Jialei Xu, Shenghong Guo, Miaolan Zhen, Zhuochen Yu, Youliang Zhu, Giuseppe Milano, Zhongyuan Lu
{"title":"PyGAMD: Python graphics processing unit-accelerated molecular dynamics software","authors":"Jialei Xu, Shenghong Guo, Miaolan Zhen, Zhuochen Yu, Youliang Zhu, Giuseppe Milano, Zhongyuan Lu","doi":"10.1002/mgea.70019","DOIUrl":"https://doi.org/10.1002/mgea.70019","url":null,"abstract":"<p>PyGAMD (Python GPU-accelerated molecular dynamics software) is a molecular simulation platform developed from scratch. It is designed for soft matter, especially for polymer by integrating coarse-grained/multi-scale models, methods, and force fields. It essentially includes an interpreter of molecular dynamics (MD) which supports secondary programming so that users can write their own functions by themselves, such as analytical potential forms for nonbonded, bond, angle, and dihedral interactions in an easy way, greatly extending the flexibility of MD simulations. The interpreter is written by pure Python language, making it easy to be modified and further developed. Some built-in libraries written by other languages that have been compiled for Python are added into PyGAMD to extend it's features, including configuration initialization, property analysis, etc. Machine learning force fields that are trained by DeePMD-kit are supported by PyGAMD for conveniently implementing multi-scale modeling and simulations. By designing an advanced framework of software, graphics processing unit-acceleration achieved by the Numba library of Python and compute unified device architecture reaches a high computing efficiency.</p>","PeriodicalId":100889,"journal":{"name":"Materials Genome Engineering Advances","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mgea.70019","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144514914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Machine learning-guided plasticity model in refractory high-entropy alloys","authors":"Shang Zhao, Jinshan Li, Weijie Liao, Ruihao Yuan","doi":"10.1002/mgea.70022","DOIUrl":"https://doi.org/10.1002/mgea.70022","url":null,"abstract":"<p>Refractory high-entropy alloys (RHEAs) represent a promising class of structural materials with significant potential for various applications. However, their limited plasticity at room temperature restricts their deformability, posing challenges for processing and industrial implementation. Traditional experimental methods for characterizing this property are time-consuming and resource-intensive, necessitating the development of efficient predictive models. In this study, we propose a machine learning approach to predict the fracture strain of RHEAs. A dataset comprising 128 RHEAs fracture strain samples is compiled from the literature and classified into two categories: “high plasticity” and “low plasticity.” Through feature selection techniques, a critical subset of features is identified, enabling a support vector classification model to achieve 96% prediction accuracy. Additionally, an interpretable machine learning algorithm is employed to derive explicit functional expressions describing the relationship between key features and fracture strain, achieving 88% accuracy. Although slightly less accurate, it provides valuable insights into the underlying mechanisms, making it a useful tool for materials design and optimization.</p>","PeriodicalId":100889,"journal":{"name":"Materials Genome Engineering Advances","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mgea.70022","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144514913","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hongyu Wu, Wenliang Shi, Ri He, Guoyong Shi, Chunxiao Zhang, Jinyun Liu, Zhicheng Zhong, Runwei Li
{"title":"Atomistic simulations of thermodynamic properties with nuclear quantum effects of liquid gallium from first principles","authors":"Hongyu Wu, Wenliang Shi, Ri He, Guoyong Shi, Chunxiao Zhang, Jinyun Liu, Zhicheng Zhong, Runwei Li","doi":"10.1002/mgea.70016","DOIUrl":"https://doi.org/10.1002/mgea.70016","url":null,"abstract":"<p>Determining thermodynamic properties in disordered systems remains a formidable challenge because of the difficulty in incorporating nuclear quantum effects into large-scale and nonperiodic atomic simulations. In this study, we employ a machine learning deep potential model in conjunction with the quantum thermal bath method, enabling machine learning molecular dynamics to simulate thermodynamic quantities of liquid materials with satisfactory accuracy without significantly increasing computational costs. Using this approach, we accurately calculate the variations in various thermodynamic quantities of liquid metal gallium at temperatures ranging from zero to room temperature. The calculated thermodynamic properties accurately capture the solid-liquid phase transition behavior of gallium, whereas classical molecular dynamics methods fail to reproduce realistic results. Through this approach, we offer a potential method for accurately calculating the thermodynamic properties of liquids and other disordered systems.</p>","PeriodicalId":100889,"journal":{"name":"Materials Genome Engineering Advances","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mgea.70016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144514882","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shuai Lv, Lei Peng, Wentiao Wu, Yufan Yao, Shizhe Jiao, Wei Hu
