Edita Sarukhanyan

• Ever since their discovery, carbon nanotubes (CNTs) have grabbed attention of the researchers from different fields of science and industry. In fact, their excellent physicochemical properties together with an ability to cross biological membranes provide innumerable possibilities for diverse applications, including biomedical and pharmacological applications. Surface modification of CNTs by biological molecules will create a new series of bioactive nanotubes which will lead to the direction of specific cell targeting. The main principles of CNT interactions with biological interfaces are still under active investigation. Experimental data suggest various ways of CNT surface modification, as well as, their pathways of internalization through the cellular membrane. Nowadays, the availability of both large computational resources and powerful computational methods, as Molecular Dynamics (MD) simulation, provides an opportunity to study these interactions at atomic level with high order of accuracy. The goal of the research work for this thesis is the multi-scale simulation study of CNTs with various biological interfaces. Initially, the study of the CNT coating mechanism by surfactants at both atomistic and coarse-grained levels has been carried out. Linear polymeric ether – based surfactants are known to coat the surface of the nanotubes and, thus, make them soluble in water. In this simulation study the distribution of the polymers of different length around CNT, as well as, the numbers of aggregated chains are found to be compatible with experimental data results. Further, investigation of the orientation and aspect ratio dependent interaction of CNT bundles with the DPPC lipid bilayer has been performed by a recently developed MD-SCF approach. The simulations have provided a molecular model of the perturbation in the structure of the lipids bilayer induced by the CNT bundles insertion process. The results have shown that strong perturbations occur only when the CNT bundles are oriented perpendicularly respect to the bilayer plane. The pore formation has also been observed with the longest CNT bundle. Finally, the atomistic MD simulations have been performed to study the structural behavior of antimicrobial hybrid peptide CA-MA in aqueous solutions under different physiological conditions. This specific hybrid peptide is of great interest to be explored, because of its bactericidal and tumoricidal abilities. The results of this study have shown that the peptide receives random coil conformation in water, which is in accordance with experimental results. Partial stabilization of the α-helix structure was found in the case of simulation in salty environment and the irreversible loss of the α-helical content was observed at the physiological temperature of 310 K. The peptide concentration plays a stabilizing role on secondary structure of the peptide. However, at these concentrations, peptide aggregation takes place. The studies of the CA-MA peptide have been further extended for the case of interactions with CNT and graphene sheet. In both cases the rapid loss of α-helical content has been observed at the time of the peptide’s contact with the solid carbon – based nanosurfaces.