Publications

@article{wild2025automatic,

title = {Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance},

author = {Romina Wild and Felix Wodaczek and Vittorio Del Tatto and Bingqing Cheng and Alessandro Laio},

year  = {2025},

date = {2025-01-01},

journal = {Nature Communications},

volume = {16},

number = {1},

pages = {270},

publisher = {Nature Publishing Group UK London},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{janevcek2025computer,

title = {Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space},

author = {Michal Janeček and Petra Kührová and Vojtěch Mlýnský and Petr Stadlbauer and Michal Otyepka and Giovanni Bussi and Jiří Šponer and Pavel Banáš},

year  = {2025},

date = {2025-01-01},

urldate = {2025-01-01},

journal = {Journal of computational chemistry},

volume = {46},

number = {1},

pages = {e27535},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{micheletti2024topology,

title = {Topology-Based Detection and Tracking of Deadlocks Reveal Aging of Active Ring Melts},

author = {Cristian Micheletti and Iurii Chubak and Enzo Orlandini and Jan Smrek},

year  = {2024},

date = {2024-01-01},

journal = {ACS Macro Letters},

volume = {13},

number = {2},

pages = {124–129},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{caraglio2024unraveling,

title = {Unraveling the Influence of Topology and Spatial Confinement on Equilibrium and Relaxation Properties of Interlocked Ring Polymers},

author = {Michele Caraglio and Cristian Micheletti and Enzo Orlandini},

year  = {2024},

date = {2024-01-01},

journal = {Macromolecules},

volume = {57},

number = {7},

pages = {3223–3233},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tagliabue2024effect,

title = {Effect of Counterion Size on Knotted Polyelectrolyte Conformations},

author = {Andrea Tagliabue and Cristian Micheletti and Massimo Mella},

year  = {2024},

date = {2024-01-01},

journal = {The Journal of Physical Chemistry B},

volume = {128},

number = {17},

pages = {4183–4194},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{luengo2024shape,

title = {Shape and Size Tunability of Sheets of Interlocked Ring Copolymers},

author = {Juan Luengo-Márquez and Salvatore Assenza and Cristian Micheletti},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2406.13561},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{suma2024unzipping,

title = {Unzipping of knotted DNA via nanopore translocation},

author = {Antonio Suma and Cristian Micheletti},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2407.11567},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zheng2024knots,

title = {When Knots are Plectonemes},

author = {Fei Zheng and Antonio Suma and Christopher Maffeo and Kaikai Chen and Mohammed Alawami and Jingjie Sha and Aleksei Aksimentiev and Cristian Micheletti and Ulrich F Keyser},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2407.16290},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{panizza2024protein,

title = {Protein Design by Integrating Machine Learning and Quantum-Encoded Optimization},

author = {Veronica Panizza and Philipp Hauke and Cristian Micheletti and Pietro Faccioli},

year  = {2024},

date = {2024-01-01},

journal = {PRX Life},

volume = {2},

number = {4},

pages = {043012},

publisher = {American Physical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gasparotto2024mapping,

title = {Mapping Cryptic Phosphorylation Sites in the Human Proteome},

author = {Dino Gasparotto and Annarita Zanon and Valerio Bonaldo and Elisa Marchiori and Massimo Casagranda and Erika Di Domenico and Laura Copat and Tommaso Fortunato Asquini and Marta Rigoli and Sirio Vittorio Feltrin and others},

year  = {2024},

date = {2024-01-01},

journal = {bioRxiv},

pages = {2024–12},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{dellostritto2024molecular,

title = {Molecular dynamics studies of knotted polymers},

author = {Mark DelloStritto and Cristian Micheletti and Michael L Klein},

year  = {2024},

date = {2024-01-01},

journal = {The Journal of Chemical Physics},

volume = {161},

number = {24},

publisher = {AIP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{zhang2024bottom,

title = {Bottom-up data integration in polymer models of chromatin organisation},

author = {Alex Chen Yi Zhang and Angelo Rosa and Guido Sanguinetti},

year  = {2024},

date = {2024-01-01},

journal = {Biophysical Journal},

volume = {123},

number = {2},

pages = {184–194},

publisher = {Cell Press},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{ubertini2024universal,

title = {Universal time and length scales of polar active polymer melts},

author = {Mattia Alberto Ubertini and Emanuele Locatelli and Angelo Rosa},

year  = {2024},

date = {2024-01-01},

journal = {ACS Macro Letters},

volume = {13},

number = {9},

pages = {1204–1210},

publisher = {American Chemical Society},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{tubiana2024topology,

