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Predicting X-ray Diffraction Quality of Protein Crystals Using a Deep-Learning Method 利用深度学习方法预测蛋白质晶体的 X 射线衍射质量
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-29 DOI: 10.3390/cryst14090771
Yujian Shen, Zhongjie Zhu, Qingjie Xiao, Kanglei Ye, Qisheng Wang, Yue Wang, Bo Sun
Over the past few decades, significant advancements in protein crystallography have led to a steady increase in the number of determined protein structures. The X-ray diffraction experiment remains one of the primary methods for investigating protein crystal structures. To obtain information about crystal structures, a sufficient number of high-quality crystals are typically required. At present, X-ray diffraction experiments on protein crystals primarily rely on manual selection by experimenters. However, each experiment is not only costly but also time-consuming. To address the urgent need for automatic selection of the proper protein crystal candidates for X-ray diffraction experiments, a protein-crystal-quality classification network, leveraging the ConvNeXt network architecture, is proposed. Subsequently, a new database is created, which includes protein crystal images and their corresponding X-ray diffraction images. Additionally, a novel method for categorizing protein quality based on the number of diffraction spots and the resolution is introduced. To further enhance the network’s focus on essential features of protein crystal images, a CBAM (Convolutional Block Attention Module) attention mechanism is incorporated between convolution layers. The experimental results demonstrate that the network achieves significant improvement in performing the prediction task, thereby effectively enhancing the probability of high-quality crystals being selected by experimenters.
在过去几十年中,蛋白质晶体学取得了重大进展,已确定的蛋白质结构数量稳步增加。X 射线衍射实验仍然是研究蛋白质晶体结构的主要方法之一。要获得晶体结构信息,通常需要足够数量的高质量晶体。目前,蛋白质晶体的 X 射线衍射实验主要依靠实验人员手动选择。然而,每次实验不仅成本高,而且耗时长。为了满足自动选择合适的候选蛋白质晶体进行 X 射线衍射实验的迫切需要,我们提出了一种利用 ConvNeXt 网络结构的蛋白质晶体质量分类网络。随后,创建了一个新的数据库,其中包括蛋白质晶体图像及其相应的 X 射线衍射图像。此外,还引入了一种基于衍射斑点数量和分辨率的蛋白质质量分类新方法。为了进一步提高网络对蛋白质晶体图像基本特征的关注,在卷积层之间加入了 CBAM(卷积块关注模块)关注机制。实验结果表明,该网络在执行预测任务方面取得了显著的改进,从而有效提高了实验人员选择高质量晶体的概率。
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引用次数: 0
Structural Insights into Phycocyanin Langmuir–Blodgett Multilayers via Serial Femtosecond Crystallography with X-ray Free-Electron Laser 利用 X 射线自由电子激光进行串行飞秒晶体学分析,揭示植物花青素朗缪尔-布洛杰特多层膜的结构奥秘
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-29 DOI: 10.3390/cryst14090767
Eugenia Pechkova, Fabio Massimo Speranza, Paola Ghisellini, Stefano Fiordoro, Cristina Rando, Roberto Eggenhöffner
Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has revolutionized classical X-ray diffraction experiments by utilizing ultra-short, intense, and coherent X-ray pulses. However, the SFX approach still requires thousands of nearly identical samples, leading to significant protein consumption. We propose utilizing Langmuir–Blodgett protein multilayers, which are characterized by long-range order, thermal stability, and the ability to induce protein crystallization, even in proteins that cannot be crystallized by conventional methods. This study aimed to combine the intrinsic properties of Langmuir–Blodgett multilayers with advanced XFEL techniques at the Linac Coherent Light Source. Since the macromolecule organization can be explored in nano or 2D crystals exploiting the properties of SFX–XFEL radiation that enable the capture of high-resolution diffraction images before radiation damage occurs, we propose Langmuir–Blodgett protein nanofilm technology as a novel approach for direct “on-chip” protein sample preparation. The present study extends previous investigations into Langmuir–Blodgett phycocyanin multilayer nanofilms using synchrotron radiation cryo-EM microscopy and second-order nonlinear imaging of chiral crystal (SONICC) experiments. We also examined the thermal stability of phycocyanin Langmuir–Blodgett multilayered films deposited on Si3N4 membranes to evaluate structural changes occurring at 150 °C compared with room temperature. Phycocyanin Langmuir–Blodgett films are worthy of investigation in view of their suitability for tissue engineering and other applications due to their thermal integrity and stability as the results of the present investigation reveal.
