10.1021/cg400741b  1
2013 Vetter T, Salvalalglio M, Mazzotti M, Parrinello M. Prediction of crystal habits of urea using molecular dynamics simulations and comparision to experimental results Engineering Sciences and Fundamentals 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 2: 1049-1050.  1
2013 Vetter T, Salvalalglio M, Mazzotti M, Parrinello M. Prediction of crystal habits of urea using molecular dynamics simulations and comparision to experimental results Engineering Sciences and Fundamentals 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 2: 1049-1050.  1
2012 Do TN, Ippoliti E, Carloni P, Varani G, Parrinello M. Counterion Redistribution upon Binding of a Tat-Protein Mimic to HIV-1 TAR RNA. Journal of Chemical Theory and Computation. 8: 688-94. PMID 26596616 DOI: 10.1021/ct2005769  0.44
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  1
2012 Salvalaglio M, Vetter T, Giberti F, Mazzotti M, Parrinello M. Uncovering molecular details of urea crystal growth in the presence of additives. Journal of the American Chemical Society. 134: 17221-33. PMID 22992035 DOI: 10.1021/ja307408x  1
2012 Gabardi S, Caravati S, Bernasconi M, Parrinello M. Density functional simulations of Sb-rich GeSbTe phase change alloys Journal of Physics Condensed Matter. 24. PMID 22945279 DOI: 10.1088/0953-8984/24/38/385803  1
2012 Eshet H, Khaliullin RZ, Kühne TD, Behler J, Parrinello M. Microscopic origins of the anomalous melting behavior of sodium under high pressure. Physical Review Letters. 108: 115701. PMID 22540486  1
2012 Hassanali AA, Cuny J, Ceriotti M, Pickard CJ, Parrinello M. The fuzzy quantum proton in the hydrogen chloride hydrates Journal of the American Chemical Society. 134: 8557-8569. PMID 22500856 DOI: 10.1021/ja3014727  1
2012 Söderhjelm P, Tribello GA, Parrinello M. Locating binding poses in protein-ligand systems using reconnaissance metadynamics Proceedings of the National Academy of Sciences of the United States of America. 109: 5170-5175. PMID 22440749 DOI: 10.1073/pnas.1201940109  1
2012 Tribello GA, Ceriotti M, Parrinello M. Using sketch-map coordinates to analyze and bias molecular dynamics simulations Proceedings of the National Academy of Sciences of the United States of America. 109: 5196-5201. PMID 22427357 DOI: 10.1073/pnas.1201152109  1
2012 Limongelli V, Marinelli L, Cosconati S, La Motta C, Sartini S, Mugnaini L, Da Settimo F, Novellino E, Parrinello M. Sampling protein motion and solvent effect during ligand binding. Proceedings of the National Academy of Sciences of the United States of America. 109: 1467-72. PMID 22238423 DOI: 10.1073/pnas.1112181108  1
2012 Grazioso G, Limongelli V, Branduardi D, Novellino E, De Micheli C, Cavalli A, Parrinello M. Investigating the mechanism of substrate uptake and release in the glutamate transporter homologue Glt(Ph) through metadynamics simulations. Journal of the American Chemical Society. 134: 453-63. PMID 22092197 DOI: 10.1021/ja208485w  1
2012 Eshet H, Khaliullin RZ, Kühne TD, Behler J, Parrinello M. Microscopic origins of the anomalous melting behavior of sodium under high pressure Physical Review Letters. 108. DOI: 10.1103/PhysRevLett.108.115701  1
2012 Verdolino V, Baldini L, Palazzesi F, Giberti F, Parrinello M. Combined computational and experimental NMR study of calix[4]arene derivatives Journal of Physical Chemistry C. 116: 23441-23452. DOI: 10.1021/jp307895x  1
2012 Muñoz-Santiburcio D, Kosa M, Hernández-Laguna A, Sainz-Díaz CI, Parrinello M. Ab initio molecular dynamics study of the dehydroxylation reaction in a smectite model Journal of Physical Chemistry C. 116: 12203-12211. DOI: 10.1021/jp301366r  1
2012 Branduardi D, Bussi G, Parrinello M. Metadynamics with adaptive gaussians Journal of Chemical Theory and Computation. 8: 2247-2254. DOI: 10.1021/ct3002464  1
2012 Do TN, Ippoliti E, Carloni P, Varani G, Parrinello M. Counterion redistribution upon binding of a tat-protein mimic to HIV-1 TAR RNA Journal of Chemical Theory and Computation. 8: 688-694. DOI: 10.1021/ct2005769  1
2011 Prakash MK, Barducci A, Parrinello M. Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations. Journal of Chemical Theory and Computation. 7: 2025-2027. PMID 26606473 DOI: 10.1021/ct200208h  0.56
