It is well known that irradiating materials with photons, heavy particles such as atoms, ions or neutrons, or light particles like electrons, produces structural and functional modifications at the atomic scale. Some areas of general interest are
- Biological matter, where irradiation has been shown to lead to DNA strand breaks and eventually cellular death
- Nuclear materials like steels for containment vessels and glasses and ceramics for nuclear waste disposal
- Semiconductor devices irradiated by cosmic rays in space
- Ices on the surface of interstellar dust grains which, when irradiated, give rise to organic molecules thus supporting one of the current theories about the origin of life
- Technological materials such as polymers that are irradiated in a controlled way to modify their properties
The goal of this research line is to use existing computational tools such as density functional molecular dynamics codes, and to develop the necessary theory and algorithmc tools to study irradiation effects in a variety of materials as itemized above. At present we are carrying out research in two areas:
- Biological systems
We aim at understanding which processes are involved in the rupture of DNA strands, from the generation of electrons and radicals by ionisation, their transport towards DNA, and their interaction with DNA that leads to single or double strand breaks. To this end we have established collaborations with other theory groups (Paris, Toulouse, Cambridge) and experimentalists mainly at QUB (CPP in Physics, Biological Sciences and CCRCB). A second goal is of applicative nature, and it consists of integrating this information into radio therapeutical models, especially ion based therapies. Here we are developing a collaboration with one of the main therapeutic centres, based in Frankfurt, and we are involved in a European network proposal that is currently under evaluation. We are also discussing joint projects with experimental colleagues in CPP to study alternative radiotherapies based on irradiation of Au nanoparticles and on short ion pulses.We simulated the first-principles molecular dynamics of an excess electron in condensed phase models of solvated DNA bases. We vertically attached an excess electron, which initially delocalized, and within a 15 fs timescale, localizes around the nucleobases. This transition requires small rearrangements in the geometry of the bases. The images below show two frames, one with the delocalised state, the second with a localised state.
The next question is what is their longer-term effect on DNA. It has been advocated that they can lead to strand breaks by cleaving the phosphodiester C3 -O3 bond. We calculated the free energy barriers for the cleavage of this bond in fully solvated nucleotides. We ﬁnd that, except for dAMP, barriers are of the order of 6 kcal/mol, suggesting that bond cleavage is a regular feature at 300K. Such low barriers are only possible due to solvent and thermal ﬂuctuations. The image below shows the free energy barriers for each of the nucleobases.
The next image shows representative snapshots of the spin density for three bond lengths. The upper panel is for 1.5 Å, which is near the equilibrium bond length. The electron is located in the nucleobase. The middle panel is for a bond length of 1.8 Å, in the region of the transition state where the barrier height is maximum. Here the electron spreads throughout the whole molecule, including the C3 – O3 bond. Finally, the lower panel shows the bond at a constrained length of 2.2 Å. The excess electron is no longer around the base component, and has localized mostly in the ribose, in particular around C3 where the bond was cleaved.
Excess Electron Localization in Solvated DNA Bases
M. Smyth and J. Kohanoff
Physical Review Letters, 106,238108 (2011).
Excess Electron Interactions with Solvated DNA Nucleotides: Strand Breaks Possible at Room Temperature
M. Smyth and J. Kohanoff
J. Am. Chem. Soc., 134,9122 (2012).
The goal is to describe electronic and nuclear stopping processes in order to simulate radiation cascades in steels, glasses and ceramics. Collaboration has been established with Cambridge, ICL, San Sebastian and Livermore.