Molecular Dynamics Simulations of Shockwave Affected STMV Virus to Measure the Frequencies of the Oscillatory Response

Abstract

Acoustic shockwaves are of interest as a possible means of the selective inactivation of viruses. It has been proposed that such inactivation may be enhanced by driving the virus particles at frequencies matching the characteristic frequency corresponding to acoustic modes of the viral structures, setting up a resonant response. Characteristic frequencies of viruses have been previously studied through opto-mechanical techniques. In contrast to optical excitation, shockwaves may be able to probe acoustic modes without the limitation of optical selection rules. This work explores molecular dynamics simulations of shockwaves interacting with a single STMV virus structure, in full atomistic detail, in order to measure the frequency of the response of the overall structure. Shockwaves of varying energy were set up in a water box containing the STMV structure by assigning water molecules at the edge of the box with an elevated velocity inward—in the direction of the virus. It was found that the structure compressed and stretched in a periodic oscillation of frequency 65 ± 6.5 GHz. This measured frequency did not show strong dependency on the energy of the shockwave perturbing the structure, suggesting the frequency is a characteristic of the structure. The measured frequency is also consistent with values predicted from elastic theory. Additionally, it was found that subjecting the virus to repeated shockwaves led to further deformation of the structure and the magnitude of the overall deformation could be altered by varying the time delay between repeated shockwave pulses.