jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Nilanjan Dey
Source: RSC Advances (article, 2025-01-01)
Field: Chemistry — Spectroscopy

Reversible color changing response of pyrenylated charge-transfer probes towards Hg<sup>2+</sup>: linker-driven modulation of sensitivity and selectivity Two easily synthesizable prenylated charge transfer probes with a terminal pyridine unit were designed. The compounds differ based on the nature of the spacer: rigid olefinic (1) and flexible hydrazo (2). Both compounds show exclusive interaction with Hg<sup>2+</sup> ions, leading to changes in visible color. Experimental analyses showed that compound 1 outperformed compound 2 in terms of sensitivity (<i>A</i>/<i>A</i> <sub>0</sub> ∼ 13-fold <i>vs.</i> ∼2-fold) and detection limit (1.2 ppm <i>vs.</i> 5.8 ppm), attributed to its rigid linker and enhanced binding affinity. Moreover, ratiometric responses (<i>r</i> <sup>2</sup> > 0.99) and excellent selectivity for Hg<sup>2+</sup> were demonstrated. This study highlights the development of robust, reusable, and cost-effective tools for mercury detection, thus addressing critical environmental and health concerns associated with mercury contamination. Environmental robustness of compound 1 was validated across solvents, counter-ions, and water mixtures, with decreasing efficacy in high-water-content systems owing to solvation effects and probe aggregation. Mechanistic studies confirmed pyridine nitrogen as the primary coordination site with reversible binding, enabling probe reuse. Practical applications were explored using paper strips modified with the probes, which facilitated rapid, cost-effective, and quantitative detection of Hg<sup>2+</sup> <i>via</i> image analysis. Selectivity ; Sensitivity (control systems) ; Modulation (music) ; Linker ; Chemistry ; Charge (physics) ; Photochemistry ; Physics ; Organic chemistry Molecular Sensors and Ion Detection ; Photochromic and Fluorescence Chemistry ; Conducting polymers and applications
Authors: Jan Janßen | Janine George | Julian Geiger | Marnik Bercx | Xing Wang | Christina Ertural | Jörg Schaarschmidt | Alex M. Ganose | Giovanni Pizzi | Tilmann Hickel | Jörg Neugebauer
Source: Digital Discovery (article, 2025-01-01)
Field: Materials Science — Materials Chemistry

A python workflow definition for computational materials design Numerous Workflow Management Systems (WfMS) have been developed in the field of computational materials science with different workflow formats, hindering interoperability and reproducibility of workflows in the field. To address this challenge, we introduce here the Python Workflow Definition (PWD) as a workflow exchange format to share workflows between Python-based WfMS, currently AiiDA, jobflow, and pyiron. This development is motivated by the similarity of these three Python-based WfMS, that represent the different workflow steps and data transferred between them as nodes and edges in a graph. With the PWD, we aim at fostering the interoperability and reproducibility between the different WfMS in the context of Findable, Accessible, Interoperable, Reusable (FAIR) workflows. To separate the scientific from the technical complexity, the PWD consists of three components: (1) a conda environment that specifies the software dependencies, (2) a Python module that contains the Python functions represented as nodes in the workflow graph, and (3) a workflow graph stored in the JavaScript Object Notation (JSON). The first version of the PWD supports Directed Acyclic Graph (DAG)-based workflows. Thus, any DAG-based workflow defined in one of the three WfMS can be exported to the PWD and afterwards imported from the PWD to one of the other WfMS. After the import, the input parameters of the workflow can be adjusted and computing resources can be assigned to the workflow, before it is executed with the selected WfMS. This import from and export to the PWD is enabled by the PWD Python library that implements the PWD in AiiDA, jobflow, and pyiron. Workflow ; Python (programming language) ; Workflow management system ; Workflow technology ; Workflow engine ; Windows Workflow Foundation ; Interoperability ; XPDL Machine Learning in Materials Science ; Additive Manufacturing and 3D Printing Technologies ; Manufacturing Process and Optimization
Authors: Srilatha Arra | Isabella Daidone | Massimiliano Aschi
Source: Journal of Computational Chemistry (article, 2025-06-20)
Field: Chemistry — Spectroscopy

