Author's posts

Making sense of complex systems through resolution, relevance, and mapping entropy

R. Holtzman, M. Giulini, R. Potestio, Making sense of complex systems through resolution, relevance, and mapping entropy, Phys. Rev. E (2022) Complex systems are characterized by a tight, nontrivial interplay of their constituents, which gives rise to a multiscale spectrum of emergent properties. In this scenario, it is practically and conceptually difficult to identify those degrees …

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Information-theoretical measures identify accurate low-resolution representations of protein configurational space

M. Mele, R. Covino, R. Potestio, Information-theoretical measures identify accurate low-resolution representations of protein configurational space, Soft Matter (2022) The steadily growing computational power employed to perform molecular dynamics simulations of biological macromolecules represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data are produced, from which useful, …

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Dynamic and facilitated binding of topoisomerase accelerates topological relaxation

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) How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most …

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Stochastic dynamics and bound states of heavy impurities in a Fermi bath

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) We investigate the dynamics of heavy impurities embedded in an ultracold Fermi gas by using a generalized Langevin equation. The latter—derived by means of influence …

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Membrane binding of pore-forming γ-hemolysin components studied at different lipid compositions

T. Tarenzi, G. Lattanzi. R. Potestio, Membrane binding of pore-forming γ-hemolysin components studied at different lipid compositions, BBA Biomembranes (2022) Methicillin-resistant Staphylococcus aureus is among those pathogens currently posing the highest threat to public health. Its host immune evasion strategy is mediated by pore-forming toxins (PFTs), among which the bi-component γ-hemolysin is one of the most common. The complexity …

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Communication pathways bridge local and global conformations in an IgG4 antibody

T. Tarenzi, M. Rigoli and R. Potestio, Communication pathways bridge local and global conformations in an IgG4 antibody, Scientific Reports (2021) The affinity of an antibody for its antigen is primarily determined by the specific sequence and structural arrangement of the complementarity-determining regions (CDRs). Recent evidence, however, points toward a nontrivial relation between the CDR …

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Honourable mention for poster presentation

Raffaele Fiorentini, SBP postdoc and member of the VARIAMOLS research group, received a honourable mention for his poster presentation at the EMBO workshop “Advances and Challenges in Biomolecular Simulations” held in October 2021. More information about this can be found at the following link.

A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules

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) A mapping of a macromolecule is a prescription to construct a simplified representation of the system in which only a subset of its constituent atoms is retained. As the specific …

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Nobel Prize in Physics 2021 awarded to Giorgio Parisi

The Nobel Prize in Physics 2021 was awarded “for groundbreaking contributions to our understanding of complex systems” with one half jointly to Syukuro Manabe and Klaus Hasselmann “for the physical modelling of Earth’s climate, quantifying variability and reliably predicting global warming” and the other half to Giorgio Parisi “for the discovery of the interplay of …

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Protein self-entanglement modulates successful folding to the native state: A multi-scale modeling study

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) The computer-aided investigation of protein folding has greatly benefited from coarse-grained models, that is, simplified representations at a resolution level lower than atomistic, providing access to qualitative and quantitative details of …

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