We carry out methodological developments in theoretical chemistry in order to tackle the problems posed by the applications that motivate us. In recent years, we have concentrated our efforts on setting up a coherent set of numerical simulations dedicated to modeling the ionizing irradiation of matter, particularly biological matter (DNA, proteins, etc.). Wherever possible, these developments are made available to the community via the deMon2k program. Please do not hesitate to contact us if you would like to collaborate with us on any level.
Real-Time Time-Dependent Density Functional Theory
Theoretical modeling of the physical and physico-chemical stages of ionizing irradiation of matter requires accounting for the response of the electron cloud on ultrashort time scales, i.e. the attosecond (10-18s) and femtosecond time domains. We are developing first-principles simulation methods based on the equations of density functional theory, with the aim of achieving high levels of performance. This is necessary to tackle the complexity of the molecular systems we are interested in (nanometric sizes, structural and chemical inhomogeneities, etc.). More specifically, we are developing an approach based on Auxiliary DFT in the deMon2k program. The RT-TD-ADFT method is compatible with many of the program’s functions, including molecular dynamics (Ehrenfest MD) and hybrid QM/MM approaches (Quantum Mechanics/Molecular Mechanics, see below).
The program can be used to simulate the irradiation of matter by fast ions or photons (UV-Vis, XUV, IR…). A recent journal article (2023) summarizes the program’s current capabilities. The program can be downloaded from Zenodo (10.5281/zenodo.8301468) for use on CPU or CPU/GPU hybrid machines. Please do not hesitate to contact us if you have any questions.
This image, taken from a paper published in 2020, shows the deformation of the electron cloud within a solvated DNA double strand during the passage of a high-energy alpha particle. RT-DT-ADFT simulations have enabled us to understand key elements in the mechanism of energy deposition by ions in DNA.
Multicomponent Dependent Density Functional Theory
Multicomponent DFT (MDFT) is an extension of electronic DFT to molecular systems comprising more than one type of quantum particle. In principle, this innovative approach makes it possible to account for nuclear quantum effects or molecules in intraction with “exotic” particles (muons, antiprotons, positrons…). We have developed a method of this type within the framework of Auxiliary DFT in the deMon2k software. This work is now continuing in collaboration with Prof. Lars Pettersson and Dr. Felix Moncada (Stockholm).
This image shows a deMon2k MDFT calculation of a micro-solvated coumarin molecule. Electrons and protons are treated in an ADFT formalism.
