jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Israt Jahan | Fatma Matpan Bekler | A. Tunç | Kemal Güven
Source: Microorganisms (article, 2024-02-17)
Field: Materials Science — Materials Chemistry

The Effects of Silver Nanoparticles (AgNPs) on Thermophilic Bacteria: Antibacterial, Morphological, Physiological and Biochemical Investigations Since thermophilic microorganisms are valuable sources of thermostable enzymes, it is essential to recognize the potential toxicity of silver nanoparticles used in diverse industrial sectors. Thermophilic bacteria <i>Geobacillus vulcani</i> 2Cx, <i>Bacillus licheniformis</i> 3CA, <i>Paenibacillus macerans</i> 3CA1, <i>Anoxybacillus ayderensis</i> FMB1, and <i>Bacillus paralicheniformis</i> FMB2-1 were selected, and their MIC and MBC values were assessed by treatment with AgNPs in a range of 62.5-1500 μg mL<sup>-1</sup>. The growth inhibition curves showed that the <i>G. vulcani</i> 2Cx, and <i>B. paralicheniformis</i> FMB2-1 strains were more sensitive to AgNPs, demonstrating a reduction in population by 71.1% and 31.7% at 62.5 μg mL<sup>-1</sup> and by 82.9% and 72.8% at 250 μg mL<sup>-1</sup>, respectively. TEM and FT-IR analysis revealed that AgNPs caused structural damage, cytoplasmic leakage, and disruption of cellular integrity. Furthermore, cell viability showed a significant decrease alongside an increase in superoxide radical (SOR; O<sub>2</sub><sup>-</sup>) production. β-galactosidase biosynthesis decreased to 28.8% level at 500 μg mL<sup>-1</sup> AgNPs for <i>G. vulcani</i> 2Cx, 32.2% at 250 μg mL<sup>-1</sup> for <i>A. ayderensis</i> FMB1, and 38.8% only at 62.5 μg mL<sup>-1</sup>, but it was completely inhibited at 500 μg mL<sup>-1</sup> for <i>B. licheniformis</i> 3CA. Moreover, <i>B. paralicheniformis</i> FMB2-1 showed a significant decrease to 11.2% at 125 μg mL<sup>-1</sup>. This study is the first to reveal the toxic effects of AgNPs on thermophilic bacteria. Bacillus licheniformis ; Silver nanoparticle ; Thermophile ; Chemistry ; Bacteria ; Microbiology ; Microorganism ; Bacillus (shape) ; Population ; Food science ; Enzyme ; Biology ; Biochemistry ; Bacillus subtilis ; Nanoparticle ; Materials science ; Nanotechnology Nanoparticles: synthesis and applications ; Graphene and Nanomaterials Applications ; Bone Tissue Engineering Materials
Authors: Chaehwa Jeong | Juhyeok Lee | Hyesung Jo | Jaewhan Oh | Hionsuck Baik | Kyoung‐June Go | Junwoo Son | Si‐Young Choi | S. A. Prosandeev | L. Bellaïche | Yongsoo Yang
Source: Nature Communications (article, 2024-05-08)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Revealing the three-dimensional arrangement of polar topology in nanoparticles In the early 2000s, low dimensional ferroelectric systems were predicted to have topologically nontrivial polar structures, such as vortices or skyrmions, depending on mechanical or electrical boundary conditions. A few variants of these structures have been experimentally observed in thin film model systems, where they are engineered by balancing electrostatic charge and elastic distortion energies. However, the measurement and classification of topological textures for general ferroelectric nanostructures have remained elusive, as it requires mapping the local polarization at the atomic scale in three dimensions. Here we unveil topological polar structures in ferroelectric BaTiO<sub>3</sub> nanoparticles via atomic electron tomography, which enables us to reconstruct the full three-dimensional arrangement of cation atoms at an individual atom level. Our three-dimensional polarization maps reveal clear topological orderings, along with evidence of size-dependent topological transitions from a single vortex structure to multiple vortices, consistent with theoretical predictions. The discovery of the predicted topological polar ordering in nanoscale ferroelectrics, independent of epitaxial strain, widens the research perspective and offers potential for practical applications utilizing contact-free switchable toroidal moments. Ferroelectricity ; Topology (electrical circuits) ; Polar ; Vortex ; Topological defect ; Polarization (electrochemistry) ; Materials science ; Nanoscopic scale ; Nanostructure ; Atomic units ; Condensed matter physics ; Physics ; Nanotechnology ; Optoelectronics ; Quantum mechanics ; Chemistry ; Dielectric Multiferroics and related materials ; Electronic and Structural Properties of Oxides ; Ferroelectric and Piezoelectric Materials
Authors: Qiong Qin | Jiangfan Wang | Yi-feng Yang
Source: The Innovation Materials (preprint, 2024-01-01)
Field: Chemistry — Physical and Theoretical Chemistry