利用 X 射线自由电子激光器(XFEL)进行的串行飞秒晶体学(SFX)利用超短、高强度和相干 X 射线脉冲彻底改变了传统的 X 射线衍射实验。然而,SFX 方法仍然需要数千个几乎完全相同的样品,导致大量蛋白质消耗。我们建议利用朗缪尔-布洛杰特蛋白质多层膜,这种多层膜具有长程有序性、热稳定性和诱导蛋白质结晶的能力,甚至能诱导传统方法无法结晶的蛋白质结晶。这项研究旨在将朗缪尔-布洛杰特多层膜的固有特性与里纳克相干光源的先进 XFEL 技术相结合。由于可以利用 SFX-XFEL 辐射的特性在纳米或二维晶体中探索大分子的组织,从而在辐射损伤发生之前捕捉到高分辨率的衍射图像,因此我们建议将朗缪尔-布洛吉特蛋白质纳米薄膜技术作为直接制备 "片上 "蛋白质样品的一种新方法。本研究利用同步辐射冷冻电子显微镜和手性晶体二阶非线性成像(SONICC)实验,扩展了之前对朗缪尔-布洛吉特藻蓝蛋白多层纳米薄膜的研究。我们还研究了沉积在 Si3N4 膜上的植物花青素朗缪尔-布洛杰特多层膜的热稳定性,以评估与室温相比在 150 °C 时发生的结构变化。本研究的结果表明,植物花青素朗缪尔-布洛吉特薄膜具有热完整性和稳定性,适用于组织工程和其他应用,因此值得研究。
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引用次数: 0
Advanced Technologies in Graphene-Based Materials 石墨烯基材料的先进技术
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-29 DOI: 10.3390/cryst14090769
Justina Gaidukevic, Jurgis Barkauskas
Graphene-based materials, including single layer graphene, laser-induced graphene, carbon nanotubes, graphene oxide, and reduced graphene oxide, have become cornerstones of modern materials science due to their exceptional properties and wide range of potential applications [...]
石墨烯基材料,包括单层石墨烯、激光诱导石墨烯、碳纳米管、氧化石墨烯和还原氧化石墨烯,因其卓越的性能和广泛的潜在应用,已成为现代材料科学的基石 [...]
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引用次数: 0
Understanding the Mechanistic Pathways of N2 Reduction to Ammonia on (110) Facets of Transition Metal Carbides 了解过渡金属碳化物 (110) 面上 N2 还原成氨的机理途径
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-29 DOI: 10.3390/cryst14090770
Atef Iqbal, Egill Skúlason, Younes Abghoui
The conversion of molecular dinitrogen into ammonia under mild conditions is a significant pursuit in chemistry due to its potential for sustainable and clean ammonia production. The electrochemical reduction of N2 offers a promising route for achieving this goal with reduced energy consumption, utilizing renewable energy sources. However, the exploration of effective electrocatalysts for this process, particularly at room temperature and atmospheric pressure, remains under exploration. This study addresses this gap by conducting a comprehensive investigation of potential catalysts for nitrogen electro-reduction to ammonia under ambient conditions. Using density functional theory calculations, we explore the (110) facets of rock salt structures across 11 transition metal carbides. Catalytic activity is evaluated through the construction of free energy diagrams for associative, dissociative, and Mars–van Krevelen reaction mechanisms. Additionally, we assess material stability against electrochemical poisoning and decomposition of parent metals during operation. Our findings suggest that a few of the candidates are promising for nitrogen reduction reactions, such as TaC and WC, with moderate onset potentials (−0.66 V and −0.82 V vs. RHE) under ambient conditions.
