Invited tutorial lecture at the 3rd School of Computational Chemistry - Theory of New Materials at Atomistic Level: Graphene, Graphene Defects and π-Conjugated Polyradical Systems.
First principles modeling as a guide for understanding microscopy and spectroscopy
Computer simulations are an invaluable tool for understanding phenomena that are not directly accessible to experiment. My research has focused particularly on two such cases with graphene, the one-atom-thick form of hexagonally bonded carbon: interpreting the core level binding energies measured by x-ray photoemission, and elucidating the mechanisms of electron-beam induced dynamics observed via transmission electron microscopy.
For the case of core level binding energies, the experimental challenge is that each measured energy corresponds to a specific chemical environment of the atoms in the material, but the technique itself cannot directly resolve the atomic structure. Although it is possible to study the bonding of, for example, heteroatom dopants by direct imaging either by electron microscopy or scanning tunneling microscopy, this is very time-consuming and there are no guarantees the painstaking local sampling faithfully represents the bulk composition of the sample. With advances in first principles modeling, and especially density functional theory, it has become possible to predict the energies with sufficient accuracy to test hypotheses and understand experiments such as synchrotron spectroscopy of nitrogen-doped graphene.
For electron irradiation, the challenge is more fundamental: when a relativistic electron that is used for imaging transfers kinetic energy to a nucleus in the material, the dynamics that follow occur on the picosecond timescale, orders of magnitude beyond the experimental time resolution. Thus even though with modern aberration-corrected instruments it is possible to directly observe the atomic structure, each image is essentially a static snapshot of a relaxed atomic configuration. To understand why a certain process occurs, such as the movement of a trivalently bonded silicon atom through the graphene lattice, density functional theory molecular dynamics modeling offers invaluable insight into the dynamics, albeit with a high computational cost.
These studies have been conducted working closely with experimentalists to solve specific challenges, illustrating the value of cross-disciplinary collaboration. In my experience, having at least a basic understanding of both experimental and theoretical tools is very useful in helping to form a full picture of the physics of the system under study.