Publications
Submitted / Under review / Under revision
64) Amoeba Monte Carlo algorithms for random trees with controlled branching activity: Efficient trial move generation and universal dynamics.
P. H. W. van der Hoek, A. Rosa, R. Everaers.
Preprint Online article
63) Assessing polymer phase behavior in explicit solvent and with vacancies.
D. Marcato, A. Giacometti, A. Maritan, A. Rosa.
Preprint Online article
62) Phase behaviour and self-assembly of semiflexible polymers in poor-solvent solutions.
T. Arcangeli, et al.
Preprint Online article
61) Universal time and length scales of polar active polymer melts.
M. A. Ubertini, E. Locatelli, A. Rosa.
Preprint Online article
In peer-reviewed journals
2024
60) Topology in soft and biological matter.
L. Tubiana, et al. (COST Action 17139 "EUTOPIA") - Physics Reports 1075, 1-137.
Preprint Online article
59) Bottom-up data integration in polymer models of chromatin organization.
A. Chen Yi Zhang, A. Rosa, G. Sanguinetti - Biophysical Journal 123, 184.
2023
58) Phase behaviour of semiflexible lattice polymers in poor-solvent solution: Mean-field theory and Monte Carlo simulations.
D. Marcato, A. Giacometti, A. Maritan, A. Rosa - Journal of Chemical Physics 159, 154901.
57) Spatial organization of slit-confined melts of ring polymers with non-conserved topology: A lattice Monte Carlo study.
M. A. Ubertini, A. Rosa - Macromolecules 56, 7860.
56) Viral RNA as a branched polymer.
D. Vaupotič, A. Rosa, R. Podgornik, L. Tubiana, A. Božič - Book Physical Virology (Springer).
55) Scaling properties of RNA as a randomly branching polymer.
D. Vaupotič, A. Rosa, L. Tubiana, A. Božič - Journal of Chemical Physics 158, 234901.
54) Topological analysis and recovery of entanglements in polymer melts.
M. A. Ubertini, A. Rosa - Macromolecules 56, 3354.
2022
53) Entanglement length scale separates threading from branching of unknotted and non-concatenated ring polymers in melts.
M. A. Ubertini, J. Smrek, A. Rosa - Macromolecules 55, 10723.
2021
52) Computer simulations of melts of ring polymers with nonconserved topology: A dynamic Monte Carlo lattice model.
M. A. Ubertini, A. Rosa - Physical Review E 104, 054503.
51) Nanorheology of active-passive polymer mixtures differentiates between linear and ring polymer topology.
A. Papale, J. Smrek, A. Rosa - Soft Matter 17, 7111.
50) The physical behavior of interphase chromosomes: Polymer theory and coarse-grain computer simulations.
A. Rosa - Book Hi-C Data Analysis: Methods and Protocols (Springer).
Preprint Online article
49) Single-molecule stretching experiments of flexible (wormlike) chain molecules in different ensembles: Theory and a potential application of finite chain length effects to nick-counting in DNA.
R. Everaers, N. B. Becker, A. Rosa - Journal of Chemical Physics 154, 024903.
2020
48) Threading-induced dynamical transition in tadpole-shaped polymers.
A. Rosa, J. Smrek, M. S. Turner, D. Michieletto - ACS Macro Letters 9, 743.
47) Randomly branching theta-polymers in two and three dimensions: Average properties and distribution functions.
I. Adroher-Benítez, A. Rosa - Journal of Chemical Physics 152, 114903.
46) Merging 1d and 3d genomic information: Challenges in modelling and validation.
A. Merlotti, A. Rosa, D. Remondini - BBA Gene Regulatory Mechanisms 1863, 194415.
2019
45) Topological constraints in eukaryotic genomes and how they can be exploited to improve spatial models of chromosomes.
A. Rosa, M. Di Stefano, C. Micheletti - Frontiers in Molecular Biosciences 6, 127.
44) Microrheology of interphase chromosomes with spatial constraints: A computational study.
A. Papale, A. Rosa - Physical Biology 16, 066002.
Preprint Online article
43) Local loop opening in untangled ring polymer melts: A detailed "Feynman test" of models for the large scale structure.
R. D. Schram, A. Rosa, R. Everaers - Soft Matter 15, 2418.
42) Conformational statistics of randomly branching double-folded ring polymers.
A. Rosa, R. Everaers - European Physical Journal E 42, 7.
41) Threading of unconcatenated ring polymers at high concentrations: Double-folded vs. time-equilibrated structures.
