5 citations · 7 across the 11 of their papers we have counts for
9 papers · 1 filter
Coarse-grained simulations of dsDNA polycatenanes and network formation in annular nanochannels with topoisomerase II
Carolina Palombo, Davide Breoni, Luca Tubiana
We numerically investigate the behavior of a system of initially unlinked nicked dsDNA rings confined into an annular square nanochannel in the presence of TopoII. Channel confinem…
Active embracement enables autonomous tweezing in active star polymers
Marco Musacchio, Davide Breoni, Iman Abdoli +3
The capacity for autonomous structural reconfiguration is a defining trait of living systems, yet it remains elusive in artificial active matter. Here, we report the discovery of a…
Controlling microalgae populations by phototactic memory
Gianni Jacucci, Davide Breoni, Pierre Illien +4
Motile microorganisms navigate environments that vary in space and time by coupling sensory inputs to internal physiological states and active motion. In photosynthetic microorgani…
The effects of solvent quality and core wetting on the circularization of star polymers
Davide Breoni, Emanuele Locatelli, Luca Tubiana
We simulate the formation of cyclical arms in star polymers, focusing on the effects of solvent quality on their resulting linking complexity and gyration radius. We find that poly…
Effects of knotting on the collapse of active ring polymers
Davide Breoni, Emanuele Locatelli, Luca Tubiana
We use numerical simulations to study tangentially active flexible ring polymers with different knot topologies. Simple, unknotted active rings display a transition from an extende…
Conformation and topology of cyclical star polymers
Davide Breoni, Emanuele Locatelli, Luca Tubiana
We study the conformation and topological properties of cyclical star polymers with ring arms, each made of beads. We find that the conformational properties of unlinked cy…
Normalized topological indices discriminate between architectures of branched macromolecules
Domen Vaupotič, Jules Morand, Luca Tubiana +1
Branching architecture characterizes numerous systems, ranging from synthetic (hyper)branched polymers and biomolecules such as lignin, amylopectin, and nucleic acids to tracheal a…
Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model
Giovanni Mattiotti, Manuel Micheloni, Lorenzo Petrolli +3
The cowpea chlorotic mottle virus (CCMV) has emerged as an exemplary model system to assess the balance between electrostatic and topological features of ssRNA viruses, specificall…
EXCOGITO, an extensible coarse-graining toolbox for the investigation of biomolecules by means of low-resolution representation
Marco Giulini, Raffaele Fiorentini, Luca Tubiana +2
Bottom-up coarse-grained (CG) models proved to be essential to complement and sometimes even replace all-atom representations of soft matter systems and biological macromolecules.…