Concepts from physics are applied to problems in molecular biology in two complementary ways. On the one hand, because the biological function of life’s molecules is constrained by their physical and chemical properties, it is important to describe the functional transformations these molecules undergo using the language of chemical physics. On the other, the most successful experimental techniques for probing the structure and dynamics of biomolecules at atomic resolution exploit the fundamental physical properties of these molecules, like their interaction with mechanical and electromagnetic forces. Research in theoretical molecular biophysics at Sabancı University touches on both of these aspects.
Employing the toolboxes of equilibrium and nonequilibrium statistical mechanics we develop efficient computational approaches for identifying and characterizing large-scale conformational transitions of biomolecules using molecular dynamics (MD) simulations. In addition, we develop a methodology for utilizing the detailed dynamical information contained in the MD trajectories to simulate electron spin resonance (ESR) spectra of the studied biomolecules. The ESR spectra computed from first principles are directly compared with experimental data provided by our international collaborators.