jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Lundgren, Kristoffer
Source: Lund University Publications (Lund University) (article, 2025-01-01)
Field: Chemistry — Inorganic Chemistry

Quantum refinement in real and reciprocal space In order to understand and manipulate biological function at the molecular level, access to high-resolution structures of biological macromolecules is essential, as structure is intimately linked to function. The two main experimental techniques that can achieve atomic, or near-atomic, resolution are crystallography and electron microscopy. Unfortunately, the experimental data alone is typically not sufficient to obtain an accurate atomic model, owing to a poor data-to-parameter ratio. Therefore, prior knowledge of the chemical nature of the system is supplemented during refinement in the form of restraints. Traditional restraints are accurate for standard amino acids and nucleic acids, less so for novel ligands and metal sites. Additionally, transferability of these restraints is commonly assumed, ignoring the specific chemical environment. A solution is to use in situ quantum mechanical calculations for small, but interesting, parts of the structure, during refinement. Such an approach, called quantum refinement, has been shown to improve structures locally, to allow determination of protonation and oxidation states of ligands and metals and discriminate between different interpretations of the structure.Previous implementations of quantum refinement have been limited to either X-ray or neutron crystallography data, using low-level quantum mechanical methods or not being able to treat metal sites. In this thesis, we present a new implementation of quantum refinement, called QRef. QRef supports X-ray, neutron and electron diffraction data, as well as cryo-EM data, and can use a wide range of quantum mechanical methods, allowing treatment of metal sites. QRef is released under a permissive license.We have subsequently applied QRef to a variety of challenging biological systems. For a recent crystal structure of Fe-nitrogenase, we determined the protonation state of the homocitrate ligand. We performed a critical evaluation of metal sites in three cryo-EM structures of particulate methane monooxygenase, showing that several sites were incorrectly interpreted. This was the first time that quantum refinement had been applied to metal sites in cryo-EM structures and we suggest that quantum refinement is the method of choice for such systems. Furthermore, we have applied quantum refinement to data from XFEL and electron diffraction experiments, showing that quantum refinement can improve structures and interpretations in these cases as well. Finally, we have applied QRef to data from neutron diffraction experiments of manganese superoxide dismutase, demonstrating the challenges associated with neutron data of limited resolution. Quantum ; Quantum chemical ; Function (biology) ; Neutron diffraction ; Quantum chemistry ; Quantum algorithm ; Quantum system ; Range (aeronautics) Metal-Catalyzed Oxygenation Mechanisms ; Metalloenzymes and iron-sulfur proteins ; Enzyme Structure and Function
Authors: Xiaochen Huang | Lin Yuan | Yue Du | Debin Shan | Qijun Li
Source: Metals (article, 2025-10-31)
Field: Materials Science — Biomaterials

Hot Deformation Behavior and Microstructure Evolution of Mg-9Li-5Al-2Sn-1.5Y (Wt%) Alloy The hot deformation behavior of the duplex structured Mg-9Li-5Al-2Sn-1.5Y alloy is investigated via hot compression tests in the temperature range of 200–350 °C and strain rate range of 0.001–1 s−1. The flow behavior of the Mg-9Li-5Al-2Sn-1.5Y alloy is defined by hyperbolic constitutive equation. The Zener–Hollomon parameter Z is used in the hyperbolic-sine-type equation to express the relationships between the peak stress, deformation temperature, and strain rate. Dynamic recovery and dynamic recrystallization are the main characteristics that affect deformation behaviors. The activation energy Q is calculated as 127.89 kJ/mol. Based on the dynamic materials model, the processing maps at strains of 0.6 and 0.8 are constructed, and the optimum processing parameters are determined as the temperature range of 320–350 °C and strain rate range of 0.001–0.007 s−1. Dynamic recrystallization ; Strain rate ; Deformation (meteorology) ; Microstructure ; Alloy ; Hot working ; Atmospheric temperature range ; Flow stress Magnesium Alloys: Properties and Applications ; Metallurgy and Material Forming ; Aluminum Alloy Microstructure Properties
Authors: Zuquan Jin | Hong Wang | Bo Pang | Shicai Li | Meiling Xu | Ao Shen
Source: Research Square (preprint, 2025-09-22)
Field: Materials Science — Biomaterials