2011 Cucinotta CS, Bernasconi M, Parrinello M. Hydrogen oxidation reaction at the Ni/YSZ anode of solid oxide fuel cells from first principles. Physical Review Letters. 107: 206103. PMID 22181748 DOI: 10.1103/PhysRevLett.107.206103  0.72
2011 Hassanali A, Prakash MK, Eshet H, Parrinello M. On the recombination of hydronium and hydroxide ions in water Proceedings of the National Academy of Sciences of the United States of America. 108: 20410-20415. PMID 22143756 DOI: 10.1073/pnas.1112486108  1
2011 Tribello GA, Cuny J, Eshet H, Parrinello M. Exploring the free energy surfaces of clusters using reconnaissance metadynamics. The Journal of Chemical Physics. 135: 114109. PMID 21950852 DOI: 10.1063/1.3628676  0.92
2011 Berteotti A, Barducci A, Parrinello M. Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism Journal of the American Chemical Society. 133: 17200-17206. PMID 21854002 DOI: 10.1021/ja202849a  1
2011 Khaliullin RZ, Eshet H, Kühne TD, Behler J, Parrinello M. Nucleation mechanism for the direct graphite-to-diamond phase transition. Nature Materials. 10: 693-7. PMID 21785417 DOI: 10.1038/nmat3078  1
2011 Grasso GI, Arena G, Bellia F, MacCarrone G, Parrinello M, Pietropaolo A, Vecchio G, Rizzarelli E. Intramolecular weak interactions in the thermodynamic stereoselectivity of copper(II) complexes with carnosine-trehalose conjugates Chemistry - a European Journal. 17: 9448-9455. PMID 21732434 DOI: 10.1002/chem.201100313  1
2011 Ceriotti M, Tribello GA, Parrinello M. From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map. Proceedings of the National Academy of Sciences of the United States of America. 108: 13023-8. PMID 21730167 DOI: 10.1073/pnas.1108486108  1
2011 Caravati S, Colleoni D, Mazzarello R, Kühne TD, Krack M, Bernasconi M, Parrinello M. First-principles study of nitrogen doping in cubic and amorphous Ge2Sb2Te5. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 23: 265801. PMID 21673401 DOI: 10.1088/0953-8984/23/26/265801  1
2011 Pietropaolo A, Branduardi D, Bonomi M, Parrinello M. A chirality-based metrics for free-energy calculations in biomolecular systems Journal of Computational Chemistry. 32: 2627-2637. PMID 21656787 DOI: 10.1002/jcc.21842  1
2011 Pietropaolo A, Parrinello M. A quantitative measure of chirality inside nucleic acid databank Chirality. 23: 534-542. PMID 21618614 DOI: 10.1002/chir.20961  1
2011 Ceriotti M, Manolopoulos DE, Parrinello M. Accelerating the convergence of path integral dynamics with a generalized Langevin equation. The Journal of Chemical Physics. 134: 084104. PMID 21361524 DOI: 10.1063/1.3556661  1
2011 Cucinotta CS, Bernasconi M, Parrinello M. Hydrogen oxidation reaction at the Ni/YSZ anode of solid oxide fuel cells from first principles Physical Review Letters. 107. DOI: 10.1103/PhysRevLett.107.206103  1
2011 Lin L, Morrone JA, Car R, Parrinello M. Momentum distribution, vibrational dynamics, and the potential of mean force in ice Physical Review B - Condensed Matter and Materials Physics. 83. DOI: 10.1103/PhysRevB.83.220302  1
2011 Miceli G, Ceriotti M, Bernasconi M, Parrinello M. Static disorder and structural correlations in the low-temperature phase of lithium imide Physical Review B - Condensed Matter and Materials Physics. 83. DOI: 10.1103/PhysRevB.83.054119  1
2011 Caravati S, Colleoni D, Mazzarello R, Kühne TD, Krack M, Bernasconi M, Parrinello M. First-principles study of nitrogen doping in cubic and amorphous Ge 2Sb2Te5 Journal of Physics Condensed Matter. 23. DOI: 10.1088/0953-8984/23/26/265801  1
2011 Ceriotti M, Tribello GA, Parrinello M. Simplifying the representation of complex free-energy landscapes using sketch-map Proceedings of the National Academy of Sciences of the United States of America. 108: 13023-13028. DOI: 10.1073/pnas.1108486108  1
2011 Tribello GA, Cuny J, Eshet H, Parrinello M. Exploring the free energy surfaces of clusters using reconnaissance metadynamics Journal of Chemical Physics. 135. DOI: 10.1063/1.3628676  1
2011 Khaliullin RZ, Eshet H, Kühne TD, Behler J, Parrinello M. Nucleation mechanism for the direct graphite-to-diamond phase transition Nature Materials. 10: 693-697. DOI: 10.1038/nmat3078  1
2011 Miceli G, Ceriotti M, Angioletti-Uberti S, Bernasconi M, Parrinello M. First-principles study of the high-temperature phase of Li2NH Journal of Physical Chemistry C. 115: 7076-7080. DOI: 10.1021/jp200076p  1
