Atomistic Assessment of Cystine Kidney Stone Behavior in a Mechanical Breakdown Process by Nanobiorobots through Classical Molecular Dynamics Simulations.

Abstract

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 SiO2, Si, and SiC nanodrills, which is about 19, 13, and 11%, respectively. In addition, the SiO2 nanodrill has more crossing time and z-direction deformation than other nanodrills due to the attractive interaction between SiO2 and stones, it shows less deformation during the process of kidney stone breaking because of repulsive interactions between the nanodrill and the kidney stone.