jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Qingqing Yan | Songyan An | Liang Yu | S S Li | Xiaonan Wu | Siqi Dong | Shunshun Xiong | Hao Wang | Sujing Wang | Jiangfeng Du
Source: Nature Communications (article, 2024-11-15)
Field: Chemistry — Inorganic Chemistry

A Ni4O4-cubane-squarate coordination framework for molecular recognition Molecular recognition is a fundamental function of natural systems that ensures biological activity. This is achieved through the sieving effect, host-guest interactions, or both in biological environments. Recent advancements in multifunctional proteins reveal a new dimension of functional organization that goes beyond single-function molecular recognition, emphasizing the need for artificial multifunctional materials in industrial applications. Herein, we have designed a porous Ni<sub>4</sub>O<sub>4</sub>-cubane squarate coordination polymer as an artificial molecular recognition host, drawing inspiration from the structural and functional features of natural enzymes. A comprehensive assessment of the material's ability to distinguish target species under different operating conditions was carried out. The results confirm its sieving function through hexane isomers separation, host-guest interaction function via xenon/krypton separation, and dual presence of sieving and interaction through carbon dioxide/nitrogen separation. Additionally, the material demonstrates good stability and feasibility for large-scale production, indicating its practical potential. Our findings provide a bio-inspired multifunctional recognition material for chemical separations as proof-of-concept while offering solutions to advance artificial multifunctional materials adaptable to other applications beyond chemical separations. Cubane ; Molecular recognition ; Computer science ; Computational biology ; Biology ; Chemistry ; Crystallography ; Molecule Metal-Organic Frameworks: Synthesis and Applications ; Computational Drug Discovery Methods ; Molecular Sensors and Ion Detection
Authors: M. Barshutina | Aleksey V. Arsenin | Valentyn S. Volkov
Source: Heliyon (review, 2024-09-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

SERS analysis of single cells and subcellular components: A review SERS is a rapidly advancing and non-destructive technique that has been proven to be more reliable and convenient than other traditional analytical methods. Due to its sensitivity and specificity, this technique is earning its place as a routine and powerful tool in biological and medical studies, especially for the analysis of living cells and subcellular components. This paper reviewed the research progress of single-cell SERS that has been made in the last few years and discussed challenges and future perspectives of this technique. The reviewed SERS platforms have been categorized according to their nature into the following types: (1) colloid-based, substrate-based, or hybrid; (2) ligand-based or ligand-free, and (3) label-based or label-free. The advantages and disadvantages of each type and their potential applications in various fields are thoroughly discussed. Nanotechnology ; Chemistry ; Computational biology ; Computer science ; Data science ; Biology ; Materials science Gold and Silver Nanoparticles Synthesis and Applications ; Advanced biosensing and bioanalysis techniques ; Biosensors and Analytical Detection
Authors: Inna Kurganskaya
Source: Minerals (article, 2024-09-02)
Field: Materials Science — Biomaterials

Dissolution Mechanisms and Surface Charge of Clay Mineral Nanoparticles: Insights from Kinetic Monte Carlo Simulations The widespread use of clay minerals and clays in environmental engineering, industry, medicine, and cosmetics largely stems from their adsorption properties and surface charge, as well as their ability to react with water. The dissolution and growth of minerals as a function of pH are closely related to acid–base reactions at their surface sites and their surface charge. The vivid tapestry of different types of surface sites across different types of clay minerals generates difficulties in experimental studies of structure–property relationships. The aim of this paper is to demonstrate how a mesoscale stochastic kinetic Monte Carlo (kMC) approach altogether with atomistic acid-base models and empirical data can be used for understanding the mechanisms of dissolution and surface charge behavior of clay minerals. The surface charge is modeled based on equilibrium equations for de/protonated site populations, which are defined by the pH and site-specific acidity constants (pKas). Lowered activation energy barriers for these sites in de/protonated states introduce pH-dependent effects into the dissolution kinetics. The V-shaped curve observed in laboratory experiments is reproduced with the new kMC model. A generic rate law for clay mineral dissolution as a function of pH is derived from this study. Thus, the kMC approach can be used as a hypothesis-testing tool for the verification of acid–base models for clay and other minerals and their influence on the kinetics of mineral dissolution and growth. Dissolution ; Monte Carlo method ; Kinetic Monte Carlo ; Mineral ; Kinetic energy ; Surface charge ; Clay minerals ; Nanoparticle ; Materials science ; Mineralogy ; Geology ; Chemistry ; Nanotechnology ; Physical chemistry ; Metallurgy ; Physics Clay minerals and soil interactions ; Soil and Unsaturated Flow ; Material Dynamics and Properties
Authors: Derrick Mirindi | James Hunter | Frédéric Mirindi | David Sinkhonde | Fatemeh Yazdandoust
Source: Nanotechnology Reviews (article, 2024-01-01)
Field: Materials Science — Biomaterials