title = {Topology in soft and biological matter},

author = {Luca Tubiana and Gareth P Alexander and Agnese Barbensi and Dorothy Buck and Julyan HE Cartwright and Mateusz Chwastyk and Marek Cieplak and Ivan Coluzza and Simon Čopar and David J Craik and others},

year  = {2024},

date = {2024-01-01},

journal = {Physics Reports},

volume = {1075},

pages = {1–137},

publisher = {North-Holland},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{arcangeli2024phase,

title = {Phase Behavior and Self-Assembly of Semiflexible Polymers in Poor-Solvent Solutions},

author = {Tobia Arcangeli and Tatjana S krbic and Somiealo Azote and Davide Marcato and Angelo Rosa and Jayanth R Banavar and Roberto Piazza and Amos Maritan and Achille Giacometti},

year  = {2024},

date = {2024-01-01},

journal = {Macromolecules},

volume = {57},

number = {18},

pages = {8940–8955},

publisher = {American Chemical Society},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{van2024amoeba,

title = {Amoeba Monte Carlo algorithms for random trees with controlled branching activity: Efficient trial move generation and universal dynamics},

author = {Pieter HW Hoek and Angelo Rosa and Ralf Everaers},

year  = {2024},

date = {2024-01-01},

journal = {Physical Review E},

volume = {110},

number = {4},

pages = {045312},

publisher = {American Physical Society},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{marcato2024theory,

title = {Theory of polymers in binary solvent solutions: mean-field free energy and phase behavior},

author = {Davide Marcato and Achille Giacometti and Amos Maritan and Angelo Rosa},

url = {https://doi.org/10.1103/PhysRevMaterials.8.125601},

year  = {2024},

date = {2024-01-01},

journal = {Physical Review Materials},

volume = {8},

pages = {125601},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{zhang2024biosbm,

title = {bioSBM: a random graph model to integrate epigenomic data in chromatin structure prediction},

author = {Alex Chen Yi Zhang and Angelo Rosa and Guido Sanguinetti},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2409.14425},

keywords = {Student Paper},

pubstate = {published},

tppubtype = {article}

}

@article{rende2024mapping,

title = {Mapping of attention mechanisms to a generalized Potts model},

author = {Riccardo Rende and Federica Gerace and Alessandro Laio and Sebastian Goldt},

year  = {2024},

date = {2024-01-01},

journal = {Physical Review Research},

volume = {6},

number = {2},

pages = {023057},

publisher = {American Physical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{del2024robust,

title = {Robust inference of causality in high-dimensional dynamical processes from the Information Imbalance of distance ranks},

author = {V Del Tatto and G Fortunato and D Bueti and A Laio and others},

year  = {2024},

date = {2024-01-01},

journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},

volume = {121},

number = {19},

pages = {1–10},

publisher = {National Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wild2024maximally,

title = {Maximally informative feature selection using Information Imbalance: Application to COVID-19 severity prediction},

author = {Romina Wild and Emanuela Sozio and Riccardo G Margiotta and Fabiana Dellai and Angela Acquasanta and Fabio Del Ben and Carlo Tascini and Francesco Curcio and Alessandro Laio},

year  = {2024},

date = {2024-01-01},

journal = {Scientific Reports},

volume = {14},

number = {1},

pages = {10744},

publisher = {Nature Publishing Group UK London},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{grafke2024metadynamics,

title = {Metadynamics for transition paths in irreversible dynamics},

author = {Tobias Grafke and Alessandro Laio},

year  = {2024},

date = {2024-01-01},

journal = {Multiscale Modeling & Simulation},

volume = {22},

number = {1},

pages = {125–141},

publisher = {Society for Industrial and Applied Mathematics University City, Philadelphia},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bernardi2024improving,

title = {Improving acute stroke assessment in non-enhanced computed tomography: automated tool for early ischemic lesion volume detection},

author = {Mara Sabina Bernardi and Alex Rodriguez and Paola Caruso and Giovanni Furlanis and Mariana Ridolfi and Gabriele Prandin and Marcello Naccarato and Alessandro Laio and Daniele Amati and Paolo Manganotti},

year  = {2024},

date = {2024-01-01},

journal = {Neurological Sciences},

pages = {1–9},

publisher = {Springer International Publishing Cham},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{springer2024unsupervised,

title = {Unsupervised detection of large-scale weather patterns in the northern hemisphere via Markov State Modelling: from blockings to teleconnections},

author = {Sebastian Springer and Alessandro Laio and Vera Melinda Galfi and Valerio Lucarini},