2011 Prakash MK, Barducci A, Parrinello M. Replica temperatures for uniform exchange and efficient roundtrip times in explicit solvent parallel tempering simulations Journal of Chemical Theory and Computation. 7: 2025-2027. DOI: 10.1021/ct200208h  1
2011 Yeung HHM, Kosa M, Parrinello M, Forster PM, Cheetham AK. Structural diversity and energetics in anhydrous lithium tartrates: Experimental and computational studies of novel chiral polymorphs and their racemic and meso analogues Crystal Growth and Design. 11: 221-230. DOI: 10.1021/cg101170k  1
2010 Caravati S, Bernasconi M, Parrinello M. First principles study of the optical contrast in phase change materials. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 22: 315801. PMID 21399368 DOI: 10.1088/0953-8984/22/31/315801  1
2010 Bonomi M, Barducci A, Gervasio FL, Parrinello M. Multiple routes and milestones in the folding of HIV-1 protease monomer. Plos One. 5: e13208. PMID 20967249 DOI: 10.1371/journal.pone.0013208  1
2010 Ceriotti M, Parrinello M, Markland TE, Manolopoulos DE. Efficient stochastic thermostatting of path integral molecular dynamics. The Journal of Chemical Physics. 133: 124104. PMID 20886921 DOI: 10.1063/1.3489925  1
2010 Tribello GA, Ceriotti M, Parrinello M. A self-learning algorithm for biased molecular dynamics Proceedings of the National Academy of Sciences of the United States of America. 107: 17509-17514. PMID 20876135 DOI: 10.1073/pnas.1011511107  1
2010 Lin L, Morrone JA, Car R, Parrinello M. Displaced path integral formulation for the momentum distribution of quantum particles. Physical Review Letters. 105: 110602. PMID 20867559 DOI: 10.1103/PhysRevLett.105.110602  1
2010 Bonomi M, Parrinello M. Enhanced sampling in the well-tempered ensemble. Physical Review Letters. 104: 190601. PMID 20866953 DOI: 10.1103/PhysRevLett.104.190601  1
2010 Metzler RA, Tribello GA, Parrinello M, Gilbert PU. Asprich peptides are occluded in calcite and permanently disorder biomineral crystals. Journal of the American Chemical Society. 132: 11585-91. PMID 20677733 DOI: 10.1021/ja103089r  1
2010 Prakash MK, Barducci A, Parrinello M. Probing the mechanism of pH-induced large-scale conformational changes in dengue virus envelope protein using atomistic simulations. Biophysical Journal. 99: 588-94. PMID 20643078 DOI: 10.1016/j.bpj.2010.04.024  1
2010 Kosa M, Tan JC, Merrill CA, Krack M, Cheetham AK, Parrinello M. Probing the mechanical properties of hybrid inorganic-organic frameworks: a computational and experimental study. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 11: 2332-6. PMID 20607713 DOI: 10.1002/cphc.201000362  1
2010 Barducci A, Bonomi M, Parrinello M. Linking well-tempered metadynamics simulations with experiments. Biophysical Journal. 98: L44-6. PMID 20441734 DOI: 10.1016/j.bpj.2010.01.033  1
2010 Mazzarello R, Caravati S, Angioletti-Uberti S, Bernasconi M, Parrinello M. Signature of tetrahedral Ge in the Raman spectrum of amorphous phase-change materials. Physical Review Letters. 104: 085503. PMID 20366945 DOI: 10.1103/PhysRevLett.104.085503  1
2010 Limongelli V, Bonomi M, Marinelli L, Gervasio FL, Cavalli A, Novellino E, Parrinello M. Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition. Proceedings of the National Academy of Sciences of the United States of America. 107: 5411-6. PMID 20215464 DOI: 10.1073/pnas.0913377107  1
2010 Leone V, Marinelli F, Carloni P, Parrinello M. Targeting biomolecular flexibility with metadynamics. Current Opinion in Structural Biology. 20: 148-54. PMID 20171876 DOI: 10.1016/j.sbi.2010.01.011  1
2010 Ceriotti M, Miceli G, Pietropaolo A, Colognesi D, Nale A, Catti M, Bernasconi M, Parrinello M. Nuclear quantum effects in ab initio dynamics: Theory and experiments for lithium imide Physical Review B - Condensed Matter and Materials Physics. 82. DOI: 10.1103/PhysRevB.82.174306  1
2010 Eshet H, Khaliullin RZ, Kühne TD, Behler J, Parrinello M. Ab initio quality neural-network potential for sodium Physical Review B - Condensed Matter and Materials Physics. 81. DOI: 10.1103/PhysRevB.81.184107  1
2010 Khaliullin RZ, Eshet H, Kühne TD, Behler J, Parrinello M. Graphite-diamond phase coexistence study employing a neural-network mapping of the ab initio potential energy surface Physical Review B - Condensed Matter and Materials Physics. 81. DOI: 10.1103/PhysRevB.81.100103  1
