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