jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Caitlin A. McCandler | Jakob C. Dahl | Kristin A. Persson
Source: ACS Nano (article, 2022-12-30)
Field: Materials Science — Materials Chemistry

Phosphine-Stabilized Hidden Ground States in Gold Clusters Investigated via a Au <sub> <i>n</i> </sub> (PH <sub>3</sub> ) <sub> <i>m</i> </sub> Database Nanoclusters are promising materials for catalysis and sensing due to their large surface areas and unique electronic structures which can be tailored through composition, geometry, and chemistry. However, relationships correlating synthesis parameters directly to outcomes are limited. While previous computational studies have mapped the potential energy surface of specific systems of bare nanoclusters by generating and calculating the energies of reasonable structures, it is known that environmental ions and ligands crucially impact the final shape and size. In this work, phosphine-stabilized gold is considered as a test system and DFT calculations are performed for clusters with and without ligands, producing a database containing >10000 structures for Au<sub><i>n</i></sub>(PH<sub>3</sub>)<sub><i>m</i></sub> (<i>n</i> ≤ 12). We find that the ligation of phosphines affects the thermodynamic stability, bonding, and electronic structure of Au nanoclusters, specifically such that "hidden" ground state cluster geometries are stabilized that are dynamically unstable in the pure gold system. Further, the addition of phosphine introduces steric effects that induce a transition from planar to nonplanar structures at 4-5 Au atoms rather than up to 13-14 Au atoms, as previously predicted for bare clusters. This work highlights the importance of considering the ligand environment in the prediction of nanocluster morphology and functionality, which adds complexity as well as a rich opportunity for tunability. Phosphine ; Database ; Materials science ; Chemistry ; Computer science ; Catalysis Nanocluster Synthesis and Applications ; Machine Learning in Materials Science ; Gold and Silver Nanoparticles Synthesis and Applications
Authors: Monika Kovačević | Dora Markulin | Matea Zelenika | Marko Marjanović | Marija Lovrić | Denis Polančec | Mirela Ivančić Šantek | Jasna Mrvčić | Krešimir Molčanov | Valentina Milašinović | Sunčica Roca | Ivan Kodrin | Lidija Barišić
Source: International Journal of Molecular Sciences (article, 2022-10-13)
Field: Chemistry — Organic Chemistry

Hydrogen Bonding Drives Helical Chirality via 10-Membered Rings in Dipeptide Conjugates of Ferrocene-1,1′-Diamine Considering the enormous importance of protein turns as participants in various biological events, such as protein-protein interactions, great efforts have been made to develop their conformationally and proteolytically stable mimetics. Ferrocene-1,1'-diamine was previously shown to nucleate the stable turn structures in peptides prepared by conjugation with Ala (<b>III</b>) and Ala-Pro (<b>VI</b>). Here, we prepared the homochiral conjugates of ferrocene-1,1'-diamine with l-/d-Phe (<b>32/35</b>), l-/d-Val (<b>33/36</b>), and l-/d-Leu (<b>34/37</b>) to investigate (1) whether the organometallic template induces the turn structure upon conjugation with amino acids, and (2) whether the bulky or branched side chains of Phe, Val, and Leu affect hydrogen bonding. Detailed spectroscopic (IR, NMR, CD), X-ray, and DFT studies revealed the presence of two simultaneous 10-membered interstrand hydrogen bonds, i.e., two simultaneous β-turns in goal compounds. A preliminary biological evaluation of d-Leu conjugate <b>37</b> showed its modest potential to induce cell cycle arrest in the G0/G1 phase in the HeLa cell line but these results need further investigation. Dipeptide ; Ferrocene ; Diamine ; Chirality (physics) ; Hydrogen bond ; Chemistry ; Conjugate ; Axial chirality ; Combinatorial chemistry ; Enantiopure drug ; Stereochemistry ; Crystallography ; Organic chemistry ; Enantioselective synthesis ; Molecule ; Amino acid ; Catalysis ; Biochemistry ; Physical chemistry ; Electrochemistry ; Mathematics Ferrocene Chemistry and Applications ; Chemical Synthesis and Analysis ; Organoboron and organosilicon chemistry
Authors: Mohammad Alboghobeish | Andrea Monforti Ferrario | Davide Pumiglia | Massimiliano Della Pietra | Stephen J. McPhail | Sergii Pylypko | Domenico Borello
Source: Energies (article, 2022-05-18)
Field: Materials Science — Materials Chemistry

