Identifying resonant frequencies of viruses for microwave-based detection and inactivation of pathogenic viruses

Abstract

The natural vibrational frequencies of biological particles encode critical information about their structures and properties. The natural vibrational frequencies have been explored for early detection and inactivation of viruses. The resonant frequency-based biophysical methods present an interesting alternative to traditional vaccine and drug treatment against the spread and infection of pathogenic viruses. However, measuring natural vibrational frequencies of a single virion in a biological environment is challenging. Assigning structural features to measured spectra is even more difficult. We have simulated the dynamic motion of SARS-CoV-2 spike protein using all-atom molecular dynamics simulation. A resonance frequency at 7.3-7.4 GHz has been identified. The finding provides a molecular-level theoretical basis for attributing the experimentally observed SARS-CoV-2 microwave absorption peak at ~ 7.5 GHz to the intrinsic vibration of the spike protein, which is different from the previously proposed viral shell-core dipole model.

Fig. 1

All-atom molecular dynamics simulations. (A) Set up of MD system. A spike protein of three chains in blue, red, and gray is embedded in a membrane (cyan). Three flexible hinges are marked in “hip”, “knee”, and “ankle”. The box size is 22.4 × 22.2 × 44.5 nm. For clarity, a portion of the water molecules is shown. (B) Evolution of radius of gyration of the spike protein in three independent simulations starting with different initial velocities.

Fig. 2

Time evolution of calculated dipole moments. The x, y and z components of the dipole moments are plotted for three independent simulations. Stronger fluctuations are seen in Z components due to flexibility in benching and stretching along Z direction.

Fig. 3

Normalized microwave absorption spectra for three independent MD simulations. The strongest absorption intensity is scaled to 1. (A–C) Spectra calculated using a whole time-series vector. Maximum intensity appears at 7.4, 7.2, and 7.3 GHz for Sim0, Sim1, and Sim2, respectively. (D–F) Spectra calculated using equally divided segments of a time-series vector and then averaging the resultant spectra. Maximum intensity appears at 7.4, 7.3, and 7.3 GHz for Sim0, Sim1, and Sim2, respectively.

Fig. 4

Significance test of the observed peaks by calculating the false-alarm probability (FAP). (A) The maximum absorption intensity in Sim0 is 0.01154 . If it is due to noise, the probability of observing the maximum intensity is < 8.61%. (B) The maximum absorption intensity in Sim1 is 0.01118 . If it is due to noise, the probability of observing the maximum intensity is < 4.34%. (C) The maximum absorption intensity in Sim2 is 0.01571 . If it is due to noise, the probability of observing the maximum intensity is < 0.05%.