2010 Caravati S, Bernasconi M, Parrinello M. First-principles study of liquid and amorphous Sb2 Te3 Physical Review B - Condensed Matter and Materials Physics. 81. DOI: 10.1103/PhysRevB.81.014201  1
2010 Miceli G, Cucinotta CS, Bernasconi M, Parrinello M. First principles study of the LiNH2/Li2NH transformation Journal of Physical Chemistry C. 114: 15174-15183. DOI: 10.1021/jp100723p  1
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  1
2010 Ceriotti M, Parrinello M. The δ-thermostat: Selective normal-modes excitation by colored-noise Langevin dynamics Procedia Computer Science. 1: 1607-1614. DOI: 10.1016/j.procs.2010.04.180  1
2010 Kosa M, Tan JC, Merrill CA, Krack M, Cheetham AK, Parrinello M. Cover picture Chemphyschem. 11: 2269. DOI: 10.1002/cphc.201090053  1
2009 Kühne TD, Krack M, Parrinello M. Static and Dynamical Properties of Liquid Water from First Principles by a Novel Car-Parrinello-like Approach. Journal of Chemical Theory and Computation. 5: 235-241. PMID 26610101 DOI: 10.1021/ct800417q  1
2009 Caravati S, Bernasconi M, Kühne TD, Krack M, Parrinello M. First-principles study of crystalline and amorphous Ge(2)Sb(2)Te(5) and the effects of stoichiometric defects. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 21: 255501. PMID 21828439 DOI: 10.1088/0953-8984/21/25/255501  1
2009 Appelhans LN, Kosa M, Radha AV, Simoncic P, Navrotsky A, Parrinello M, Cheetham AK. Phase selection and energetics in chiral alkaline Earth tartrates and their racemic and meso analogues: synthetic, structural, computational, and calorimetric studies. Journal of the American Chemical Society. 131: 15375-86. PMID 19795897 DOI: 10.1021/ja905690t  1
2009 Cucinotta CS, Miceli G, Raiteri P, Krack M, Kühne TD, Bernasconi M, Parrinello M. Superionic conduction in substoichiometric LiAl alloy: an ab initio study. Physical Review Letters. 103: 125901. PMID 19792446 DOI: 10.1103/PhysRevLett.103.125901  1
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  1
2009 Ceriotti M, Bussi G, Parrinello M. Nuclear quantum effects in solids using a colored-noise thermostat. Physical Review Letters. 103: 030603. PMID 19659261  1
2009 Tribello GA, Bruneval F, Liew C, Parrinello M. A molecular dynamics study of the early stages of calcium carbonate growth. The Journal of Physical Chemistry. B. 113: 11680-7. PMID 19650654 DOI: 10.1021/jp902606x  1
2009 Pfaendtner J, Branduardi D, Parrinello M, Pollard TD, Voth GA. Nucleotide-dependent conformational states of actin. Proceedings of the National Academy of Sciences of the United States of America. 106: 12723-8. PMID 19620726 DOI: 10.1073/pnas.0902092106  1
2009 Caravati S, Bernasconi M, Kühne TD, Krack M, Parrinello M. Unravelling the mechanism of pressure induced amorphization of phase change materials. Physical Review Letters. 102: 205502. PMID 19519039 DOI: 10.1103/PhysRevLett.102.205502  1
2009 Bonomi M, Barducci A, Parrinello M. Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics. Journal of Computational Chemistry. 30: 1615-21. PMID 19421997 DOI: 10.1002/jcc.21305  1
2009 Tribello GA, Liew C, Parrinello M. Binding of calcium and carbonate to polyacrylates. The Journal of Physical Chemistry. B. 113: 7081-5. PMID 19400592 DOI: 10.1021/jp900283d  1
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  1
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  1
2009 Berteotti A, Cavalli A, Branduardi D, Gervasio FL, Recanatini M, Parrinello M. Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations. Journal of the American Chemical Society. 131: 244-50. PMID 19067513 DOI: 10.1021/ja806846q  1
2009 Ceriotti M, Bussi G, Parrinello M. Nuclear quantum effects in solids using a colored-noise thermostat Physical Review Letters. 103. DOI: 10.1103/PhysRevLett.103.030603  1
2009 Ceriotti M, Kühne TD, Parrinello M. A hybrid approach to Fermi operator expansion Aip Conference Proceedings. 1148: 658-661. DOI: 10.1063/1.3225396  1
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  1
2008 Zykova-Timan T, Raiteri P, Parrinello M. Investigating the polymorphism in PR179: a combined crystal structure prediction and metadynamics study. The Journal of Physical Chemistry. B. 112: 13231-7. PMID 18826187 DOI: 10.1021/jp802977t  1
