Publications

2018

41) Stretching worm-like chains.
R. Everaers, N. B. Becker, A. Rosa – In preparation.
Preprint     Online article

40) Conformational statistics of randomly-branching double-folded ring polymers.
A. Rosa, R. Everaers – In preparation.
Preprint     Online article

39) Structure and microrheology of genome organization: From experiments to physical modeling.
A. Papale, A. Rosa  Under review.
Preprint     Online article

38) Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains.
N. Nahali, A. Rosa – Submitted.
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.
Preprint     Online article

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, October 2017).

35) Flory theory of randomly branched polymers.
R. Everaers, A. Yu. Grosberg, M. Rubinstein, A. Rosa – Soft Matter 13, 1223.
Online article

34) Beyond Flory theory: Distribution functions for interacting lattice trees.
A. Rosa, R. Everaers – Physical Review E 95, 012117.


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.
Preprint     Online article

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.
Preprint     Online article


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.
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.
Preprint     
Online article

26) Computational models of large-scale genome architecture.
A. Rosa, C. Zimmer – International Review of Cell and Molecular Biology 307, 275.
Online article

Press highlights:
1) "Science Daily" (Jan, 3 2014): link
2) "Genetic Engineering & Biotechnology News" (Jan, 6 2014): link
3) "Il Sole 24 Ore" (Jan, 12 2014)
4) "Il Piccolo" (Jan, 22 2014)
5) "Il Piccolo" (Jan, 28 2014)
6) "La Gazzetta del Mezzogiorno" (Ed. Basilicata; Jan, 28 2014)
7) "Il Settimanale" (Rai 3 - Friuli-Venezia Giulia; Feb, 22 2014): link


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
.
Online article

MONTHLY COVER (issue 11 - June 2013)




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
.
Online article

MONTHLY COVER (March 2013)




23) Topological constraints and chromosome organization in eukaryotes: A physical point of view.

A. Rosa – Biochemical Society Transactions 41, 612.

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.
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.
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.
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.
Online article


18) Looping probabilities in model interphase chromosomes.

A. Rosa, N. B. Becker, R. Everaers – Biophysical Journal 98, 2410.
Online article 


2008

17) Structure and dynamics of interphase chromosomes.
A. Rosa, R. Everaers – Plos Computational Biology 4, e1000153.
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.
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.
Online article


14) Long time behavior of diffusing particles in constrained geometries.

A. Rosa, F. R. Neumann, S. M. Gasser, A. Stasiak – Journal of Physics: Condensed Matter 18, S235.
Online article


13) Stretching a self-interacting semi-flexible polymer.

A. Rosa, D. Marenduzzo, S. Kumar – Europhysics Letters 75, 818.
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.
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.
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.
Online article


9) A new interpolation formula for semi-flexible polymers.

A. Rosa, T.-X. Hoang, D. Marenduzzo, A. Maritan – Biophysical Chemistry 115, 251.
Online article 


2004

8) Stepwise unfolding of collapsed polymers.
D. Marenduzzo, A. Maritan, A. Rosa, F. Seno – European Physical Journal E 15, 83.
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.
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.
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.
Online article


4) Stretching of a polymer below the theta-point.

D. Marenduzzo, A. Maritan, A. Rosa, F. Seno – Physical Review Letters 90, 088301.
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.
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.
Online article


1) Trajectory versus probability density entropy.

M. Bologna, P. Grigolini, M. Karagiorgis, A. Rosa – Physical Review E 64, 016223.
Online article
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