Apr 20
Single-Molecule Structure and Topology of Kinetoplast DNA NetworksPinyao He, Allard J. Katan, Luca Tubiana, Cees Dekker, and Davide Michieletto Phys. Rev. X 13, 021010 – Published 19 April 2023 Trypanosomes are unique single-cell parasites: Their mitochondrial genome is made of thousands of DNA minicircles interlinked to form a giant 2D Olympic-ring-like network, known as a “kinetoplast …
Mar 06
On March 1st, 2023 our friend, colleague, and SBP group founding member Pietro Faccioli made a big step towards a new phase in his career: the University of Milan Bicocca! The SBP group has dedicated a day to look back to Pietro’s achievements in Trento and wish him all the best for this thrilling change! …
Feb 07
R. Fiorentini, T. Tarenzi, R. Potestio, Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins, J. Chem. Inf. Model. (2023) In recent years, a few multiple-resolution modeling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, with the remainder of the system being concurrently treated using a coarse-grained …
Nov 25
Rings of rings of molecules: how they stretch and twist, and what they can be used for L. Tubiana, F. Ferrari, E. Orlandini “Circular polycatenanes: Supramolecular structures with topologically tunable properties“, Phys. Rev. Lett (2022). Press-release: Italian / English The polymers that make up our bodies, such as proteins and DNA, are molecules made up …
Nov 02
The XVI International Workshop on Complex Systems will take place in Andalo from 13 to 17 March 2023. The workshop will point out new directions, challenges and opportunities in the following fields: Andalo is a beautiful village about 30 km far from Trento close to the ski slopes of the Paganella ski area. The program will be interdisciplinary and it will …
Oct 26
The SBP group members affiliated to the VARIAMOLS and HAMMOCK research projects have gathered in Fontana dei Gai, a mountain lodge near Trento, for a three-days group retreat. This event was aimed at both carrying out research work and team building. The event flyer can be seen here. A few pictures taken during the retreat …
Oct 26
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 …
Oct 26
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, …
Jun 29
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 …
Jun 29
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 …