year  = {2024},

date = {2024-01-01},

journal = {npj Climate and Atmospheric Science},

volume = {7},

number = {1},

pages = {105},

publisher = {Nature Publishing Group UK London},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cheng2024emergence,

title = {Emergence of a High-Dimensional Abstraction Phase in Language Transformers},

author = {Emily Cheng and Diego Doimo and Corentin Kervadec and Iuri Macocco and Jade Yu and Alessandro Laio and Marco Baroni},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2405.15471},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{di2024beyond,

title = {Beyond the noise: intrinsic dimension estimation with optimal neighbourhood identification},

author = {Antonio Di Noia and Iuri Macocco and Aldo Glielmo and Alessandro Laio and Antonietta Mira},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2405.15132},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carli2024density,

title = {Density estimation via binless multidimensional integration},

author = {Matteo Carli and Alex Rodriguez and Alessandro Laio and Aldo Glielmo},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2407.08094},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{macocco2024intrinsic,

title = {Intrinsic dimension as a multi-scale summary statistics in network modeling},

author = {Iuri Macocco and Antonietta Mira and Alessandro Laio},

year  = {2024},

date = {2024-01-01},

journal = {Scientific Reports},

volume = {14},

number = {1},

pages = {17756},

publisher = {Nature Publishing Group UK London},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gerace2024choose,

title = {How to choose the right transfer learning protocol? A qualitative analysis in a controlled set-up},

author = {Federica Gerace and Diego Doimo and Stefano Sarao Mannelli and Luca Saglietti and Alessandro Laio and others},

year  = {2024},

date = {2024-01-01},

journal = {Transactions on Machine Learning Research},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{barone2024unsupervised,

title = {Unsupervised domain classification of AlphaFold2-predicted protein structures},

author = {Federico Barone and Alessandro Laio and Marco Punta and Stefano Cozzini and Alessio Ansuini and Alberto Cazzaniga},

year  = {2024},

date = {2024-01-01},

journal = {bioRxiv},

pages = {2024–08},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tamagnone2024coarse,

title = {Coarse-Grained Molecular Dynamics with Normalizing Flows},

author = {Samuel Tamagnone and Alessandro Laio and Marylou Gabrié},

year  = {2024},

date = {2024-01-01},

journal = {Journal of Chemical Theory and Computation},

volume = {20},

number = {18},

pages = {7796–7805},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{rende2024distributional,

title = {A distributional simplicity bias in the learning dynamics of transformers},

author = {Riccardo Rende and Federica Gerace and Alessandro Laio and Sebastian Goldt},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2410.19637},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{acevedo2024unsupervised,

title = {Unsupervised detection of semantic correlations in big data},

author = {Santiago Acevedo and Alex Rodriguez and Alessandro Laio},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2411.02126},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{thiel2024sampling,

title = {Sampling globally and locally correct rna 3d structures using ernwin, spqr and experimental saxs data},

author = {Bernhard C Thiel and Giovanni Bussi and Simón Poblete and Ivo L Hofacker},

year  = {2024},

date = {2024-01-01},

journal = {Nucleic Acids Research},

pages = {gkae602},

publisher = {Oxford University Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{wild2024automatic,

title = {Automatic feature selection and weighting using Differentiable Information Imbalance},

author = {Romina Wild and Vittorio Del Tatto and Felix Wodaczek and Bingqing Cheng and Alessandro Laio},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2411.00851},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gilardoni2024boosting,

title = {Boosting Ensemble Refinement with Transferable Force-Field Corrections: Synergistic Optimization for Molecular Simulations},

author = {Ivan Gilardoni and Thorben Fro hlking and Giovanni Bussi},

year  = {2024},

date = {2024-01-01},

journal = {The Journal of Physical Chemistry Letters},

volume = {15},

number = {5},

pages = {1204–1210},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pokorna2024molecular,

title = {Molecular dynamics simulations reveal the parallel stranded d (GGGA) 3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble},

author = {Pavlína Pokorná and Vojtěch Ml`ynsk`y and Giovanni Bussi and Jiří Šponer and Petr Stadlbauer},

year  = {2024},

date = {2024-01-01},

journal = {International Journal of Biological Macromolecules},

volume = {261},

pages = {129712},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{bussi2024rna,

title = {RNA Dynamics from Experimental and Computational Approaches},

author = {Giovanni Bussi and Massimiliano Bonomi and Paraskevi Gkeka and Michael Sattler and Hashim M Al-Hashimi and Pascal Auffinger and Maria Duca and Yann Foricher and Danny Incarnato and Alisha N Jones and others},

