Here are listed the publications of the SBP group since January 1st, 2018 (the first being the most recent).
For a complete list of publications by each group member you are encouraged to check their personal web pages.
2026
- B. Romano and R. Menichetti and N. Paracini and P. Gutfreund and B. Bracco and P. Sassi and A. Orecchini and R. Potestio and A. Luchini, Phosphatidylserine lipids reduce the adsorption of chondroitin sulphate at the membrane surface, Journal of Colloid and Interface Science (2026)
- J. Gliksberg et al., NET4EXA: Toward Ethernet-native interconnects for exascale HPC and AI systems, Microprocessors and Microsystems (2026)
- M. Micheloni, R. Potestio, L. Petrolli, Dynamical insights on the role of supercoiling on DNA radiosensitivity, Physics in Medicine & Biology (2026)
- M. Mele, R. Fiorentini, T. Tarenzi, G. Mattiotti, R. Potestio, Determining the optimal structural resolution of proteins through an information-theoretic analysis of their conformational ensemble, JCTC (2026)
2025
- M. Micheloni, L. Tubiana, R. Potestio, L. Petrolli, Sequence- and supercoiling-dependent effects on the structural dynamics of DNA minicircles, accepted for publication in Biophys. Reports (2025) [cover article]
- G. Mattiotti, V. Nanna, M. Giulini, D. Alberga, G. F. Mangiatordi, N. Sánchez-Puig, M. Saviano, L. Tubiana, R. Potestio, G. Lattanzi, D. Siliqi, Structural Implications of Missense Point Mutations in Shwachman-Bodian-Diamond Syndrome Protein (SBDS): A Combined SAXS/MD Investigation, ACS Omega (2025)
- R. Aldrigo, R. Menichetti, R. Potestio, Low-resolution descriptions of model neural activity reveal hidden features and underlying system properties, Phys. Rev. E (2025)
- R. Rusková, L. Tubiana, R. Potestio, D. Račko, Controlling knot interactions through confinement, Macromolecules (2025) [cover article]
- M. Mele, R. Menichetti, A. Ingrosso, R. Potestio, Density of states in neural networks: an in-depth exploration of learning in parameter space, TMLR (2025)
- M. Rigoli, R. Potestio, R. Menichetti, A multi-scale analysis of the CzrA transcription repressor highlights the allosteric changes induced by metal ion binding, JPCB (2025)
2024
- G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model, Macromol. Rapid Commun. (2024)
- M. Giulini, R. Fiorentini, L. Tubiana, R. Potestio, R. Menichetti, EXCOGITO, an Extensible Coarse-Graining Toolbox for the Investigation of Biomolecules by Means of Low-Resolution Representations, J. Chem. Inf. Model. (2024)
- L. Tubiana et al., Topology in soft and biological matter, Phys. Rep. (2024)
- J. Morand, S. Yip, Y. Velegrakis, G. Lattanzi, R. Potestio, L. Tubiana, Quality assessment and community detection methods for anonymized mobility data in the Italian Covid context, Sci. Rep. (2024)
2023
- D. Vapoutic, […] L. Tubiana, […], Viral RNA as a branched polymer, book chapter in “Physical Virology”, Springer series in Biophysics 24 (2023)
- N.A. Taklimi, F. Ferrari, M.R. Piatek, L. Tubiana, Thermal properties of knotted block copolymer rings with charged monomers subjected to short-range interactions, Phys. Rev. E (2023)
- D. Vaupotič, A. Rosa, L. Tubiana, A. Božič, Scaling properties of RNA as a randomly branching polymer, J. Chem. Phys. (2023)
- M. Micheloni, L. Petrolli, G. Lattanzi, R. Potestio, Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations, Biophys. J. (2023)
- C. Paternoster, T. Tarenzi, R. Potestio, G. Lattanzi, Gamma-Hemolysin Components: Computational Strategies for LukF-Hlg2 Dimer Reconstruction on a Model Membrane, Int. J. Mol. Sci. (2023)
- G. Novi Inverardi, F. Carnovale, L. Petrolli, S. Taioli, G. Lattanzi, Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography, Biophysica (2023)
- R. Fiorentini, T. Tarenzi, R. Potestio, Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins, J. Chem. Inf. Model. (2023)
2022
