3 ECTS credits
80 u studietijd
Aanbieding 1 met studiegidsnummer 4023202DNR voor alle studenten in het 1e semester met een inleidend master niveau.
In several lectures, the underlying principles are introduced of the techniques applied in the practical sessions; the aim is to understand, not to be able to reproduce. In addition, the lectures are structured entirely in function of the computational applications. In the practical sessions, conventional packages in the field will be used: VMD, NAMD, Gromacs, CP2K - all freely available for academic users.
Construction of a molecular model: the structure of a pdb file, visualization.
Description of atomic/molecular interactions in biomolecular systems: classical (force fields), quantum-mechanical (ab initio) and semi-empirical.
Multiscale approaches: QM/MM
Molecular dynamics: minimization, equilibration, annealing
Analysis of dynamics: energy contributions, RMSD, normal mode analysis, principal component analysis
The function of biological macromolecules is determined by their three-dimensional structure and dynamics. With molecular simulations, it is possible to calculate microscopic properties and to link them to macroscopic variables, such as thermodynamic properties. Molecular modeling is increasingly used as a valuable tool by biologists and (bio)chemists. Due to the ever-increasing computer capabilities, these simulations have become accessible to end-users. In addition, simulations can often provide answers to fundamental scientific questions in a relatively inexpensive way, not requiring many (costly) chemical reactions or purifications. Within the academic world but also in the industry, modeling is frequently applied to biomolecules such as proteins, polynucleotides, pharmaceuticals, pesticides, etc.
Understand and reproduce recent scientific literature, and implement these methods in own research.
Independently set up a computer simulation and perform a meaningful analysis.
Directly connect with the current research of different labs at home and abroad.
De beoordeling bestaat uit volgende opdrachtcategorieën:
Examen Andere bepaalt 100% van het eindcijfer
Binnen de categorie Examen Andere dient men volgende opdrachten af te werken:
End-of-term evaluation. Assignment with oral evaluation. A project paper is required and the project is defended in a short oral presentation.
Deze aanbieding maakt deel uit van de volgende studieplannen:
Master of Chemistry: Analytical and Environmental Chemistry (enkel aangeboden in het Engels)
Master of Chemistry: Chemical Theory, (Bio)Molecular Design and Synthesis (enkel aangeboden in het Engels)