Group Members:
We aim at providing sound mathematical
modeling
of DNA dynamics,
in particular for what concerns the transcription
process.
This subject is linked, since the
pioneering
work by Englander et al.,
with the theory of solitons
travelling
along the DNA double chain.
Recently, we provided a new model
overcoming
the main obstacle the
theory is confronted to, i.e.
exhibiting
a mechanism which allows
solitary waves in the presence of
disorder
(the latter being a result
of the base sequence along the helix).
The work on this model uncovered some
general
mechanisms for
multi-component nonlinear wave
equations,
valid outside the realm
of DNA or Biology.
Our work, prompted by advances
directly related
to DNA modeling
by Saccomandi and Sgura, also considers
the existence of solitary wave
solutions with strictly compact support
(compactons) for certain classes
of nonlinear wave equations.
Research on Mathematical Modelling of
DNA
Dynamics was fostered by a grant
from the Italian Ministery for
University
and Research in the framework of the
PRIN (National Interest Reasearch
Programs)
covering the years 2005 & 2006.
The Research Unit based in Milano
(actually
including also a substantial group
from Cagliari) was part of a national
project
coordinated by prof. Giuseppe
Saccomandi from Lecce (he now moved to
Perugia).
Two meetings were held in the
framework of
this Project. Here you can access
information about these meetings.
| Meeting
on
DNA Dynamics
Lecce, may 2005 |
Meeting
on
DNA Dynamics
Cagliari, september 2006 |
Here is a description of the (old, to a large extent realized) research program for the Milano unit, in italian and english
| Papers by G. Gaeta | Papers by M. Cadoni | Papers by R. De Leo | Papers by S. Demelio |
G. Derks and G. Gaeta:
``A minimal model of DNA dynamics in interaction with
RNA-Polymerase'',
Physica D 240 (2011), 1805-1817
G. Gaeta:
``Biology, Physics and Nonlinear Science''
(preface to the Special Issue of JNMP devoted to Nonlinear
Mathematical Biophysics),
J.
Nonlin.
Math. Phys. 18-S2
(2011), v-xii
M. Cadoni, R. De Leo, S. Demelio and G. Gaeta,
``Propagation of twist
solitons in real DNA chains'',
J.
Nonlin.
Math. Phys. 17
(2010), 557-569
M. Cadoni, R. De Leo, S. Demelio and G. Gaeta, Nonlinear
torsional dynamics of macromolecules: from DNA to polyethylene,
International Journal of Non-Linear Mechanics 43 (2008),
1094-1107
Roberto De Leo, Sergio Demelio, Numerical analysis of
solitons
profiles in a composite model for DNA torsion dynamics,
International Journal of Non-Linear Mechanics 43 (2008),
1029--1039
G. Gaeta and L. Venier, Solitary waves in twist-opening
models
of DNA dynamics,
Physical Review E 78
(2008),
011901 (9pp)
G. Gaeta and L. Venier, Solitary waves in helicoidal models
of
DNA dynamics,
Journal
of Nonlinear Mathematical Physics 15 (2008), 186-204
M. Cadoni, R. De Leo and G. Gaeta, Sine-Gordon solitons,
auxiliary fields, and singular limit of a double pendulums
chain,
Journal of Physics
A
40 (2007), 12917-12929
M. Cadoni, R. De Leo and G. Gaeta, A symmetry breaking
mechanism for selecting the speed of relativistic solitons,
Journal of Physics
A
40 (2007), 8517-8534
M. Cadoni, R. De Leo and G. Gaeta, A composite model
for DNA torsion dynamics,
Physical Review E 75 (2007),
021919
M. Cadoni, R. De Leo and G. Gaeta, Solitons in a double
pendulums chain model, and DNA roto-torsional dynamics,
Journal
of Nonlinear Mathematical Physics 14 (2007),
128-146
G. Gaeta, Solitons in Yakushevich-like models of DNA
dynamics with improved intrapair potential,
Journal
of Nonlinear Mathematical Physics 14
(2007),
57-81
G. Gaeta, Compact travelling waves and non-smooth
potentials,
EuroPhysics Letters
79 (2007), 20003 (6 pp)
M. Destrade. G. Gaeta and G. Saccomandi,
Weierstrass's criterion and compact solitary waves,
Physical Review E 75
(2007),
047601 (4 pp)
G. Gaeta, T. Gramchev and S. Walcher, Compact solitary waves
in linearly elastic chains with non-smooth on-site potential,
Journal of Physics
A
40 (2007), 4493-4509
G. Gaeta, Solitons in the Yakushevich model of DNA
beyond the contact approximation,
Physical Review E 74 (2006),
021921
R.W. Ogden, G. Saccomandi and I. Sgura,
Computational aspects of Worm-Like-Chain interpolation formulas,
Computers
and
Mathematics with Applications 53 (2007), 276-286
G. Saccomandi and I. Sgura,
The Relevance of nonlinear stacking interactions
in simple models of double-stranded DNA,
Journal
of
Royal Society Interface 3 (2006), 655–667
F. Maggioni and R.L. Ricca, Writhing and coiling
of closed filaments,
Proceedings
Royal
Society A, 462 (2006), 3151–3166
F. Maggioni and R.L. Ricca, Multiple folding and
packing in DNA modelling,
Computers
and
Mathematics with Applications in press