Engineering topics
Publications and source records attributed to Han, T. Yong-Jin.
A molecular crystal structure prediction workflow, based on the random structure generator, Genarris, and the genetic algorithm (GA), GAtor, is successfully applied to two energetic materials and a chiral arene.
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To expedite new molecular compound development, a long-sought goal within the chemistry community has been to predict molecules’ bulk properties of interest a priori to synthesis from a chemical structure alone. In this work, we demonstrate that machine learning methods can indeed be used to directly learn the relationship between chemical structures and bulk crystalline properties of molecules, even in the absence of any crystal structure information or quantum mechanical calculations. We focus specifically on a class of organic compounds categorized as energetic materials called high explosives (HE) and predicting their crystalline density. An ongoing challenge within the chemistry machine learning community is deciding how best to featurize molecules as inputs into machine learning models—whether expert handcrafted features or learned molecular representations via graph-based neural network models—yield better results and why. We evaluate both types of representations in combination with a number of machine learning models to predict the crystalline densities of HE-like molecules curated from the Cambridge Structural Database, and we report the performance and pros and cons of our methods. Our message passing neural network (MPNN) based models with learned molecular representations generally perform best, outperforming current state-of-the-art methods at predicting crystalline density and performing well even when testing on a data set not representative of the training data. However, these models are traditionally considered black boxes and less easily interpretable. Here, to address this common challenge, we also provide a comparison analysis between our MPNN-based model and models with fixed feature representations that provides insights as to what features are learned by the MPNN to accurately predict density.
Packing motifs—patterns in how molecules orient relative to one another in a crystal structure—are an important concept in many subdisciplines of materials science because of correlations observed between specific packing motifs and properties of interest. That said, packing motif data sets have remained small and noisy due to intensive manual labeling processes and insufficient labeling schemes. The most prominent labeling algorithms calculate relative interplanar angles of nearest neighbor molecules to determine the packing motif of a molecular crystal, but this simple approach can fail when neighbors are naively sampled isotropically around the crystal structure. To remedy this issue, here we propose an optimization algorithm, which rotates the molecular crystal structure to find representative molecules that inform the packing motif. We package this algorithm into an automated framework—Autopack—which both optimally rotates the crystal structure and labels the packing motif based on the appropriate neighboring molecules. In this work, we detail the Autopack framework and its performance, which shows improvements compared to previous state-of-the-art labeling methods, providing the first quantitative point of comparison for packing motif labeling algorithms. Furthermore, using Autopack (available at https://ipo.llnl.gov/technologies/software/autopack), we perform the first large-scale study of potential relationships between chemicals’ compositions and packing motifs, which shows that these relationships are more complex than previously hypothesized from studies that used only tens of polycyclic aromatic hydrocarbon molecules. Autopack’s capabilities help pose next steps for crystal engineering research focusing not only on a molecule’s adoption of a specific packing motif but also on new structure–property relationships.
A comprehensive framework to automatically perform size and morphology recognition of nanoparticles in SEM images in a high-throughput manner.
Electrophoretic deposition (EPD) is an industrially relevant and scalable technique used to form particle deposits from colloidal suspensions. Highly concentrated particle suspensions generally prevent real-time in situ microscopy observations which limit the characterization of EPD films to ex situ, or postprocessed, laboratory techniques. For dynamic systems, such as tunable amorphous photonic crystals (APCs), only reversible deposits are formed during the EPD process. Since reversible deposits cannot be characterized with standard ex situ methods, the particle-particle and particle-field interactions that govern the displayed color and crystallinity of these systems are not well understood. In this paper, we present in situ small-angle x-ray scattering and UV-Vis techniques for measuring both the structural and optical response of an APC under applied electric fields. Furthermore, we also develop a computational model based on colloidal interactions to explain the observed change in the interparticle spacing of APCs due to the applied electric field which correlates to displayed color. Ultimately, this work provides a new in situ characterization method that could be expanded for other dynamic, tunable colloidal systems.