Developing an Automated Tool for Quantitative Analysis of the Deconvoluted Electrochemical Impedance Response of a Solid Oxide Fuel Cell Despite being commercially available, solid oxide fuel cell (SOFC) technology requires further study to understand its physicochemical processes for diagnostics, prognostics, and quality assurance purposes. Electrochemical impedance spectroscopy (EIS), a widely used characterization technique for SOFCs, is often accompanied by the distribution of relaxation times (DRT) as a method for deconvoluting the contribution of each physicochemical process from the aggregated impedance response spectra. While EIS yields valuable information for the operation of SOFCs, the quantitative analysis of the DRT and its shifts remains cumbersome. To address this issue, and to create a replicable benchmark for the assessment of DRT results, a custom tool was developed in MATLAB to numerically analyze the DRT spectra, identify the DRT peaks, and assess their deviation in terms of peak frequency and DRT amplitude from nominal operating conditions. The preliminary validation of the tool was carried out by applying the tool to an extensive experimental campaign on 23 SOFC button-sized samples from three production batches in which EIS measurements were performed in parametric operating conditions. It was concluded that the results of the automated analysis via the developed tool were in accordance with the qualitative analysis of previous studies. It is capable of providing adequate additional quantitative results in terms of DRT shifts for further analysis and provides the basis for better interoperability of DRT analyses between laboratories. Dielectric spectroscopy ; Electrical impedance ; Parametric statistics ; Solid oxide fuel cell ; Benchmark (surveying) ; MATLAB ; Quantitative analysis (chemistry) ; Quality assurance ; Computer science ; Materials science ; Process engineering ; Engineering ; Electrical engineering ; Electrochemistry ; Chemistry ; Mathematics Advancements in Solid Oxide Fuel Cells ; Fuel Cells and Related Materials ; Analytical Chemistry and Sensors
Authors: Aleksandra A. Petelski | Nikolai Slavov | Harrison Specht
Source: Journal of Visualized Experiments (article, 2022-12-09)
Field: Chemistry — Spectroscopy

Single-Cell Proteomics Preparation for Mass Spectrometry Analysis Using Freeze-Heat Lysis and an Isobaric Carrier Single-cell proteomics analysis requires sensitive, quantitatively accurate, widely accessible, and robust methods. To meet these requirements, the Single-Cell ProtEomics (SCoPE2) protocol was developed as a second-generation method for quantifying hundreds to thousands of proteins from limited samples, down to the level of a single cell. Experiments using this method have achieved quantifying over 3,000 proteins across 1,500 single mammalian cells (500-1,000 proteins per cell) in 10 days of mass spectrometer instrument time. SCoPE2 leverages a freeze-heat cycle for cell lysis, obviating the need for clean-up of single cells and consequently reducing sample losses, while expediting sample preparation and simplifying its automation. Additionally, the method uses an isobaric carrier, which aids protein identification and reduces sample losses. This video protocol provides detailed guidance to enable the adoption of automated single-cell protein analysis using only equipment and reagents that are widely accessible. We demonstrate critical steps in the procedure of preparing single cells for proteomic analysis, from harvesting up to injection to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Additionally, viewers are guided through the principles of experimental design with the isobaric carrier, quality control for both isobaric carrier and single-cell preparations, and representative results with a discussion of limitations of the approach. Isobaric labeling ; Mass spectrometry ; Isobaric process ; Proteomics ; Sample preparation ; Computer science ; Lysis ; Shotgun proteomics ; Chromatography ; Orbitrap ; Chemistry ; Tandem mass spectrometry ; Tandem mass tag ; Protocol (science) ; Quantitative proteomics ; Protein mass spectrometry ; Biochemistry ; Medicine Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Single-cell and spatial transcriptomics
Authors: Tongqiang Jiang | Wang ZHENG | Qing‐chuan Zhang | Zu‐zheng Wang | Baolian Cheng
Source: Food Science & Nutrition (article, 2022-01-19)
Field: Chemistry — Analytical Chemistry

