Modelling nanotoxicity of engineered nanomaterials by molecular dynamics simulations (Dublin)
Thesis in external company Thesis abroad
External reference persons Dr. Nicolae-Viorel Buchete (https://people.ucd.ie/nicolae-viorel.buchete)
Research Groups Multi-Scale Modeling Laboratory – SMaLL (www.polito.it/small)
Thesis type MODELING AND DATA ANALYSIS
Description This thesis proposal is part of the European project H2020 called NanoInformaTIX. NanoInformaTIX aims to create a comprehensive, sustainable, multi-scale modelling framework for exposure and (eco)-toxicity of Engineered Nanomaterials (ENM) to facilitate cost-effective risk assessment, less reliant on animal testing, and to support the design of safer materials and products. In particular, this thesis will focus on Molecular Dynamics (MD) simulations and coarse-grained MD (CGMD) techniques to study protein-protein interactions (PPIs) near the surface of model nanoparticles. The goal is to use MD and CGMD simulations to map specific PPIs on a network of Markovian dynamic transitions between CG states, and to estimate computationally the corresponding thermodynamic and kinetic parameters of the resulting Markov State Models. Similar techniques have been developed by Dr. Nicolae-Viorel Buchete and hence, interacting with him, the student will have the opportunity to learn this approach. The ultimate goal is to investigate computationally the interaction between ENMs and living structures (e.g. cell membrane). The screening of different types of engineered nanomaterials and biomolecules will be considered.
See also http://www.nanoinformatix.eu/
Required skills La competenza in programmazione (ad esempio Matlab, Python) ed in termodinamica è desiderabile. Si prevede che il candidato abbia un atteggiamento / curiosità significativa nei confronti della modellizzazione, in particolare in relazione ai fenomeni di trasporto su scala nanometrica. Ci aspettiamo una forte volontà e attitudine a collaborare e interagire con esperti sulle simulazioni atomistiche. La lingua di comunicazione preferenziale sarà l'inglese.
Notes The period abroad will last from 3 to 6 months at University College Dublin in Ireland. A preliminary training of 3 months at Politecnico di Torino will be done, to become confident with the computational tools required for the thesis activities. Dublin is an expensive city and the monthly rent for only a room in Dublin is currently about 750 Eur/month. The minimum amount needed/recommended for a student to visit UCD /month is thus about 1000 Eur/month.
Deadline 23/04/2020 PROPONI LA TUA CANDIDATURA