2008 Bonomi M, Branduardi D, Gervasio FL, Parrinello M. The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin. Journal of the American Chemical Society. 130: 13938-44. PMID 18811160 DOI: 10.1021/ja803652f  1
2008 Eshet H, Bruneval F, Parrinello M. New Lennard-Jones metastable phase. The Journal of Chemical Physics. 129: 026101. PMID 18624562 DOI: 10.1063/1.2953327  1
2008 Ceriotti M, Kühne TD, Parrinello M. An efficient and accurate decomposition of the Fermi operator. The Journal of Chemical Physics. 129: 024707. PMID 18624552 DOI: 10.1063/1.2949515  1
2008 Domene C, Klein ML, Branduardi D, Gervasio FL, Parrinello M. Conformational changes and gating at the selectivity filter of potassium channels. Journal of the American Chemical Society. 130: 9474-80. PMID 18588293 DOI: 10.1021/ja801792g  1
2008 Pagliai M, Cavazzoni C, Cardini G, Erbacci G, Parrinello M, Schettino V. Anharmonic infrared and Raman spectra in Car-Parrinello molecular dynamics simulations. The Journal of Chemical Physics. 128: 224514. PMID 18554036 DOI: 10.1063/1.2936988  1
2008 Behler J, Martonák R, Donadio D, Parrinello M. Metadynamics simulations of the high-pressure phases of silicon employing a high-dimensional neural network potential. Physical Review Letters. 100: 185501. PMID 18518388 DOI: 10.1103/PhysRevLett.100.185501  1
2008 Donadio D, Martonák R, Raiteri P, Parrinello M. Influence of temperature and anisotropic pressure on the phase transitions in alpha-cristobalite. Physical Review Letters. 100: 165502. PMID 18518214 DOI: 10.1103/PhysRevLett.100.165502  1
2008 Molina-Montes E, Donadio D, Hernández-Laguna A, Sainz-Díaz CI, Parrinello M. DFT research on the dehydroxylation reaction of pyrophyllite 1. First-principle molecular dynamics simulations. The Journal of Physical Chemistry. B. 112: 7051-60. PMID 18489137 DOI: 10.1021/jp711278s  1
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  1
2008 Karamertzanis PG, Raiteri P, Parrinello M, Leslie M, Price SL. The thermal stability of lattice-energy minima of 5-fluorouracil: metadynamics as an aid to polymorph prediction. The Journal of Physical Chemistry. B. 112: 4298-308. PMID 18341322 DOI: 10.1021/jp709764e  1
2008 Buch V, Dubrovskiy A, Mohamed F, Parrinello M, Sadlej J, Hammerich AD, Devlin JP. HCl hydrates as model systems for protonated water. The Journal of Physical Chemistry. A. 112: 2144-61. PMID 18288820 DOI: 10.1021/jp076391m  1
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  1
2008 Petraglio G, Bartolini M, Branduardi D, Andrisano V, Recanatini M, Gervasio FL, Cavalli A, Parrinello M. The role of Li+, Na+, and K+ in the ligand binding inside the human acetylcholinesterase gorge. Proteins. 70: 779-85. PMID 17729290 DOI: 10.1002/prot.21560  1
2008 Pietrucci F, Bernasconi M, Laio A, Parrinello M. Vacancy-vacancy interaction and oxygen diffusion in stabilized cubic ZrO2 from first principles Physical Review B - Condensed Matter and Materials Physics. 78. DOI: 10.1103/PhysRevB.78.094301  1
2008 Kosa M, Krack M, Cheetham AK, Parrinello M. Modeling the hydrogen storage materials with exposed M2+ coordination sites Journal of Physical Chemistry C. 112: 16171-16173. DOI: 10.1021/jp806394g  1
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  1
2008 Behler J, Martoňák R, Donadio D, Parrinello M. Pressure-induced phase transitions in silicon studied by neural network-based metadynamics simulations Physica Status Solidi (B) Basic Research. 245: 2618-2629. DOI: 10.1002/pssb.200844219  1
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  1
2008 Pfaendtner J, Branduardi D, Parrinello M, Voth GA. Multiscale investigation of nucleotide effects in actin structures Aiche Annual Meeting, Conference Proceedings 1
2007 Ensing B, Nielsen SO, Moore PB, Klein ML, Parrinello M. Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics. Journal of Chemical Theory and Computation. 3: 1100-5. PMID 26627429 DOI: 10.1021/ct600323n  0.88
2007 Delle Site L, Ghiringhelli LM, Andreussi O, Donadio D, Parrinello M. The interplay between surface-water and hydrogen bonding in a water adlayer on Pt(111) and Ag(111). Journal of Physics. Condensed Matter : An Institute of Physics Journal. 19: 242101. PMID 21694030 DOI: 10.1088/0953-8984/19/24/242101  1
2007 Mantz YA, Gervasio FL, Laino T, Parrinello M. Solvent effects on charge spatial extent in DNA and implications for transfer. Physical Review Letters. 99: 058104. PMID 17930798 DOI: 10.1103/PhysRevLett.99.058104  1
