The molecular dynamics simulation of peptide-based structure adsorption inside nanochannel with surface roughness

Abstract

Peptides result from partial hydrolysis of protein polypeptide chains. These atomic structures are the main section of various protein compounds. So, the adsorption process of these structures can be used in various medical applications. The small peptide structure is absorbed using a platinum nanochannel with cubic roughness in an aqueous environment in the present computational examination. Technically, the simulation of the nanochannel- peptide system is done using the Molecular Dynamics (MD) method. The different atoms' interactions in our systems are defined by DREIDING/Universal Force-Field (UFF), TIP3P, and Embedded Atom Model (EAM). Temperature, total energy (TE), Radial Distribution Function (RDF), profiles of density/velocity/temperature, absorption ratio, interaction energy, and volume were presented for t = 30 ns in order to provide a physical description of the peptide adsorption process. Our simulation results show the atomic stability of P-nanochannel system in the attendance of H2O molecules. Moreover, peptide absorption ratio inside the MD box reached a 78 % value. This result shows the appropriate behavior of a metallic nanochannel with rectangular roughness to adsorption of various protein-based structures, such as Ps for medical aims.