Frustrated superconductivity and intrinsic reduction of &lt;i&gt;T&lt;/i&gt;&lt;sub&gt;&lt;i&gt;c&lt;/i&gt;&lt;/sub&gt; in trilayer nickelate &lt;p&gt;Identifying the key factors controlling the magnitude of &lt;i&gt;T&lt;/i&gt;&lt;sub&gt;&lt;i&gt;c&lt;/i&gt;&lt;/sub&gt; is of critical importance in the pursuit of high-temperature superconductivity. In cuprates, &lt;i&gt;T&lt;/i&gt;&lt;sub&gt;&lt;i&gt;c&lt;/i&gt;&lt;/sub&gt; reaches its maximal value in trilayer structure, leading to the belief that interlayer coupling may help promote the pairing. In contrast, for the recently discovered nickelate superconductors under high pressure, the maximum &lt;i&gt;T&lt;/i&gt;&lt;sub&gt;&lt;i&gt;c&lt;/i&gt;&lt;/sub&gt; is reduced from about 80 K in the bilayer La&lt;sub&gt;3&lt;/sub&gt;Ni&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;7&lt;/sub&gt; to 30 K in the trilayer La&lt;sub&gt;4&lt;/sub&gt;Ni&lt;sub&gt;3&lt;/sub&gt;O&lt;sub&gt;10&lt;/sub&gt;. Motivated by this opposite trend, we propose an interlayer pairing scenario for the superconductivity of La&lt;sub&gt;4&lt;/sub&gt;Ni&lt;sub&gt;3&lt;/sub&gt;O&lt;sub&gt;10&lt;/sub&gt;. Our theory reveals intrinsic frustration in the spin-singlet pairing that the inner layer tends to form with both of the two outer layers respectively, leading to strong superconducting fluctuations between layers. This explains the reduction of its maximum &lt;i&gt;T&lt;/i&gt;&lt;sub&gt;&lt;i&gt;c&lt;/i&gt;&lt;/sub&gt; compared to that of the bilayer La&lt;sub&gt;3&lt;/sub&gt;Ni&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;7&lt;/sub&gt;. Our findings support a fundamental distinction between multilayer nickelate and cuprate superconductors, and ascribe it to their different (interlayer versus intralayer) pairing mechanisms. Furthermore, our theory predicts extended &lt;i&gt;s&lt;/i&gt;&lt;sup&gt;&lt;i&gt;±&lt;/i&gt;&lt;/sup&gt;-wave gap structures in La&lt;sub&gt;4&lt;/sub&gt;Ni&lt;sub&gt;3&lt;/sub&gt;O&lt;sub&gt;10&lt;/sub&gt;, with varying signs and possible nodes on different Fermi pockets. We also find an intrinsic Josephson coupling with potentially interesting consequences that may be examined in future experiments. Our work reveals the possibility of rich novel physics in multilayer superconductors with interlayer pairing.&lt;/p&gt; Superconductivity ; Reduction (mathematics) ; Condensed matter physics ; Materials science ; Physics ; Mathematics ; Geometry Advanced Physical and Chemical Molecular Interactions ; Theoretical and Computational Physics
Authors: Jia‐wei Zhang | Xiaohong Wu | Chengyu He | Bin Wu | Shuyu Zhang | Jun Sun
Source: Foods (article, 2024-05-07)
Field: Chemistry — Analytical Chemistry

Near-Infrared Spectroscopy Combined with Fuzzy Improved Direct Linear Discriminant Analysis for Nondestructive Discrimination of Chrysanthemum Tea Varieties The quality of chrysanthemum tea has a great connection with its variety. Different types of chrysanthemum tea have very different efficacies and functions. Moreover, the discrimination of chrysanthemum tea varieties is a significant issue in the tea industry. Therefore, to correctly and non-destructively categorize chrysanthemum tea samples, this study attempted to design a novel feature extraction method based on the fuzzy set theory and improved direct linear discriminant analysis (IDLDA), called fuzzy IDLDA (FIDLDA), for extracting the discriminant features from the near-infrared (NIR) spectral data of chrysanthemum tea. To start with, a portable NIR spectrometer was used to collect NIR data for five varieties of chrysanthemum tea, totaling 400 samples. Secondly, the raw NIR spectra were processed by four different pretreatment methods to reduce noise and redundant data. Thirdly, NIR data dimensionality reduction was performed by principal component analysis (PCA). Fourthly, feature extraction from the NIR spectra was performed by linear discriminant analysis (LDA), IDLDA, and FIDLDA. Finally, the K-nearest neighbor (KNN) algorithm was applied to evaluate the classification accuracy of the discrimination system. The experimental results show that the discrimination accuracies of LDA, IDLDA, and FIDLDA could reach 87.2%, 94.4%, and 99.2%, respectively. Therefore, the combination of near-infrared spectroscopy and FIDLDA has great application potential and prospects in the field of nondestructive discrimination of chrysanthemum tea varieties. Linear discriminant analysis ; Principal component analysis ; Pattern recognition (psychology) ; Artificial intelligence ; Mathematics ; Near-infrared spectroscopy ; Chemometrics ; Fuzzy logic ; Computer science ; Physics ; Machine learning Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Advanced Chemical Sensor Technologies
Authors: Ricardo Cortez | Marco Antonio Sandoval-Chileño | Norma Lozada‐Castillo | Alberto Luviano‐Juárez
Source: Biomimetics (article, 2024-03-16)
Field: Materials Science — Materials Chemistry

