Large scale coarse-grained simulations of supramolecular systems containing DNA and proteins in solution.

Project: PHD

Project Details


This projects aims at constructing coarse-grained models of biologically relevant biomolecular systems as to study the structural dynamics and the interactions between DNA and proteins by mean of molecular mechanics methods.
Effective start/end date1/10/091/10/13

Research Output

  • Systematic Hierarchical Coarse-Graining with the Inverse Monte Carlo Method

    Lyubartsev, A. P., Naome, A., Vercauteren, D. P. & Laaksonen, A., 28 Dec 2015, In : The journal of chemical physics. 143, 24, 8 p., 243120.

    Research output: Contribution to journalArticle

  • Molecular Dynamics Simulation of 8-Oxoguanine Containing DNA Fragments Reveals Altered Hydration and Ion Binding Patterns

    Naome, A., Schyman, P., Laaksonen, A. & Vercauteren, D. P., 15 Apr 2010, In : Journal of physical chemistry B. 114, p. 4789-4801 13 p.

    Research output: Contribution to journalArticle

  • Student Theses

    Theoretical study of healthy and damaged DNA fragments in solution using molecular dynamics simulations

    Author: Naômé, A., 2008

    Supervisor: Vercauteren, D. (Co-Supervisor) & Laaksonen, A. (External person) (Co-Supervisor)

    Student thesis: Master typesMaster in Chemistry