Establishment and application of risk classification model for lead in vegetables based on spectral clustering algorithms This study aims to evaluate the risk of lead pollution in 9 kinds of vegetables consumed by residents in 20 provinces/cities of China. Sampling data and vegetable consumption data from 20 provinces/cities in 2019 were used. Combined with dietary exposure assessment, the vegetable categories and provinces were paired, and a risk classification model based on spectral clustering algorithms was proposed. The results of the spectral clustering algorithm showed that the risk level of lead pollution in vegetables can be divided into five levels. The combination of vegetable-province/cities at the risk level of 1 and 2 accounted for 92.78%, and that at the risk level of 4 and 5 accounted for 2.22%. The high-risk combinations were fresh edible fungus-Shaanxi, fresh edible fungus-Sichuan, and fresh edible fungus-Shanghai and bean sprouts-Guangdong. In the proposed model, objective data were used as the classification index, and the spectral clustering algorithm was employed to select the optimal risk classification in a data-driven way. As a result, the influence of subjective factors was effectively reduced, the risk of lead pollution in vegetables was classified, and the results were scientific and accurate. This study provides a scientific basis of supervision priorities for regulatory departments. Cluster analysis ; Computer science ; Lead (geology) ; Spectral clustering ; Artificial intelligence ; Data mining ; Algorithm ; Pattern recognition (psychology) ; Biology Heavy Metals in Plants ; Heavy metals in environment
Authors: Maxim Ziatdinov | Yongtao Liu | Sergei V. Kalinin
Source: arXiv (Cornell University) (preprint, 2022-03-18)
Field: Materials Science — Materials Chemistry

Active learning in open experimental environments: selecting the right information channel(s) based on predictability in deep kernel learning Active learning methods are rapidly becoming the integral component of automated experiment workflows in imaging, materials synthesis, and computation. The distinctive aspect of many experimental scenarios is the presence of multiple information channels, including both the intrinsic modalities of the measurement system and the exogenous environment and noise signals. One of the key tasks in experimental studies is hence establishing which of these channels is predictive of the behaviors of interest. Here we explore the problem of discovery of the optimal predictive channel for structure-property relationships (in microscopy) using deep kernel learning for modality selection in an active experiment setting. We further pose that this approach can be directly applicable to similar active learning tasks in automated synthesis and the discovery of quantitative structure-activity relations in molecular systems. Predictability ; Computer science ; Artificial intelligence ; Modality (human–computer interaction) ; Machine learning ; Property (philosophy) ; Workflow ; Active learning (machine learning) ; Kernel (algebra) ; Component (thermodynamics) ; Channel (broadcasting) ; Mathematics Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Shingo Urata | Rikiya Kado
Source: Journal of the American Ceramic Society (article, 2022-11-12)
Field: Materials Science — Ceramics and Composites

Effect of Al <sub>2</sub> O <sub>3</sub> addition on the thermal expansion of sodium alkaline‐earth silicate glasses: A molecular dynamics study Abstract Coefficient of thermal expansion (CTE) is an important property to consider when utilizing oxide glasses in thermal treatment processes to avoid thermal damage at the interfaces of the glasses with heterogeneous materials. It is thus important to know the effect of additives on CTE for designing glasses. The use of alumina efficiently improves chemical and mechanical durability of oxide glasses while maintaining the functionality and productivity; however, alumina‐doping often induces nonlinear variation of CTE. In this work, we therefore tried to investigate the relationship between CTE and the microstructure of sodium alkaline‐earth aluminosilicate glasses using classical molecular dynamics (MD) simulations. To accurately model the glasses, we extended a force‐matching potential by optimizing the parameter sets for Ca–O, Mg–O, and Na–O pair interactions using Bayesian optimization. The MD simulations reproduced the nonlinear variation of CTE as a function of alumina content, and detailed structural analyses identified inhomogeneous expansion in the glasses. It was found that the nonuniform CTE change at the nanoscale was related to the formation of an alumina‐rich region, in which more fivefold‐coordinated aluminum exist, when alumina content exceeded Na 2 O content. Accordingly, the microstructural change by alumina‐doping was identified as the origin of the nonlinear variation in the CTE of the glasses. Thermal expansion ; Materials science ; Aluminosilicate ; Molecular dynamics ; Oxide ; Doping ; Sodium oxide ; Aluminium oxides ; Microstructure ; Sodium aluminosilicate ; Mineralogy ; Composite material ; Chemical engineering ; Thermodynamics ; Metallurgy ; Chemistry ; Catalysis ; Computational chemistry Glass properties and applications ; Nuclear materials and radiation effects ; Luminescence Properties of Advanced Materials
Authors: Bhargavi Bhat | Silabrata Pahari | Shuhao Liu | Yuting Lin | Joseph Sang‐Il Kwon | Mustafa Akbulut
Source: Colloids and Surfaces A Physicochemical and Engineering Aspects (article, 2022-08-28)
Field: Chemistry — Organic Chemistry

