Plasma medicine, or the biomedical application of cold atmospheric plasma (CAP), is an expanding field within plasma research. CAP has demonstrated remarkable versatility in diverse biological applications, including cancer treatment, wound healing, microorganism inactivation, and skin disease therapy. However, the precise mechanisms underlying the effects of CAP remain incompletely understood. The therapeutic effects of CAP are largely attributed to the generation of reactive oxygen and nitrogen species (RONS), which play a crucial role in the biological responses induced by CAP. Specifically, RONS produced during CAP treatment have the ability to chemically modify cell membranes and membrane proteins, causing nitro-oxidative stress, thereby leading to changes in membrane permeability and disruption of cellular processes. To gain atomic-level insights into these interactions, non-reactive molecular dynamics (MD) simulations have emerged as a valuable tool. These simulations facilitate the examination of larger-scale system dynamics, including protein-protein and protein-membrane interactions. In this comprehensive review, we focus on the applications of non-reactive MD simulations in studying the effects of CAP on cellular components and interactions at the atomic level, providing a detailed overview of the potential of CAP in medicine. We also review the results of other MD studies that are not related to plasma medicine but explore the effects of nitro-oxidative stress on cellular components and are therefore important for a broader understanding of the underlying processes.

In this review article, statistical mechanisms of oxidative modification reactions in various organic compounds under the influence of reactive oxygen species (ROS) generated by cold atmospheric plasma (CAP) are investigated and analyzed based on reactive molecular dynamics (MD) simulations. As an efficient and hygienic advanced oxidation technology, CAP demonstrates tremendous potential in fields such as biomedicine and environmental protection. Through simulations, this paper provides a detailed analysis of the interaction mechanisms between ROS and components of biological tissues and environmental toxins. In this paper, we review the reactions involving four major ROS (OH radicals, O atoms, ${\mathrm{O}}_3$ molecules, and ${\mathrm{H}}_2{\mathrm{O}}_2$ molecules) and organic compounds, including proteins, DNA, polysaccharides, fatty acids, antibiotics, and mycotoxins. Atomic-level analysis reveals various oxidative modification reactions induced by ROS and their resulting products, including dehydrogenation reactions, bond-formation reactions, oxygen-addition reactions, and bond-cleavage reactions. Additionally, the study elucidates the role of active functional groups in various organic compounds, the presence of special elements, and the specific reactive nature of ${\mathrm{H}}_2{\mathrm{O}}_2$. Furthermore, the influence of different ROS species and concentrations on reaction types is explored, aiming to provide a solid theoretical foundation for the application of CAP technology in biomedicine and environmental remediation.