12:17 p.m.
TITLE: Molecular Modeling as virtual microscope at the nanoscale: some
examples
SPEAKER: Prof. Andrea Danani (SUPSI - IDSIA)
WHEN: Monday, October 19th, 14:00
WHERE: IDSIA Meeting room - Galleria 1, Manno
ABSTRACT:
In this talk, several examples will be presented showing how Molecular
Modeling can act as virtual microscope to have insight on molecular
mechanisms. The first part will be devoted to some examples where we show
how the modifications of some structural parameters can affect the
efficiency of a special class of hyperbranched polymers called dendrimers
as delivery systems. Recently, five parameters, called Critical Nanoscale
Design Parameters (CNDP) that characterize the behavior of well-defined
nanoscale building blocks such as dendrimers: size, shape, surface
chemistry, flexibility/rigidity and architecture. These quantities
constitute the first real attempt to propose formal parameters allowing, in
principle, to control the final behavior of a given molecule. However, the
CDNP are somewhat entangled, and they do not take into account explicitly
the influence of the external environment as thought as the presence of
polar solvent molecules, salt ions and eventually other charged molecules.
In this context, we have performed many different modeling studies to
explore how the efficiency of the dendrimers in binding siRNA and DNA
changes upon CDNPs modification. The effect on the affinity for nucleic
acids of different dendritic generations, architecture modification,
flexibility of the dendritic scaffold and changing of the ligands that
decorate the surface were explored in detail.
In the second part, some preliminary results will be presented about the
investigation of the interaction of Cell-Penetrating Peptides (CPPs) with
iron oxide nanoparticles in order to assess their potential as
functionalization strategies. Magnetite protonation state strongly
influences the interaction with dendrimers and CPPs. In the case of CPPs,
it is interesting to notice that, the final adsorbed conformations are
characterized by peptides flattened over the NP surface mainly interacting
through arginine, a key residue for the peptide’s function.
In the last part, we show some preliminary results concerning a new
approach that we proposed for the implementation of the Multiscale Coarse
Graining method, using Wavelets as set of functions for the approximation
of the force fields.
SHORT BIO:
Prof. Andrea Danani received the Dipl.-Ing degree in Physics from ETH in
Zurich in 1987. After the Ph.D. degree at SISSA/ISAS in Trieste in 1992,
Dr. Danani worked with a post-doctoral position for many years at several
Physics departments (Politecnico di Torino, Università Statale di Milano
and Università di Genova) and as scientific collaborator by the Swiss
National Supercomputing Center (CSCS) in Manno. Since 2001, he works at the
Unversity of Applied Sciences of Southern Switzerland – SUPSI, as
scientific collaborator and teacher and he received the Professor title in
2005. After many years of affiliation partly at ICIMSI Institute and partly
at Laboratory of Applied Mathematics and Physics in the Department of
Innovative Technologies, from September 2015, he is part of IDSIA staff.
His scientific activity was first centered on the modellization of
many-electron systems and their phase transitions and later on the
description of surface diffusion of adatoms in metals using analytical
models and several numerical simulation methods, mainly MonteCarlo,
Molecular dynamics and Cluster Variation Method. In SUPSI, after some
projects centered on the study and improvement of polymeric nanocomposites
properties, the research activities in the last six years have been mainly
focused on the numerical simulation of nanoscaled drug delivery systems
(special polymers and decorated nanoparticles) and on virtual screening
with the study of interactions between drugs and proteins to optimize
performance and safety of the drug delivery with projects in collaboration
with pharmaceutical companies.
Prof. Danani has been swiss MC member for two recently closed european COST
actions: TD 0802 (Dendrimers for biomedical applications) and TD1003
(Bioinspired Materials), and is currently MC member for two other running
actions: TP1202 (Hybrid Interfaces) and MP1404 (Simulation and
pharmaceutical technologies for advanced patient-tailored inhaled
medicines). He has published more than 100 scientific publications among
papers in peer refereed journals, book chapters and proceedings.
--
Prof. Dr. Andrea Danani
Istituto Dalle Molle di studi sull'Intelligenza Artificiale (IDSIA)
Scuola universitaria professionale della Svizzera italiana (SUPSI)
Università della Svizzera italiana (USI)
Galleria 2, CH-6928 Manno
Uff. : +41 58 666 65 68
Segr: +41 58 666 66 66
email: andrea.danani(a)supsi.ch
Home : http://www.dti.supsi.ch/~danani
URL: http://m3.dti.supsi.ch