4.8 Article

Bandgap prediction by deep learning in configurationally hybridized graphene and boron nitride

期刊

NPJ COMPUTATIONAL MATERIALS
卷 5, 期 -, 页码 -

出版社

NATURE PORTFOLIO
DOI: 10.1038/s41524-019-0165-4

关键词

-

资金

  1. University of Missouri-Columbia
  2. NASA Missouri Space Consortium [00049784]
  3. Unite States Department of Agriculture [2018-67017-27880]
  4. Department of Energy National Energy Technology Laboratory [DE-FE0031645]
  5. National Science Foundation [DBI1759934, IIS1763246]
  6. NSF [1429294]

向作者/读者索取更多资源

It is well-known that the atomic-scale and nano-scale configuration of dopants can play a crucial role in determining the electronic properties of materials. However, predicting such effects is challenging due to the large range of atomic configurations that are possible. Here, we present a case study of how deep learning algorithms can enable bandgap prediction in hybridized boron-nitrogen graphene with arbitrary supercell configurations. A material descriptor that enables correlation of structure and bandgap was developed for convolutional neural networks. Bandgaps calculated by ab initio calculations, and corresponding structures, were used as training datasets. The trained networks were then used to predict bandgaps of systems with various configurations. For 4 x 4 and 5 x 5 supercells they accurately predict bandgaps, with a R-2 of > 90% and root-mean-square error of similar to 0.1 eV. The transfer learning was performed by leveraging data generated from small supercells to improve the prediction accuracy for 6 x 6 supercells. This work will pave a route to future investigation of configurationally hybridized graphene and other 2D materials. Moreover, given the ubiquitous existence of configurations in materials, this work may stimulate interest in applying deep learning algorithms for the configurational design of materials across different length scales.

作者

我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。

评论

主要评分

4.8
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

Article Chemistry, Multidisciplinary

Direct Freeform Laser Fabrication of 3D Conformable Electronics

Bujingda Zheng, Ganggang Zhao, Zheng Yan, Yunchao Xie, Jian Lin

Summary: 3D conformable electronic devices on freeform surfaces have superior performance and have witnessed exponential growth in various applications. However, their potential is limited by a lack of advanced fabrication techniques. To overcome this challenge, a new direct freeform laser fabrication method for directly fabricating 3D conformable electronics on targeted arbitrary surfaces is reported.

ADVANCED FUNCTIONAL MATERIALS (2023)

Article Engineering, Environmental

A two-sorbent system for fast uptake of arsenate from water: Batch and column studies

Zhengyang Wang, Xiangyu Bi, Xiaoqing He, Yunchao Xie, Jian Lin, Baolin Deng

Summary: Decentralized and/or point-of-use systems are crucial for addressing challenging water quality issues. Sorption-based approaches, with their simplicity in operation, are ideal for such applications. This study presents a two-sorbent system consisting of Fe2O3-coated mesoporous carbon and nano-Fe2O3-coated activated carbon, which effectively removes arsenate through a capture-and-storage process with a short empty bed contact time.

WATER RESEARCH (2023)

Article Plant Sciences

High-throughput identification of novel heat tolerance genes via genome-wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii

Erin M. Mattoon, William E. McHargue, Catherine E. Bailey, Ningning Zhang, Chen Chen, James Eckhardt, Chris G. Daum, Matt Zane, Christa Pennacchio, Jeremy Schmutz, Ronan C. O'Malley, Jianlin Cheng, Ru Zhang

Summary: By conducting genome-wide screens and transcriptomics/proteomics analysis, we identified a list of 933 high/medium-confidence genes with putative roles in heat tolerance in photosynthetic cells of the green alga Chlamydomonas. This provides potential engineering targets to improve thermotolerance in algae and crops.

PLANT CELL AND ENVIRONMENT (2023)

Review Engineering, Electrical & Electronic

Efficient Acceleration of Deep Learning Inference on Resource-Constrained Edge Devices: A Review

Md. Maruf Hossain Shuvo, Syed Kamrul Islam, Jianlin Cheng, Bashir I. Morshed

Summary: The successful integration of deep neural networks has led to breakthroughs in various fields, but deploying these accurate models for practical machine learning solutions remains challenging. Deep learning algorithms are often computationally expensive, power-hungry, and require large memory. Edge devices, such as mobile phones and IoT devices, have limited resources but can reduce cloud transmission cost.

PROCEEDINGS OF THE IEEE (2023)

Review Materials Science, Multidisciplinary

Toward autonomous laboratories: Convergence of artificial intelligence and experimental automation

Yunchao Xie, Kianoosh Sattari, Chi Zhang, Jian Lin

Summary: The increasing demand for novel materials has led to the retrofitting of traditional research paradigms with artificial intelligence and automation. An autonomous experimental platform (AEP) has emerged as a research frontier that integrates data-driven algorithms and experimental automation for material development. This review provides insights into developing data-driven algorithms, recent progress in automated material synthesis, ML-enabled data analysis, and decision-making, and the challenges and opportunities in developing the next-generation AEP for autonomous laboratories.

PROGRESS IN MATERIALS SCIENCE (2023)

Article Biochemical Research Methods

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Tianqi Wu, Zhiye Guo, Jianlin Cheng

Summary: A deep learning-based method called ATOMRefine is developed to improve the quality and nativeness of predicted protein structures. It directly refines protein atomic coordinates to enhance the initial structural models generated by AlphaFold, outperforming state-of-the-art refinement methods.

