Application Overview

The ability to model and understand electron-molecule scattering processes is of fundamental relevance in a variety of research and technology areas: astrophysics, plasma physics, the understanding of the damage process initiated by ionising radiation in biological environments (the cell), etc.. The methodology to treat these processes at low projectile kinetic energies (below the ionisation threshold) is fairly well developed. In particular, the UK has been at the forefront of the field, with use of the R-matrix method to treat the problem in an ab initio manner. Specifically, the UK R-matrix polyatomic suite [1], UKRMol, is one of the most accurate codes in the world to describe the electronic part of the problem. These codes are also used to study positron scattering. Radiation uses in medicine (for treatment and diagnosis) have been developed for many decades mostly as empirical macroscopic techniques. However, recent important biomedical advances involving radiation are demanding an increasingly detailed level of description of the nanoscale, molecular interaction processes involved. Experiments confirmed almost a decade ago that secondary electrons with energies up to 20 eV can damage DNA [2]. Detailed experimental studies with DNA strands and DNA/RNA constituents have confirmed that electron collisional mechanisms (such as dissociative electron attachment) are highly efficient in producing structural changes leading to biological and physiological alterations. This intense experimental activity [3] has not been matched by theoretical studies, with such work tackling only the completely elastic process. Exceptions are the studies of uracil [4] and the sugar molecule tetrahydrofuran using the R-matrix codes [5]. Application of UKRMol to other new fields like near threshold ionisation [6] have also recently been pioneered.

The atomic versions of the R-matrix codes (PRMAT) have been ported and optimized on HECToR (by Dr M Plummer and Dr A G Sunderland) in a previous dCSE project and there is further dCSE funded work to interface the PFARM part of PRMAT with the UKRMOL-in suite of codes and to parallelize the construction of the atomic Hamiltonian (Dr M Plummer).

Figure 1: A flowchart of the main programs of UKRMol-in.

The UKRMol-in suite contains a series of programs, see Figure , which perform the following tasks:

1. The calculation of integrals over target and continuum orbitals (and corrections due to the finite size of the R-matrix) and orthogonalisation of the set of orbitals (the SW- and GAUSTAIL programs in Figure );
2. The construction and diagonalization of the Inner Region Hamiltonian (the CONGEN and SCATCI programs);
3. In the ``target run'' mode, the calculation of density matrices and from them target properties (GAUSPROP and DENPROP programs, not included in Figure ).

The suite also contains modules to generate Hartree Fock-SCF or pseudonatural orbitals and the basis sets for the description of the continuum. The former is now being superseded by the use of standard quantum chemistry codes to generate more sophisticated orbitals (in particular MOLPRO). The latter are run infrequently as normally these basis sets only depend on the radius of the R-matrix sphere and the charge of the target. The computational requirements to run these programs are very modest. The UKRMol codes are available to UK academics and to non-UK scientists through the CCPForge website [8] The code is currently used by groups in India, the US, Canada, France and Japan. A user community for the codes is being developed using the tools available in the site (mailing lists, forums, bug reporting and tracking, etc.). In addition, UKRMol-in will form the basis for the time-dependent suite to treat the dynamics of molecules in ultra-short light pulses.