Structural performance of boards through nanoparticle reinforcement: An advance review Abstract Under the turbulence of global change, the production of boards has been influenced by the rising demand and price of wood-based materials. To improve the structural performance of boards, reinforcement materials have been added, such as nanoparticles. The purpose of this review is to explore the application of nanomaterials, including nano-SiO 2 , nano-Al 2 O 3 , nano-ZnO, nano-Fe 2 O 3 , nano-cellulose, nano-lignin, and nano-chitosan, to evaluate the physical and mechanical properties of particleboards. These nanoparticles have demonstrated their ability to reduce formaldehyde emissions, enhance the dimensional stability, bending strength, bending stiffness, fire resistance, and resistance to thermal conductivity in board production. For example, the addition of nano-SiO 2 , known for its hydrophilicity, attracts and holds water molecules and acts as a thermal barrier due to its high melting point and low thermal conductivity. In contrast, nano-Al 2 O 3 is known for its high compressive strength (up to 3 GPa), hardness strength (9 Mohs scale), and high thermal conductivity, which helps to dissipate heat more effectively. This comprehensive evaluation brings together recent advances in producing particleboards and medium density fiberboard reinforced with nanoparticles, which are essential for future research and industry applications. The study emphasizes how innovative nanoparticles can contribute to sustainable urban development and construction practices, reduce deforestation, preserve natural habitats, and provide affordable housing. The research indicates that nanoparticle boards meet ( e.g. , nanoclay and nanoalumina panels) and in some cases exceed the minimum requirement for general-purpose panels set standards such as the ANSI/A208.1-1999, including water absorption of 8%, thickness swelling of 3% and EN 312 for the bending strength (15–16 MPa) and bending stiffness (2.2–2.4 GPa) for P4 and P6 boards, respectively. These results support the transformative power of nanomaterials in promoting a more sustainable and future solution for boards in the building construction industry. Reinforcement ; Nanoparticle ; Materials science ; Nanotechnology ; Composite material Advanced Cellulose Research Studies ; Electrospun Nanofibers in Biomedical Applications ; Innovative concrete reinforcement materials
Authors: Igor N. Pyagay | Yana A. Svakhina | Marina E. Titova | V. V. MIROSHNICHENKO
Source: International Journal of Engineering (article, 2024-09-01)
Field: Chemistry — Inorganic Chemistry

Synthesis of Linde Type A Zeolites Based on Silica Gel for Petrochemical Industry The demand for various types of zeolites in the oil and gas industry is associated with their high ion exchange and adsorption properties. This study is aimed to identify the regularities of the process of obtaining zeolite precursors from waste silica gel and industrial aluminium hydroxide since water glass and aluminate solution are the initial hydrogel components for the hydrothermal synthesis of zeolites. In addition, the process of hydrothermal synthesis of zeolites was investigated, namely, the effect of the molar ratio of SiO2:Al2O3 between hydrogel components on the structure and type of zeolite produced was determined. Identification of phases and study of the morphology of initial substances and obtained samples were carried out using X-ray diffraction and scanning electron microscopy methods. For the sample representing the monophase of LTA zeolite, the value of ion exchange capacity for Ca2+ ion and the particle size of the main fraction were determined to be 550 mEq/100g and less than 10 μm, respectively. Petrochemical ; Materials science ; Waste management ; Chemical engineering ; Metallurgy ; Process engineering ; Environmental science ; Engineering Zeolite Catalysis and Synthesis ; Mesoporous Materials and Catalysis ; Catalysis and Hydrodesulfurization Studies
Authors: F. Koua | Huijong Han | Richard Bean
Source: ACS Catalysis (article, 2024-07-04)
Field: Materials Science — Materials Chemistry

