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Numerical simulations of ionising radiation induced damages to biomolecules

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Français - Anglais

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General information

Reference : UMR8000-AURDEL-001
Workplace : ORSAY
Date of publication : Friday, September 27, 2019
Scientific Responsible name : Aurélien de la Lande
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 February 2020
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

Radiolysis of cell induces production of a plethora of extremely chemically reactive species that in turn degrade DNA, proteins and lipid membranes. This leads to accelerated aging and eventually to the emergence of cancers. On the other hand certain types of ionizing radiations, for instance heavy atom nuclei with kinetic energies within the keV-MeV range, are promising in the context of radiotherapies. Little is known about the first responses of complex biological structure to irradiation. Experimental approaches are limited by the extraordinary molecular complexity of biological systems and by the fugacity of the chemical intermediates produced by irradiation. Computer simulations thus represent a powerful and promising alternative to experiments.
The objective of this PhD thesis is to explore the physical-chemistry responses of various molecules of biological interest subjected to ionizing radiations composed of mass particles (alpha, beta, protons, hadrons). We will start by investigating small molecules (peptides, oligonucleotides) and eventually go toward larger molecular systems like protein/DNA complexes. One goal will be to decipher the mechanisms of energy deposition on the sub-femtosecond time scales, and on the other hand to investigate the subsequent ultrafast chemical reactivity. The PhD work program will build on experimental data obtained at LCP by our collaborators. The candidate will use simulation algorithms developped in the past in the group. The PhD student will be trained to explicit simulations of the electron density (Real Time TD-DFT), to ground-state and to non-adiabatic mixed quantum-classical molecular dynamics and to classical and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) molecular dynamics simulations.

Work Context

LCP is a joint research unit between CNRS and Université Paris Sud. The study of the effects of ionizing radiation on matter is an historical research project of the Laboratory.
LCP host both experimental and theoretical research groups.
The PhD student will integrate the Theorie and Simulation group. He will be supervised by Dr. A. de la Lande (http://hebergement.u-psud.fr/delalandecnrs)

Constraints and risks

The successful applicant must have a good theoretical background in physical-chemistry and/or quantum chemistry, be motivated and hard-working. Previous training to numerical simulations in Master internship (eg. molecular dynamics simulations, either with classical force fields, ab initio of QM/MM) will be an advantage, as well as some preliminary basic knowledge in computer coding. This PhD grant is funded by the French Agence Nationale de la Recherche in the context of the RUBI project. The candidate will tus have to show his-her capability to work within a research team and within a consortium of research groups.

Additional Information

Funding from French Agence NAtionale pour la Recherche

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