Starts 6 Mar 2024 11:00
Ends 6 Mar 2024 12:00
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CMSP Seminar (Atomistic Simulation Webinar Series): First Principles Simulations of Biological Matter under Ionizing Radiations
Luigi Stasi Seminar Room (and via Zoom)
Angela Parise
(CNR-IOM at SISSA)
Abstract:
In-depth knowledge of the consequences of interaction of biomolecules with ionizing radiations is of fundamental importance for progress in medicine, radiotherapy and radioprotection as well as for addressing the panspermia hypothesis. The physicochemical events taking place during the first picoseconds after irradiation have so far escaped the scrutiny of researchers. Yet the plethora of vibrationally hot, electronically excited and highly reactive species formed upon irradiation is likely to trigger rich and non-conventional chemistry. For complex biostructures such as DNA or proteins irradiation could undergo currently unknown chemical damages with dramatic consequences for health. In the field of astrochemistry, ionizing radiations could have played a crucial role. The bombardment of the early Earth by comets that have captured organic rich interstellar icy grains is thought to have provided the molecular precursors at the origin of life on Earth. Such an assumption depends on the survival of these precursor under cosmic irradiations.
The propagation of time-dependent Kohn-Sham equations provides a mean to access the realm of attosecond electron dynamics [1]. Our group has implemented in deMon2k a RT-TD-DFT module [2]. In this contribution, I will present the details of this methodology. It will be shown how the physical sense of the method was validated by calculating the cross-section of the first ionization of water molecule in the gaseous phase and comparing it with the experimental data [3]. Finally I will show first examples with deMon2k of effect induced by radiation to the electron cloud of bio-molecules [4].
References
The propagation of time-dependent Kohn-Sham equations provides a mean to access the realm of attosecond electron dynamics [1]. Our group has implemented in deMon2k a RT-TD-DFT module [2]. In this contribution, I will present the details of this methodology. It will be shown how the physical sense of the method was validated by calculating the cross-section of the first ionization of water molecule in the gaseous phase and comparing it with the experimental data [3]. Finally I will show first examples with deMon2k of effect induced by radiation to the electron cloud of bio-molecules [4].
References
[1] Runge, E.; Gross, E. K. U., Phys.Rev.lettt. 1984, 52(12), 997-1000.
[2] Wu, X.; Teuler, J.-M.; Cailliez, F.; Clavaguéra, C.; Salahub, D. R.; de la Lande, A., J. Chem. Theory Comput, 2017,13(9), 3985–4002.
[3] Parise, A.; Alvarez-Ibarra, A.; Wu , X.; Zhao, X.; Pilme, J.; de la Lande, A., J. Phys. Chem. Lett., 2018, 9, 844−850.
[4] Alvarez-Ibarra, A.; Parise, A.; Hasnaoui, K.; de La Lande, A., Phys. Chem. Chem. Phys., 2020, 22, 7747-7758.
[2] Wu, X.; Teuler, J.-M.; Cailliez, F.; Clavaguéra, C.; Salahub, D. R.; de la Lande, A., J. Chem. Theory Comput, 2017,13(9), 3985–4002.
[3] Parise, A.; Alvarez-Ibarra, A.; Wu , X.; Zhao, X.; Pilme, J.; de la Lande, A., J. Phys. Chem. Lett., 2018, 9, 844−850.
[4] Alvarez-Ibarra, A.; Parise, A.; Hasnaoui, K.; de La Lande, A., Phys. Chem. Chem. Phys., 2020, 22, 7747-7758.