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Analysis of chemical graphs is a major research topic in computational molecular biology due to its potential applications to drug design. One approach is inverse quantitative structure activity/property relationship (inverse QSAR/QSPR)…

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Crystal-graph attention networks have emerged recently as remarkable tools for the prediction of thermodynamic stability and materials properties from unrelaxed crystal structures. Previous networks trained on two million materials…

Supervised machine learning algorithms, such as graph neural networks (GNN), have successfully predicted material properties. However, the superior performance of GNN usually relies on end-to-end learning on large material datasets, which…

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Machine learning models for molecular property prediction generally rely on representations -- such as SMILES strings and molecular graphs -- that overlook the surface-local phenomena driving intermolecular behavior. 3D-based approaches…

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Grain boundaries have been shown to dramatically influence the behavior of relatively simple materials such as monatomic metals and binary alloys. The increased chemical complexity associated with multi-principal element alloys is…

Property prediction on molecular graphs is an important application of Graph Neural Networks. Recently, unlabeled molecular data has become abundant, which facilitates the rapid development of self-supervised learning for GNNs in the…

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The use of polymer nanocomposites as gas barrier materials has seen increasing interest, including applications involving hydrogen transport and storage. Better understanding of gas transport through those polymeric systems requires 3D…

Coarse-graining offers a means to extend the achievable time and length scales of molecular dynamics simulations beyond what is practically possible in the atomistic regime. Sampling molecular configurations of interest can be done…

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Predicting self-assembly in multi-component amphiphilic systems is challenging due to the complexity of intercomponent interactions and the combinatorial growth of possible formulations. In this study, we develop a unified machine-learning…

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Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…

Atomic migration from metallic contacts, and subsequent filament formation, is recognised as a prevailing mechanism leading to resistive switching in memristors based on two-dimensional materials (2DMs). This study presents a detailed…

Recent advances in scanning transmission electron and scanning tunneling microscopies allow researchers to measure materials structural and electronic properties, such as atomic displacements and charge density modulations, at an Angstrom…

We present an accurate machine learning (ML) model for atomistic simulations of carbon, constructed using the Gaussian approximation potential (GAP) methodology. The potential, named GAP-20, describes the properties of the bulk crystalline…

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Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a…

Biomolecules · Quantitative Biology 2021-09-15 Vy Duong , Elizabeth Diessner , Gianmarc Grazioli , Rachel W. Martin , Carter T. Butts

Computer-aided molecular design (CAMD) studies quantitative structure-property relationships and discovers desired molecules using optimization algorithms. With the emergence of machine learning models, CAMD score functions may be replaced…

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Granular materials (GMs) are ubiquitous in daily life. Understanding their properties is also important, especially in agriculture and industry. However, existing works require dedicated measurement equipment and also need large human…

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Predicting materials properties from composition or structure is of great interest to the materials science community. Deep learning has recently garnered considerable interest in materials predictive tasks with low model errors when…

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In precision agriculture, one of the most important tasks when exploring crop production is identifying individual plant components. There are several attempts to accomplish this task by the use of traditional 2D imaging, 3D…

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Graph neural networks (GNNs) have shown promise in learning the ground-state electronic properties of materials, subverting ab initio density functional theory (DFT) calculations when the underlying lattices can be represented as small…

Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds. However, because of the large temporal and…

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