Computer simulation of DNA radiation damage

Computer simulation of DNA radiation damage

Background: The effect of radiation on biological systems has been intensely studied since the discovery of X-rays in 1895. The early observation that X-ray exposure causes damage (sometimes unrecoverable) to biological tissue, was the basis for the subsequent use of radiation for therapeutic purposes. A large body of knowledge has been accumulated about the underlying chemical mechanisms. The most important biological effect of radiation is to cause damage to DNA, mainly in the form of double strand breaks. We have been studying this problem using computer simulation at the atomic level for some time now. We have learnt a great deal, but we are still far from understanding how the damage is produced and what determines it. This year has seen the creation at QUB of the Centre for Advanced Interdisciplinary Radiation Research (CAIRR), which constitutes a natural framework to further develop this project, in collaboration with experimentalists in Physics and Pharmacy.

The long-term goal is to simulate the various stages of the radiation damage process:

  1. Generation of reactive species like electrons, holes, and free radicals;
  2. Transport of electrons and radicals through the biological medium depositing energy via secondary ionisation, and electronic and vibrational excitation;
  3. End-point biological effects (DNA damage) caused by low-energy electrons, ions and radicals in a realistic environment.

Our recent work has focused on the modelling of excess electron capture in small DNA fragments, including also chemotherapeutic drugs, and the subsequent bond breaking due to the excess electron [1-6]. We have also made a start in the development of a methodology to study electron transport [7] in these systems. It is now time to capitalize on this and start assessing the various possible processes and which ones are most likely to happen in the physiological environment.

Aims and objectivesof the project To study in detail, using computer simulation techniques at the molecular level, the effects of radiation (mostly ions and electrons) on biological systems. To develop and implement the necessary computational technologies to achieve the above goal. To improve our understanding of the reasons for single and double strand breaks in DNA under realistic biological conditions.

Training: The student will be trained in state-of-the-art methods for electronic structure calculations, electron dynamics and atomistic simulation. More formal training will be offered through participation in appropriate Schools and Workshops in the UK and elsewhere. We have collaborative links with Toulouse (France), Sherbrooke (Canada), and Livermore (USA), and several other groups, and we will encourage the student to travel and spend some time in those labs, and to attend appropriate Workshops to present their work and to meet other people working in the field.

[1] M. Smyth and J. Kohanoff, Phys. Rev. Lett. 106, 238108 (2011).
[2] M. Smyth and J. Kohanoff, J. Am. Chem. Soc. 134, 9122 (2012).
[3] M. Smyth, J. Kohanoff and I. Fabrikant, J. Chem. Phys. 140, 184313 (2014).
[4] Bin Gu, M. Smyth and J. Kohanoff, Phys. Chem. Chem. Phys. 16, 24350 (2014).
[5] M. McAllister, M. Smyth, Bin Gu, G. Tribello, and J. Kohanoff, J. Phys. Chem. Lett. 6, 3091 (2015)
[6] P. M. Dinh, L Bouëssel du Bourg, C.-Z. Gao, Bin Gu, L. Lacombe, M. McAllister, M. Smyth, G. Tribello, M. Vincendon, J. Kohanoff, P.-G. Reinhard, L. Sanche, and, E. Suraud, in Nanoscale Insights into Ion-Beam Cancer Therapy, ed. A. V. Solovy’ov (Springer, 2017), pp. 277-309.
[7] V. RIzzi, T. N. Todorov, J. Kohanoff, and A. A. Correa, Phys. Rev. B 93, 024306 (2016).