Search for: All records

The rapid spread of SARS-CoV-2 required immediate actions to control the transmission of the virus and minimize its impact on humanity. An extensive mutation rate of this viral genome contributes to the virus’ ability to quickly adapt to environmental changes, impacts transmissibility and antigenicity, and may facilitate immune escape. Therefore, it is of great interest for researchers working in vaccine development and drug design to consider the impact of mutations on virus-drug interactions. Here, we propose a multitarget drug discovery pipeline for identifying potential drug candidates which can efficiently inhibit the Receptor Binding Domain (RBD) of spike glycoproteins from different variants of SARS-CoV-2. Eight homology models of RBDs for selected variants were created and validated using reference crystal structures. We then investigated interactions between host receptor ACE2 and RBDs from nine variants of SARS-CoV-2. It led us to conclude that efficient multi-variant targeting drugs should be capable of blocking residues Q(R)493 and N487 in RBDs. Using methods of molecular docking, molecular mechanics, and molecular dynamics, we identified three lead compounds (hesperidin, narirutin, and neohesperidin) suitable for multitarget SARS-CoV-2 inhibition. These compounds are flavanone glycosides found in citrus fruits – an active ingredient of Traditional Chinese Medicines. The developed pipeline can be further used to (1) model mutants for which crystal structures are not yet available and (2) scan a more extensive library of compounds against other mutated viral proteins. 

Micro vortex generator (MVG) is a currently facile, robust, and feasible device for supersonic and hypersonic flow control. The purpose of this study is to investigate the impact on SWBLI from the streamwise location of MVG. Large eddy simulation (LES) was conducted on MVG controlled supersonic ramp flow to reveal the sensitivity of MVG streamwise position on shock-wave boundary-layer interaction (SWBLI) control. Numerical cases with minor different distances between MVG and ramp corner are carried out. The results are analyzed in time-averaged and instantaneous view, respectively. The results show that streamwise position has a significant effect on SWBLI in some aspects. With minor changes on the streamwise position, the ring-like vortices generated by MVG were very similar, with only small changes in height and intensity. However, the small changes made on the ring-like vortices produced relatively significant changes to the separation region in front of the ramp. In terms of the time-averaged solution, the farther the MVG is from the ramp, the higher the ring-like vortices are lifted, and the shock wave is also disturbed/reduced more strongly. Further, the flow separation zone on the wall also appears smaller. The results of this study play a guiding role for further optimal configuration of MVG in flow control. 

Modal analysis on micro-vortex generator (MVG)-controlled supersonic flow at different Mach numbers is performed in this paper. The purpose of this investigation is to clarify the different properties of streamwise and ring-like vortical modes, and the effects of different Mach numbers on these modes, to further understand the vortical structures as they travel from MVG down to the shock wave/boundary-layer interaction (SWBLI) region. To this end, a high order and high resolution large eddy simulation (LES) was carried out, which identified the vortical structures behind the MVG and in the shock wave/boundary-layer interaction (SWBLI) region in the supersonic ramp flow with flow speeds of three different Mach numbers 1.5, 2.0, and 2.5. The proper orthogonal decomposition (POD) then was adopted to investigate the modes of the fluctuation flow field. It emerged that the streamwise and ring-like vortical modes were disparate in energy distribution, structural order, frequency and amplitude. Furthermore, it showed that as the Mach number increased, the energy of the streamwise modes increased while the opposite was true for ring-like modes; and the streamwise modal structures were altered more significantly than the ring-like modes, and the frequency of each mode scarcely varied. It was also found that the streamwise vortices absorbed energy from the ring-like vortices while they traveled from the MVG down to the SWBLI region, but the dominant frequency of each mode rarely changed during this process.