Revisiting the “Cluster‐In‐Solvent” Approach for Computational Spectroscopy: The Vibrational Circular Dichroism as a Test Case The cluster-in-solvent approach, that is, the use of the quantum-mechanical calculation of a spectral observable on a significant number of solute-solvent clusters extracted from semi-classical simulations, is widely used in computational spectroscopy. However, identifying relevant coordinates for cluster selection remains a challenge. We previously developed the Ellipsoid Method for Cluster-in-Solvent (EMCS), an automated strategy for unbiased identification and statistical weighting of clusters. Yet, for larger solutes, EMCS can yield overly large solvent clusters that hinder conformational analysis. Here, we introduce a simple extension of EMCS that reduces cluster size, enabling its application to medium-to-large solutes. The method is validated through the computation of Vibrational Circular Dichroism (VCD) spectra, which are highly sensitive to solute-solvent interactions. Test cases include aqueous L-alanine, aqueous dialanine, and (1S,2S)-trans-1-amino-2-indanol in DMSO. For L-alanine and trans-1-amino-2-indanol, computed spectra closely match experiment, with root-mean-square-deviation (RMSD) values of 10.3 and 8.0, respectively, consistent with previous benchmarks. For aqueous dialanine, the main spectral features were reproduced, though discrepancies in the fine structure remain, likely due to limitations in capturing subtle solvation effects. Overall, the refined EMCS protocol enables efficient and non-arbitrary sampling of solute-solvent clusters, offering a valuable tool for the structural analysis of solvation shells in complex molecular systems. Solvation ; Cluster (spacecraft) ; Chemistry ; Solvent ; Vibrational circular dichroism ; Spectroscopy ; Aqueous solution ; Computational chemistry ; Circular dichroism ; Crystallography ; Physical chemistry ; Computer science ; Physics ; Organic chemistry Molecular spectroscopy and chirality ; Spectroscopy and Quantum Chemical Studies ; Protein Structure and Dynamics
Authors: S. Paulsingarayar | S. Seenivasan | P. Satishkumar | Jayant Giri | T. Sathish | Muhammad Imam Ammarullah
Source: Scientific Reports (article, 2025-08-13)
Field: Materials Science — Polymers and Plastics

Investigation of the mechanical properties of pineapple leaf fibre-reinforced biocomposites This study explores the production process and mechanical properties of biocomposites reinforced with pineapple leaf fibres. The biocomposite fabrication involves the use of various techniques, including compression moulding, to integrate the natural fibres into a polyester matrix. The mechanical performance of the resulting composites is evaluated through a comprehensive set of tests, including tensile strength measurements and Energy Dispersive X-Ray Spectroscopy (EDX). Key factors influencing mechanical behaviour, such as fibre content, orientation, and production variables, are systematically examined. Additionally, the chemical composition of the composites is assessed to understand its role in their performance. The findings provide valuable insights into the potential applications of pineapple leaf fibre-based biocomposites in industries requiring lightweight, sustainable materials with enhanced mechanical properties. This paper aims to establish a clear link between production techniques and mechanical performance, highlighting the practical potential of these biocomposites for environmentally-conscious material solutions. Composite material ; Materials science Natural Fiber Reinforced Composites ; Nanocomposite Films for Food Packaging ; Advanced Cellulose Research Studies
Authors: Shuang Liu | Kangning Liu | Jing Wu | Sheliang Wang
Source: Buildings (article, 2025-05-21)
Field: Materials Science — Materials Chemistry