year  = {2024},

date = {2024-01-01},

journal = {Structure},

volume = {32},

pages = {1281},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{piomponi2024molecular,

title = {Molecular simulations to investigate the impact of N6-methylation in RNA recognition: Improving accuracy and precision of binding free energy prediction},

author = {Valerio Piomponi and Miroslav Krepl and Jiri Sponer and Giovanni Bussi},

year  = {2024},

date = {2024-01-01},

journal = {The Journal of Physical Chemistry B},

volume = {128},

number = {37},

pages = {8896–8907},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{amaro2024need,

title = {The need to implement FAIR principles in biomolecular simulations},

author = {Rommie Amaro and Johan Åqvist and Ivet Bahar and Federica Battistini and Adam Bellaiche and Daniel Beltran and Philip C Biggin and Massimiliano Bonomi and Gregory R Bowman and Richard Bryce and others},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2407.16584},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mykuliak2024molecular,

title = {Molecular dynamics simulations reveal how vinculin refolds partially unfolded talin rod helices to stabilize them against mechanical force},

author = {Vasyl V Mykuliak and Rolle Rahikainen and Neil J Ball and Giovanni Bussi and Benjamin T Goult and Vesa P Hytönen},

year  = {2024},

date = {2024-01-01},

journal = {PLOS Computational Biology},

volume = {20},

number = {8},

pages = {e1012341},

publisher = {Public Library of Science},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{boccalini2024exploring,

title = {Exploring RNA destabilization mechanisms in biomolecular condensates through atomistic Simulations},

author = {Matteo Boccalini and Yelyzaveta Berezovska and Giovanni Bussi and Matteo Paloni and Alessandro Barducci},

year  = {2024},

date = {2024-01-01},

journal = {bioRxiv},

pages = {2024–09},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{silva2024characterizing,

title = {Characterizing RNA oligomers using Stochastic Titration Constant-pH Metadynamics simulations},

author = {Tomas FD Silva and Giovanni Bussi},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2410.16064},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{posani2024ensemble,

title = {Ensemble Refinement of mismodeled cryo-EM RNA Structures Using All-Atom Simulations},

author = {Elisa Posani and Pavel Janos and Daniel Haack and Navtej Toor and Massimiliano Bonomi and Alessandra Magistrato and Giovanni Bussi},

year  = {2024},

date = {2024-01-01},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{di2024all,

title = {All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions},

author = {Salvatore Di Marco and Jana Aupič and Giovanni Bussi and Alessandra Magistrato},

year  = {2024},

date = {2024-01-01},

journal = {bioRxiv},

pages = {2024–11},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gilardoni2024mdrefine,

title = {MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data},

author = {Ivan Gilardoni and Valerio Piomponi and Thorben Fröhlking and Giovanni Bussi},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2411.07798},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{tribello2024plumed,

title = {PLUMED Tutorials: a collaborative, community-driven learning ecosystem},

author = {Gareth A Tribello and Massimiliano Bonomi and Giovanni Bussi and Carlo Camilloni and Blake I Armstrong and Andrea Arsiccio and Simone Aureli and Federico Ballabio and Mattia Bernetti and Luigi Bonati and others},

year  = {2024},

date = {2024-01-01},

journal = {arXiv preprint arXiv:2412.03595},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{sorichetti2023structure,

title = {Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks},

author = {Valerio Sorichetti and Andrea Ninarello and José Ruiz-Franco and Virginie Hugouvieux and Emanuela Zaccarelli and Cristian Micheletti and Walter Kob and Lorenzo Rovigatti},

year  = {2023},

date = {2023-01-01},

journal = {The Journal of Chemical Physics},

volume = {158},

number = {7},

publisher = {AIP Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{suma2023nonequilibrium,

title = {Nonequilibrium thermodynamics of DNA nanopore unzipping},

author = {Antonio Suma and Vincenzo Carnevale and Cristian Micheletti},

year  = {2023},

date = {2023-01-01},

journal = {Physical Review Letters},

volume = {130},

number = {4},

pages = {048101},

publisher = {American Physical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{chen2023protein,

title = {Protein folds vs. protein folding: Differing questions, different challenges},

author = {Shi-Jie Chen and Mubashir Hassan and Robert L Jernigan and Kejue Jia and Daisuke Kihara and Andrzej Kloczkowski and Sergei Kotelnikov and Dima Kozakov and Jie Liang and Adam Liwo and others},

year  = {2023},

date = {2023-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {120},

number = {1},

pages = {e2214423119},

publisher = {National Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}