Structural Dynamics of Metalloproteins and Redox Enzymology with Mix-and-Inject Time-Resolved Serial Femtosecond Crystallography Time-resolved serial femtosecond crystallography (tr-SFX) enables the study of biomolecules in action at room temperature, thus facilitating the construction of in crystallo mini-3D biomolecular series (a stop-motion series) of biochemical reactions with unprecedented spatiotemporal details. One of the challenges encountered in expanding this method is the insufficient tools available for triggering the biomacromolecular reaction. Here, we highlight recent advances and challenges in the mix-and-inject (diffusion-based) tr-SFX (MISC) as a promising triggering method for studying the structural dynamics of metalloproteins, redox enzymes, and their reaction kinetics. We further discuss the results obtained using MISC tr-SFX and propose complex MISC (cMISC) as a tool to study complex reaction kinetics such as theenzyme-catalyzed bisubstrate (sequential and ping-pong) reactions. Redox ; Kinetics ; Chemistry ; Femtosecond ; Biomolecule ; Catalysis ; Metalloprotein ; Nanotechnology ; Materials science ; Enzyme ; Biochemistry ; Physics ; Organic chemistry Enzyme Structure and Function ; Metal-Catalyzed Oxygenation Mechanisms ; Protein Structure and Dynamics
Authors: João Paulo Cerqueira Felix | Gabriel Reynald Da Silva | Gláucio R. Nagurniak | Alexandre C. Dias | Renato P. Orenha | Celso R. C. Rêgo | Renato L. T. Parreira | Diego Guedes‐Sobrinho | Maurício J. Piotrowski
Source: ACS Omega (article, 2024-09-18)
Field: Materials Science — Materials Chemistry

Investigating Molecular Adsorption on Graphene-Supported Platinum Subnanoclusters: Insights from DFT + D3 Calculations Platinum (Pt) subnanoclusters have become pivotal in nanocatalysis, yet their molecular adsorption mechanisms, particularly on supported versus unsupported systems, remain poorly understood. Our study employs detailed density functional theory (DFT) calculations with D3 corrections to investigate molecular adsorption on Pt subnanoclusters, focusing on CO, NO, N<sub>2</sub>, and O<sub>2</sub> species. Gas-phase and graphene-supported scenarios are systematically characterized to elucidate adsorption mechanisms and catalytic potential. Gas-phase Pt <sub><i>n</i></sub> clusters are first analyzed to identify stable configurations and assess size-dependent reactivity. Transitioning to graphene-supported Pt <sub><i>n</i></sub> clusters, both periodic and nonperiodic models are employed to study interactions with graphene substrates. Strong adsorbate interactions predominantly occur at single top sites, revealing distinct adsorption geometries and stabilization effects for specific molecules on Pt<sub>6</sub> clusters. Energy decomposition analysis highlights the paramount role of graphene substrates in enhancing stability and modulating cluster-adsorbate interactions. The interaction energy emerges as a critical criterion within the Sabatier principle, crucial for distinguishing between physisorption and chemisorption. Hybridization indices and charge density flow tendencies establish direct relationships with stabilization processes, underscoring graphene's influence in stabilizing highly reactive subnanoclusters. This comprehensive investigation provides critical insights into molecular adsorption mechanisms and the catalytic potential of graphene-supported Pt nanoclusters. Our findings contribute to a deeper understanding of nanocatalysis, emphasizing the essential role of substrates in optimizing catalytic performance for industrial applications. Graphene ; Adsorption ; Platinum ; Materials science ; Nanotechnology ; Chemical physics ; Computational chemistry ; Chemistry ; Physical chemistry ; Organic chemistry ; Catalysis Graphene research and applications ; Catalytic Processes in Materials Science ; Machine Learning in Materials Science
Authors: Pratyush Tiwary
Source: Proceedings of the National Academy of Sciences (article, 2024-05-29)
Field: Materials Science — Materials Chemistry

Modeling prebiotic chemistries with quantum accuracy at classical costs Molecular Dynamics (MD) simulations using classical force-fields are commonly employed in numerous scientific investigations. However, many natural processes involve bond breaking and quantum forces. This complexity is compounded by the presence of multiple competing length and timescales. For example, accurately modeling the thermodynamics and dynamics of a chemical reaction requires accounting for the concerted movements of numerous solvent molecules and ions with their own fast or slow timescales. While widely used static Density Functional Theory (DFT) calculations at 0 temperature can be beneficial for such investigations, they do not account for dynamics, and lack precision in describing the molecular environments. They particularly fail at correct, rigorous treatments of finite-temperature fluctuations, and thus generalization to experimentally relevant conditions. In PNAS Benayad et al develop a scalable, generalizable approach for designing Neural Network Potentials (NNPs) that can handle chemical reactivity in solvated systems with quantum accuracy at classical costs. Specifically, they study phosphoester bond formation and rupture, which is fundamentally relevant to the Phosphorus-Oxygen bond formation central to life, and especially for the RNA world hypothesis. The framework developed here has the potential to generalize to different chemical reactions of energy and biological relevance. Prebiotic ; Quantum ; Astrobiology ; Biochemical engineering ; Chemistry ; Physics ; Quantum mechanics ; Engineering ; Food science Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Protein Structure and Dynamics
Authors: Elhassan A. Allam | Mohamed A. Ghamry | Mohamed A. Gizawy | Rehab M. El‐Sharkawy | Mohamed E. Mahmoud
Source: Journal of Inorganic and Organometallic Polymers and Materials (article, 2024-07-12)
Field: Chemistry — Inorganic Chemistry

