PhD defense of Karwan Ali Omar – Wednesday, November 22 2023 in salle Magat

07 November 2023 par clavaguera
Karwan Ali Omar from the ThéoSim group will defend his thesis on Wednesday, November 22 2023 at 2:00 p.m.

“Numerical simulations of ultra-fast response of biological molecules subjected to light fast ions and XUV pulses”, supervised by Aurélien de la Lande.

The defense will be held on the 22 of November at 2 pm, in Salle Magat. The defense will be in English.


In this thesis, we study the physical stage of ionizing irradiation of biomolecular systems, a process taking place on a time scale ranging from attoseconds to a few femtoseconds. The physical stage covers energy deposition and charge migration, laying the foundations for all subsequent physico-chemical events. We use Real-Time Time-Dependent Auxiliary Density Functional Theory (RT-TD-ADFT) to study energy deposition and ultrafast electron responses of biomolecules exposed to ions and XUV pulses. Chapter 1 presents a brief overview of biomolecule damage mechanisms. We discuss the main theoretical models of energy deposition and first-principles numerical simulation approaches dedicated to their study. This chapter describes the theoretical methods used in the rest of the work. In Chapters 2 and 3, we explore the impact of relativistic effects of charged particles and hydrogen bonds on energy deposition for a model guanine-cytosine system in hydrogen bond with two water molecules. We show the need to incorporate relativistic effects for protons of more than one mega-electronvolt kinetic energy. We show that the relativistic effect exacerbates energy deposition, via a modification of the ion-electron interaction mechanism. We find that energy deposition decreases in the presence of hydrogen bonds. This influence diminishes with increasing proton kinetic energy up to 2 MeV, before gradually increasing again. These fluctuations had not previously been observed in the TD-DFT literature. In chapter 3 we study the physical stage of a protein/DNA complex irradiated by an α-particle. We adopt a hybrid QM/MM approach that couples RT-TD-ADFT and molecular mechanics (MM) in non-polarizable and polarizable force fields. We show that electrostatic induction in the MM part has a negligible effect on energy deposition, but is likely to influence charge migrations between molecular fragments. We identify ultra-rapid (fs) hole migrations in the protein/DNA system, occurring at the fs scale. Finally, in order to analyze charge migrations occurring within systems comprising several hundred quantum atoms, we propose tools based on correlation matrices. This is a powerful tool for extracting relevant information from RT-TD-ADFT simulations on large-scale systems. The final chapter focuses on the ultrafast response of insulin and a peptide to an XUV pulse in an experimental collaboration. We first identify that RT-TD-ADFT simulation of the photo-ionization of small molecules like N2 is difficult with standard Gaussian basis functions. However, it can be significantly improved by enriching them with continuum-optimized atomic orbitals. However, these difficulties are largely mitigated when simulating larger molecules. We have carried out calculations for electron ejection and hole creation over a period of 50 fs for peptides. The results show that the hole distribution covers the entire molecular structure, although there are marked disparities between the different amino acids. The probability of ionization increases in rough correlation with the number of valence electrons. Within a specific amino acid, the environment plays a key role in determining its ionization probability. A remarkable observation of our study is the increased susceptibility to ionization of amino acids present on the surface compared to those deeply embedded in the structure. The manuscript concludes with a general summary of the work and a proposal for possible future research avenues.

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