J. Smrek, K. Kremer, A. Rosa - ACS Macro Letters 8, 155.
Preprint Online article
2018
40) The Ising model in swollen vs. compact polymers: Mean-field approach and computer simulations.
A. Papale, A. Rosa - European Physical Journal E 41, 144.
Preprint Online article
39) Structure and microrheology of genome organization: From experiments to physical modeling.
A. Papale, A. Rosa - Book Modeling the 3D Conformation of Genomes (CRC Press, Jan 2019).
Preprint Online article
38) Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains.
N. Nahali, A. Rosa - Journal of Chemical Physics 148, 194902.
Preprint Online article
2017
37) Glassiness and heterogeneous dynamics in dense solutions of ring polymers.
D. Michieletto, N. Nahali, A. Rosa - Physical Review Letters 119, 197801.
36) A polymer physics view on universal and sequence-specific aspects of chromosome folding.
D. Jost, A. Rosa, C. Vaillant, R. Everaers - Book Nuclear Architecture and Dynamics (Elsevier).
Preprint Online article
35) Flory theory of randomly branched polymers.
R. Everaers, A. Yu. Grosberg, M. Rubinstein, A. Rosa - Soft Matter 13, 1223.
Preprint Online article
34) Beyond Flory theory: Distribution functions for interacting lattice trees.
A. Rosa, R. Everaers - Physical Review E 95, 012117.
Preprint Online article (Editors' Suggestion)
2016
33) Computer simulations of melts of randomly branching polymers.
A. Rosa, R. Everaers - Journal of Chemical Physics 145, 164906.
32) Computer simulations of randomly branching polymers: Annealed vs. quenched branching structures.
A. Rosa, R. Everaers - Journal of Physics A: Mathematical and Theoretical 49, 345001.
31) Large scale chromosome folding is stable against local changes in chromatin structure.
A.-M. Florescu, P. Therizols, A. Rosa - Plos Computational Biology 12, e1004987.
Preprint (arXiv) Preprint (bioRxiv) Online article
30) Density effects in entangled solutions of linear and ring polymers.
N. Nahali, A. Rosa - Journal of Physics: Condensed Matter 28, 065101.
2015
29) Pore translocation of knotted polymer chains: How friction depends on knot complexity.
A. Suma, A. Rosa, C. Micheletti - ACS Macro Letters 4, 1420.
Preprint Online article
2014
28) Viscoelasticity of model interphase chromosomes.
M. Valet, A. Rosa - Journal of Chemical Physics 141, 245101.
Accepted after only 3 weeks since submission, based on the reports by 2 independent reviewers!!!
27) Ring polymers in the melt state: The physics of crumpling.
A. Rosa, R. Everaers - Physical Review Letters 112, 118302.
26) Computational models of large-scale genome architecture.
A. Rosa, C. Zimmer - International Review of Cell and Molecular Biology 307, 275.
Preprint Online article
Press highlights:
"Science Daily" (Jan, 3 2014): link
"Genetic Engineering & Biotechnology News" (Jan, 6 2014)
"Il Sole 24 Ore" (Jan, 12 2014)
"Il Piccolo" (Jan, 22 2014)
"Il Piccolo" (Jan, 28 2014)
"La Gazzetta del Mezzogiorno" (Ed. Basilicata; Jan, 28 2014)
"Il Settimanale" (Rai 3 - Friuli-Venezia Giulia; Feb, 22 2014)
2013
25) Spontaneous knotting and unknotting of flexible linear polymers: Equilibrium and kinetic aspects.
L. Tubiana, A. Rosa, F. Fragiacomo, C. Micheletti - Macromolecules 46, 3669.
Preprint Online article
24) Colocalization of coregulated genes: A steered molecular dynamics study of human chromosome 19.
M. Di Stefano, A. Rosa, V. Belcastro, D. di Bernardo, C. Micheletti - Plos Computational Biology 9, e1003019.
Preprint Online article
23) Topological constraints and chromosome organization in eukaryotes: A physical point of view.
A. Rosa - Biochemical Society Transactions 41, 612.
Preprint Online article
2012
22) Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore.
A. Rosa, M. Di Ventra, C. Micheletti - Physical Review Letters 109, 118301.
Preprint Online article
21) Multi-scale modeling of diffusion-controlled reactions in polymers: Renormalisation of reactivity parameters.
