Multiscale Modeling of Nanoparticles Growth, Self-assembly and Applications in Nanomedicine

In this thesis, we use quantum and classical methods to precisely model nanoscale materials on their own and in contact with biological components (nanomedicines). Most of the studies have been performed in close collaborations with experimentalists. First, we perform multiscale modeling of materials, using quantum ab initio methods and classical atomistic molecular dynamics (MD) simulations. We study (1) the nucleation of gold nanocrystals from its aqueous solution (Au(Cl4)-), (2) the dynamics of reaction intermediates (Si(OH)4) during wet etching of silicon nanopillars, (3) a capacitive gas sensing at the interface of an ionic liquid and a gold electrode, and (4) a reversible self-assembly of azobenzene-functionalized gold nanoparticles (NPs) in toluene. Second, we use atomistic MD simulations to model the interactions of nanoscale systems (NPs, micelles) with proteins and lipid bilayers. We investigate (5) irreversible interactions of functionalized NPs with selected viruses (HPV, dengue virus), (6) interactions of predesigned NPs with an Aβ40 amyloid fibril, (7) the enhancement of an enzymatic activity on the surfaces of ligated quantum dots, (8) the effect of PEG chain length in dendron micelles (DM) on the charge-dependent DM-cellular interactions, and (9) the effect of structural properties of DMs on their target-mediated cellular interactions.