|
Biosystems
Head:
Paolo Ruggerone
Research topics
Ab initio, classical, and QM/MM
calculations on biological systems
Biomimics:
study of artificial
photosynthetic systems
Drug-DNA interactions:
principles of small molecule-DNA recognition
Myoglobin and hemoglobin:
effects of mutants on dynamics and ligand interactions
Antibiotics: dynamics of
antibiotic
molecules through membrane channels
Ion channels and pumps
Molecular machines:
conformational
changes and interactions with surfaces
Methods to beat time: approaches
to perform long time simulations
People
Paolo
Ruggerone, associate professor (personal
page)
Matteo
Ceccarelli, assistent professor
Attilio
Vittorio Vargiu, PhD student (at
SISSA, Triest)
Thesis
students: Francesca Collu,
Enrico Spiga
Collaborators:
Manuela Mura
Selected publications
M.
Ceccarelli, C. Danelon, A. Laio and M. Parrinello: Microscopic mechanism of antibiotics
translocation through a porin, Biophys. J. 87, 58-64 (2004).
A.
Laio, A. Rodriguez-Fortea, F.L. Gervasio, M. Ceccarelli and M. Parrinello: Assessing the accuracy of metadynamics, J.Phys.Chem. B 109, 6714-6721 (2005).
G.
Petraglio, Matteo Ceccarelli, and M. Parrinello: Non-periodic boundary conditions for
solvated systems, J. Chem. Phys. in
press.
M.
Ceccarelli, F. Mercuri, D. Passerone and M. Parrinello: The Microscopic switching mechanism of a
[2]catenane, submitted to J.
Phys. Chem. B
K. Spiegel, A. Magistrato, P. Ruggerone, P. Carloni, J. Reedijk: Binding of Novel Azole-Bridged Dinuclear Platinum(II) Antica
ncer Drugs to DNA: Insights from Hybrid QM/MM Molecular Dynamics Simulations, J. P
hys. Chem. B110, 3604-3613 (2006)
A. Vargiu, P. Ruggerone, A. Magistrato, P. Carloni: Anthramycin-DNA bind
ing explored by molecular simulations, submitted to Nuc.
Acid. Res.
M. Ceccarelli, P. Ruggerone, R. Anedda, M. Casu, A. Fais, B. Era, M.C. Sollaino, M. Corda
:
Structure-function relationship in a variant haemoglobin: a combined
computational-experimental approach, submitted to Biophys. J.
Active projects
Collaborations
P. Carloni, Sissa, Triest
(Italy)
A.
Seitsonen,CNRS & IMPMC,
Université Pierre et Marie Curie, Paris (France)
O.
Pulci, University of Roma II (Italy)
Parrinello
Group, ETHZ, Zurich (Switzerland)
G. Sava,
University of Trieste and Callerio Foundation, Trieste (Italy)
M.
Winterhalter,
International University Bremen, Bremen (Germany)
C.
Danelon, EPFL, Lausanne
(Switzerland)
F.
Mercuri, CNR-ISTM
Perugia (Italy)
|
SLACS 