Due to unique and tunable optical properties, gold nanoparticles (GNPs) are becoming more widely used in biological and biomedical applications. However, nanoparticles in fluid tend to lose the specific function because of aggregation in the transport process of use. Therefore, it is necessary to investigate the aggregation behavior for having a good understanding of aggregation mechanism and inhibiting GNPs aggregation. A MD simulation in this study was performed to investigate the physical aggregation behavior of GNPs in biological media. By analyzing the aggregation proportion of GNPs in different conditions and the changes in center-to-center distance between GNPs with the time, the effects of the hydrophilic/hydrophobic characteristics of GNPs, velocity of ionic solution, size of GNPs, initial distance between two GNPs, and surface charge were discussed. The simulation results indicate that the aggregation proportion of GNPs with hydrophilic modification is 62.5%, which is less than 87.5% in the model without surface modification, while the final aggregation proportion of GNPs with hydrophobic modification increased to 100%. When the velocity of the NaCl aqueous solution is 0.1 m/s, the final aggregation proportion of GNPs is 87.5%, which is similar with the model without flow velocity. But the final aggregation proportion increased to 100% when the velocity is 1m/s. Under the same conditions, the GNPs of 1 nm diameter aggregated at 0.16 ns, but the GNPs of 1.5 nm and 2 nm diameters aggregated at 0.6 ns and 0.8 ns, respectively. For the GNPs of 1 nm diameter, the GNPs can only get close to each other very slowly when the distance between the surfaces of GNPs is within the range of 0.8–1.2 nm, whereas the GNPs will aggregate quickly when the distance is close enough. GNPs can retain stable by modified with appropriate negative charge. But ions in the solution will weaken this effect.

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