Recent environmental studies have shown the impact of air quality on human health and in particular, toxicological effect of particulate matter (PM) and ultrafine particles (UFPs) on progression of neurodegenerative diseases. While in-vivo experiments reveal enhanced concentration of amyloid beta peptides in the brains of animals after the exposure to PM and UFPs, the molecular interactions between peptides and atmospheric pollutants remain obscure. In this study, molecular dynamics simulations were performed to investigate the effect of UFPs on the aggregation of amyloid beta peptides, associated with the development of Alzheimer’s Disease (AD) in human brain. In particular, the changes in the structure of eight Aß16-21 peptides, the segment of Aß1-42 peptide with the high propensity to aggregate were investigated. The aggregation kinetics of Aß16-21 peptides and amount of beta sheets in their secondary structures were studied in the presence of varying concentrations of NH4+ and SO4-2 ions, common secondary inorganic ions found in the environmental realm from the different sources of atmospheric pollution. Moreover, the effect of hydrophobic UFP, modelled by C60 molecule, on the structure of peptides was analysed. The aggregation kinetics was calculated by estimating the time necessary to reach Solvent Accessible Surface Area (SASA) of peptides of 60 nm2. The study demonstrated that, although, the inhibitory effect of hydrophobic UFP on the formation of beta sheets was revealed, there could be a synergistic effect of the concentration of (NH4)2SO4 salt and presence of UFP on the aggregation kinetics of peptides. Among three different salt concentrations of 0.15 M, 0.25 M and 0.35 M, the slowest aggregation of peptides in the absence of C60 molecule and the fastest aggregation in the presence of C60 were observed at 0.25 M of (NH4)2SO4.