Stokes-Mueller polarization-based analysis of model SARS-CoV-2 virions

Abstract

Understanding the virology of the coronavirus at the structural level has gained utmost importance to overcome the constant and long-term health complications induced by them. In this work, the light scattering properties of SARS-CoV-2 of size 140 nm were simulated by using discrete dipole approximation (DDA) for two incident wavelengths 200 nm and 350 nm, respectively. Three different 3-dimensional (3D) models of SARS-CoV-2 corresponding to 15, 20, and 40 numbers of spike proteins on the viral capsid surface were constructed as target geometries for the DDA calculations. These models were assessed by employing Stokes-Mueller polarimetry to obtain individual polarization properties such as degree of polarization (DOP), degree of linear polarization (DOLP), and degree of circular polarization (DOCP). Irrespective of its spike numbers, all the coronavirus models were found to display higher DOP and DOCP values and negligibly small DOLP values for circularly polarized incident light, indicating the presence of chiral structures. On the other hand, the lack of understanding about the dependence of the Mueller matrix on its microstructural properties was overcome by transforming 16 Mueller elements into sub-matrices with specific structural and physical properties using Lu-Chipman-based Mueller matrix polar decomposition method. The obtained properties such as retardance, diattenuation, and depolarization were used for investigating the composition and microstructural information. The approach presented in this work has the potential to understand the virology of the coronavirus at the structural level and, therefore, will be beneficial in developing effective detection strategies by exploiting their characteristic electromagnetic scattering signatures.

Keywords: Discrete dipole approximation; Lu-Chipman decomposition; Mueller matrix; Polarimetry; SARS-CoV-2; Stokes vector.

Fig. 1

Schematic representation of Stokes–Mueller analysis with various SARS-CoV-2 models

Fig. 2

(A) The blender representation of the target shapes of SARS-COV-2 with different spike numbers used in DDA computations. Model references: PDB ID 6VXX, CHARMM-GUI Archive-COVID-19 Proteins Library. (B) 3D rendered dipole representation of the target geometries (SARS-CoV-2) with 15, 20, and 40 spike proteins

Fig. 3

Graphs of Stokes vector polarization parameters such as DOP, DOLP, and DOCP as a function of spike numbers with 0° and RCP excitation polarization states at two incident wavelengths 200 nm and 350 nm for (a) 0°, (b) 45°, and (c) 90° scattering angle

Fig. 4

Graph of Lu–Chipman decomposition parameters such as diattenuation (d), linear retardance (δ), and optical rotation (ψ), as a function of spikes number at different wavelengths 200 nm and 350 nm for (a) 0°, (b) 45°, and (c) 90° scattering angle