Although remarkable attempts have already been made to automate the AFM-based manipulation of biological cells, there are still many ambiguous points regarding the interactions between biological nanoparticles and manipulation tools, especially in different biological environments. As micro/nanoparticles of different shapes are placed in different biological environments, thus, it is necessary to accurately investigate the effects of the target nanoparticle’s geometry and material as well as the impact of the biomanipulation environment on the values of critical force and time of AFM-based manipulation. Therefore, in this article the cylindrical contact models of Hertz, JKR and viscoelastic model are developed for use in the AFMbased manipulation process conducted within different biological environments. Then, these models are applied to simulate the manipulation of gold and yeast nanoparticles in various environments such as air, water, alcohol and plasma. By comparing the results obtained in this paper, it is concluded that the movement of particles in different biological environments starts later and by a force of higher magnitude relative to the air medium. Also, it is found that the critical force and time of manipulation increase considerably for cylindrical particles relative to the spherical ones. At the end, the results are compared with the existing empirical results and their reliability is verified.
