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  1. Neural-network quantum molecular dynamics (NNQMD) simulations based on machine learning are revolutionizing atomistic simulations of materials by providing quantum-mechanical accuracy but orders-of-magnitude faster, illustrated by ACM Gordon Bell prize (2020) and finalist (2021). State-of-the-art (SOTA) NNQMD model founded on group theory featuring rotational equivari- ance and local descriptors has provided much higher accuracy and speed than those models, thus named Allegro (meaning fast). On massively parallel super- computers, however, it suffers a fidelity-scaling problem, where growing number of unphysical predictions of interatomic forces prohibits simulations involving larger numbers of atoms for longer times. Here, we solve this problem by com- bining the Allegro model with sharpness aware minimization (SAM) for enhanc- ing the robustness of model through improved smoothness of the loss landscape. The resulting Allegro-Legato (meaning fast and “smooth”) model was shown to elongate the time-to-failure tfailure, without sacrificing computational speed or accuracy. Specifically, Allegro-Legato exhibits much weaker dependence of time- to-failure on the problem size, t_failure = N^−0.14 (N is the number of atoms) compared to the SOTA Allegro model (t_failure ∝ N^−0.29), i.e., systematically delayed time-to-failure, thus allowing much larger and longer NNQMD simulations without failure. The model also exhibits excellent computational scalabil- ity and GPU acceleration on the Polaris supercomputer at Argonne Leadership Computing Facility. Such scalable, accurate, fast and robust NNQMD models will likely find broad applications in NNQMD simulations on emerging exaflop/s computers, with a specific example of accounting for nuclear quantum effects in the dynamics of ammonia to lay a foundation of the green ammonia technology for sustainability. 
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    Free, publicly-accessible full text available May 10, 2024
  2. Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which ami-no-acid residues are in close spatial proximity given the amino-acid sequence of a protein. Despite recent progresses in ML-based protein contact prediction, predict-ing contacts with a wide range of distances (commonly classified into short-, me-dium- and long-range contacts) remains a challenge. Here, we propose a multiscale graph neural network (GNN) based approach taking a cue from multiscale physics simulations, in which a standard pipeline involving a recurrent neural network (RNN) is augmented with three GNNs to refine predictive capability for short-, medium- and long-range residue contacts, respectively. Test results on the Pro-teinNet dataset show improved accuracy for contacts of all ranges using the pro-posed multiscale RNN+GNN approach over the conventional approach, including the most challenging case of long-range contact prediction. 
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