在温和条件下将分子二氮转化为氨是化学领域的一个重要追求,因为它具有可持续和清洁生产氨的潜力。N2 的电化学还原为利用可再生能源、降低能耗实现这一目标提供了一条前景广阔的途径。然而,对这一过程的有效电催化剂的探索,尤其是在室温和常压下的探索,仍处于探索阶段。本研究针对这一空白,对环境条件下氮气电还原为氨气的潜在催化剂进行了全面研究。利用密度泛函理论计算,我们探索了 11 种过渡金属碳化物的岩盐结构 (110) 面。通过构建关联、离解和 Mars-van Krevelen 反应机制的自由能图,对催化活性进行了评估。此外,我们还评估了材料在运行过程中防止电化学中毒和母体金属分解的稳定性。我们的研究结果表明,在环境条件下,一些候选材料(如 TaC 和 WC)具有适中的起始电位(-0.66 V 和 -0.82 V 对 RHE),有望用于氮还原反应。
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引用次数: 0
A Review of Additively Manufactured Iron-Based Shape Memory Alloys 铁基形状记忆合金快速成型综述
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-29 DOI: 10.3390/cryst14090773
Qian Sun, Xiaojun Tan, Mingjun Ding, Bo Cao, Takeshi Iwamoto
Iron-based shape memory alloys (Fe-SMAs), traditionally manufactured, are favored in engineering applications owing to their cost-effectiveness and ease of fabrication. However, the conventional manufacturing process of Fe-SMAs is time-consuming and raw-material-wasting. In contrast, additive manufacturing (AM) technology offers a streamlined approach to the integral molding of materials, significantly reducing raw material usage and fabrication time. Despite its potential, research on AMed Fe-SMAs remains in its early stages. This review provides updated information on current AM technologies utilized for Fe-SMAs and their applications. It provides an in-depth discussion on how printing parameters, defects, and post-printing microstructure control affect the mechanical properties and shape memory effect (SME) of AMed Fe-SMAs. Furthermore, this review identifies existing challenges in the AMed Fe-SMA approach and proposes future research directions, highlighting potential areas for development. The insights presented aim to guide improvements in the material properties of AMed Fe-SMAs by optimizing printing parameters and enhancing the SME through microstructure adjustment.
传统制造的铁基形状记忆合金(Fe-SMA)因其成本效益高、易于制造而在工程应用中备受青睐。然而,铁基形状记忆合金的传统制造工艺既耗时又浪费原材料。相比之下,快速成型制造(AM)技术提供了一种简化的材料整体成型方法,可显著减少原材料用量和制造时间。尽管具有潜力,但有关 AMed Fe-SMA 的研究仍处于早期阶段。本综述提供了当前用于铁-SMA 的 AM 技术及其应用的最新信息。它深入探讨了打印参数、缺陷和打印后微结构控制如何影响 AMed Fe-SMA 的机械性能和形状记忆效应 (SME)。此外,本综述还指出了 AMed Fe-SMA 方法中的现有挑战,并提出了未来的研究方向,同时强调了潜在的发展领域。本文提出的见解旨在通过优化印刷参数和调整微观结构来提高 SME,从而改善 AMed Fe-SMA 的材料性能。
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引用次数: 0
Study on the Wear Resistance Performance of the Hot-Rolled BTW1/Q345 Composite Plate under Different Annealing Temperatures 不同退火温度下热轧 BTW1/Q345 复合板材的耐磨性能研究
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-29 DOI: 10.3390/cryst14090772
Lei Huang, Ke Wang, Wenjun Meng, Zhixia Wang, Pengtao Liu
Wear-resistant steel/carbon steel composite plates not only have the double performance advantages of high strength and wear resistance but can also reduce energy consumption and production costs. Based on a 50% reduction rate, the wear resistance of the BTW1/Q345 composite was studied at different annealing temperatures, and the dry friction and wear tests of the BTW1/Q345 composite at different annealing temperatures were carried out using RETC MFT-5000. By using the white-light interference three-dimensional surface profiler, scanning electron microscope (SEM), and backscattered electron diffraction (EBSD) technology, we carried out a detailed analysis of the macroscopic and microscopic morphology and wear mechanism of wear traces at different annealing temperatures. The effects of the annealing process on the thickness and composition of the wear layer were studied, and the causes of wear failure were analyzed based on the results of scanning electron microscopy. It was found that as the annealing temperature gradually increased, the particle size near the scratch of BTW1 in the wear-resistant layer of the composite plate became smaller. On this basis, the effects of different annealing temperatures on the friction and wear characteristics of the composite plate were further studied. At the annealing temperature of 860 ° C, the wear resistance of the material was the best.