- L. Tubiana, F. Ferrari, E. Orlandini, Circular polycatenanes: Supramolecular structures with topologically tunable properties, Phys. Rev. Lett. (2022)
- R. Holtzman, M. Giulini, R. Potestio, Making sense of complex systems through resolution, relevance, and mapping entropy, Phys. Rev. E (2022)
- M. Mele, R. Covino, R. Potestio, Information-theoretical measures identify accurate low-resolution representations of protein configurational space, Soft Matter (2022)
- M. Rigoli, G. Spagnolli, G. Lorengo, P. Monti, R. Potestio, E. Biasini and A. Inga, Structural Basis of Mutation-Dependent p53 Tetramerization Deficiency, Int. J. Mol. Sci. (2022)
- T. Tarenzi, G. Mattiotti, M. Rigoli and R. Potestio, In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins, Applied Sciences (2022)
- T. Tarenzi, G. Lattanzi and R. Potestio, Membrane binding of pore-forming γ-hemolysin components studied at different lipid compositions, BBA Biomembranes (2022)
- D. Michieletto, Y. A. G. Fosado, E. Melas, M. Baiesi, L. Tubiana, E. Orlandini, Dynamic and facilitated binding of topoisomerase accelerates topological relaxation, Nucleic Acids Research (2022)
- M. Sighinolfi, D. De Boni, A. Roggero, G. Garberoglio, P. Faccioli, and A. Recati, Stochastic dynamics and bound states of heavy impurities in a Fermi bath, Phys Rev A (2022)
- E. Spinetti, P. Delre, M. Saviano, D. Siliqui, G. Lattanzi, and G.F. Mangiatordi, A comparative molecular dynamics study of selected point mutations in the Schwachman-Bodian-Diamond syndrome protein SBDS, Int. J. Mol. Sci.
- V. Agostiniani, M. Fogagnolo, and L.Mazzieri, Minkowski Inequalities via Nonlinear Potential Theory, ARMA
- V. Agostiniani, L.Mazzieri, and F. Oronzio A geometric capacitary inequality for sub-static manifolds with harmonic potentials, MinE
2021
- T. Tarenzi, M. Rigoli and R. Potestio, Communication pathways bridge local and global conformations in an IgG4 antibody, Scientific Reports (2021)
- V. Agostiniani, S. Borghini, L. Mazzieri, On the Serrin problem for ring-shaped domains, arxiv preprint (2021)
- R. Menichetti, M. Giulini and R. Potestio, A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules, EPJB (2021)
- L. F. Signorini, C. Perego and R. Potestio, Protein self-entanglement modulates successful folding to the native state: A multi-scale modeling study, J. Chem. Phys. (2021)
- V. Agostiniani, L. Mazzieri, and F. Oronzio, A Green’s function proof of the Positive Mass Theorem (2021) [arXiv preprint]
- V. Agostiniani, L. Mazzieri, and F. Oronzio, A geometric capacitary inequality for sub-static manifolds with harmonic potentials, Mathematics in Engineering (2021)
- M. Giulini, M. Rigoli, G. Matiotti, R. Menichetti, T. Tarenzi, R. Fiorentini and R. Potestio, From system modelling to system analysis: the impact of resolution level and resolution distribution in the computer-aided investigation of biomolecules, Front. Mol. Biosci. (2021)
- L. Tubiana, H. Kobayashi, R. Potestio, B. Duenweg, K. Kremer, P. Virnau and K. Daoulas, Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators, Journal of Physics: Condensed Matter (2021)
- F. Errica, M. Giulini, D. Bacciu, R. Menichetti, A. Micheli and R. Potestio, A deep graph network-enhanced sampling approach to efficiently explore the space of reduced representations of proteins, Front. Mol. Biosci. (2021)
- A. Baptista, R. Chandra Dutta, M. Sevilla, M. Heidari, R. Potestio, K. Kremer and R. Cortes-Huerto, Density-Functional-Theory Approach to the Hamiltonian Adaptive Resolution Simulation Method, Journal of Physics: Condensed Matter (2021)
2020
- M. Turelli, D. Alberga, G. Lattanzi, I. Ciofini and C. Adamo, Theoretical insights on acceptor–donor dyads for organic photovoltaics, Physical Chemistry Chemical Physics (2020)
- L. Petrolli, F. Tommasino, E. Scifoni and G. Lattanzi, Can We Assess Early DNA Damage at the Molecular Scale by Radiation Track Structure Simulations? A Tetranucleosome Scenario in Geant4-DNA, Frontiers in Physics (2020)