Biomimetically-engineered FRP composites: integration of nanostructured resin matrix with hybrid fiber networks towards ultrahigh chemical stability and mechanical strengthening Epoxy ; Shear strength (soil) ; Fibre-reinforced plastic ; Corrosion ; Polymer ; Shear (geology) ; Fiber ; Aramid ; Composite number Electrospun Nanofibers in Biomedical Applications ; Silk-based biomaterials and applications ; Advanced Sensor and Energy Harvesting Materials
Authors: A. Cagri Aydinkarahaliloglu | Arifin Nur Alif | Xiao-Jun Wang | Mariano Troccoli | Anthony J. Hoffman
Source: Research Square (preprint, 2025-11-25)
Field: Chemistry — Spectroscopy

Predicting premature failure of quantum cascade lasers with different quantum designs using active machine learning Cascade ; Laser ; Quantum cascade laser ; Quantum ; Quantum dot laser ; Support vector machine Spectroscopy and Laser Applications ; Semiconductor Lasers and Optical Devices ; Semiconductor Quantum Structures and Devices
Authors: Yiming Li | En-zhi GAO | D. S. Xue | Jie Wang | Zhigang Zhu | Rongzheng Xu
Source: Journal of Physics Conference Series (article, 2025-07-01)
Field: Materials Science — Materials Chemistry

Diffusion characteristics of Cu/Al/Cu interface based on molecular dynamics Abstract Based on molecular dynamics simulation, the interfacial diffusion process of the Cu /Al /Cu system is simulated. The diffusion characteristics and evolution law of interfacial atoms are analyzed using mean square displacement, diffusion coefficient, radial distribution function, and atomic concentration distribution. The results show that the Cu atomic energy is deeply diffused into Al, while the Al atom is only diffused to the Cu side, and the diffusion range is limited to the interface. With the increase in temperature, the thickness of the interfacial transition layer increases and expands to both sides gradually. At the Cu /Al /Cu interface, the ordered structure of Al is destroyed in the diffusion process, showing disorder. At the same time, the Cu layer as a whole maintains a high order, only the structure near the interface is slightly disordered. At the same time, three diffusion mechanisms of Cu atoms in the Al lattice have been found, and the main diffusion mechanism is the first neighbor transition. Lattice diffusion coefficient ; Diffusion ; Molecular dynamics ; Mean squared displacement ; Diffusion layer ; Atom (system on chip) ; Lattice (music) ; Materials science ; Chemical physics ; Copper ; Radial distribution function ; Diffusion process ; Atomic diffusion ; Embedded atom model ; Effective diffusion coefficient ; Crystallography ; Thermodynamics ; Chemistry ; Layer (electronics) ; Nanotechnology ; Computational chemistry ; Metallurgy ; Physics ; Innovation diffusion Microstructure and mechanical properties ; Aluminum Alloy Microstructure Properties ; Aluminum Alloys Composites Properties
Authors: Zakiah Mohd Yusoff | Nurlaila Ismail
Source: Science, Engineering and Health Studies (article, 2025-12-16)
Field: Chemistry — Organic Chemistry

Sesquiterpenoids in Aquilaria oil and their medicinal insights: A structured review Aquilaria oil, widely used in traditional Chinese medicine, has long been valued for its aromatic and therapeutic properties in treating ailments such as pain, inflammation, and fever. Despite extensive studies on its sesquiterpenoid content, the full medicinal potential of these compounds remains underexplored. This structured review systematically analyzed 177 articles from Scopus and Web of Science, of which 18 met the inclusion criteria, focusing on three main themes: biological activities, chemical characterization, and ethnobotanical and medicinal insights. The findings show that sesquiterpenoids in Aquilaria oil are predominantly humulane- and eudesmane-type compounds, frequently linked to anti-inflammatory, antimicrobial, and anticancer properties. Current trends also highlight growing use of DNA barcoding and chemical profiling for species authentication and oil quality evaluation. Moreover, ethnobotanical evidence consistently supports its role as a sedative and immune-modulating agent, increasingly validated by pharmacological studies. Collectively, these insights underscore the therapeutic relevance of Aquilaria sesquiterpenoids and identify promising pathways for drug discovery and sustainable utilization. Ethnobotany ; Chemical constituents ; Medicinal plants ; Web of science ; Bioprospecting Wood and Agarwood Research ; Ginger and Zingiberaceae research ; Psychiatry, Mental Health, Neuroscience
Authors: Pham Thanh Ha | Bui Ngoc Tram | Nguyen Thi Lan
Source: Journal of Biohybrid Systems Engineering (article, 2025-11-17)
Field: Materials Science — Biomaterials