Erosion Resistance of Iron Ore Tailings as Aggregate for Manufacturing of Cement-Based Materials Cement-based materials used in China’s coastal and salt lake areas in the northwest are exposed to long-term chloride corrosion, which deteriorates the materials and substantially reduces the durability of the structures. This study investigates the chlorine ion erosion resistance in salt spray environments of cement-based materials made with iron ore tailings (IOTs) as an aggregate (namely, IOTCs). The compressive strength, mass loss, and relative dynamic elastic modulus (RDEM) macroscopic performance of IOTC undergoing different chloride diffusion times (0–180 d) were explored in detail. Chloride ion profiles at 0–180 d were analyzed via chemical titration, while X-ray computed tomography (CT) and scanning electron microscopy (SEM) were employed to characterize microstructural evolution. The results demonstrate that IOTC exhibited superior chloride resistance compared to conventional concrete (GC). While both materials showed early strength gain (&lt;60 d) due to hydration and pore-filling effects, IOTC experienced only a 23.9% strength loss after long-term exposure (180 d) significantly less than the 37.2% reduction in GC. Chloride profiling revealed that IOTC had 43.5% lower free chloride ions (Cf) and 32% lower total chloride ions (Ct) at 1 mm depth after 180 d, alongside reduced chloride diffusion coefficients (Da). The CT analysis revealed that IOTC exhibited a significantly denser and more uniformly distributed pore structure than GC, with a porosity of only 0.67% under chloride-free conditions. SEM confirmed IOTC’s more intact matrix and fewer microcracks. Tailings ; Cement ; Iron ore ; Aggregate (composite) ; Erosion ; Metallurgy ; Materials science ; Mining engineering ; Geology ; Composite material Magnesium Oxide Properties and Applications ; Tailings Management and Properties ; Concrete and Cement Materials Research
Authors: S. Stepanović | Romain Giraud | Gérard Hopfgartner
Source: ChemRxiv (preprint, 2025-06-11)
Field: Chemistry — Spectroscopy

Integrative data science in mass spectrometry: connecting molecular structures with diverse mass spectrometry fragmentation behaviours We investigated how molecular structure influences ultraviolet photon dissociation (UVPD), at 266 nm and electron activated dissociation (EAD) of small molecules using a dataset of 178 pesticides. Logistic regression revealed distinct structure–fragmentation relationships and simple models can predict the likelihood of distinct UVPD fragmentation events based purely on molecular structure, while density functional theory (DFT)-based analysis showed that the appearance of [M+H]²⁺• radicals in EAD at energies above 10 eV correlates with their thermodynamic stability. These results support a partial electron removal mechanism in EAD and highlight the predictive value of simple models. Mass spectrometry ; Fragmentation (computing) ; Chemistry ; Computer science ; Chromatography Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Elvar M. S. Jóhönnuson | Henriette P. Sennels | Henrik L. Jørgensen | Jens Hannibal | Ching‐Yan Chloé Yeung | Christine Rasmussen | Gabriela Pruś | Nicolai J. Wewer Albrechtsen | Annelaura Bach Nielsen
Source: Clinical Proteomics (article, 2025-08-22)
Field: Chemistry — Spectroscopy

Diurnal rhythm of the human plasma proteome These findings demonstrate that over one-quarter of the human plasma proteome is under diurnal control. Such oscillations might have direct clinical implications, as the time-of-day may alter biomarker accuracy. Incorporating diurnal timing into diagnostic and research protocols, through standardized sampling or time-sensitive reference intervals, could improve patient care and inform future biomarker discoveries. Further research in larger, more diverse populations is needed to generalize these results and streamline practices in a way that takes diurnal variation into account. Circadian rhythm ; Human plasma ; Proteome ; Rhythm ; Proteomics ; Human proteome project ; Computational biology ; Bioinformatics ; Biology ; Medicine ; Chemistry ; Neuroscience ; Internal medicine ; Biochemistry ; Chromatography Advanced Proteomics Techniques and Applications ; Genetic Associations and Epidemiology ; Erythropoietin and Anemia Treatment
Authors: Nilo Antônio de Souza Sampaio | José Cláudio Caraschi | Glaucia Aparecida Prates | Fabíola Freitas de Miranda | Lesley Carina do Lago Attadia Galli | R. Rocha | Helenita Rodrigues da Silva Tamashiro
Source: Revista de Gestão Social e Ambiental (article, 2025-05-12)
Field: Chemistry — Analytical Chemistry