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  1
2007 Bruneval F, Donadio D, Parrinello M. Molecular dynamics study of the solvation of calcium carbonate in water. The Journal of Physical Chemistry. B. 111: 12219-27. PMID 17915911 DOI: 10.1021/jp0728306  1
2007 Shamay ES, Buch V, Parrinello M, Richmond GL. At the water's edge: nitric acid as a weak acid. Journal of the American Chemical Society. 129: 12910-1. PMID 17915872 DOI: 10.1021/ja074811f  1
2007 Biarnés X, Ardèvol A, Planas A, Rovira C, Laio A, Parrinello M. The conformational free energy landscape of beta-D-glucopyranose. Implications for substrate preactivation in beta-glucoside hydrolases. Journal of the American Chemical Society. 129: 10686-93. PMID 17696342 DOI: 10.1021/ja068411o  1
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  1
2007 Bonomi M, Gervasio FL, Tiana G, Provasi D, Broglia RA, Parrinello M. Insight into the folding inhibition of the HIV-1 protease by a small peptide. Biophysical Journal. 93: 2813-21. PMID 17573430 DOI: 10.1529/biophysj.107.106369  1
2007 Behler J, Parrinello M. Generalized neural-network representation of high-dimensional potential-energy surfaces. Physical Review Letters. 98: 146401. PMID 17501293 DOI: 10.1103/PhysRevLett.98.146401  1
2007 Kühne TD, Krack M, Mohamed FR, Parrinello M. Efficient and accurate Car-Parrinello-like approach to Born-Oppenheimer molecular dynamics. Physical Review Letters. 98: 066401. PMID 17358962 DOI: 10.1103/PhysRevLett.98.066401  1
2007 Buch V, Mohamed F, Parrinello M, Devlin JP. Elusive structure of HCl monohydrate. The Journal of Chemical Physics. 126: 074503. PMID 17328616 DOI: 10.1063/1.2436870  1
2007 Branduardi D, Gervasio FL, Parrinello M. From A to B in free energy space. The Journal of Chemical Physics. 126: 054103. PMID 17302470 DOI: 10.1063/1.2432340  1
2007 Buch V, Mohamed F, Parrinello M, Devlin JP. A new glance at HCl-monohydrate spectroscopy, using on-the-fly dynamics. The Journal of Chemical Physics. 126: 021102. PMID 17228930 DOI: 10.1063/1.2426333  1
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  1
2007 Mantz YA, Gervasio FL, Laino T, Parrinello M. Charge localization in stacked radical cation DNA base pairs and the benzene dimer studied by self-interaction corrected density-functional theory. The Journal of Physical Chemistry. A. 111: 105-12. PMID 17201393 DOI: 10.1021/jp063080n  1
2007 Martoňák R, Donadio D, Oganov AR, Parrinello M. From four- to six-coordinated silica: Transformation pathways from metadynamics Physical Review B - Condensed Matter and Materials Physics. 76. DOI: 10.1103/PhysRevB.76.014120  1
2007 Krajewski FR, Parrinello M. Linear scaling electronic structure Monte Carlo method for metals Physical Review B - Condensed Matter and Materials Physics. 75. DOI: 10.1103/PhysRevB.75.235108  1
2007 Stirling A, Bernasconi M, Parrinello M. Defective pyrite (100) surface: An ab initio study Physical Review B - Condensed Matter and Materials Physics. 75. DOI: 10.1103/PhysRevB.75.165406  1
2007 Boero M, Gervasio FL, Parrinello M. Charge localisation and hopping in DNA Molecular Simulation. 33: 57-60. DOI: 10.1080/08927020601052849  1
2007 Cavalli A, Berteotti A, Branduardi D, Gervasio FL, Recanatini M, Parrinello M. Protein conformational plasticity: The "off-on" switching movement in CDK5 Aip Conference Proceedings. 963: 598. DOI: 10.1063/1.2836152  1
2007 Caravati S, Bernasconi M, Kühne TD, Krack M, Parrinello M. Coexistence of tetrahedral- and octahedral-like sites in amorphous phase change materials Applied Physics Letters. 91. DOI: 10.1063/1.2801626  1
2007 Michel C, Laio A, Mohamed F, Krack M, Parrinello M, Milet A. Free energy ab Initio metadynamics: A new tool for the theoretical study of organometallic reactivity? Example of the C-C and C-H reductive eliminations from platinum(IV) complexes Organometallics. 26: 1241-1249. DOI: 10.1021/om060980h  1
2007 Bulo RE, Donadio D, Laio A, Molnar F, Rieger J, Parrinello M. "Site binding" of Ca2+ ions to polyacrylates in water: A molecular dynamics study of coiling and aggregation Macromolecules. 40: 3437-3442. DOI: 10.1021/ma062467l  1
2007 Rodríguez-Fortea A, Iannuzzi M, Parrinello M. Ab initio molecular dynamics study of heterogeneous nitric acid decomposition reactions on graphite surfaces Journal of Physical Chemistry C. 111: 2251-2258. DOI: 10.1021/jp066581h  1
