Supervisors info:
Ζωή Κούρνια, Ερευνήτρια Γ', Βοηθός Καθηγητή, Ίδρυμα Ιατροβιολογικών Ερευνών, Ακαδημίας Αθηνών
Summary:
Nanoparticles have various applications in medicine, physics, optics, and electronics. Modeling nanoparticles is an essential first step to assess their capacity in different uses such as in energy storage or drug delivery. However, creating an initial starting conformation for modeling and simulation is tedious, because every crystalline material grows with a different crystal habit and different symmetry in nature.
In this diploma thesis, a web-based crystallographic tool has been created, which creates nanoparticle models from any crystal structure guided by their preferred equilibrium shape in standard conditions according to Wulff morphology (crystal habit).
The algorithm uses input from quantum mechanical calculations based on the Wulff construction. The Wulff construction employs energy minimization arguments to demonstrate that specific crystal planes are preferred over others, with their distance from the origin being proportional to their surface energy. The input parameters for determining this equilibrium nanoparticle structure are the preferred growing planes as Miller indices, the energy of each plane, and the desired size of the nanoparticle.
After inputting this data, the equilibrium shape is created with the following methodology. First, based on the crystallographic point group, the symmetric planes are produced based on the Miller indices, the fractional coordination system, and the lattice parameters. In this procedure, we place the origin on the negative side of these planes, and then we calculate the intersection points per three of the planes, discarding those that are on the positive side of at least one of the planes. Then, we obtain the faces of the equilibrium shape using the Quickhull algorithm on the remaining intersection points, and the equilibrium shape is constructed by connecting these faces. The symmetric unit cell of the crystal structure is produced from the asymmetric one, using the lattice parameters and the symmetry operations of the crystallographic space group on the coordinates of the atoms again. Finally, the nanoparticle is constructed by replication of the unit cell across all three spatial directions, until the equilibrium shape is filled, and the coordinates of the atoms are output to the user.
This tool may be used to construct nanoparticles for simulation of any material given the crystal structure as input, the size of the nanoparticle, and the preferred growing planes and energies. It has been implemented as a website using C++ and PHP and can be accessed and used at: http://nanocrystal.vi-seem.eu/CrystalTool.
SUBJECT AREA: Condensed Matter Physics
KEYWORDS: crystallography, nanoparticles, Wulff construction, modeling nanoparticles, web development
Keywords:
crystallography, nanoparticles, Wulff construction, modeling nanoparticles, web development
