Silicon is one of the most abundant elements on Earth with around 78% of Earth’s crust consisting of varioussilicon and oxygen compounds [1]. Due to this, silica nanoparticles (SNPs) are widely used nanostructures fordrug delivery, bonding and coating applications and others [2].The properties of nanoparticles strongly correlate with their size hence it is critical to have an accurateway of measuring it. Commonly used techniques such as small angle x-ray scattering (SAXS), transmissionelectron microscopy (TEM) or dynamic light scattering (DLS) have drawbacks, such as being expensive andrequiring complex sample preparation. Additionally, they might be inaccurate for particles under 10 nm size.Potential methods that can be used to measure sizes of such constructs are time-resolved fluorescenceanisotropy [3], and fluorescence recovery after photobleaching (FRAP) however, due to the size of the systemit is impossible to determine experimentally how the dye is oriented on the SNP surface. As a result, its contri-bution to the measured complex size is unknown. Fortunately, the dye and SNP interaction mechanism can bestudied using computational methods, such as molecular dynamics, which allow full insight into such processeson an atomistic scale.In this work we used molecular dynamics simulations to get an insight into the rhodamine 6G (R6G) ad-sorption process to assess the most favourable conditions for successful adsorption and determine the impactof the dye to the measured complex size. Furthermore, we found that due to the geometric constraints and therequirement of correct dipole moment orientation, only one R6G molecule can adsorb on any sized SNP, andthe R6G layer formation on the nanoparticle surface is not possible. Similar restrictions lead to the fact that thehighest stable R6G oligomer is a dimer [4]