Spider Silk and Composites: Forging a New Generation of High-Toughness, Lightweight Structures The escalating demand for advanced materials that combine exceptional mechanical properties with low density is a driving force in aerospace, automotive, and biomedical engineering. While synthetic fibers like carbon and aramid have dominated high-performance applications, their inherent brittleness and energy-absorbing limitations present significant drawbacks. Nature, through millions of years of evolution, offers a paradigm-shifting solution: spider silk. Spider silk exhibits an unparalleled combination of high tensile strength and extreme extensibility, resulting in a toughness that surpasses most known natural and synthetic materials. This review delves into the convergence of spider silk and composite engineering, presenting a comprehensive overview of the pathway towards next-generation lightweight structures. We begin by deconstructing the hierarchical structure of spider silk, linking its nano-scale and molecular architecture-specifically, the arrangement of β-sheet crystallites within an amorphous glycine-rich matrix-to its macroscopic mechanical supremacy. The core of this article critically examines the two primary routes for harnessing this natural marvel: the direct integration of natural silk fibers into composite matrices and the engineering of recombinant spider silk proteins (spidroins) for processing into synthetic fibers, films, and hydrogels. We explore a variety of composite fabrication techniques, including laminate stacking and solution casting, and analyze the critical interface between silk and polymer matrices (e.g., epoxy, polyester) or natural polymers (e.g., chitosan, cellulose). A significant focus is placed on the enhancement of interfacial adhesion through chemical and physical surface modifications to achieve optimal stress transfer. Furthermore, the article presents a detailed mechanical analysis, highlighting how silk-reinforced composites achieve synergistic improvements in fracture toughness, impact resistance, and damage tolerance without compromising weight. The discussion extends to emerging applications, from failure-resistant aerospace components and lightweight body armor to biodegradable biomedical implants and tissue scaffolds. Finally, we address the formidable challenges of scalable spidroin production and material processing, outlining future research directions in metabolic engineering, advanced spinning techniques, and the development of multifunctional, bio-hybrid composite systems. The integration of spider silk into composite materials marks a pivotal step in emulating nature's genius, paving the way for a new era of high-toughness, lightweight engineering solutions. Spider silk ; SILK ; Toughness ; Composite number ; Brittleness ; Ultimate tensile strength ; Elastomer ; Spider ; Damage tolerance Silk-based biomaterials and applications ; Electrospun Nanofibers in Biomedical Applications ; Hemostasis and retained surgical items
Authors: R. D. Panwar | Shin‐Ping Lin | Shyh‐Hsiang Lin | Jer‐An Lin | Yu-Jen Wang | Yung‐Kun Chuang
Source: Foods (article, 2025-06-12)
Field: Chemistry — Analytical Chemistry

