Research in The Kirmizialtin Lab involves computational modeling of (bio)molecular processes using computer simulations, with the aim of learning the physical principles governing these phenomena. Quantitative understanding of biophysical mechanisms increasingly requires analysis of dynamical changes and the changes occur at distinct points in time and space. To achieve our goal, we focus on developing and employing novel computational methods to enhance conformational sampling. We also use methods to extend the timescales of MD simulations to compute the kinetics and thermodynamics of processes using all atom simulations.
Our lab also integrates simulations and experiments to study the structure and dynamics of biomolecular machinery. Using experiments such as Cryo-EM, SAXS, and FRET, our aim is to develop computational tools and methods to guide MD simulations toward the direction where they meet the experimental data, providing an accurate description of physical interactions and allowing atomic-level visualization of experiments.
As model systems, we study nucleic acids (DNA/RNA) and protein/nucleic acid complexes. We look at the aspects of the mechanism of action of these biomolecular machines, their folding/unfolding processes, their conformational changes coupled to their interactions with their environment.
Current activity in our lab can be grouped in two main categories:
(i) Computational and theoretical modelling of poly-nucleotides and their environment
(ii) Studying the mechanism of actions of enzymes.
In addition, due to the demand and the regional relevance, we initiated a new area of research in our lab on material science.