2007 Ensing B, Nielsen SO, Moore PB, Klein ML, Parrinello M. Energy conservation in adaptive hybrid atomistic/coarse-grain molecular dynamics Journal of Chemical Theory and Computation. 3: 1100-1105. DOI: 10.1021/ct600323n  1
2006 Laino T, Mohamed F, Laio A, Parrinello M. An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations. Journal of Chemical Theory and Computation. 2: 1370-8. PMID 26626844 DOI: 10.1021/ct6001169  1
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  1
2006 Trudu F, Donadio D, Parrinello M. Freezing of a Lennard-Jones fluid: from nucleation to spinodal regime. Physical Review Letters. 97: 105701. PMID 17025828 DOI: 10.1103/PhysRevLett.97.105701  0.8
2006 Park JM, Laio A, Iannuzzi M, Parrinello M. Dissociation mechanism of acetic acid in water. Journal of the American Chemical Society. 128: 11318-9. PMID 16939231 DOI: 10.1021/ja060454h  1
2006 Röhrig UF, Laio A, Tantalo N, Parrinello M, Petronzio R. Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer. Biophysical Journal. 91: 3217-29. PMID 16920832 DOI: 10.1529/biophysj.106.088542  1
2006 Gervasio FL, Boero M, Parrinello M. Double proton coupled charge transfer in DNA. Angewandte Chemie (International Ed. in English). 45: 5606-9. PMID 16888729 DOI: 10.1002/anie.200602106  0.64
2006 Fiorin G, Pastore A, Carloni P, Parrinello M. Using metadynamics to understand the mechanism of calmodulin/target recognition at atomic detail. Biophysical Journal. 91: 2768-77. PMID 16877506 DOI: 10.1529/biophysj.106.086611  0.44
2006 Martonák R, Donadio D, Oganov AR, Parrinello M. Crystal structure transformations in SiO2 from classical and ab initio metadynamics. Nature Materials. 5: 623-6. PMID 16845414 DOI: 10.1038/nmat1696  0.8
2006 Gervasio FL, Parrinello M, Ceccarelli M, Klein ML. Exploring the gating mechanism in the ClC chloride channel via metadynamics. Journal of Molecular Biology. 361: 390-8. PMID 16843488 DOI: 10.1016/j.jmb.2006.06.034  0.88
2006 Zipoli F, Laino T, Laio A, Bernasconi M, Parrinello M. A QUICKSTEP-based quantum mechanics/molecular mechanics approach for silica. The Journal of Chemical Physics. 124: 154707. PMID 16674251 DOI: 10.1063/1.2187485  1
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  1
2006 Raiteri P, Laio A, Gervasio FL, Micheletti C, Parrinello M. Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics. The Journal of Physical Chemistry. B. 110: 3533-9. PMID 16494409 DOI: 10.1021/jp054359r  1
2006 Rodríguez-Fortea A, Iannuzzi M, Parrinello M. Ab initio molecular dynamics study of heterogeneous oxidation of graphite by means of gas-phase nitric acid. The Journal of Physical Chemistry. B. 110: 3477-84. PMID 16494401 DOI: 10.1021/jp052526h  1
2006 Barducci A, Chelli R, Procacci P, Schettino V, Gervasio FL, Parrinello M. Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding. Journal of the American Chemical Society. 128: 2705-10. PMID 16492057 DOI: 10.1021/ja057076l  0.64
2006 Pagliai M, Iannuzzi M, Cardini G, Parrinello M, Schettino V. Lithium hydroxide phase transition under high pressure: an ab initio molecular dynamics study. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 7: 141-7. PMID 16331720 DOI: 10.1002/cphc.200500272  1
2006 Krajewski FR, Parrinello M. Linear scaling for quasi-one-dimensional systems Physical Review B - Condensed Matter and Materials Physics. 74. DOI: 10.1103/PhysRevB.74.125107  1
2006 Devlin JP, Buch V, Mohamed F, Parrinello M. The amorphous analogs of the crystalline monohydrate of HCl: Structures and spectra Chemical Physics Letters. 432: 462-467. DOI: 10.1016/j.cplett.2006.11.001  1
2006 Laio A, Parrinello M. Computing free energies and accelerating rare events with metadynamics Lecture Notes in Physics. 703: 315-347. DOI: 10.1007/3-540-35273-2_9  1
2005 Laino T, Mohamed F, Laio A, Parrinello M. An Efficient Real Space Multigrid QM/MM Electrostatic Coupling. Journal of Chemical Theory and Computation. 1: 1176-84. PMID 26631661 DOI: 10.1021/ct050123f  1
2005 Ceccarelli M, Mercuri F, Passerone D, Parrinello M. The microscopic switching mechanism of a [2]catenane. The Journal of Physical Chemistry. B. 109: 17094-9. PMID 16853180 DOI: 10.1021/jp051609v  0.44
