Research Group
PostDoc: A. Murugan Natarajan.

Former Research
Ph.D. studies: Electronic Structure of Designer Hard Materials , in the Condensed Matter Theory Group of Prof. Börje Johansson at Uppsala University, Sweden, under the supervision of Prof. Olle Eriksson .

Research interests
My current field of research is Car-Parrinello Molecular Dynamics (CPMD) on biological systems, with focus on nucleic acid systems (RNA and DNA) . In these electronic structure studies, based on Density Functional Theory (DFT), I employ force-field based molecular dynamics (MD), first-principles MD (here CPMD), and the hybrid/mixed CPMD/classical MD. The use of a mixed/hybrid QM/MM method is essential when one wants to study large biologically relevant systems (not accessible to pure first-principles methods) and systems under-going chemical reactions (not accessible to force-field methods).

Ribozymes: My main subject of interest is RNA, e.g. simulations of the Hammerhead Ribozyme (HRz) mediated cleavage of RNA, metal ion positions in the DomainV of a group II intron, and other studies of metal ions in ribonucleic acids.  The HRz is a small RNA catalytically active by cleaving the backbone (phosphodiester bond) of itself, or other RNAs. Since the HRz can be designed to cleave sequence-specific strands of RNA (e.g. m-RNA) it carries great potential in novel anti-viral treatments.

DNA: Radiative damage of DNA from Low Energy Electrons (LEE) is studied in collaboration with Patric Schyman and Prof. Aatto Laaksonen at Stockholm University.

Pharmaceutical drugs: Atomistic studies, both classical MD and hybrid QM/MM, of the solvation of drug molecules is pursued together with Laban Bondesson at our department.

Published papers and patents
CV
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