Correlation Effect of the Van-der-Waals and Intramolecular Forces for the Nucleotide Chain - Metallic Nanoparticles Binding in a Carbon Nanotube Matrix of Periodic Boundaries

Abstract

Using molecular dynamics simulation method we investigated the correlation effects between the weak Van der Waals forces and intramolecular vibrations for the molecular system consisting of a small nucleotide chain, gold nanoparticles and carbon nanotube with periodic boundaries. The molecular system represents a great interest in many aspects of modern research and applied sciences. For example, in bio-nano-technologies the application aspects include the development of electronic mobile diagnostic facilities, nanorobotic design for a drug delivery inside living cell, and so on. For the molecular system we have built up a series of the models with different configurations and performed their analysis. The entire system was allowed to interact with each other by the only VdW forces. The Lennard-Jones short-ranged interaction was assumed between the nucleotide chain, nanoparticles and carbon nanotube. For the carbon nanotube a many-body Tersoff potential having a quantum-chemistry nature was used. So far, the so-called hybrid MD approach was realized, where the quantum-chemistry potential in combination with a classical trajectory calculation applied. The peculiarities of the nucleotide chain – nanoparticle interaction and bond formation inside of a carbon nanotube matrix of the periodic boundaries were investigated along with the structural and dynamical behavior.