Department of Molecular Simulations of Polymers

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The research is oriented towards theoretical aspects of polymers. Structure, thermodynamics, mechanical, and other properties of synthetic polymers and biopolymers are investigated using the molecular Monte Carlo and molecular dynamics simulations which produce unique independent information, sometimes out-of-reach for experiment. Recently, the focus is on three main topics.

1. Coarse-grained simulations of a single chain confined in a channel of asymmetric cross-section or in a channel with crowded environment represented by parallel posts which are relevant to DNA-linearization experiments or to biological systems with spatially heterogeneous confinements encountered in various nano- and bio-structures. Related mainly to the behavior of principal biopolymers like DNA, semiflexible macromolecules are investigated under confinement; the problem for which the theory is much less developed than that for flexible polymers.

2. Atomistic simulations of PEO or PNIPAAm chains end-grafted onto solid surfaces with the application to the protection of surfaces against protein adsorption or bacteria adhesion or to wetting, adhesion, colloid stabilization or dispersion of nanoparticles. (Cooperation with the Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Prof. M. Natália D. S. Cordeiro)

3. Coarse-grained simulations of supercoiled knotted DNA molecules studied in order to shed light on the role of DNA supercoiling in DNA unknotting. This research provides understanding how the DNA supercoiling directs type II DNA topoisomerases to preferentially act on knotted portions of DNA molecules. (Cooperation with the Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne and the Swiss Institute of Bioinformatics in Lausanne, Prof. Andrzej Stasiak)