Effect of Pressure and Temperature on the Retention Time of Crude Oil Inside the Three-Phase Separator Using the Response Surface Methodology Objective: The aim of this paper is to show the application of the Surface Experiment to a petrochemical industry in the northern region of the state of Rio de Janeiro, Brazil. Theoretical framework: One of the tools provided by statistics for process optimization is the Response Surface Methodology, which has been widely applied in recent years for the study of optimization (Bas &amp; Boyaci, 2007). Response surface methodology is a set of statistical and mathematical techniques that aim to predict, improve and optimize the response of interest. It is applied when this response or a set of responses of interest are influenced by various parameters or variables, and can define this effect separately or together. Furthermore, this methodology generates a mathematical model that can be represented graphically(Ba &amp; Boyaci, 2007) Method: Experimental data was taken from a petrochemical industry in the northern region of the state of Rio de Janeiro and the data was treated with a Response Surface Experiment. Final Considerations: It can be concluded that Response Surface Methodology is a very viable option for optimizing the performance of industrial processes. In this specific case of the plant, it can be concluded that, although the only significant interaction is Pressure-Pressure, the pressure and temperature factors lead to optimal retention time values if they are at their minimum values, i.e. pressure less than 200 mmHg and temperature less than 30oC. Implications of the research: The use cases of Response Surface Experiments are multiplying in the scientific literature and are proving to be highly effective for treating data in which the assumptions of Normality are confirmed. Originality/value: Despite being well-known statistical tools, the Response Surface Experiment is widely used and can bring innovations in its application, as in the case of the company in question. Separator (oil production) ; Materials science ; Crude oil ; Chromatography ; Petroleum engineering ; Retention time ; Mechanics ; Environmental science ; Chemistry ; Thermodynamics ; Engineering ; Physics Petroleum Processing and Analysis ; Crystallization and Solubility Studies ; Minerals Flotation and Separation Techniques
Authors: Ruhao Yang | Han Ye | Qi Wang | Yumin Liu | Wenjun Liu | Zhenping Wu
Source: Small Structures (article, 2025-01-28)
Field: Materials Science — Materials Chemistry

Complex Janus MoSSe Nanoscrolls Spontaneously Formed from Flat Nanoflakes: A Theoretical Exploration Janus transition metal dichalcogenide (TMD) monolayers with out‐of‐plane atomic asymmetry have been experimentally observed to scroll into unique 1D nanoscrolls with diverse complex structures, while the underlying mechanism has not been unveiled. In this work, the entire scrolling process of triangular and hexagonal MoSSe nanoflakes is successfully simulated based on molecular dynamics, demonstrating the formation of five distinct nanoscroll structures. From flat configuration, the nanoflakes are released along typical directions (including edge‐to‐vertex, vertex‐to‐vertex, and vertex‐to‐edge) accounting for the time‐dependent break of van der Waals (vdW) interaction between substrate and nanoflakes. Key structural parameters such as inner radii are found to be closely related to the nanoflake shapes, sizes, and release directions. Additionally, the regions with various layer numbers in nanoscrolls are projected on the flat nanoflakes to demonstrate the local contribution to the vdW stacked multilayer structures. For each nanoflake shape and release direction, the quantitative relations between the area of specific layer number and both inner radius and interlayer distance are obtained. The results provide a fundamental understanding of complex nanoscrolls spontaneously formed from Janus TMD nanoflakes. Janus ; Materials science ; Nanotechnology ; Geology 2D Materials and Applications ; Advanced Photocatalysis Techniques ; Quantum Dots Synthesis And Properties
Authors: Xiao-Fei Liu | Ruohui Chen | Yilin Lu | Chenxu Zhu | Yang Qiu | Xingyan Zhao | Shaonan Zheng | Qize Zhong | Bo Cui | Yuan Dong | Ting Hu
Source: Chinese Optics Letters (article, 2025-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Optical performances of near-infrared metalenses with process-induced defects Defects are inevitably induced during the fabrication process of a metalens, which will affect the metalens's yield and optical performances.Thus, investigations on the fabrication defects are becoming increasingly important for the mass production of metalenses.In this Letter, the optical performances of near-infrared metalenses with four types of fabrication defects are investigated.The results show that the process-induced defects obviously affect the focusing efficiency at = 940 nm, but they have less impact on the quality of the focal spot.This work provides fabrication guidance for largescale manufacturing of metalenses in the future. Optics ; Infrared ; Process (computing) ; Materials science ; Computer science ; Physics Metamaterials and Metasurfaces Applications ; Optical and Acousto-Optic Technologies ; Photonic Crystals and Applications
Authors: Leixiao Wu | Wei Cai | Jie Yang
Source: Polymers (article, 2025-07-19)
Field: Materials Science — Polymers and Plastics

