Modelling energy transfer during irradiation of matter by swift particles

Two fully-funded studentships available.

Background

Two four-year PhD positions are available in the Atomistic Simulation Centre (ASC). Both students will work as part of a research project that aims to model irradiation of biological molecules in the presence of solvents and metal nanoparticles (MNPs). Such irradiation processes occur over a wide range of time and length scales and so a range of theoretical and computational approaches are required that bridge these different regimes. The team involved in this work have developed a range of techniques to do this and the goal of this project is to join these methods together into a unified approach. Each student will work on different aspects of the problem, as set out the individual project descriptions below, before joining these strands together to study photon irradiation of nucleobases (the fundamental elements of genetic codes) and radiosensitisers in the presence of solvents and MNPs.

Project 1: Stochastic quantum descriptions of correlations

Supervisors: Daniel Dundas, Myrta Grüning, Lorenzo Stella

This project involves implementation of a stochastic method for describing electron-electron and electron-ion correlations beyond the standard mean-field description of time-dependent density functional theory (TDDFT). This approach, developed by Prof. Eric Suraud and co-workers at Université Paul Sabatier in Toulouse, will be used to describe the initial energy absorption processes.

The stochastic method extends the description of electron correlation by including two-particle (2p2h) excitations within a Kohn-Sham style formalism. In order to do this, it goes beyond a single mean-field state theory to one in which an ensemble of mean-field states is considered. A similar approach can also be used to describe electron-ion correlations beyond a mean-field picture.

The stochastic method for both electron-electron and electron-ion correlations will be incorporated into a parallel computer code that has been developed by Dr Dundas 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.

As part of this work, the student will spend time in Toulouse with Prof. Suraud to learn about the stochastic method in more detail.

Project 2: Hybrid approaches for coupling to complex environments

Supervisors: Lorenzo Stella, Myrta Grüning, Daniel Dundas

The goal of this project is to design, implement, and parameterise a frequency-dependent polarisable embedding scheme based on the projected equation of motion (PEOM) formalism. The work will be organised in two main stages.

Stage 1 will involve modelling of a polarisable environment.  The molecular susceptibility will be fitted using high-level electronic structure calculations, with the possibility to include only the most relevant molecular dipole transitions. The molecular susceptibility is not constant, but depends on the electric field generated by the embedded absorber. This dependency is non-trivial and history dependent. Using the PEOM formalism, the direct calculation of the convolution integral is avoided by introducing a set of fictitious oscillators that effectively reproduces the molecular susceptibility.

Stage 2 will involve embedding of a molecular absorber. This extended formalism will result in a frequency-dependent quantum mechanics/molecular mechanics (QM/MM) scheme exemplified in cover image. The PEOM formalism can be straightforwardly extended to numerically integrate all the MM degrees of freedom.

The Application Process

Applicants must demonstrate a first or upper second-class honours degree or an equivalent academic qualification, preferably in Physics, Chemistry, Engineering, or Mathematics.  An ability to program in either Fortran, C, or Python is desirable but not a prerequisite.

All applications must be submitted before the deadline through the QUB online application portal: https://dap.qub.ac.uk/portal/user/u_login.php. Please state clearly in your application which project you are applying for.

The deadline for applications is 5 March 2021. Short-listed candidates will be contacted shortly after the deadline. The starting date for both projects is 1 July 2021.

For further information and queries, please email Dr D. Dundas (d.dundas@qub.ac.uk).

The Environment

The ASC works in one of the most dynamical areas in the physical sciences – the theory and simulation of molecules, liquids, solids and materials at the level of the constituent electrons and nuclei. Students in our group emerge with forefront knowledge in the theoretical and computational methods involved. This project will harness a range of ASC themes, resulting in a qualification that is difficult to obtain otherwise, yet in high demand at the academia/industry interface.

Funding notes

Two fully-funded (fees and maintenance) studentships are available. Eligible candidates must be either UK or Republic of Ireland residents. EU citizens that satisfy a requirement of being ordinarily resident in the UK for the three years prior to the start of the studentship are also eligible. Further details of the eligibility criteria can be found here: http://go.qub.ac.uk/pgrfees. Potential candidates are strongly recommended to verify their eligibility before applying.