Informative Wavelength Selection for Evaluation of Bacterial Spoilage in Raw Salmon (Salmo salar) Fillet Using FT-NIR Spectroscopy This study highlights the potential of Fourier-transform near-infrared (FT-NIR) spectroscopy for the on-site, nondestructive detection of spoilage caused by bacterial action in raw salmon (<i>Salmo salar</i>) fillets. A stepwise multiple linear regression model with first-derivative spectrum transformation was combined with the standard normal variate and detrend preprocessing techniques. The model achieved correlation values of 0.97 in both the calibration and validation sample sets, with root mean square error values of 0.18 and 0.20 log CFU/mL, respectively. These accurate results reveal the precision of FT-NIR spectroscopy for assessing the spoilage caused by bacteria. The most informative wavelengths (885.27 nm, 1026.27 nm, 1039.93 nm, 1068.38 nm, 1257.55 nm, 1267.75 nm, and 1453.49 nm) related to the total bacterial count's identification were obtained. The innovative, cost-effective, and feasible approach outlined in this article is a promising methodology for enhancing the safety and quality standards of various fishery products. Salmo ; Fillet (mechanics) ; Food spoilage ; Fish fillet ; Selection (genetic algorithm) ; Raw material ; Spectroscopy ; Food science ; Biological system ; Fishery ; Environmental science ; Biology ; Materials science ; Computer science ; Artificial intelligence ; Fish <Actinopterygii> ; Physics ; Ecology ; Bacteria ; Composite material Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Water Quality Monitoring and Analysis
Authors: Huan Li | Zhentao Tang | Jian Chen | Qiao Fan | Huiying Xu | Song Miao | Yanbo Wang
Source: Food Science and Human Wellness (article, 2025-12-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Sandwich-Type SERS Aptasensor Based on Aptamer-functionalized Magnetic Capture Probe and AuNPs@MIL-101 Signal Enhancement Probe for Ultrasensitive Detection of <em>Bifidobacterium bifidum</em> Rapid and on-site detection of <em>Bifidobacterium bifidum </em><em>(</em><em>B. bifidum</em><em>)</em> throughout the food manufacturing process serves as an essential sentinel for assessing product quality and healthy potency. Herein, we introduce a sandwich-type surface-enhanced Raman scattering (SERS) aptasensor for <em>B. bifidum</em> quantification, which integrates aptamer-functionalized magnetic beads (Apt-Fe<sub>3</sub>O<sub>4</sub>) for target-specific capture and aptamer-modified gold nanoparticles/metal-organic framework composites (Apt-AuNPs@MIL-101) for SERS-based signal amplification. Experimental results revealed a strong linear correlation between the intensity of the characteristic Raman peak and the logarithmic of the <em>B. bifidum</em> concentrations within the range of 2.0 × 10<sup>1</sup> to 2.0 × 10<sup>6</sup> CFU/mL, and the limit of detection was as low as 2.5 CFU/mL. In addition to superior sensitivity, the proposed approach demonstrated exceptional specificity against non-target bacterial strains, particularly in multi-strain coexistent systems. The method further demonstrated great potential in analysis of <em>B. bifidum</em> in commercial samples, showing high consistency with the results obtained from the classic qPCR method. The study established an innovative analytical platform for rapid and on-site probiotic assessment, highlighting its applicability in probiotic food products’ quality control and evaluation. Detection limit ; Aptamer ; Raman scattering ; Logarithm ; SIGNAL (programming language) ; Raman spectroscopy ; Limit (mathematics) ; Linear range Gold and Silver Nanoparticles Synthesis and Applications ; Biosensors and Analytical Detection ; Advanced biosensing and bioanalysis techniques
Authors: Daniel Cozzolino | Louwrens C. Hoffman
Source: Journal of the Science of Food and Agriculture (article, 2025-09-15)
Field: Chemistry — Analytical Chemistry

The contribution of vibrational spectroscopy and data analytics towards the achievement of the global sustainability goals The United Nations Sustainable Development Goals (UN SDGs) were defined to improve the quality of life of the global population particularly regarding social and economic aspects, with a major focus on environmental sustainability. The incorporation of digital technologies into the agri-food sector has become a key enabler in increasing the efficiency, productivity, and sustainability of food production and processing systems. Digital technologies and innovations including artificial intelligence (AI), robotics, in-ground and remote sensors, connectivity, and internet of things (IoT) have been recognized as also being critical for the successful implementation of the UN SDGs. In particular, the utilization of sensing technologies (e.g., in-ground and remote sensors) has been shown to be of great importance to achieve these goals. The use of vibrational spectroscopy and data analytics have shown potential to contribute with the development and implementation of UN SDGs. An overview of the contribution of sensing technologies based on the utilization of vibrational spectroscopy (e.g., near- and mid-infrared spectroscopy, hyperspectral imaging) and data analytics to achieve the UN SDGs is provided. Advantages and limitations of these techniques are also discussed. The incorporation of technology will provide tools that can be used to monitor and predict the safety and quality of foods. Furthermore, digital technologies are enabling the development of novel decision-management systems along the food supply and value chain. Ultimately, the goal will be to assure the consumers the use of these technologies plays a key role in the applicability of the UN SDG. © 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. Enabling ; Sustainability ; Analytics ; Emerging technologies ; Population ; Quality (philosophy) ; Sustainable development ; Big data Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Identification and Quantification in Food
Authors: Sachin S Chourasia
Source: Integrative Journal of Conference Proceedings (article, 2025-02-19)
Field: Materials Science — Biomaterials