Temperature/Stress-Dependent Fractional Creep Models of Thermoplastic Polymers The creep behavior of thermoplastic polymeric materials is highly dependent on loading conditions, which must be accounted for in the intrinsic model. In this paper, fractional creep models have been developed to describe the temperature/stress-dependent creep/creep-recovery and accelerated creep damage behavior, with the construction of a criterion correlating model parameters with temperature and initial stress. The fractional order in the fractional creep/creep-recovery model can be physically interpreted by the well-known master curve, and the creep rupture time can be predicted by combining the Monkman-Grant law with the fractional creep damage model. Extensive experimental data are employed to substantiate the model's applicability under different loading conditions. Moreover, a comparative analysis highlights the proposed model's superior simplicity and performance over existing models. Creep ; Materials science ; Composite material ; Thermoplastic ; Stress (linguistics) ; Thermoplastic polymer ; Polymer Polymer Nanocomposites and Properties ; Polymer crystallization and properties ; Rheology and Fluid Dynamics Studies
Authors: 干崇昊 Gan Chonghao | 卢翔孟 Lu Xiangmeng | 崔大健 Cui Dajian | 冯文林 Feng Wenlin | 杨晓占 Yang Xiaozhan | 刘相志 Liu Xiangzhi
Source: Acta Optica Sinica (article, 2025-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

近红外波段消色差超构透镜的设计与仿真 随着微纳光子学技术的快速发展，超构透镜作为一种新型的光学元件，因其独特的光波调控特性，在高度集成的成像系统和光通信领域中展现出巨大的应用潜力。针对超构透镜因工作带宽的限制产生的色差问题，设计一种基于传输相位和几何相位联合调控的消色差超构透镜，针对1450~1650 nm的圆偏振光，实现宽带消色差聚焦功能。所设计的超构透镜数值孔径可达0.8165，平均聚焦效率约为24%，平均偏振转化效率约为45.5%，旁瓣比约为0.04。该超构透镜有望在红外探测、显微成像、光通信等领域发挥作用。 Computer science Metamaterials and Metasurfaces Applications ; Advanced Antenna and Metasurface Technologies ; Antenna Design and Analysis
Authors: Kaylie I. Kirkwood‐Donelson | Prashant Rai | L. Perera | Michael B. Fessler | Alan K. Jarmusch
Source: Journal of the American Society for Mass Spectrometry (article, 2025-03-07)
Field: Chemistry — Spectroscopy

Bromine-Based Derivatization of Carboxyl-Containing Metabolites for Liquid Chromatography–Trapped Ion Mobility Spectrometry–Mass Spectrometry The analysis of small carboxyl-containing metabolites (CCMs), such as tricarboxylic acid (TCA) cycle intermediates, provides highly useful information about the metabolic state of cells. However, their detection using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) methods can face sensitivity and specificity challenges given their low ionization efficiency and the presence of isomers. Ion mobility spectrometry (IMS), such as trapped ion mobility spectrometry (TIMS), provides additional specificity, but further signal loss can occur during the mobility separation process. We, therefore, developed a solution to boost CCM ionization and chromatographic separation as well as leverage specificity of IMS. Inspired by carbodiimide-mediated coupling of carboxylic acids with 4-bromo-<i>N</i>-methylbenzylamine (4-BNMA) for quantitative analysis, we newly report the benefits of this reagent for TIMS-based measurement. We observed a pronounced (orders of magnitude) increase in signal and enhanced isomer separations, particularly by LC. We found that utilization of a brominated reagent, such as 4-BNMA, offered unique benefits for untargeted CCM measurement. Derivatized CCMs displayed shifted mobility out of the metabolite and lipid region of the TIMS-MS space as well as characteristic isotope patterns, which were leveraged for data mining with Mass Spectrometry Query Language (MassQL) and indication of the number of carboxyl groups. The utility of our LC-ESI-TIMS-MS/MS method with 4-BMA derivatization was demonstrated via the characterization of alterations in CCM expression in bone marrow-derived macrophages upon activation with lipopolysaccharide. While metabolic reprogramming in activated macrophages has been characterized previously, especially with respect to TCA cycle intermediates, we report a novel finding that isomeric itaconic, mesaconic, and citraconic acid increase after 24 h, indicating possible roles in the inflammatory response. Chemistry ; Derivatization ; Ion-mobility spectrometry ; Mass spectrometry ; Chromatography ; Bromine ; Ion-mobility spectrometry–mass spectrometry ; Liquid chromatography–mass spectrometry ; Protein mass spectrometry ; Tandem mass spectrometry ; Selected reaction monitoring ; Organic chemistry Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Analytical Chemistry and Chromatography