Publications
2025
Das S., Raucci U., Trizio E., Kang P., Neves R.P., Ramos M.J., Parrinello M.
A Machine Learning-Driven, Probability-Based Approach to Enzyme Catalysis
ACS Catalysis, vol. 15, (no. 11), pp. 9785-9792
2025
Raucci U.
Capturing Excited State Proton Transfer Dynamics with Reactive Machine Learning Potentials
Journal of Physical Chemistry Letters, pp. 4900-4906
2025
Visigalli A., Trizio E., Bonati L., Vidossich P., Parrinello M., De Vivo M.
Coordinated Residue Motions at the Enzyme-Substrate Interface Promote DNA Translocation in Polymerases
Journal of the American Chemical Society
2025
Parrinello M., Greed S.
Discussions with a dignitary of molecular dynamics
Nature Reviews Chemistry, vol. 9, (no. 9)
Note
Journal
2025
Trizio E., Kang P., Parrinello M.
Everything everywhere all at once: a probability-based enhanced sampling approach to rare events
Nature Computational Science
Article
Journal
2025
Novelli P., Meanti G., Buigues P., Rosasco L., Parrinello M., Pontil M., Bonati L.
Fast and Fourier Features for Transfer Learning of Interatomic Potentials
npj Computational Materials
Article
Journal
2025
Tokita A.M., Devergne T., Saitta A.M., Behler J.
Free energy profiles for chemical reactions in solution from high-dimensional neural network potentials: The case of the Strecker synthesis
Journal of Chemical Physics, vol. 162, (no. 17)
Article
Journal
2025
Tosello Gardini A., Raucci U., Parrinello M.
Machine learning-driven molecular dynamics unveils a bulk phase transformation driving ammonia synthesis on barium hydride
Nature Communications, vol. 16, (no. 1)
2025
Yang H., Raucci U., Iyer S., Hasan G., Golin Almeida T., Barua S., Savolainen A., Kangasluoma J., Rissanen M., Vehkamaki H., Kurten T.
Molecular dynamics-guided reaction discovery reveals endoperoxide-to-alkoxy radical isomerization as key branching point in α-pinene ozonolysis
Nature Communications, vol. 16, (no. 1)
2025
Perego S., Purcel M., Baum Y., Chen S., Muller A.S., Parrinello M., Behrens M., Muhler M., Bonati L.
No Time for Nitrides: How Cobalt Alloying Promotes Iron Catalysts for Ammonia Decomposition
ACS Catalysis, vol. 15, pp. 16690-16702
Article
Journal
2025
Tribello G.A., Bonomi M., Bussi G., Camilloni C., Armstrong B.I., Arsiccio A., Aureli S., Ballabio F., Bernetti M., Bonati L., Brookes S.G.H., Brotzakis Z.F., Capelli R., Ceriotti M., Chan K.-T., Cossio P., Dasetty S., Donadio D., Ensing B., Ferguson A.L., Fraux G., Gale J.D., Gervasio F.L., Giorgino T., Herringer N.S.M., Hocky G.M., Hoff S.E., Invernizzi M., Languin-Cattoen O., Leone V., Limongelli V., Lopez-Acevedo O., Marinelli F., Febrer Martinez P., Masetti M., Mehdi S., Michaelides A., Murtada M.H., Parrinello M., Piaggi P.M., Pietropaolo A., Pietrucci F., Pipolo S., Pritchard C., Raiteri P., Raniolo S., Rapetti D., Rizzi V., Rydzewski J., Salvalaglio M., Schran C., Seal A., Shayesteh Zadeh A., Silva T.F.D., Spiwok V., Stirnemann G., Sucerquia D., Tiwary P., Valsson O., Vendruscolo M., Voth G.A., White A.D., Wu J.
