Development of multiscale simulation methods

PhD ceremony: Mr. A.J. Rzepiela, 13.15 uur, Aula Academiegebouw, Broerstraat 5, Groningen

Dissertation: Development of multiscale simulation methods

Promotor(s): prof. S.J. Marrink

Faculty: Mathematics and Natural Sciences

Multiscale techniques bridge what is often mutually excluding in computer models: accuracy and efficiency. Thus, complex systems can be studied with ease, without compromising quality of a research. However, the high complexity of studied phenomenon requires often very specific methods, aimed at the particular problem. In this thesis we developed, tested and presented applications of three novel multiscale algorithms for biomolecular simulations. The focus was on methods in which the MARTINI coarse-grained forcefield could have been employed. The back mapping method helps to reconstruct atomistic structures from their corresponding coarse grained representations. In the hybrid multiscale simulation protocol only a part of a system is represented in a lower resolution and the crucial details are kept explicitly in the model. In the ‘constant lambda' approach potential energy has a mixed atomistic coarse-grained form and the level of coarse-graining is adjusted with the lambda parameter. All three methods are carefully characterized on pages of this thesis and selected applications on biomolecular systems are also presented. Programs with the described algorithms can be downloaded from the cgmartini.nl web page.