149 citations · 469 across the 18 of their papers we have counts for
19 papers
On the thermal properties of knotted block copolymer rings
Neda Abbasi Taklimi, Franco Ferrari, Marcin R. Piątek +1
We investigate the thermal and structural properties of knotted diblock copolymer rings using a coarse-grained lattice model in an implicit solvent. The system is studied by means…
Organisation and dynamics of individual DNA segments in topologically complex genomes
Saminathan Ramakrishnan, Auro Varat Patnaik, Guglielmo Grillo +2
Capturing the physical organisation and dynamics of genomic regions is one of the major open challenges in biology. The kinetoplast DNA (kDNA) is a topologically complex genome, ma…
A contact map method to capture the features of knot conformations
Neda Abbasi Taklimi, Franco Ferrari, Marcin Radosław Piątek +1
Inspired by recent advances in the chromosome capture techniques, a method is proposed to study the structural organization of systems of polymers rings with topological constraint…
Single-Molecule Morphology of Topologically Digested Olympic Networks
Saminathan Ramakrishnan, Zihao Chen, Yair Augusto Gutierrez Fosado +5
The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The…
Emergent circulation patterns from anonymized mobility data: Clustering Italy in the time of Covid
Jules Morand, Shoichi Yip, Yannis Velegrakis +3
Using anonymized mobility data from Facebook users and publicly available information on the Italian population, we model the circulation of people in Italy before and during the e…
Scaling properties of RNA as a randomly branching polymer
Domen Vaupotič, Angelo Rosa, Luca Tubiana +1
Formation of base pairs between the nucleotides of an RNA sequence gives rise to a complex and often highly branched RNA structure. While numerous studies have demonstrated the fun…
Viral RNA as a branched polymer
Domen Vaupotič, Angelo Rosa, Rudolf Podgornik +2
Myriad viruses use positive-strand RNA molecules as their genomes. Far from being only a repository of genetic material, viral RNA performs numerous other functions mediated by its…
On the thermal properties of knotted block copolymer rings
Neda Abbasi Taklimi, Franco Ferrari, Marcin Radosław Piątek +1
The thermal properties of coarse grained knotted polymers containing two kinds of monomers and fluctuating in a solution are investigated on a simple cubic lattice using th…
Single-Molecule Structure and Topology of Kinetoplast DNA Networks
Pinyao He, Allard J. Katan, Luca Tubiana +2
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understandi…
Ring-o-rings: a new category of supramolecular structures with topologically tunable properties
Luca Tubiana, Franco Ferrari, Enzo Orlandini
Macrochains of topologically interlocked rings with unique physical properties have recently gained considerable interest in supramolecular chemistry, biology, and soft matter. Mos…
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation
Davide Michieletto, Yair Fosado, Elias Melas +3
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in biophysics. Most of the existing models…
Chirality modifies the interaction between knots
Saeed Najafi, Luca Tubiana, Rudolf Podgornik +1
In this study we consider an idealization of a typical optical tweezers experiment involving a semiflexible double-knotted polymer, with steric hindrance and persistence length mat…
Universal criterion for designability of heteropolymers
Chiara Cardelli, Valentino Bianco, Lorenzo Rovigatti +4
Proteins are an example of heteropolymers able to self-assemble in specific target structures. The self-assembly of designed artificial heteropolymers is still, to the best of our…
Synonymous mutations reduce genome compactness in icosahedral ssRNA viruses
Luca Tubiana, Anže Lošdorfer Božič, Cristian Micheletti +1
Recent studies have shown that single-stranded viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based…
On the factorization of composite polymer knots into separated prime components
Luca Tubiana
Using Monte Carlo simulations and advanced knot localization methods, we analyze the length and distribution of prime components in composite knots tied on Freely Jointed Rings (FJ…
Spontaneous knotting and unknotting of flexible linear polymers: equilibrium and kinetic aspects
Luca Tubiana, Angelo Rosa, Filippo Fragiacomo +1
We report on a computational study of the statics and dynamics of long flexible linear polymers that spontaneously knot and unknot. Specifically, the equilibrium self-entanglement…
Structure and dynamics of ring polymers: entanglement effects because of solution density and ring topology
Angelo Rosa, Enzo Orlandini, Luca Tubiana +1
The effects of entanglement in solutions and melts of unknotted ring polymers have been addressed by several theoretical and numerical studies. The system properties have been typi…
Multiscale entanglement in ring polymers under spherical confinement
Luca Tubiana, Enzo Orlandini, Cristian Micheletti
The interplay of geometrical and topological entanglement in semiflexible knotted polymer rings confined inside a spherical cavity is investigated using advanced numerical methods.…
Probing the entanglement and locating knots in ring polymers: a comparative study of different arc closure schemes
Luca Tubiana, Enzo Orlandini, Cristian Micheletti
The interplay between the topological and geometrical properties of a polymer ring can be clarified by establishing the entanglement trapped in any portion (arc) of the ring. The t…