BIOINFORMATICS (2023)

Article Biochemistry & Molecular Biology

Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions

Nabin Giri, Raj S. Roy, Jianlin Cheng

Summary: Cryo-Electron Microscopy (cryo-EM) is a crucial technology for determining protein structures, especially large complexes and assemblies. The challenge lies in automatically reconstructing accurate protein structures from cryo-EM density maps. This review provides an overview of deep learning methods used for building protein structures from cryo-EM density maps, analyzes their impact, and discusses the challenges in preparing high-quality training data sets. Advanced deep learning models that integrate cryo-EM data with other complementary sources such as protein sequences and AlphaFold-predicted structures need to be developed for future advancements in the field.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2023)

Article Multidisciplinary Sciences

A large expert-curated cryo-EM image dataset for machine learning protein particle picking

Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng

Summary: Cryo-electron microscopy is a powerful technique for accurately determining biological macromolecular complexes. However, the process of picking single-protein particles from cryo-EM micrographs is time-consuming. To address this issue, we introduce CryoPPP, a large, diverse, expert-curated cryo-EM image dataset for efficient protein particle picking and analysis.

SCIENTIFIC DATA (2023)

Article Engineering, Manufacturing

3D-printing of selectively porous, freestanding structures via humidity-induced rapid phase change

Jacob Search, Alireza Mahjoubnia, Andy C. Chen, Heng Deng, Aik Jong Tan, Shi-you Chen, Jian Lin

Summary: The emergence of 3D printing has advanced the fabrication of 3D structures, but current techniques have limitations in print time and versatility. This study introduces a new approach using a rapid liquid-to-solid phase change mechanism enabled by humidity to print selectively porous, freestanding structures without support. Various structures were successfully printed, and the printed material showed great biocompatibility.

ADDITIVE MANUFACTURING (2023)

Article Biochemistry & Molecular Biology

Genomic imbalance modulates transposable element expression in maize

Hua Yang, Xiaowen Shi, Chen Chen, Jie Hou, Tieming Ji, Jianlin Cheng, James A. Birchler

Summary: Genomic imbalance refers to the more severe phenotypic consequences of changing part of a chromosome compared with the whole genome set. Studies have found that aneuploidy often shows an inverse modulation of transposable elements (TEs), while reductions in monosomy and increases in disomy and trisomy are also common. The ploidy series, on the other hand, showed little TE modulation. The modulation of TEs and genes in the same experimental group were compared, and TEs showed greater modulation than genes, especially in disomy.

PLANT COMMUNICATIONS (2023)

Article Biochemical Research Methods

Predicted structural proteome of Sphagnum divinum and proteome-scale annotation

Russell B. Davidson, Mark Coletti, Mu Gao, Bryan Piatkowski, Avinash Sreedasyam, Farhan Quadir, David J. Weston, Jeremy Schmutz, Jianlin Cheng, Jeffrey Skolnick, Jerry M. Parks, Ada Sedova

Summary: This study utilizes AlphaFold to predict the structural proteome of Sphagnum divinum, and provides structure alignment and enzyme classification, filling the gaps in the field of protein structure for Sphagnum species.

BIOINFORMATICS (2023)

Article Biochemistry & Molecular Biology

Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15

Raj S. Roy, Jian Liu, Nabin Giri, Zhiye Guo, Jianlin Cheng

Summary: In this study, a new method (MULTICOM_qa) was proposed to estimate the accuracy of protein complex models by combining pairwise similarity score (PSS) and interface contact probability score (ICPS) based on deep learning inter-chain contact prediction. The method performed well in estimating the global structure accuracy of assembly models and demonstrated the effectiveness of combining PSS and ICPS.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2023)

Article Multidisciplinary Sciences

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

Cole E. E. McKay, Jianlin Cheng, John J. J. Tanner

Summary: The crystal structure of the domain of unknown function family 507 protein from Aquifex aeolicus was determined, revealing a Y-shaped α-helical structure with pseudo-twofold symmetry. The structures differ in their C-terminal arm rotation, suggesting a potential functional site.

SCIENTIFIC REPORTS (2023)

Article Biochemical Research Methods

Single-cell Hi-C data enhancement with deep residual and generative adversarial networks

Yanli Wang, Zhiye Guo, Jianlin Cheng

Summary: In this study, we developed a new deep learning method called ScHiCEDRN for improving single-cell Hi-C data using deep residual networks and generative adversarial networks. Experimental results showed that ScHiCEDRN outperforms other four deep learning methods in enhancing raw single-cell Hi-C data of human and Drosophila, and it can generate single-cell Hi-C data more suitable for identifying topologically associating domain boundaries and reconstructing 3D chromosome structures.

BIOINFORMATICS (2023)

Article Biochemical Research Methods

3D-equivariant graph neural networks for protein model quality assessment

Chen Chen, Xiao Chen, Alex Morehead, Tianqi Wu, Jianlin Cheng

Summary: The researchers developed a new graph-based 3D-equivariant neural network method to estimate the accuracy of protein structural models. Their approach achieved state-of-the-art performance on protein structural models predicted by both traditional protein structure prediction methods and the latest end-to-end deep learning method-AlphaFold2. This suggests that 3D-equivariant graph neural network is a promising approach for the evaluation of protein structural models.

BIOINFORMATICS (2023)

暂无数据