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.

#### 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018

## 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)