{"title":"Bridging language models and computational materials science: A prompt-driven framework for material property prediction","authors":"Shuai Lv, Lei Peng, Wentiao Wu, Yufan Yao, Shizhe Jiao, Wei Hu","doi":"10.1002/mgea.70013","DOIUrl":"https://doi.org/10.1002/mgea.70013","url":null,"abstract":"<p>Large language models (LLMs) have demonstrated effectiveness in interpreting complex data. However, they encounter challenges in specialized applications, such as predicting material properties, due to limited integration with domain-specific knowledge. To overcome these challenges, we introduce MatAgent, an artificial intelligence (AI) agent that combines computational chemistry tools, such as first-principles (FP) calculations, with the capabilities of LLMs to predict key properties of materials. By leveraging prompt engineering and advanced reasoning techniques, MatAgent integrates a series of tools and acquires domain-specific knowledge in the field of material property prediction, enabling it to accurately predict the properties of materials without the need for predefined input structures. The experimental results indicate that MatAgent achieves a significant improvement in prediction accuracy and efficiency. As a novel approach that integrates LLMs with FP calculation tools, MatAgent highlights the potential of combining advanced computational techniques to enhance material property predictions, representing a significant advancement in computational materials science.</p>","PeriodicalId":100889,"journal":{"name":"Materials Genome Engineering Advances","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mgea.70013","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144514880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Revolutionizing materials design through advanced artificial intelligence-assisted multiscale simulation","authors":"Hui Wang, Xingqiu Chen","doi":"10.1002/mgea.70017","DOIUrl":"https://doi.org/10.1002/mgea.70017","url":null,"abstract":"<p>Materials science is currently at the forefront of technological development, which enables remarkable advancements in various aspects of our society. For the past few decades, multiscale computational simulations ranging from accurate first principles calculation and atomistic molecular dynamics to mesoscopic and macroscopic continuum models have been essential tools for understanding, predicting, and ultimately designing materials with desired properties.</p><p>Today, multiscale modeling/simulation is entering an exciting era where recent rapid advances in artificial intelligence (AI)/data-driven approach are beginning to converge with well-established multiscale computational simulation toolset. This convergence opens unprecedented opportunities not only for accelerating high-throughput screening of vast compositional and structural space across a wide variety of length/time scales but also for discovering new structure–property relationships for efficient designing and synthesizing materials for practical applications.</p><p>There is no doubt that AI/data-driven approaches are a central pillar within today's materials genome engineering paradigm for rapid materials discovery and design, which inspires us with honor and immense pleasure to bring forth the special issue of <i>Materials Genome Engineering Advances</i> (MGE Advances) entitled “Revolutionizing Materials Discovery by Advanced AI-Assisted Multiscale Computational Modeling” to realize its mission of breaking the barrier between disciplines and fostering digital, smart materials R&D. The following thematic selection highlights the active state-of-the-art advances in applications involving advanced machine learning/AI algorithms applied to a variety of multiscale computational modeling/numerical simulation efforts.</p><p>Materials discovery accelerated with high-throughput computing: For example, benefiting from high-throughput density functional theory calculations to search for candidates of antiperovskites possessing desired properties (such as large spin Hall conductivity) or guiding the design of particular alloy systems (for instance, easily separable Fe-containing intermetallics in Al–Si alloy).</p><p>The development and application of advanced ML potentials: Developing deep learning- or machine learning-based potentials enables atomistic simulations for complicated events at larger length/time scales or in harsh environments (e.g., investigating finite-temperature behaviors of materials such as NbO<sub>2</sub> or deciphering high-temperature deforming mechanisms of intermetallics such as Ni<sub>3</sub>Al).</p><p>Data-aided design of novel materials: Adopting a data-driven strategy based on existing simulation or experimental datasets to design novel materials with desired functions (e.g., optimizing mechanical properties of biodegradable deformed zinc alloys).</p><p>Developing new computational methods/tools for science innovations: Improving existing computational infra","PeriodicalId":100889,"journal":{"name":"Materials Genome Engineering Advances","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mgea.70017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144514929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Accelerating the design of highly separable Fe-containing intermetallics in Al–Si alloys via DFT calculations and experimental validation","authors":"Xiaozu Zhang, Dongtao Wang, Hiromi Nagaumi, Rui Wang, Zibin Wu, Minghe Zhang, Dongsheng Gao, Hao Chen, Pengfei Wang, Pengfei Zhou, Yunxuan Zhou, Zhixiu Wang, Tailin Li","doi":"10.1002/mgea.70008","DOIUrl":"https://doi.org/10.1002/mgea.70008","url":null,"abstract":"<p>The detrimental Fe element in Al-Si cast alloy can be effectively removed by Fe-containing intermetallics separation. However, the formation temperature of Fe-containing intermetallics can be further improved to increase the removal efficiency of Fe element. The effects of the Cr/Mn atomic ratio on the stability, theoretical melting point, elastic modulus, and thermal properties were calculated with the aim of improving the stability of the α-Al(FeMnCr)Si phase. An increased Cr/Mn atomic ratio effectively increased the stability, theoretical melting point, elastic modulus, isobaric heat capacity, and reduced the volumetric thermal expansion coefficient of α-Al(FeMnCr)Si phase, which can be explained by the strengthened Al-Cr and Si-Cr chemical bonds. The experimental study results revealed that the formation temperature and Young's modulus of the α-Al(FeMnCr)Si phase increase from 673.0°C and 228.5 GPa to 732.0°C and 272.1 GPa with the Cr/Mn atomic ratio increasing from 0.11 to 0.8, which better validates the thermodynamic stability, theoretical melting point and elastic modulus calculation results. These results provide a new strategy for designing Fe-containing intermetallics with the desired properties, which contributes to guiding the development of high-performance recycled Al-Si alloys.