"Revolutionizing Cancer Treatment with Nano QSAR: A Mini Review of Computational Modeling and Nanomedicine" Recent developments in nanotechnology and computational modelling have opened new avenues to address these challenges of treating cancer.One such innovation is NanoQSAR (Quantitative Structure-Activity Relationship) modelling, a powerful tool that combines the predictive capabilities of QSAR with nanotechnology's precision.This mini review discusses how NanoQSAR intersects cancer treatment and how it holds the potential to revolutionize drug design, optimization, and personalized therapy.Key methodologies of NanoQSAR, its application in the prediction of biological activity in nanomaterials, and how it enhances targeted cancer therapies are discussed.Also, the potential integration of NanoQSAR with machine learning and artificial intelligence to help accelerate the discovery of novel anticancer agents has been investigated.Finally, challenges and directions for future research in the field are presented, suggesting that further research is urgently needed to fully realize the promise of NanoQSAR in cancer therapy. Cancer treatment ; Nano- ; Cancer ; Cancer therapy Nanoparticle-Based Drug Delivery ; Computational Drug Discovery Methods ; Cancer Research and Treatment
Authors: Aryan Soniya Duge | Punam Roy Suprio | E. S. | Jeetu S. Babu | Karthik V. Shankar | Karthik Manu
Source: Journal of King Saud University - Engineering Sciences (article, 2025-12-01)
Field: Materials Science — Materials Chemistry

Influence of pre-existing stacking fault on the mechanical and microstructural behavior of Cu–Zn alloys—a molecular dynamics study Abstract This study explores the impact of pre-existing stacking fault defects on the mechanical behavior and microstructural evolution of Cu–Zn alloys under uniaxial tensile loading through Molecular Dynamics (MD) simulations. It further examines the influence of varying zinc concentrations (6 at %, 12 at %, and 24 at %) on the alloy’s mechanical properties. The MD simulations are used to evaluate key mechanical parameters, including Young’s modulus, ultimate tensile strength (UTS), and toughness. A detailed comparison of these properties is carried out to identify inherent trends associated with changes in composition. Additionally, the temperature dependence analysis conducted over the range of 200 K to 800 K shows that higher temperatures accelerate failure, reduce UTS, and lower toughness, while system size has a stabilizing effect on stress–strain response. Zn concentration further amplifies these effects, particularly in alloys with pre-existing stacking faults. Complementary to these analyses, Common Neighbor Analysis (CNA) is performed to investigate atomic structural changes within the predominantly FCC solid solution under varying conditions. The results indicate that increasing Zn content in defect-free Cu–Zn alloys leads to a decline in mechanical performance. However, the introduction of pre-existing stacking faults results in a reduction in UTS but an increase in Young’s modulus, suggesting improved resistance to elastic deformation. Ultimate tensile strength ; Stacking ; Stacking fault ; Molecular dynamics ; Stacking-fault energy ; Microstructure ; Dislocation ; Zinc Microstructure and mechanical properties ; Metallurgy and Material Science ; Aluminum Alloy Microstructure Properties
Authors: Dmitry V. Alimov | Artem S. Poryvaev | Matvey V. Fedin
Source: Molecules (article, 2025-05-21)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Pressure Sensitivity of UiO-66 Framework with Encapsulated Spin Probe: A Molecular Dynamics Study Probes sensitive to mechanical stress are in high demand for analyzing pressure distributions in materials. Metal-organic frameworks (MOFs) are especially promising for designing pressure sensors due to their structural tunability. In this work, using classical molecular dynamics (MD) simulations, we clarified the mechanism of exceptional pressure sensitivity of the material based on the UiO-66 framework with a trace amount of spin probes encapsulated in cavities. The role of defects in the MOF structure has been revealed using a combination of electron paramagnetic resonance (EPR) spectroscopy and MD calculations, and potential degradation pathways under mechanical stress have been proposed. The combined MD and EPR study provides valuable insights for further development of new MOF-based sensors applicable for non-destructive pressure mapping in various materials. Electron paramagnetic resonance ; Molecular dynamics ; Chemical physics ; Stress (linguistics) ; Electron paramagnetic resonance spectroscopy ; Materials science ; Sensitivity (control systems) ; Metal-organic framework ; Spin probe ; Paramagnetism ; Spin (aerodynamics) ; Nanotechnology ; Chemistry ; Physical chemistry ; Computational chemistry ; Nuclear magnetic resonance ; Condensed matter physics ; Physics ; Thermodynamics Magnetism in coordination complexes ; Metal-Organic Frameworks: Synthesis and Applications ; Lanthanide and Transition Metal Complexes