R. Everaers, A. Rosa - Journal of Chemical Physics 136, 014902.
Preprint Online article
2011
20) Structure and dynamics of ring polymers: Entanglement effects because of solution density and ring topology.
A. Rosa, L. Tubiana, E. Orlandini, C. Micheletti - Macromolecules 44, 8668.
Preprint Online article
2010
19) The radial distribution function of worm-like chains.
N. B. Becker, A. Rosa, R. Everaers - European Physical Journal E 32, 53.
Preprint Online article
18) Looping probabilities in model interphase chromosomes.
A. Rosa, N. B. Becker, R. Everaers - Biophysical Journal 98, 2410.
Preprint Online article
2008
17) Structure and dynamics of interphase chromosomes.
A. Rosa, R. Everaers - Plos Computational Biology 4, e1000153.
Preprint Online article
2006
16) Measuring limits of telomere movements on nuclear envelopes.
A. Rosa, J. H. Maddocks, F. R. Neumann, S. M. Gasser, A. Stasiak - Biophysical Journal 90, L24.
Preprint Online article
15) Spatially confined polymer chains: Implication of chromatin fiber flexibility and peripheral anchoring on telomere-telomere interaction.
L. Gehlen, A. Rosa, K. Klenin, J. Langowski, S. M. Gasser, K. Bystricky - Journal of Physics: Condensed Matter 18, S245.
Preprint Online article
14) Long time behavior of diffusing particles in constrained geometries: Application to chromatin motion.
A. Rosa, F. R. Neumann, S. M. Gasser, A. Stasiak - Journal of Physics: Condensed Matter 18, S235.
Preprint Online article
13) Stretching a self-interacting semi-flexible polymer.
A. Rosa, D. Marenduzzo, S. Kumar - Europhysics Letters 75, 818.
Preprint Online article
2005
12) Scaling exponents and probability distributions of DNA end-to-end distance.
F. Valle, M. Favre, P. De Los Rios, A. Rosa, G. Dietler - Physical Review Letters 95, 158105.
Preprint Online article
11) Correlation function and generalized master equation of arbitrary age.
P. Allegrini, G. Aquino, P. Grigolini, L. Palatella, A. Rosa, B. J. West - Physical Review E 71, 066109.
Preprint Online article
10) Non-Poisson processes: Regression to equilibrium versus equilibrium correlation functions.
P. Allegrini, P. Grigolini, L. Palatella, A. Rosa, B. J. West - Physica A 347, 268.
Preprint Online article
9) A new interpolation formula for semi-flexible polymers.
A. Rosa, T.-X. Hoang, D. Marenduzzo, A. Maritan - Biophysical Chemistry 115, 251.
Preprint Online article
2004
8) Stepwise unfolding of collapsed polymers.
D. Marenduzzo, A. Maritan, A. Rosa, F. Seno - European Physical Journal E 15, 83.
Preprint Online article
2003
7) Generalized master equation via aging continuous-time random walks.
P. Allegrini, G. Aquino, P. Grigolini, L. Palatella, A. Rosa - Physical Review E 68, 056123.
Preprint Online article
6) Elasticity of semi-flexible polymers with and without self-interactions.
A. Rosa, T.-X. Hoang, D. Marenduzzo, A. Maritan - Macromolecules 36, 10095.
Preprint Online article
5) Mechanical unfolding of a partially directed walk in a poor solvent: Critical exponents.
A. Rosa, D. Marenduzzo, A. Maritan, F. Seno - Physical Review E 67, 041802.
Preprint Online article
4) Stretching of a polymer below the theta-point.
D. Marenduzzo, A. Maritan, A. Rosa, F. Seno - Physical Review Letters 90, 088301.
Preprint Online article
2002
3) Decoherence, wave function collapses, non ordinary statistical mechanics, and the second principle.
P. Allegrini, G. Aquino, M. Bologna, P. Grigolini, M. Ignaccolo, M. G. Pala, L. Palatella, A. Rosa, B. J. West - AIP Proceeding 643, 72.
Preprint Online article
2001
2) Sporadic randomness: The transition from the stationary to the non-stationary condition.
M. Ignaccolo, P. Grigolini, A. Rosa - Physical Review E 64, 026210.
Preprint Online article
1) Trajectory versus probability density entropy.
M. Bologna, P. Grigolini, M. Karagiorgis, A. Rosa - Physical Review E 64, 016223.
Preprint Online article