</p>","PeriodicalId":100889,"journal":{"name":"Materials Genome Engineering Advances","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mgea.70008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144514554","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Machine learning-accelerated computational screening of CrNiCu ternary alloy as superior cocatalyst for photocatalytic hydrogen evolution","authors":"Shouwei Sang, Kangyu Zhang, Lichang Yin, Gang Liu","doi":"10.1002/mgea.70014","DOIUrl":"https://doi.org/10.1002/mgea.70014","url":null,"abstract":"<p>The development of cost-effective noble-metal-free cocatalysts with exceptional hydrogen evolution reaction (HER) activity is critical for advancing scalable and sustainable photocatalytic hydrogen production. Although platinum (Pt) remains a benchmark HER catalyst, its scarcity and high cost stimulates the search for viable alternatives. In this work, a machine learning (ML)-accelerated strategy is presented to screen highly active ternary CrNiCu alloys. Combining with density functional theory calculations, XGBoost regression models were trained to predict hydrogen adsorption energies and water dissociation energy barriers on CrNiCu alloy surfaces. Consequently, the theoretical exchange current densities were predicted for all possible compositions of CrNiCu alloys, enabling the identification of alloy catalysts with composition of 10∼30 at.% Cr, 30–50 at.% Ni, and 20–60 at.% Cu that exhibits superior HER activity than Pt. Stability assessment of optimal ternary CrNiCu alloys further confirms their excellent resistance to element segregation and hydroxyl poisoning under operational conditions. This work not only identifies promising ternary CrNiCu alloys of non-noble HER catalysts but also establishes an efficient ML-accelerated computational framework for the discovery of durable high-activity alloys for renewable energy applications.</p>","PeriodicalId":100889,"journal":{"name":"Materials Genome Engineering Advances","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mgea.70014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144514509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xinhang Li, Yongqiang Wang, Tianyu Jiao, Zhaoxin Liu, Chuanle Yang, Ri He, Liang Si
{"title":"Finite-temperature properties of \u0000 \u0000 \u0000 \u0000 NbO\u0000 2\u0000 \u0000 \u0000 ${text{NbO}}_{2}$\u0000 from a deep-learning interatomic potential","authors":"Xinhang Li, Yongqiang Wang, Tianyu Jiao, Zhaoxin Liu, Chuanle Yang, Ri He, Liang Si","doi":"10.1002/mgea.70011","DOIUrl":"https://doi.org/10.1002/mgea.70011","url":null,"abstract":"<p>Using first-principles-based machine-learning potential, molecular dynamics (MD) simulations are performed to investigate the micro-mechanism in phase transition of <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mtext>NbO</mtext>\u0000 <mn>2</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation> ${text{NbO}}_{2}$</annotation>\u0000 </semantics></math>. Treating the DFT results of the low- and intermediate-temperature phases of <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mtext>NbO</mtext>\u0000 <mn>2</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation> ${text{NbO}}_{2}$</annotation>\u0000 </semantics></math> as training data in the deep-learning model, we successfully constructed an interatomic potential capable of accurately reproducing the phase transitions from low-temperature (pressure) to high-temperature (pressure) regimes. Notably, our simulations predict a high-pressure monoclinic phase (>14 GPa) without treating its information in the training set, consistent with previous experimental findings, demonstrating the reliability of the constructed interatomic potential. We identified the Nb-dimers as the key structural motif governing the phase transitions. At low temperatures, the displacements of the Nb-dimers drive the transition between the <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>I</mi>\u0000 <msub>\u0000 <mn>4</mn>\u0000 <mn>1</mn>\u0000 </msub>\u0000 <mo>/</mo>\u0000 <mi>a</mi>\u0000 </mrow>\u0000 <annotation> $I{4}_{1}/a$</annotation>\u0000 </semantics></math> (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>α</mi>\u0000 </mrow>\u0000 <annotation> $alpha $</annotation>\u0000 </semantics></math>-<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <msub>\u0000 <mtext>NbO</mtext>\u0000 <mn>2</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation> ${text{NbO}}_{2}$</annotation>\u0000 </semantics></math>) and <span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>I</mi>\u0000 <msub>\u0000 <mn>4</mn>\u0000 <mn>1</mn>\u0000 </msub>\u0000 </mrow>\u0000 <annotation> $I{4}_{1}$</annotation>\u0000 </semantics></math> (<span></span><math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>β</mi>\u0000 <","PeriodicalId":100889,"journal":{"name":"Materials Genome Engineering Advances","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/mgea.70011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144514615","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}