Journal of Basic and Applied Research International

The interaction process between the nucleotides and gold nanoparticles (NPs) has been investigated inside of a carbon nanotube (CNT) matrix using molecular dynamics (MD) simulation method. This work has been aimed to study the correlation effects between the weak Van der Waals (VdW) nonbonding forces and intramolecular bond vibrations for the nucleotides interacting with the NP in a confined CNT environment. A specific nucleotide (of purine or pyrimidine base) has been located within a range of VdW forces in a vicinity of NPs and their interaction dynamics and binding process in a matrix of the CNT with periodic boundaries were traced up. The entire system (the nucleotide, gold NPs and CNT) were allowed to interact with each other by the VdW forces only. The Lennard-Jones short-ranged interaction was assumed between the nucleotide, NP and CNT. For the CNT a many body Tersoff potential having a quantum-chemistry nature was used. So far, the so-called hybrid MD approach, where the quantum-chemistry potential in combination with a classical trajectory calculation applied, was realized. The nucleotide – metallic nanoparticles – carbon nanotube system represents a great interest in many aspects of modern electronic and bio-nano-technologies, for example, in DNA nanotechnology, in nanorobotic design for a drug delivery inside living cell, for the development of electronic mobile diagnostic facilities and so on. For the nucleotide–NP–CNT system we have performed a series of the MD simulations under different temperatures and initial configurations. The peculiarities of the nucleotide–NP interaction and binding inside of a CNT matrix of the periodic boundaries were investigated along with the structural and dynamical behavior.