耐磨钢/碳钢复合板不仅具有高强度和耐磨性的双重性能优势,还能降低能耗和生产成本。在降低 50%的基础上,研究了 BTW1/Q345 复合材料在不同退火温度下的耐磨性,并利用 RETC MFT-5000 对 BTW1/Q345 复合材料在不同退火温度下进行了干摩擦磨损试验。利用白光干涉三维表面轮廓仪、扫描电子显微镜(SEM)和背散射电子衍射(EBSD)技术,对不同退火温度下磨损痕迹的宏观和微观形貌及磨损机理进行了详细分析。研究了退火过程对磨损层厚度和成分的影响,并根据扫描电子显微镜的结果分析了磨损失效的原因。研究发现,随着退火温度的逐渐升高,复合板耐磨层中 BTW1 划痕附近的颗粒尺寸变小。在此基础上,进一步研究了不同退火温度对复合板摩擦磨损特性的影响。退火温度为 860 ° C 时,材料的耐磨性最好。
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引用次数: 0
Additive Manufacturing: Experiments, Simulations, and Data-Driven Modelling 快速成型制造:实验、模拟和数据驱动建模
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-28 DOI: 10.3390/cryst14090763
Muhammad Arif Mahmood, Asif Ur Rehman, Marwan Khraisheh, Metin U. Salamci, Rashid Ur Rehman, Uzair Sajjad, Carmen Ristoscu, Andrei C. Popescu, Mihai Oane, Ion N. Mihailescu
Additive manufacturing (AM) has profoundly impacted modern engineering and materials science by enabling unparalleled control over microstructures, customization, and material properties [...]
快速成型制造(AM)通过实现对微结构、定制和材料特性的无与伦比的控制,对现代工程和材料科学产生了深远的影响 [...] 。
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引用次数: 0
Semiconductive Tendency of the Passive Film Formed on Super Austenitic Stainless Steel SR-50A in Acidic or Alkaline Chloride Solutions 超级奥氏体不锈钢 SR-50A 在酸性或碱性氯化物溶液中形成的无源膜的半导体倾向
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-28 DOI: 10.3390/cryst14090766
Seung-Heon Choi, Young-Ran Yoo, Young-Sik Kim
Stainless steel is widely used in various industrial fields due to its excellent corrosion resistance and mechanical properties. The key to this corrosion resistance is the thin passive film that naturally forms on the metal surface. Passive films are characterized by oxide film theory and adsorption theory, each uniquely explaining the structure and mechanism of the protective film on the metal surface. Research on the semiconductive properties of passive films on stainless steel offers diverse viewpoints, classifying theories into the point defect model and the bipolar fixed charge-induced passivity. Specific changes in passive film attributes that lead to degradation, however, are not fully understood. In this study, we analyzed the inner and outer layers of the passive film on super austenitic stainless steel SR-50A under various conditions in acidic and alkaline chloride environments. The interpretations of these results were based on the point defect model and the bipolar model for the passivation mechanism, and correlations between p-type and n-type semiconductor properties and passivation behavior were examined. The surface of the stainless steel forms a passive film comprising two layers with p-type and n-type semiconductive properties, independent of the pH of the solutions. The corrosion resistance increases as the p-type and n-type semiconductive tendencies become more balanced, consequently enhancing the properties of the passive film.
不锈钢具有优异的耐腐蚀性和机械性能,因此被广泛应用于各个工业领域。这种耐腐蚀性的关键在于金属表面自然形成的一层薄薄的被动膜。氧化膜理论和吸附理论分别对金属表面保护膜的结构和机理做出了独特的解释。有关不锈钢被动膜半导体特性的研究提供了多种观点,将理论分为点缺陷模型和双极固定电荷诱导钝化。然而,人们对导致降解的无源薄膜属性的具体变化并不完全了解。在本研究中,我们分析了超级奥氏体不锈钢 SR-50A 在酸性和碱性氯化物环境中各种条件下被动膜的内层和外层。对这些结果的解释基于钝化机理的点缺陷模型和双极模型,并研究了 p 型和 n 型半导体特性与钝化行为之间的相关性。不锈钢表面形成了一层钝化膜,由具有 p 型和 n 型半导体特性的两层膜组成,与溶液的 pH 值无关。随着 p 型和 n 型半导体特性趋于平衡,耐腐蚀性也随之增强,从而提高了被动膜的特性。
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引用次数: 0
Synthesis of Samarium Nitride Thin Films on Magnesium Oxide (001) Substrates Using Molecular Beam Epitaxy 利用分子束外延技术在氧化镁 (001) 基质上合成氮化钐薄膜
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-28 DOI: 10.3390/cryst14090765
Kevin D. Vallejo, Zachery E. Cresswell, Volodymyr Buturlim, Brian S. Newell, Krzysztof Gofryk, Brelon J. May
Rare-earth nitrides are an exciting family of materials with a wide variety of properties desirable for new physics and applications in spintronics and superconducting devices. Among them, samarium nitride is an interesting compound reported to have ferromagnetic behavior coupled with the potential existence of p-wave superconductivity. Synthesis of high-quality thin films is essential in order to manifest these behaviors and understand the impact that vacancies, structural distortions, and doping can have on these properties. In this study, we report the synthesis of samarium nitride monocrystalline thin films on magnesium oxide (001) substrates with a chromium nitride capping layer using molecular beam epitaxy (MBE). We observed a high-quality monocrystalline SmN film with matching orientation to the substrate, then optimized the growth temperature. Despite the initial 2 nm of growth showing formation of a potential samarium oxide layer, the subsequent layers showed high-quality SmN, with semiconducting behavior revealed by an increase in resistivity with decreasing temperature. These promising results highlight the importance of studying diverse heteroepitaxial schemes and open the door for integration of rare-earth nitrides and transition metal nitrides for future spintronic devices.
