Continuum Modeling with Functional Lennard–Jones Parameters for DNA‐Graphene Interactions

• Published in: Advanced theory and simulations Vol. 6; no. 5
• Main Authors: Stevens, Kyle, Thamwattana, Ngamta, Tran‐Duc, Thien
• Format: Journal Article
• Language: English
• Published: 01.05.2023
• Subjects: continuum modeling; DNA; graphene; Lennard‐Jones potential
• ISSN: 2513-0390; 2513-0390
• DOI: 10.1002/adts.202200896

Carbon nanostructures are of particular interest as platforms for molecular storage and adsorption. In this paper, the adsorption of a single stranded DNA molecule onto a graphene sheet is considered. Even though DNA molecules are complicated heterogeneous structures comprising several types of atoms, it is found that the repeated patterns within the DNA molecules enable the use of a continuum approach to model the DNA‐graphene sheet interaction. Here, a model is proposed such that the heterogeneity across the DNA molecule is captured by interaction functions, which are used to replace the attractive and repulsive constants in the Lennard‐Jones potential. Result from this new model shows better agreement to molecular dynamics simulations compared to the traditional continuum approach where atoms on the DNA are averaged evenly across the molecule. Finally, the paper comments on the model, its parameters, and suggests ways for improvement. The interaction between a single‐stranded DNA (deoxyribonucleic acid) and a graphene sheet is modeled using the Lennard‐Jones potential and a new continuum approximation. The Lennard‐Jones's constants are replaced by interaction functions to capture both heterogeneity and repeated pattern of the DNA. Analytical expressions for the interaction energy are obtained and results are compared with molecular dynamics simulations.