Nanostructural and rheological transitions of pH-responsive supramolecular systems involving a zwitterionic amphiphile and a triamine Differential scanning calorimetry ; Supramolecular chemistry ; Small-angle X-ray scattering ; Chemical engineering ; Rheology ; Dynamic light scattering ; Bilayer ; Viscoelasticity ; Micelle ; Vesicle ; Thermotropic crystal ; Chemistry ; Lamellar structure ; Rheometer ; Aqueous solution ; Small-angle neutron scattering ; Phase (matter) ; Crystallography ; Materials science ; Nanoparticle ; Neutron scattering ; Thermodynamics ; Physical chemistry ; Organic chemistry ; Nanotechnology ; Scattering ; Membrane ; Crystal structure ; Composite material Surfactants and Colloidal Systems ; Lipid Membrane Structure and Behavior ; Protein Interaction Studies and Fluorescence Analysis
Authors: Mengwei Yu | Cheng Chen | Xi Jiang
Source: Fuel (article, 2022-04-29)
Field: Chemistry — Analytical Chemistry

Understanding the miscibility of polyoxymethylene dimethyl ethers (OMEn) and diesel blend using molecular dynamics simulation Polyoxymethylene ; Miscibility ; Molecular dynamics ; Omen ; Diesel fuel ; Materials science ; Thermodynamics ; Physical chemistry ; Organic chemistry ; Chemistry ; Computational chemistry ; Physics ; Polymer Petroleum Processing and Analysis ; Polymer crystallization and properties ; Phase Equilibria and Thermodynamics
Authors: Xingsheng Sun
Source: Materials (article, 2022-10-07)
Field: Materials Science — Materials Chemistry

Uncertainty Quantification of Material Properties in Ballistic Impact of Magnesium Alloys The design and development of cutting-edge light materials for extreme conditions including high-speed impact remains a continuing and significant challenge in spite of steady advances. Magnesium (Mg) and its alloys have gained much attention, due to their high strength-to-weight ratio and potential of further improvements in material properties such as strength and ductility. In this paper, a recently developed computational framework is adopted to quantify the effects of material uncertainties on the ballistic performance of Mg alloys. The framework is able to determine the largest deviation in the performance measure resulting from a finite variation in the corresponding material properties. It can also provide rigorous upper bounds on the probability of failure using known information about uncertainties and the system, and then conservative safety design and certification can be achieved. This work specifically focuses on AZ31B Mg alloys, and it is assumed that the material is well-characterized by the Johnson-Cook constitutive and failure models, but the model parameters are uncertain. The ordering of uncertainty contributions for model parameters and the corresponding behavior regimes where those parameters play a crucial role are determined. Finally, it is shown that how this ordering provides insight on the improvement of ballistic performance and the development of new material models for Mg alloys. Magnesium ; Materials science ; Ballistic impact ; Metallurgy ; Composite material ; Projectile High-Velocity Impact and Material Behavior ; Energetic Materials and Combustion ; Structural Response to Dynamic Loads
Authors: Khim Hoong Chu | Mohd Ali Hashim | Ackmez Mudhoo | Jean Debord
Source: Chemical Papers (article, 2022-11-14)
Field: Chemistry — Organic Chemistry

Beyond Freundlich and Langmuir: the Ruthven–virial equilibrium isotherm for aqueous-solid adsorption systems Freundlich equation ; Virial theorem ; Thermodynamics ; Langmuir ; Virial coefficient ; Langmuir adsorption model ; Chemistry ; Adsorption ; Aqueous solution ; Materials science ; Physical chemistry ; Physics ; Quantum mechanics Surfactants and Colloidal Systems ; Groundwater flow and contamination studies ; Spectroscopy and Quantum Chemical Studies
Authors: Pavel Ferkl | Pavel Hrma | Alexander W. Abboud | Donna Post Guillen | Miroslava Vernerová | Jaroslav Kloužek | Mark Hall | Albert A. Kruger | Richard Pokorný
Source: International Journal of Applied Glass Science (article, 2022-09-17)
Field: Materials Science — Materials Chemistry

