The thermophoresis of nanoparticles in the free molecule regime plays an important role in the nucleation, collision and coagulation of nanoparticles. In this contribution, on the basis of a rigorous gas kinetic theory, the theoretical expressions for the thermophoretic force on nanoparticles suspended in dilute gas mixtures are derived, wherein the non-rigid-body interactions between the gas molecules and the nanoparticle are taken into account. The analytical formulas in the present work are consistent with those under the rigid-body collision assumption. Negative thermophoresis, is found to be possible for nanoparticles in the free molecule regime, by which the thermophoretic force exerted on the suspended nanoparticle is from low to high temperature, i.e., opposite to the direction of normal thermophoresis.

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