Prediction of Diblock Copolymer Morphology via Machine Learning

A machine learning approach is presented to accelerate the computation of block polymer morphology evolution for large domains over long timescales. The strategy exploits the separation of characteristic times between coarse-grained particle evolution on the monomer scale and slow morphological evolution over mesoscopic scales. In contrast to empirical continuum models, the proposed approach learns stochastically driven defect annihilation processes directly from particle-based simulations. A UNet architecture that respects different boundary conditions is adopted, thereby allowing periodic and fixed substrate boundary conditions of arbitrary shape. Physical concepts are also introduced via the loss function and symmetries are incorporated via data augmentation. The model is validated using three different use cases. Explainable artificial intelligence methods are applied to visualize the morphology evolution over time. This approach enables the generation of large system sizes and long trajectories to investigate defect densities and their evolution under different types of confinement. As an application, we demonstrate the importance of accessing late-stage morphologies for understanding particle diffusion inside a single block. This work has implications for directed self-assembly and materials design in micro-electronics, battery materials, and membranes.

APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics

The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics, and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The advent of AI models, such as AlphaFold, is revolutionizing applications that depend on robust protein structure prediction algorithms. To maximize the impact, and ease the usability, of these novel AI tools we introduce APACE, AlphaFold2 and advanced computing as a service, a novel computational framework that effectively handles this AI model and its TB-size database to conduct accelerated protein structure prediction analyses in modern supercomputing environments. We deployed APACE in the Delta supercomputer, and quantified its performance for accurate protein structure predictions using four exemplar proteins: 6AWO, 6OAN, 7MEZ, and 6D6U. Using up to 200 ensembles, distributed across 50 nodes in Delta, equivalent to 200 A100 NVIDIA GPUs, we found that APACE is up to two orders of magnitude faster than off-the-shelf AlphaFold2 implementations, reducing time-to-solution from weeks to minutes. This computational approach may be readily linked with robotics laboratories to automate and accelerate scientific discovery.

GHP-MOFassemble: Diffusion modeling, high throughput screening, and molecular dynamics for rational discovery of novel metal-organic frameworks for carbon capture at scale

We introduce GHP-MOFassemble, a Generative artificial intelligence (AI), High Performance framework to accelerate the rational design of metal-organic frameworks (MOFs) with high CO2 capacity and synthesizable linkers. Our framework combines a diffusion model, a class of generative AI, to generate novel linkers that are assembled with one of three pre-selected nodes into MOFs in a primitive cubic (pcu) topology. The CO2 capacities of these AI-generated MOFs are predicted using a modified version of the crystal graph convolutional neural network model. We then use the LAMMPS code to perform molecular dynamics simulations to relax the AI-generated MOF structures, and identify those that converge to stable structures, and maintain their porous properties throughout the simulations. Among 120,000 pcu MOF candidates generated by the GHP-MOFassemble framework, with three distinct metal nodes (Cu paddlewheel, Zn paddlewheel, Zn tetramer), a total of 102 structures completed molecular dynamics simulations at 1 bar with predicted CO2 capacity higher than 2 mmol/g at 0.1 bar, which corresponds to the top 5% of hMOFs in the hypothetical MOF (hMOF) dataset in the MOFX-DB database. Among these candidates, 18 have change in density lower than 1% during molecular dynamics simulations, indicating their stability. We also found that the top five GHP-MOFassemble's MOF structures have CO2 capacities higher than 96.9% of hMOF structures. This new approach combines generative AI, graph modeling, large-scale molecular dynamics simulations, and extreme scale computing to open up new pathways for the accelerated discovery of novel MOF structures at scale.

End-to-end AI Framework for Hyperparameter Optimization, Model Training, and Interpretable Inference for Molecules and Crystals

We introduce an end-to-end computational framework that enables hyperparameter optimization with the DeepHyper library, accelerated training, and interpretable AI inference with a suite of state-of-the-art AI models, including CGCNN, PhysNet, SchNet, MPNN, MPNN-transformer, and TorchMD-Net. We use these AI models and the benchmark QM9, hMOF, and MD17 datasets to showcase the prediction of user-specified materials properties in modern computing environments, and to demonstrate translational applications for the modeling of small molecules, crystals and metal organic frameworks with a unified, stand-alone framework. We deployed and tested this framework in the ThetaGPU supercomputer at the Argonne Leadership Computing Facility, and the Delta supercomputer at the National Center for Supercomputing Applications to provide researchers with modern tools to conduct accelerated AI-driven discovery in leadership class computing environments.