Application of High Performance Computing for Comparison of Two Highly Branched Lysine Molecules of Different Topology

High performance computations were performed for comparison of size and other properties of big heavily charged biocompatible molecules of complex topology in water. Lysine dendrimer and short dendritic brush of the same molecular weight were studied by molecular dynamics simulation method and GROMACS software package. The size and structural properties of these two systems were compared. It was shown that dendritic brush has smaller size and more dense core than the dendrimer. Radial density profile for both molecules is not monotonous and has minimum near core of molecules. This minimum is wider and deeper for dendrimer than for dendritic brush. Thus dendrimer has larger region of low density than dendritic brush and is more suitable for use for encapsulation and delivery of hydrophobic drugs.