Modelling energy deposition in biomolecules on ultrafast timescales

Supervisors: Daniel Dundas and Jorge Kohanoff


The energy deposited when molecules interact with radiation sources can initiate a range of electronic and ionic processes in the molecule. These processes can result in the ionization and subsequent fragmentation of the molecule on ultrafast timescales ranging from the attosecond timescale for electronic processes to the femtosecond timescale for fragmentation processes. Over the fragmentation timescale, the evolving electronic dynamics can interact with the ionic dynamics and this interplay can greatly influence the final reaction pathway [1]. These basic interactions lie at the heart of many ultrafast technologies: examples include the design of electronic devices [2], probes and sensors [3], biological repair and signalling processes and development of optically-driven ultrafast electronics [4].

´╗┐Aims and Objectives

Describing these processes on an equal footing is notoriously difficult and several (often quite severe) approximations are usually required. However, accurate modelling of the basic processes is crucial: at the very least it will act as an input or benchmark for other less demanding computational approaches. One ab initio method that is widely used to treat the irradiation of molecules is time-dependent density functional theory (TDDFT) [5]. In many cases this quantum approach for treating the electron dynamics is coupled to a classical treatment of the ionic dynamics, thus allowing for a non-adiabatic treatment of the electron-ion dynamics [6, 7]. Over the last several years, a parallel computer code that implements this formalism has been developed in the ASC. EDAMAME (Ehrenfest DynAMics on Adaptive MEshes) solves the time-dependent Kohn-Sham equations of TDDFT to describe the irradiation of complex molecules [8]. To date irradiation of molecules by ultrashort laser pulses has been considered, but the generalisation to treat irradiation by charged projectiles is fairly straightforward. The electronic dynamics are calculated on a 3D finite difference mesh while the ionic dynamics are described using Ehrenfest dynamics. Thus the irradiation of arbitrary molecules can be studied. Already this code has been used to study dissociation processes in organic molecules [9] and high-harmonic generation in both chiral molecules [10] and organic molecules [11]. In this project, fragmentation processes in amino acids and dipeptides (such as Leu-Trp and Gly-Gly-NH-CH3) will be studied.


The solution of this problem is formidable using high-performance modern computing technology. The project would therefore suit someone highly skilled in mathematical and computational techniques. A background in physics or physical chemistry would be a distinct advantage. The skills and experience developed during the project are at the leading edge of current technology and will be invaluable in the job market whether in research or industry.


[1] A. I. Kuleff and L. S. Cederbaum. J Phys B: At Mol Opt Phys , 47:100, 2014.
[2] C. Joachim et al. Nature, 408:541, 2000.
[3] D. M. Willard and A. van Orden. Nature Materials, 2:575, 2003.
[4] F. Krausz and M. I. Stockman. Nature Photonics, 8:205, 2014.
[5] E. Runge and E. K. U. Gross. Phys Rev Lett, 52:997, 1984.
[6] F. Calvayrac et al. Phys Rep, 337:493, 2000.
[7] A. Castro et al. Eur. Phys. J. D, 28:211, 2004.
[8] D. Dundas. J Chem Phys , 136:194303, 2012.
[9] A. Wardlow and D. Dundas. Phys Rev A , 93:023428, 2016.
[10] D. Dundas et al. Phys Chem Chem Phys, 19:19619, 2017.
[11] P. Mulholland and D. Dundas. Phys Rev A , 97:043428, 2018.