Investigation of Adsorption Optimization, Kinetic and Isotherm Behaviors of 60Co and 152+154Eu Radioisotopes from Nuclear Radioactive Wastewater onto a Novel Co0.5Ni0.5O–Co2Mo3O8–CuO–ZnO Perovskite Metal Oxides Nanosorbent Abstract Herein in this study, a new nanosorbent consisted of perovskite cobalt–nickel oxide Co 0.5 Ni 0.5 O and perovskite cobalt–molybdenum oxide Co 2 Mo 3 O 8 , copper oxide CuO, and zinc oxide ZnO, has been synthesized. The structural and morphological properties of the nanosorbent were established by using FT-IR, PXRD, TGA, HR-TEM, SEM, and EDX. The nanosorbent was implemented to adsorb 60 Co and 152+154 Eu radioactive isotopes under diverse conditions using different pH values, contact times, radioactive nuclides concentrations, and temperatures. The highest adsorption removal for both radionuclides was obtained at pH 6.0 as 83.65 and 122.50 mg/g for 60 Co(II), and 152+154 Eu(III), respectively. The adsorption models for 60 Co(II) were fitted with Temkin only, on the other hand, the adsorption of 152+154 Eu(III) was fitted with four adsorption models. The kinetics for 60 Co(II) were fitted with the Pseudo first order (PFO), Pseudo second order (PSO), and Intraparticle models on the other hand 152+154 Eu(III) were found to agree with the P seudo first order ( P FO) and intraparticle models. Adsorption ; Perovskite (structure) ; Kinetic energy ; Metal ; Radioactive waste ; Materials science ; Inorganic chemistry ; Chemistry ; Nuclear chemistry ; Physical chemistry ; Metallurgy ; Crystallography ; Physics Radioactive element chemistry and processing ; Chemical Synthesis and Characterization ; Covalent Organic Framework Applications
Authors: О. О. Дідур | Н. О. Хромых | О. А. Drehval | Т. V. Sklyar | Volodymyr Dzhagan | Nazar Mazur | Mykola Skoryk | V. Kurahina
Source: Biosystems Diversity (article, 2024-08-19)
Field: Materials Science — Materials Chemistry

Influence of silver nanoparticles synthesized from Chaenomeles leaf extracts on pathogenic microorganisms Klebsiella pneumoniae, Staphylococcus aureus, and Fusarium culmorum Herein, we report for the first time the biosynthesis of silver nanoparticles (AgNPs) using leaf extracts of Chaenomeles Lindl. (Rosaceae) plants and its spectral characteristics, as well as antifungal and antibacterial activity. Phytosynthesis of silver nanoparticles on the base of aqueous plant extracts and silver nitrate solution was carried out by an ecofriendly and cost-effective approach. UV-Vis spectroscopy was applied to validate the plant-mediated biosynthesis of AgNPs colloidal solutions by the Surface Plasmon Resonance (SPR) bands in the region of 450–500 nm, characteristic of polycrystalline silver nanoparticles. Scanning microscopy (SEM) revealed a wide variation in range 5–58 nm and a close to spherical shape of plant-derived AgNPs. Raman scattering spectroscopy revealed the suitability of biosynthesized silver nanoparticles as the substrates for surface-enhanced Raman scattering (SERS) spectroscopy with the highest efficiency of AgNPs, biosynthesized from leaf extract of Ch. × superba, which enhanced the Rhodamine 6G dye applied at a concentration of 10–7 M. Assay of antifungal activity performed by well diffusion method revealed the dose-dependent effect of all AgNPs against the phytopathogenic fungus Fusarium culmorum. The most effective AgNPs (Ch. speciosa-AgNPs, Ch. cathayensis-AgNPs, and Ch. japonica-AgNPs) achieved a 1.42–1.63 times greater zone of inhibition of the F. culmorum colonies’ growth compared to the corresponding doses of the known chemical fungicide "Quadris". Micro preparations of the zones of incomplete growth inhibition presented changes in the mycelium morphology of F. culmorum due to the action of nanoparticles, such as deformation (curvature, expansion), and a decrease in the hyphae length and density compared to the control sample. Disc-diffusion assay showed notable species-specific antibacterial activity of AgNPs both against Gram-negative (Klebsiella pneumoniae) and Gram-positive (Staphylococcus aureus) strains. Summarizing, the results indicate the undeniable suitability of aqueous leaf extracts of the genus Chaenomeles species for the successful biosynthesis of silver nanoparticles with many useful properties, whose diverse applications require further research. Klebsiella pneumoniae ; Staphylococcus aureus ; Fusarium culmorum ; Microbiology ; Microorganism ; Biology ; Fusarium ; Bacteria ; Botany ; Escherichia coli Nanoparticles: synthesis and applications ; Essential Oils and Antimicrobial Activity ; Medicinal Plants and Neuroprotection
Authors: Adam M. Krajewski | Allison M. Beese | Wesley F. Reinhart | Zi‐Kui Liu
Source: npj Unconventional Computing (article, 2024-11-05)
Field: Materials Science — Materials Chemistry

