A THEORETICAL STUDY OF INTERACTION OF NANOPARTICLES WITH BIOMOLECULE

Many types of materials at nanoscale are currently being used in everyday life. The production and use of such products based on engineered nanomaterials have raised concerns of the possible risks and hazards associated with these nanomaterials. In order to evaluate and gain a better understanding of their effects on living organisms, we have performed first-principles quantum mechanical calculations and molecular dynamics simulations. Specifically, we will investigate the interaction of nanomaterials including semiconducting quantum dots and metallic nanoparticles with various biological molecules, such as dopamine, DNA nucleobases and lipid membranes. Firstly, interactions of semiconducting CdSe/CdS quantum dots (QDs) with the dopamine and the DNA nucleobase molecules are investigated using similar quantum mechanical approach to the one used for the metallic nanoparticles. A variety of interaction sites are explored. Our results show that small-sized Cd4Se4 and Cd4S4 QDs interact strongly with the DNA nucleobase if a DNA nucleobase has the amide or hydroxyl chemical group. These results indicate that these QDs are suitable for detecting subcellular structures, as also reported by experiments. The next two chapters describe a preparation required for the simulation of nanoparticles interacting with membranes leading to accurate structure models for the membranes. We develop a method for the molecular crystalline structure prediction of 1,2-Dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC), 1,2-Dimyristoyl-sn-glycero-3-phosphorylethanolamine (DMPE) and cyclic di-amino acid peptide using first-principles methods. Since an accurate determination of the structure of an organic crystal is usually an extremely difficult task due to availability of the large number of its conformers, we propose a new computational scheme by applying knowledge of symmetry, structural chemistry and chemical bonding to reduce the sampling size of the conformation space. The interaction of metal nanoparticles with cell membranes is finally carried out by molecular dynamics simulations, and the results are reported in the last chapter. A new force field is developed which accurately describes the interaction forces between the clusters representing small-sized metal nanoparticles and the lipid bilayer molecules. The permeation of nanoparticles into the cell membrane is analyzed together with the RMSD values of the membrane modeled by a lipid bilayer. The simulation results suggest that the AgNPs could cause the same amount of deformation as the AuNPs for the dysfunction of the membrane.

Computational prediction of the influence of crosslink distribution on the thermo-mechanical properties of epoxies

Experimental studies on epoxies report that the microstructure consists of highly crosslinked localized regions connected with a dispersed phase of low crosslink density. The various thermo-mechanical properties of epoxies might be affected by the crosslink distribution. But as experiments cannot report the exact number of crosslinked covalent bonds present in the structure, molecular dynamics is thus being used in this work to determine the influence of crosslink distribution on thermo-mechanical properties. Molecular dynamics and molecular mechanics simulations are used to establish wellequilibrated molecular models of EPON 862-DETDA epoxy system with a range of crosslink densities and various crosslink distributions. Crosslink distributions are being varied by forming differently crosslinked localized clusters and then by forming different number of crosslinks interconnecting the clusters. Simulations are subsequently used to predict the volume shrinkage, thermal expansion coefficients, and elastic properties of each of the crosslinked systems. The results indicate that elastic properties increase with increasing levels of overall crosslink density and the thermal expansion coefficient decreases with overall crosslink density, both above and below the glass transition temperature. Elastic moduli and coefficients of linear thermal expansion values were found to be different for systems with same overall crosslink density but having different crosslink distributions, thus indicating an effect of the epoxy nanostructure on physical properties. The values of thermo-mechanical properties for all the crosslinked systems are within the range of values reported in literature.