Journeys into the 3rd dimension (and beyond!): transferring atomic structures from HR-TEM into MD simulations

High-resolution transmission electron microscopy (HR-TEM) is a powerful tool for visualizing atomic structures and characterizing material behavior. Its natural companion in the modeling and simulation space is molecular dynamics (MD), which matches HR-TEM length scales and can provide a wealth of complementary information. A common approach in HR-TEM studies using MD is to identify a set of defects of interest in the physical sample, then reconstruct said defects virtually in an MD-friendly file format by hand or via atomistic simulation tools. While this approach has numerous advantages, the need to isolate highly specific structural features can limit the scope of study or introduce confounding structural artifacts. These limitations can especially hinder the study of larger-scale defect complexes such as those seen in highly deformed metals, which can involve dislocations, stacking faults, twins, grains, and even additional phases within a single two-dimensional micrograph.

In this talk, I will discuss the development of new tools designed to transfer complex defect structures from HR-TEM micrographs of metals, specifically deformed 304L steels, directly into accurate, three-dimensional structures ready for MD (LAMMPS) simulation environments. We will cover the general approach, current capabilities, development challenges, and demonstrate its use in several contexts. Finally, we will explore potential applications of this approach beyond forward simulation, such as uncertainty reduction, hypothesis testing, and training data generation.