Efficient generation of grids and traversal graphs in compositional spaces towards exploration and path planning Abstract Diverse disciplines across science and engineering deal with problems related to compositions, which exist in non-Euclidean simplex spaces, rendering many standard tools inaccurate or inefficient. This work explores such spaces conceptually in the context of materials discovery, quantifies their computational feasibility, and implements several essential methods specific to simplex spaces through a new high-performance open-source library . Most significantly, we derive and implement an algorithm for constructing a novel n-dimensional simplex graph data structure, containing all discretized compositions and possible neighbor-to-neighbor transitions. Critically, no distance or neighborhood calculations are performed, instead leveraging pure combinatorics and order in procedurally generated simplex grids, keeping the algorithm $${\mathcal{O}}(N)$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>O</mml:mi> <mml:mrow> <mml:mo>(</mml:mo> <mml:mrow> <mml:mi>N</mml:mi> </mml:mrow> <mml:mo>)</mml:mo> </mml:mrow> </mml:mrow> </mml:math> , with minimal memory, enabling rapid construction of graphs with billions of transitions in seconds. Additionally, we demonstrate how such graph representations can be combined to homogeneously express complex path-planning problems, while facilitating efficient deployment of existing high-performance gradient descent, graph traversal, and other optimization algorithms. Tree traversal ; Simplex ; Computer science ; Graph traversal ; Algorithm ; Graph ; Discretization ; Theoretical computer science ; Mathematics ; Combinatorics Machine Learning in Materials Science
Authors: Ming Qiao | Huimin Wang | Heng Guo | Ma Luo | Yuzhi Zhao | Haoze Han | Jianfeng Yan | Yingying Zhang
Source: Light Advanced Manufacturing (article, 2024-01-01)
Field: Materials Science — Biomaterials

Ultrafast laser processing of silk films by bulging and ablation for optical functional devices Organic proteins are attractive owing to their unique optical properties, remarkable mechanical characteristics, and biocompatibility. Manufacturing multifunctional structures on organic protein films is essential for practical applications; however, the controllable fabrication of specific structures remains challenging. Herein, we propose a strategy for creating specific structures on silk film surfaces by modulating the bulging and ablation of organic materials. Unique surface morphologies such as bulges and craters with continuously varying diameters were generated based on the controlled ultrafast laser-induced crystal-form transition and plasma ablation of the silk protein. Owing to the anisotropic optical properties of the bulge/crater structures with different periods, the fabricated organic films can be used for large-scale inkless color printing. By simultaneously engineering bulge/crater structures, we designed and demonstrated organic film-based optical functional devices that achieves holographic imaging and optical focusing. This study provides a promising strategy for the fabrication of multifunctional micro/nanostructures that can broaden the potential applications of organic materials. Ultrashort pulse ; Laser ablation ; SILK ; Materials science ; Ablation ; Laser ; Optoelectronics ; Optics ; Composite material ; Engineering ; Physics Silk-based biomaterials and applications ; Neurobiology and Insect Physiology Research ; Nonlinear Optical Materials Studies