Abstract Chemical disorder and point defects critically influence the properties of two-dimensional (2D) materials, but their theoretical description is limited by the vast configurational space of possible atomic arrangements, which is intractable for conventional first-principles methods such as density functional theory (DFT). Here, we develop and validate a method for accelerated assessment of thermodynamic stability of alloyed transition metal dichalcogenide monolayers with and without vacancies. A combination of DFT and graph neural networks (GNNs) is applied across the composition/configuration space (CCS) representing structured collections of symmetry-unique atomic arrangements. First, using the method proposed and convex-hull-based analysis, we show that quaternary alloys are thermodynamically unstable at 0 K. This problem is further addressed by finite-temperature analysis. Second, we demonstrate that random sampling underestimates the configurational entropy contribution for highly defective quaternaries, while considering systematically sampled CCS delivers accurate assessments. Furthermore, structured training data are shown to improve GNN generalization and out-of-domain accuracy relative to random sampling. Third, reconstructing finite-temperature free-energy convex hulls for low-defect alloys, many quaternary compositions become thermodynamically stable. Chalcogen vacancies emerge as the dominant favored intrinsic defect in the studied systems, remaining only ≈20-30 meV/atom above the free-energy hull at temperatures up to 1200 K, whereas metal vacancies stay less favorable (≈70-90 meV/atom). Altogether these results establish a scalable route for finite-temperature thermodynamic screening of chemically disordered 2D materials with defects.
Agile methods continue to gain popularity. In particular, the Scrum method appears to be on the verge of becoming a de-facto standard in the industry, leading the so called Agile movement. While there are success stories and recommendations, there is little scientifically valid evidence of the challenges in the adoptio...
A. Marchenko, P. Abrahamsson· Agile Conference· 59 citations· ⚡11
A comprehensive taxonomy of the challenges faced when a medium-scale organization decided to adopt software platforms is provided, namely: business challenges, organizational challenges, technical challenges, and people challenges.
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It is shown that high article processing charges are not sufficiently justified by the publishers, which often lack transparency and may prevent authors from adopting OA.
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MCGLPPI, a novel geometric representation learning framework that combines graph neural networks (GNNs) with the MARTINI molecular coarse-grained (CG) model to predict overall PPI properties accurately and efficiently, offers an effective and efficient solution for PPI overall property predictions.
Yang Yue, Shu Li, Yihua Cheng et al.· bioRxiv· 15 citations
PepPCBench enables a robust evaluation of PFNN-based methods and supports their continued development for peptide-protein structure prediction, and highlights the influence of peptide length, conformational flexibility, and training set similarity on prediction accuracy.
Si-Long Zhai, Huifeng Zhao, Ji-Ke Wang et al.· Journal of Chemical Informat...· 13 citations· ⚡1
Abstract Predicting properties from coordinate–category data—sets of vectors paired with categorical information—is fundamental to computational science, manifesting in materials science as predicting formation energies or elastic moduli from crystal structures. While large language models (LLMs) have increasingly been...
Nawaf Alampara, Santiago Miret, Kevin Maik Jablonka· Nature Computational Science· 13 citations
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