- M. Giulini, R. Menichetti, M. Scott Shell and R. Potestio, An information theory-based approach for optimal model reduction of biomolecules, J. Chem. Theor. Comput. (2020)
- F. Errica, M. Giulini, D. Bacciu, R. Menichetti, A. Micheli, R. Potestio, Accelerating the identification of informative reduced representations of proteins with deep learning for graphs, Front. Mol. Biosci. (2021) [arxiv preprint here]
- R. Fiorentini, K. Kremer and R. Potestio, Ligand-protein interactions in lysozyme investigated through a dual-resolution model, Proteins (2020)
- M. Heidari, K. Kremer, R. Golestanian, R. Potestio, and R. Cortes-Huerto, Open-Boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations, J. Chem. Phys. (2020)
2019
- M. Giulini and R. Potestio, A deep learning approach to the structural analysis of proteins, Royal Society Interface Focus (2019)
- A. Borsatto, V. Marino, G. Abrusci, G. Lattanzi and D. Dell’Orco, Effects of Membrane and Biological Target on the Structural and Allosteric Properties of Recoverin: A Computational Approach, Int. J. Mol. Sci. (2019)
- M. Heidari, R. Cortes-Huerto, R. Potestio, and K. Kremer, Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences, J. Chem. Phys. (2019)
- C. Perego and R. Potestio, Computational methods in the study of self-entangled proteins: a critical appraisal, Journal of Physics: Condensed Matter (2019)
- C. Perego and R. Potestio, Searching the Optimal Folding Routes of a Complex Lasso Protein, Biophysical Journal (2019)
- G. Spagnolli, M. Rigoli, S. Orioli, A. M. Sevillano, P. Faccioli, H. Wille, E. Biasini, J. R. Requena, “Full Atomistic Model of Prion Structure and Conversion”, PLoS Pathogens (2019) [biorxiv preprint here]
- S. J. Wodak et al, Allostery in Many Disguises and Applications, Structure 27, 566 (2019)
- M. Carli, M. Turelli and P. Faccioli, Microscopic Calculation of Absorption Spectra of Macromolecules: an Analytic Approach, J. Chem Phys. 150, 144103 (2019).
- M. Rigoli et al., “OK Google, How Could I Design Therapeutics Against Prion Diseases?” Curr. Opin. Structr. Biol. 44, 39 (2019) (journal cover)
- A. Ianeselli, G. Spagnolli, S. Orioli and P. Faccioli, “ERRATUM: All-atom calculation of protein free energy profiles“, J. Chem. Phys, 150(5), 05990 (2019=
2018
- F. Segatta, G. Lattanzi and P. Faccioli, Predicting Charge Mobility of Organic Semiconducors with Complex Morphology, Macromolecules, in press (2018)
- G. Bartolucci, S. Orioli and P. Faccioli, “Transition Path Theory from Biased Simulations”, J. Chem. Phys. 149, 072336 (2018)
- M. Praprotnik, R. Cortes-Huerto, R.Potestio, Luigi Delle Site, Adaptive Resolution Molecular Dynamics Technique, Handbook of Materials Modeling: Methods: Theory and Modeling, 1-15 (2018)
- M. Heidari, K. Kremer, R. Cortes-Huerto and R. Potestio, Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids, J. Chem. Theor. Comput. (2018)
- M. Heidari, K. Kremer, R. Potestio and Robinson Cortes-Huerto, Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations, Molecular Physics, special issue in honour of Daan Frenkel, DOI: 10.1080/00268976.2018.1482429 (2018)
- M. Heidari, K. Kremer, R. Cortes-Huerto and R. Potestio, Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations, Eur. Phys. J. E 41:64 (2018) [JOURNAL HIGHLIGHT]
- F. Wang, S. Orioli, A. Ianeselli, G. Spagnolli, S. a Beccara, A. Gershenson, P. Faccioli and P. L. Wintrode, “All-Atom Simulations Reveal How Single-Point Mutations Promote Serpin Misfolding“, Biophys. J. 114, 2083 (2018)
- M. Heidari, K. Kremer, R. Potestio and R. Cortes-Huerto, Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method, Entropy 20(4) (2018)
- A. Ianeselli, S. Orioli, G. Spagnolli, P. Faccioli, L. Cupellini, S. Jurinovich, B. Mennucci, Atomic Detail of Protein Folding Revealed by an Ab Initio Reappraisal of Circular Dichroism, J. Am. Chem. Soc. 140, 3674−3682 (2018)
