In collaboration with colleagues from the Swiss Federal Institute of Technology Zurich (ETHZ) and from the Swiss National Centre of Competence in Research (NCCR) I have participated in the organization and as a tutor at a winter workshop on how molecular dynamics simulations can be used to interpret experimental data.
F.18 Transfer of new know-how to direct users (seminars, fora, conferences)
COBISS.SI-ID: 30057733In this lecture I presented how the single-step perturbation techniqe can be used to estimate the relative stability of netropsin-DNA complexes. I discussed the approximations and limitations of the method. Moreover, I estimated the accuracy of the single-step perturbation technique by comparing its results with the results obtained with the well-validated thermodynamic integration method.
B.04 Guest lecture
COBISS.SI-ID: 29075205The primary result obtained with molecular dynamics simulations are trajectories in which the positions and energies of all the particles of a simulated system are stored. The extraction of physical and chemical properties of a simulated system from the coordinate and energy trajectories is called a trajectory analysis. In this lecture I have shown how various chemical properties can be extracted from the trajectories calculated with the GROMOS simulation program, which I use and develop myself as well.
B.04 Guest lecture
COBISS.SI-ID: 30053637In this lecture I have used the exploration of conserved water sites in the vicinity of a coiled coil as an example to show how computer simulations can complement experiment in the field of biomolecular structure determination.
B.04 Guest lecture
COBISS.SI-ID: 29462277Nowadays people read and hear a lot about different molecules, however, seldomly can one imagine how these molecules actually look like. At the exhibition we presented pictures of structures of different molecules from various chemical and biochemical fields. Every picture had a short explanation. I contributed to the exhibition with a picture titled "In water". In the picture, the structure of liquid water calculated using molecular dynamics simulations was presented.
F.28 Organising an exhibition
COBISS.SI-ID: 29168133