Using atomistic simulations together with neutron scattering measurements is of great importance in molecular biophysics because such an approach provides a complementary information about structural and dynamical details of biological systems. In this talk we examine several examples of application of classical and ab initio MD simulations to the interpretation of neutron scattering experiments and discuss the resulting ideas on the general characteristics of biomolecular motions in terms of their functional implications. As an example we demonstrate the softening effect of the protein dynamics upon ligand binding. Next, the DNA neutron scattering experimental data is interpreted with the aid of MD simulations and large scale, all-atom, phonon calculations opening a view into the stiffness of DNA and its structural integrity on different length scales. Small peptides in aqueous solution are analyzed for their conformational preferences using ab-initio MD simulations IR-spectroscopy and neutron diffraction experiments.
B.04 Guest lecture
COBISS.SI-ID: 38448901In the three block-lectures the following topics were presented: Introduction to computer simulations, Quantum mechanical and classical level of theory, Local properties of complex systems and experiments, Advanced molecular dynamics and coarse graining approach, Free energies and phase equilibria, Statistical mechanics of fluids, Water and hydration effects, Biological macromolecules.
B.05 Guest lecturer at an institute/university
COBISS.SI-ID: 6105626Vibrational spectra possess all information about the structure and dynamics of the probed system. However, the high density of vibrational states encumbers the application of vibrational spectroscopy. For small molecules, especially when corresponding theoretical treatment is available, structural vibrational parameters can be retrieved from the spectra. For larger systems only partial information is available. We presented on selected examples from our research how to retrieve accurate information from the complex vibrations spectra and correlate it with a molecular structure. We discussed about the infrared spectroscopy, Raman spectroscopy and vibrational circular dichroism.
B.04 Guest lecture
COBISS.SI-ID: 6003738