Three-dimensional modeling and simulation of the AFM-based manipulation of spherical biological micro/nanoparticles with the consideration of contact mechanics theories

Abstract

By using an atomic force microscope as an ideal instrument for the manipulation of biological particles, the user deprives herself of the direct observation of the manipulation process in real time. In order to understand this process and to remove this limitation, an auxiliary method should be adopted which itself is not hampered by such a constraint. One of the approaches that has become of interest in this regard is the atomic force microscope based modeling and simulation of the manipulation process. Up to now, two-dimensional simulations have been performed using this technique; and as for three-dimensional modeling, only non-biological particles with cylindrical geometries have been investigated without the consideration of contact mechanics. For the first time, the present research has focused on the three-dimensional modeling and simulation of spherical biological particles in air medium while considering the mechanics of contact. Based on the simulation results, the manipulation force and indentation depth values that are produced in the contacts made during the manipulation process depend on the properties of the biological micro/nanoparticles involved; and in comparison with the two-dimensional case, increased values of manipulation force, contact radius and indentation depth have been observed in the three-dimensional models.