Molecular Dynamics Simulation Of Interaction Mechanisms Between Cold Atmospheric Plasmas And Virus

Currently,the application of Cold Atmospheric Plasma(CAP)in health has attracted a lot of attention from researchers.Plasma medicine is a rapidly developing and relatively new multidisciplinary field that includes chemistry,physics,medicine and bioengineering.Experimental studies have shown that atmospheric pressure cold plasma can inactivate various viral microorganisms.Reactive Oxygen Species(ROS)is considered to be one of the key factors in sterilization among various active components that may be produced in atmospheric cold plasma.However,the existing experimental detection methods are mainly used to characterize the killing effect of atmospheric pressure cold plasma on viral microorganisms,etc.,and are limited in explaining its potential microscopic mechanism.As an important supplement to experimental research,molecular simulation technology has been frequently used in plasma medical and health care,and has been widely recognized by the academic community.Based on reactive molecular dynamics,the interaction between reactive oxygen species(ROS)particles in atmospheric cold plasma and the molecular structure of viral microorganism was studied.In this paper,the interaction between ROS and viral structure(genetic material DNA,viral capsid protein)was simulated at the atomic level,which was used as the microscopic characteristic quantity to characterize the effect of ROS in the process of sterilization and disinfection.Molecular dynamics simulation can theoretically study the mechanism of atmospheric pressure cold plasma sterilization at the atomic level and serve as mutual verification and supplement to macroscopic experimental phenomena.The main contents of this paper are as follows:(1)In this paper,the basic concept and classification of plasma are summarized,and the research status of atmospheric pressure cold plasma in the inactivation of viruses and microorganisms as well as the mechanism of sterilization and disinfection are summarized.The molecular dynamics simulation methods and Reactive Force Field(ReaxFF)used in this research are introduced.The simulation software Materials Studio used in this paper is introduced,and the functional modules involved in the simulation are also introduced.The simulation reaction between chitin molecules and reactive oxygen species(O,OH,H2O2,and H2O)in the cell wall of fungi was taken as an example.The process setup of the simulation method and the result analysis process method used in this paper were introduced.(2)As the genetic material of some viruses and all cellular organisms,DNA molecules play a key role in the survival and reproduction of viral microorganisms.The interaction of reactive oxygen species(O,OH and H2O2)with DNA fragments in atmospheric cold plasma was studied by molecular dynamics simulation based on ReaxFF reaction field.The simulation results show that ROS and DNA molecules have two kinds of hydrogen stripping reactions.The O and OH take the H atom from the DNA molecular structure,while the H atom of H2O2 is taken from the O atom of the DNA molecule.O,OH free radicals and H2O2 damage DNA molecules at different locations,causing irreversible damage to the molecular structure of DNA.(3)Molecular dynamics was used to investigate the damage of O atom and OH radical in cold plasma to the receptor binding region of S protein of novel Coronavirus(SARS-CoV-2).The destruction of RBD molecular structure by reactive oxygen particles is first initiated by hydrogen stripping reaction.In the process of inducing the destruction of RBD molecular structure,the RBD molecule after the hydrogen stripping reaction presents an unstable state,which may further trigger a series of important chemical bond breakage and formation reactions,which will destroy the original protein molecular structure and cause the receptor binding protein to lose its physiological functions such as recognition and binding.If the original molecular structure of viral capsid protein is destroyed,minor damage or conformational change of viral capsid protein may terminate the binding of the virus to the receptor on the surface of the host cell,thus resulting in the loss of viral infectivity.