Conversion degree and heat transfer in the cold cap and their effect on glass production rate in an electric melter Abstract A predictive model of melt rate in waste glass vitrification operations is needed to inform melter operations during normal and off‐normal operations. This paper describes the development of a model of the cold cap (the reacting melter feed floating on molten glass in a glass melter) that couples heat transfer with the feed‐to‐glass conversion kinetics. The model was applied to four melter feeds designed for high‐level and low‐activity nuclear waste feeds using the material properties, either measured or estimated, to obtain temperature and conversion distribution within the cold cap. The cold cap model, when coupled with a computational fluid dynamics model of a Joule‐heated glass melter, allows the prediction of the glass production rate and power consumption. The results show reasonable agreement with the melting rates measured during pilot‐scale melter tests. Vitrification ; Materials science ; Heat transfer ; Nuclear engineering ; Radioactive waste ; Glass melting ; Glass production ; Glass furnace ; Waste management ; Metallurgy ; Thermodynamics Nuclear materials and radiation effects ; Recycling and utilization of industrial and municipal waste in materials production ; Iron and Steelmaking Processes
Authors: João A. Paulo
Source: PROTEOMICS (article, 2022-09-12)
Field: Chemistry — Spectroscopy

Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing Isobaric labeling has rapidly become a predominant strategy for proteome-wide abundance measurements. Coupled to mass spectrometry, sample multiplexing techniques using isobaric labeling are unparalleled for profiling proteins and posttranslational modifications across multiple samples in a single experiment. Here, I highlight aspects of isobaric labeling in the context of expanding the breadth of multiplexing, improving quantitative accuracy and proteome depth, and developing a wide range of diverse applications. I underscore two facets that enhance quantitative accuracy and reproducibility, specifically the availability of quality control standards for isobaric labeling experiments and the evolution of data acquisition methods. I also emphasize the necessity for standardized methodologies, particularly for emerging high-throughput workflows. Future developments in sample multiplexing will further strengthen the importance of isobaric labeling for comprehensive proteome profiling. Isobaric process ; Isobaric labeling ; Multiplexing ; Proteome ; Context (archaeology) ; Computational biology ; Computer science ; Workflow ; Sample (material) ; Quantitative proteomics ; Data mining ; Biology ; Proteomics ; Chromatography ; Bioinformatics ; Chemistry ; Database ; Physics ; Genetics Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Helong Si | Quan Wang | Yuanyuan Guo | Yuxin Zhao | Hongya Li | Shuna Li | Shuxiang Wang | Baocheng Zhu
Source: Frontiers in Chemistry (review, 2022-08-05)
Field: Chemistry — Spectroscopy

Functionalized monolithic columns: Recent advancements and their applications for high-efficiency separation and enrichment in food and medicine The chromatographic column is the core of a high-performance liquid chromatography (HPLC) system, and must have excellent separation efficiency and selectivity. Therefore, functional modification materials for monolithic columns have been rapidly developed. This study is a systematic review of the recently reported functionalized monolithic columns. In particular, the study reviews the types of functional monomers under different modification conditions, as well as the separation and detection techniques combined with chromatography, and their development prospects. In addition, the applications of functionalized monolithic columns in food analysis, biomedicine, and the analysis of active ingredient of Chinese herbal medicines in recent years are also discussed. Also reviewed are the functionalized monolithic columns for qualitative and quantitative analysis. It provided a reference for further development and application of organic polymer monolithic columns. Monolithic HPLC column ; High-performance liquid chromatography ; Ingredient ; Active ingredient ; Chromatography ; Materials science ; Nanotechnology ; Chemistry Analytical Chemistry and Chromatography ; Microfluidic and Capillary Electrophoresis Applications ; Analytical chemistry methods development
Authors: Miwa Suzuki | Shun’ichi Ishii | Kohei Gonda | Hiroyuki Kashima | Shino Suzuki | Katsuyuki Uematsu | Takahiro Arai | Yuya Tachibana | Tadahisa Iwata | Ken‐ichi Kasuya
Source: Research Square (preprint, 2022-09-09)
Field: Materials Science — Biomaterials

Marine biodegradation mechanism of biodegradable plastics revealed by plastisphere analysis Biodegradation ; Gammaproteobacteria ; Adipate ; Esterase ; Chemistry ; Enzyme ; Polyhydroxyalkanoates ; Environmental chemistry ; Biochemistry ; Biology ; Bacteria ; Organic chemistry ; 16S ribosomal RNA ; Polymer chemistry ; Gene biodegradable polymer synthesis and properties ; Microplastics and Plastic Pollution