The investigation of energy management and atomic interaction between coronavirus structure in the vicinity of aqueous environment of H2O molecules via molecular dynamics approach

Abstract

The coronavirus pandemic is caused by intense acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Identifying the atomic structure of this virus can lead to the treatment of related diseases in medical cases. In the current computational study, the atomic evolution of the coronavirus in an aqueous environment using the Molecular Dynamics (MD) approach is explained. The virus behaviors by reporting the physical attributes such as total energy, temperature, potential energy, interaction energy, volume, entropy, and radius of gyration of the modeled virus are reported. The MD results indicated the atomic stability of the simulated virus significantly reduced after 25.33 ns. Furthermore, the volume of simulated virus changes from 182397 Å3 to 372589 Å3 after t = 30 ns. This result shows the atomic interaction between various atoms in coronavirus structure decreases in the vicinity of H2O molecules. Numerically, the interaction energy between virus and aqueous environment converges to −12387 eV and −251 eV values in the initial and final time steps of the MD study procedure, respectively.