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Abstract The Normal Mode Analysis (NMA) is a standard approach to elucidate the anisotropic vibrations of macromolecules at their folded states, where low-frequency collective motions can reveal rearrangements of domains and changes in the exposed surface of macromolecules. Recent advances in structural biology have enabled the resolution of megascale macromolecules with millions of atoms. However, the calculation of their vibrational modes remains elusive due to the prohibitive cost associated with constructing and diagonalizing the underlying eigenproblem and the current approaches to NMA are not readily adaptable for efficient parallel computing on graphic processing unit (GPU). Here, we present eigenproblem construction and diagonalization approach that implements level-structure bandwidth-reducing algorithms to transform the sparse computation in NMA to a globally-sparse-yet-locally-dense computation, allowing batched tensor products to be most efficiently executed on GPU. We map, optimize, and compare several low-complexity Krylov-subspace eigensolvers, supplemented by techniques such as Chebyshev filtering, sum decomposition, external explicit deflation and shift-and-inverse, to allow fast GPU-resident calculations. The method allows accurate calculation of the first 1000 vibrational modes of some largest structures in PDB ( > 2.4 million atoms) at least 250 times faster than existing methods. 

Abstract Surface acoustic waves (SAWs) propagate along solid-air, solid-liquid, and solid-solid interfaces. Their characteristics depend on the elastic properties of the solid. Combining transmission electron microscopy (TEM) experiments with molecular dynamics (MD) simulations, we probe atomic environments around intrinsic defects that generate SAWs in vertically stacked two-dimensional (2D) bilayers of MoS₂. Our joint experimental-simulation study provides insights into SAW-induced structural and dynamical changes and thermomechanical responses of MoS₂bilayers. Using MD simulations, we compute mechanical properties from the SAW velocity and thermal conductivity from thermal diffusion of SAWs. The results for Young’s modulus and thermal conductivity of an MoS₂monolayer are in good agreement with experiments. The presence of defects, such as nanopores which generate SAWs, reduces the thermal conductivity of 2D-MoS₂by an order of magnitude. We also observe dramatic changes in moiré patterns, phonon focusing, and cuspidal structures on 2D-MoS₂layers. 

Machine learning represents a milestone in data-driven research, including material informatics, robotics, and computer-aided drug discovery. With the continuously growing virtual and synthetically available chemical space, efficient and robust quantitative structure–activity relationship (QSAR) methods are required to uncover molecules with desired properties. Herein, we propose variable-length-array SMILES-based (VLA-SMILES) structural descriptors that expand conventional SMILES descriptors widely used in machine learning. This structural representation extends the family of numerically coded SMILES, particularly binary SMILES, to expedite the discovery of new deep learning QSAR models with high predictive ability. VLA-SMILES descriptors were shown to speed up the training of QSAR models based on multilayer perceptron (MLP) with optimized backpropagation (ATransformedBP), resilient propagation (iRPROP‒), and Adam optimization learning algorithms featuring rational train–test splitting, while improving the predictive ability toward the more compute-intensive binary SMILES representation format. All the tested MLPs under the same length-array-based SMILES descriptors showed similar predictive ability and convergence rate of training in combination with the considered learning procedures. Validation with the Kennard–Stone train–test splitting based on the structural descriptor similarity metrics was found more effective than the partitioning with the ranking by activity based on biological activity values metrics for the entire set of VLA-SMILES featured QSAR. Robustness and the predictive ability of MLP models based on VLA-SMILES were assessed via the method of QSAR parametric model validation. In addition, the method of the statistical H0 hypothesis testing of the linear regression between real and observed activities based on the F2,n−2 -criteria was used for predictability estimation among VLA-SMILES featured QSAR-MLPs (with n being the volume of the testing set). Both approaches of QSAR parametric model validation and statistical hypothesis testing were found to correlate when used for the quantitative evaluation of predictabilities of the designed QSAR models with VLA-SMILES descriptors. 

Computing landscape is evolving rapidly. Exascale computers have arrived, which can perform 10^18 mathematical operations per second. At the same time, quantum supremacy has been demonstrated, where quantum computers have outperformed these fastest supercomputers for certain problems. Meanwhile, artificial intelligence (AI) is transforming every aspect of science and engineering. A highly anticipated application of the emerging nexus of exascale computing, quantum computing and AI is computational design of new materials with desired functionalities, which has been the elusive goal of the federal materials genome initiative. The rapid change in computing landscape resulting from these developments has not been matched by pedagogical developments needed to train the next generation of materials engineering cyberworkforce. This gap in curricula across colleges and universities offers a unique opportunity to create educational tools, enabling a decentralized training of cyberworkforce. To achieve this, we have developed training modules for a new generation of quantum materials simulator, named AIQ-XMaS (AI and quantum-computing enabled exascale materials simulator), which integrates exascalable quantum, reactive and neural-network molecular dynamics simulations with unique AI and quantum-computing capabilities to study a wide range of materials and devices of high societal impact such as optoelectronics and health. As a singleentry access point to these training modules, we have also built a CyberMAGICS (cyber training on materials genome innovation for computational software) portal, which includes step-by-step instructions in Jupyter notebooks and associated tutorials, while providing online cloud service for those who do not have access to adequate computing platform. The modules are incorporated into our open-source AIQ-XMaS software suite as tutorial examples and are piloted in classroom and workshop settings to directly train many users at the University of Southern California (USC) and Howard University—one of the largest historically black colleges and universities (HBCUs), with a strong focus on underrepresented groups. In this paper, we summarize these educational developments, including findings from the first CyberMAGICS Workshop for Underrepresented Groups, along with an introduction to the AIQ-XMaS software suite. Our training modules also include a new generation of open programming languages for exascale computing (e.g., OpenMP target) and quantum computing (e.g., Qiskit) used in our scalable simulation and AI engines that underlie AIQ-XMaS. Our training modules essentially support unique dual-degree opportunities at USC in the emerging exa-quantum-AI era: Ph.D. in science or engineering, concurrently with MS in computer science specialized in high-performance computing and simulations, MS in quantum information science or MS in materials engineering with machine learning. The developed modular cyber-training pedagogy is applicable to broad engineering education at large. 

Optoelectronic properties of devices made of two-dimensional materials depend largely on the dielectric constant and thickness of a substrate. To systematically investigate the thickness dependence of dielectric constant from first principles, we have implemented a double-cell method based on a theoretical framework by Martyna and Tuckerman [J. Chem. Phys. 110, 2810 (1999)] and therewith developed a general and robust procedure to calculate dielectric constants of slab systems from electric displacement and electric field, which is free from material-specific adjustable parameters. We have applied the procedure to a prototypical substrate, Al 2 O 3 , thereby computing high-frequency and static dielectric constants of a finite slab as a function of the number of crystalline unit-cell layers. We find that two and four layers are sufficient for the high-frequency and static dielectric constants of (0001) Al 2 O 3 slabs to recover 90% of the respective bulk values computed by a Berry-phase method. This method allows one to estimate the thickness dependence of dielectric constants for various materials used in emerging two-dimensional nanophotonics, while providing an analytic formula that can be incorporated into photonics simulations.