稀土氮化物是一个令人兴奋的材料家族,它具有各种各样的特性,是自旋电子学和超导设备中新物理学和应用的理想材料。其中,氮化钐是一种有趣的化合物,据报道它不仅具有铁磁性,还可能具有 p 波超导性。为了体现这些行为,了解空位、结构畸变和掺杂对这些特性的影响,合成高质量的薄膜至关重要。在本研究中,我们报告了利用分子束外延(MBE)技术在带有氮化铬封盖层的氧化镁(001)基底上合成氮化钐单晶薄膜的情况。我们观察到了与基底取向匹配的高质量单晶 SmN 薄膜,然后优化了生长温度。尽管在最初 2 纳米的生长过程中形成了潜在的氧化钐层,但随后的薄膜层显示出高质量的 SmN,电阻率随温度降低而增加,显示出半导体特性。这些充满希望的结果凸显了研究各种异质外延方案的重要性,并为未来自旋电子器件整合稀土氮化物和过渡金属氮化物打开了大门。
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引用次数: 0
Effect of Solution and Aging Heat Treatment on the Microstructure and Mechanical Properties of Inconel 625 Deposited Metal 溶解和老化热处理对铬镍铁合金 625 沉积金属微观结构和机械性能的影响
IF 2.7 4区 材料科学 Q2 CRYSTALLOGRAPHY Pub Date : 2024-08-28 DOI: 10.3390/cryst14090764
Yingdi Wang, Yunhai Su, Zhiyong Dai
Inconel 625 deposited metal was prepared by gas metal arc welding. The solid solution treatment temperature was set at 1140 °C for 4 h using the DSC test method, followed by secondary aging at 750 °C/4 h and 650 °C/24 h. The specimens in the prepared state and after heat treatment were subjected to high temperature tensile at 600 °C, respectively. The fracture morphology, thermal deformation behavior, and strengthening mechanism of the samples in different states were analyzed. The results showed that the stress–strain curves of the deposited metals exhibited obvious work-hardening behavior at 600 °C. The solid solution and aging heat-treated samples have higher tensile and yield strength, but the plasticity is obviously lower than that of the deposited metal. It was also found that the γ″ phase and M23C6 carbides, as well as the continuous stacking faults in the alloy, were the main reasons for the increase in tensile strength of the solution and aging heat-treated sample.
Inconel 625 熔敷金属是通过气体金属弧焊制备的。采用 DSC 试验方法将固溶处理温度设定为 1140 ℃,持续 4 小时,然后在 750 ℃/4 小时和 650 ℃/24 小时条件下进行二次时效。分析了不同状态下试样的断口形貌、热变形行为和强化机制。结果表明,沉积金属在 600 ℃ 时的应力-应变曲线表现出明显的加工硬化行为。固溶和时效热处理样品具有较高的拉伸强度和屈服强度,但塑性明显低于沉积金属。研究还发现,γ″相和 M23C6 碳化物以及合金中的连续堆叠断层是固溶和时效热处理样品抗拉强度提高的主要原因。
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引用次数: 0
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Crystals
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