Preferential Adsorption of Single-Stranded DNA on Graphene Oxide with Hydroxyl and Epoxy Groups
Abstract
1. Introduction
2. Method and Model
2.1. Simulation Workflow
- (a)
- All essential input files and parameters were prepared, including the configuration file, simulation parameter file, and force field file.
- (b)
- Energy minimization was carried out to eliminate unfavorable atomic contacts, followed by a 2 ns isothermal-isobaric (NPT) equilibration at 300 K and 1 atm to stabilize the system density.
- (c)
- The production phase consisted of a 400 ns canonical ensemble (NVT) simulation at 300 K to investigate the adsorption mechanism of ssDNA onto GO. The carbon atoms of GO were frozen at their initial positions while the other atoms were free to move. Five independent simulation replicates with identical initial configurations were performed to obtain statistically averaged results.
- (d)
- The simulation outcomes were then validated to ensure physical plausibility and consistency with the initial research objectives.
- (e)
- Finally, statistical analyses were performed using multiple independent replicas to extract reliable metrics, including HBs, HB lifetimes, and interaction energies, and so on.
2.2. System Settings
2.3. Simulation Parameters
3. Result and Discussion
4. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Ma, H.; Huang, X.; Wang, S.; Wu, M.; Wang, H.; Shao, G.; Zhao, L.; Lei, X. Preferential Adsorption of Single-Stranded DNA on Graphene Oxide with Hydroxyl and Epoxy Groups. Crystals 2025, 15, 800. https://doi.org/10.3390/cryst15090800
Ma H, Huang X, Wang S, Wu M, Wang H, Shao G, Zhao L, Lei X. Preferential Adsorption of Single-Stranded DNA on Graphene Oxide with Hydroxyl and Epoxy Groups. Crystals. 2025; 15(9):800. https://doi.org/10.3390/cryst15090800
Chicago/Turabian StyleMa, Huishu, Xiaodan Huang, Shijun Wang, Mei Wu, Hanbing Wang, Guowei Shao, Liang Zhao, and Xiaoling Lei. 2025. "Preferential Adsorption of Single-Stranded DNA on Graphene Oxide with Hydroxyl and Epoxy Groups" Crystals 15, no. 9: 800. https://doi.org/10.3390/cryst15090800
APA StyleMa, H., Huang, X., Wang, S., Wu, M., Wang, H., Shao, G., Zhao, L., & Lei, X. (2025). Preferential Adsorption of Single-Stranded DNA on Graphene Oxide with Hydroxyl and Epoxy Groups. Crystals, 15(9), 800. https://doi.org/10.3390/cryst15090800