Because cystine kidney stones are a more serious challenge for health-related quality of life than other types of kidney stones, the search for a new treatment for cystinuria is considered the main goal of this study. To achieve the defined goal, classical molecular dynamics simulations and quantum mechanics calculations were implemented in this study. Three nanodrills with different stiffnesses (i.e., silicon, silica, and silicon carbide) were selected to find the efficient nanodrill to break the kidney stones into smaller pieces. The related nanodrills under various forces from 20 to 100 eV/Å inclusive were exerted on the cystine kidney stones to determine the effect of the force magnitude on the rate of destruction. The exerted forces were modeled via a hypothetical spring force. To bring this investigation closer to reality, the urinary tract and the bulk of cystine kidney stones were modeled by simulation of the real blockage of the kidney stones. The obtained results from quantum mechanics calculations reveal the strong interaction (chemisorption) between the cystine stone components. Moreover, the molecular dynamics simulations show that an increase in force does not necessarily lead to more destruction of cystine kidney stones. The maximum rate of cystine kidney stone destruction occurs under forces of 80, 70, and 60 eV/Å for SiO 2 , Si, and SiC nanodrills, which is about 19, 13, and 11%, respectively. In addition, the SiO 2 nanodrill has more crossing time and z-direction deformation than other nanodrills due to the attractive interaction between SiO 2 and stones, it shows less deformation during the process of kidney stone breaking because of repulsive interactions between the nanodrill and the kidney stone.

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Since the manipulation of particles using atomic force microscopy is not observable in real-time, modeling the manipulation process is of notable importance, enabling us to investigate the dynamical behavior of nanoparticles. To model this process, previous studies employed classical continuum mechanics and molecular dynamics simulations which had certain limitations; the former does not consider size effects at the nanoscale while the latter is time consuming and faces computational restrictions. To optimize accuracy and computational costs, a new nonclassical modeling of the nanomanipulation process based on the modified couple stress theory is proposed that includes the size effects. To this end, after simulating the critical times and forces that are required for the onset of nanoparticle motion on the substrate, along with the dominant motion mode, the nonclassical theory of continuum mechanics and a developed von Mises yield criterion are employed to investigate the dynamical behavior of a cylindrical gold nanoparticle during manipulation. Timoshenko and Euler–Bernoulli beam theories based on the modified couple stress theory are used to model the dynamics of cylindrical gold nanoparticles while the finite element method is utilized to solve the governing equations of motion. The results show a difference of 90% between the classical and nonclassical models in predicting the maximum deflection before the beginning of the dominant mode and a difference of more than 25% in the dynamic modeling of a 200 nm manipulation of a gold nanoparticle with a length of 25 µm and aspect ratio of 30. This difference increases with each increment of the aspect ratio and reduction of manipulation distance. Furthermore, by applying an extended von Mises criterion on the modified couple stress theory, it is found that the failure aspect ratio of a cylindrical gold nanoparticle based on nonclassical models is 212% more than that of the classical model. In the end, the results are compared with those of the classical method on polystyrene nanorods. The results for cylindrical gold nanoparticles indicate that the material length scale has a major effect on the exact positioning of cylindrical nanoparticles.