We use molecular dynamics (MD) simulations to model selected biotechnological problems in collaboration with experimentalists. First, we investigate a disintegration of viruses by virucidal nanoparticles, and show that these processes are very sensitive to the structures of ligands and nanoparticles, due to a highly specific multivalent binding. We also show that functionalized cyclodextrines can perform similar tasks, but they are more likely to be applied as nanomedicines. Then, atomistic MD simulations are used to explain the increased reaction rates of oligo-anionic molecular sliders with their conjugates (bromo-substituted N-methyl-Maleimide) in the presence of poly-cationic tracks. The simulations reveal that molecular sliders not only diffuse, but also loop and hop efficiently along or between several polymer tracks, thereby significantly increasing the meeting and reaction rates with their conjugates, in comparison to the bulk solvent.

Modeling of nanoparticles nanomedicines and molecular sliders on biopolymers

2019 Spring National Meeting

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