2005 Laio A, Rodriguez-Fortea A, Gervasio FL, Ceccarelli M, Parrinello M. Assessing the accuracy of metadynamics. The Journal of Physical Chemistry. B. 109: 6714-21. PMID 16851755 DOI: 10.1021/jp045424k  1
2005 Ensing B, Laio A, Parrinello M, Klein ML. A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions. The Journal of Physical Chemistry. B. 109: 6676-87. PMID 16851750 DOI: 10.1021/jp045571i  1
2005 Donadio D, Raiteri P, Parrinello M. Topological defects and bulk melting of hexagonal ice. The Journal of Physical Chemistry. B. 109: 5421-4. PMID 16851575 DOI: 10.1021/jp050690z  0.8
2005 Oganov AR, Martonák R, Laio A, Raiteri P, Parrinello M. Anisotropy of Earth's D'' layer and stacking faults in the MgSiO3 post-perovskite phase. Nature. 438: 1142-4. PMID 16372006 DOI: 10.1038/nature04439  1
2005 Petraglio G, Ceccarelli M, Parrinello M. Nonperiodic boundary conditions for solvated systems. The Journal of Chemical Physics. 123: 044103. PMID 16095342 DOI: 10.1063/1.1955449  0.44
2005 Branduardi D, Gervasio FL, Cavalli A, Recanatini M, Parrinello M. The role of the peripheral anionic site and cation-pi interactions in the ligand penetration of the human AChE gorge. Journal of the American Chemical Society. 127: 9147-55. PMID 15969593 DOI: 10.1021/ja0512780  0.72
2005 Gervasio FL, Laio A, Parrinello M, Boero M. Charge localization in DNA fibers. Physical Review Letters. 94: 158103. PMID 15904193 DOI: 10.1103/PhysRevLett.94.158103  1
2005 Raiteri P, Martonák R, Parrinello M. Exploring polymorphism: the case of benzene. Angewandte Chemie (International Ed. in English). 44: 3769-73. PMID 15887199 DOI: 10.1002/anie.200462760  0.6
2005 Gervasio FL, Laio A, Parrinello M. Flexible docking in solution using metadynamics. Journal of the American Chemical Society. 127: 2600-7. PMID 15725015 DOI: 10.1021/ja0445950  1
2005 VandeVondele J, Mohamed F, Krack M, Hutter J, Sprik M, Parrinello M. The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water. The Journal of Chemical Physics. 122: 14515. PMID 15638682 DOI: 10.1063/1.1828433  0.72
2004 Stirling A, Iannuzzi M, Laio A, Parrinello M. Azulene-to-naphthalene rearrangement: the Car-Parrinello metadynamics method explores various reaction mechanisms. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 5: 1558-68. PMID 15535555 DOI: 10.1002/cphc.200400063  1
2004 Raiteri P, Laio A, Parrinello M. Correlations among hydrogen bonds in liquid water. Physical Review Letters. 93: 087801. PMID 15447226 DOI: 10.1103/PhysRevLett.93.087801  1
2004 Gervasio FL, Laio A, Iannuzzi M, Parrinello M. Influence of DNA structure on the reactivity of the guanine radical cation Chemistry - a European Journal. 10: 4846-4852. PMID 15372666 DOI: 10.1002/chem.200400171  1
2004 Ensing B, Laio A, Gervasio FL, Parrinello M, Klein ML. A minimum free energy reaction path for the E2 reaction between fluoro ethane and a fluoride ion. Journal of the American Chemical Society. 126: 9492-3. PMID 15291524 DOI: 10.1021/ja048285t  1
2004 Ceccarelli M, Danelon C, Laio A, Parrinello M. Microscopic Mechanism of Antibiotics Translocation through a Porin. Biophysical Journal. 87: 58-64. PMID 15240444 DOI: 10.1529/biophysj.103.037283  1
2004 Micheletti C, Laio A, Parrinello M. Reconstructing the density of states by history-dependent metadynamics. Physical Review Letters. 92: 170601. PMID 15169135 DOI: 10.1103/PhysRevLett.92.170601  1
2003 Iannuzzi M, Laio A, Parrinello M. Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. Physical Review Letters. 90: 238302. PMID 12857293 DOI: 10.1103/PhysRevLett.90.238302  1
2002 Laio A, Parrinello M. Escaping free-energy minima. Proceedings of the National Academy of Sciences of the United States of America. 99: 12562-6. PMID 12271136 DOI: 10.1073/pnas.202427399  1
2002 Tuckerman ME, Marx D, Parrinello M. The nature and transport mechanism of hydrated hydroxide ions in aqueous solution Nature. 417: 925-929. PMID 12087398 DOI: 10.1038/nature00797  1
1997 Tuckerman ME, Marx D, Klein ML, Parrinello M. On the Quantum Nature of the Shared Proton in Hydrogen Bonds Science (New York, N.Y.). 275: 817-20. PMID 9012345 DOI: 10.1126/science.275.5301.817  1
1990 Zhang Q, Chiarotti G, Selloni A, Car R, Parrinello M. Atomic structure and bonding in liquid GaAs from Iab-initioP molecular dynamics. Physical Review. B, Condensed Matter. 42: 5071-5081. PMID 9996067  0.8
Show low-probability matches.