The absence of sub-grid scale (SGS) motions leads to severe errors in particle pair dynamics, which represents a great challenge to the large eddy simulation of particle-laden turbulent flow. In order to address this issue, data from direct numerical simulation (DNS) of homogenous isotropic turbulence coupled with Lagrangian particle tracking are used as a benchmark to evaluate the corresponding results of filtered DNS (FDNS). It is found that the filtering process in FDNS will lead to a non-monotonic variation of the particle collision statistics, including radial distribution function, radial relative velocity, and the collision kernel. The peak of radial distribution function shifts to the large-inertia region due to the lack of SGS motions, and the analysis of the local flowstructure characteristic variable at particle position indicates that the most effective interaction scale between particles and fluid eddies is increased in FDNS. Moreover, this scale shifting has an obvious effect on the odd-order moments of the probability density function of radial relative velocity, i.e. the skewness, which exhibits a strong correlation to the variance of radial distribution function in FDNS. As a whole, the radial distribution function, together with radial relative velocity, can compensate the SGS effects for the collision kernel in FDNS when the Stokes number based on the Kolmogorov time scale is greater than 3.0. However, it still leaves considerable errors for $${ St}_\mathrm{k }<3.0$$ .
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