PLUMED Tutorials: A collaborative, community-driven learning ecosystem
Journal of Chemical Physics, vol. 162, (no. 9)
2025
Cigrang L.L.E., Curchod B.F.E., Ingle R.A., Kelly A., Mannouch J.R., Accomasso D., Alijah A., Barbatti M., Chebbi W., Doslic N., Eklund E.C., Fernandez-Alberti S., Freibert A., Gonzalez L., Granucci G., Hernandez F.J., Hernandez-Rodriguez J., Jain A., Janos J., Kassal I., Kirrander A., Lan Z., Larsson H.R., Lauvergnat D., Le De B., Lee Y., Maitra N.T., Min S.K., Pelaez D., Picconi D., Qiu Z., Raucci U., Robertson P., Sangiogo Gil E., Sapunar M., Schurger P., Sinnott P., Tretiak S., Tikku A., Vindel-Zandbergen P., Worth G.A., Agostini F., Gomez S., Ibele L.M., Prlj A.
Roadmap for Molecular Benchmarks in Nonadiabatic Dynamics
Journal of Physical Chemistry A, vol. 129, (no. 31), pp. 7023-7050
Review
Journal
2025
Devergne T., Kostic V., Pontil M., Parrinello M.
Slow dynamical modes from static averages
Journal of Chemical Physics, vol. 162, (no. 12)
Article
Journal
2025
Amaro R.E., Aqvist J., Bahar I., Battistini F., Bellaiche A., Beltran D., Biggin P.C., Bonomi M., Bowman G.R., Bryce R.A., Bussi G., Carloni P., Case D.A., Cavalli A., Chang C.-E.A., Cheatham T.E., Cheung M.S., Chipot C., Chong L.T., Choudhary P., Cisneros G.A., Clementi C., Collepardo-Guevara R., Coveney P., Covino R., Crawford T.D., Dal Peraro M., de Groot B.L., Delemotte L., De Vivo M., Essex J.W., Fraternali F., Gao J., Gelpi J.L., Gervasio F.L., Gonzalez-Nilo F.D., Grubmuller H., Guenza M.G., Guzman H.V., Harris S., Head-Gordon T., Hernandez R., Hospital A., Huang N., Huang X., Hummer G., Iglesias-Fernandez J., Jensen J.H., Jha S., Jiao W., Jorgensen W.L., Kamerlin S.C.L., Khalid S., Laughton C., Levitt M., Limongelli V., Lindahl E., Lindorff-Larsen K., Loverde S., Lundborg M., Luo Y.L., Luque F.J., Lynch C.I., MacKerell A.D., Magistrato A., Marrink S.J., Martin H., McCammon J.A., Merz K., Moliner V., Mulholland A.J., Murad S., Naganathan A.N., Nangia S., Noe F., Noy A., Olah J., O'Mara M.L., Ondrechen M.J., Onuchic J.N., Onufriev A., Osuna S., Palermo G., Panchenko A.R., Pantano S., Parish C., Parrinello M., Perez A., Perez-Acle T., Perilla J.R., Pettitt B.M., Pietropaolo A., Piquemal J.-P., Poma A.B., Praprotnik M., Ramos M.J., Ren P., Reuter N., Roitberg A., Rosta E., Rovira C., Roux B., Rothlisberger U., Sanbonmatsu K.Y., Schlick T., Shaytan A.K., Simmerling C., Smith J.C., Sugita Y., Swiderek K., Taiji M., Tao P., Tieleman D.P., Tikhonova I.G., Tirado-Rives J., Tunon I., van der Kamp M.W., van der Spoel D., Velankar S., Voth G.A., Wade R., Warshel A., Welborn V.V., Wetmore S.D., Wheeler T.J., Wong C.F., Yang L.-W., Zacharias M., Orozco M.
The need to implement FAIR principles in biomolecular simulations
Nature Methods, vol. 22, (no. 4), pp. 641-645
Note
Journal
2025
Seal A., Perego S., Hennefarth M.R., Raucci U., Bonati L., Ferguson A.L., Parrinello M., Gagliardi L.
Weighted active space protocol for multireference machine-learned potentials
Proceedings of the National Academy of Sciences of the United States of America, vol. 122, (no. 38)
Article
Journal