Snake Robot with Motion Based on Shape Memory Alloy Spring-Shaped Actuators This study presents the design and evaluation of a prototype snake-like robot that possesses an actuation system based on shape memory alloys (SMAs). The device is constructed based on a modular structure of links connected by two degrees of freedom links utilizing Cardan joints, where each degree of freedom is actuated by an agonist-antagonist mechanism using the SMA spring-shaped actuators to generate motion, which can be easily replaced once they reach a degradation point. The methodology for programming the spring shape into the SMA material is described in this work, as well as the instrumentation required for the monitoring and control of the actuators. A simplified design is presented to describe the way in which the motion is performed and the technical difficulties faced in manufacturing. Based on this information, the way in which the design is adapted to generate a feasible robotic system is described, and a mathematical model for the robot is developed to implement an independent joint controller. The feasibility of the implementation of the SMA actuators regarding the motion of the links is verified for the case of a joint, and the change in the shape of the snake robot is verified through the implementation of a set of tracking references based on a central pattern generator. The generated tracking results confirm the feasibility of the proposed mechanism in terms of performing snake gaits, as well as highlighting some of the drawbacks that should be considered in further studies. Actuator ; Robot ; SMA* ; Modular design ; Controller (irrigation) ; Computer science ; Shape-memory alloy ; Mechanism (biology) ; Control engineering ; Motion control ; Control theory (sociology) ; Kinematics ; Engineering ; Artificial intelligence ; Control (management) Shape Memory Alloy Transformations ; Soft Robotics and Applications ; Innovations in Concrete and Construction Materials
Authors: Michele Stofella | Anna Grimaldi | Jochem H. Smit | Jürgen Claesen | Emanuele Paci | Frank Sobott
Source: Chemical Reviews (review, 2024-10-31)
Field: Chemistry — Spectroscopy

Computational Tools for Hydrogen–Deuterium Exchange Mass Spectrometry Data Analysis Hydrogen-deuterium exchange (HDX) has become a pivotal method for investigating the structural and dynamic properties of proteins. The versatility and sensitivity of mass spectrometry (MS) made the technique the ideal companion for HDX, and today HDX-MS is addressing a growing number of applications in both academic research and industrial settings. The prolific generation of experimental data has spurred the concurrent development of numerous computational tools, designed to automate parts of the workflow while employing different strategies to achieve common objectives. Various computational methods are available to perform automated peptide searches and identification; different statistical tests have been implemented to quantify differences in the exchange pattern between two or more experimental conditions; alternative strategies have been developed to deconvolve and analyze peptides showing multimodal behavior; and different algorithms have been proposed to computationally increase the resolution of HDX-MS data, with the ultimate aim to provide information at the level of the single residue. This review delves into a comprehensive examination of the merits and drawbacks associated with the diverse strategies implemented by software tools for the analysis of HDX-MS data. Chemistry ; Hydrogen–deuterium exchange ; Mass spectrometry ; Deuterium ; Hydrogen ; Chromatography ; Nuclear physics ; Organic chemistry Mass Spectrometry Techniques and Applications ; Analytical Chemistry and Chromatography ; Radioactive element chemistry and processing
Authors: Vaishali Waman | Nicola Bordin | Andy M. Lau | Shaun M. Kandathil | Jude Wells | David Miller | Sameer Velankar | David T. Jones | Ian Sillitoe | Christine Orengo
Source: Nucleic Acids Research (article, 2024-11-20)
Field: Chemistry — Spectroscopy

CATH v4.4: major expansion of CATH by experimental and predicted structural data CATH (https://www.cathdb.info) is a structural classification database that assigns domains to the structures in the Protein Data Bank (PDB) and AlphaFold Protein Structure Database (AFDB) and adds layers of biological information, including homology and functional annotation. This article covers developments in the CATH classification since 2021. We report the significant expansion of structural information (180-fold) for CATH superfamilies through classification of PDB domains and predicted domain structures from the Encyclopedia of Domains (TED) resource. TED provides information on predicted domains in AFDB. CATH v4.4 represents an expansion of ∼64 844 experimentally determined domain structures from PDB. We also present a mapping of ∼90 million predicted domains from TED to CATH superfamilies. New PDB and TED data increases the number of superfamilies from 5841 to 6573, folds from 1349 to 2078 and architectures from 41 to 77. TED data comprises predicted structures, so these new folds and architectures remain hypothetical until experimentally confirmed. CATH also classifies domains into functional families (FunFams) within a superfamily. We have updated sequences in FunFams by scanning FunFam-HMMs against UniProt release 2024_02, giving a 276% increase in FunFams coverage. The mapping of TED structural domains has resulted in a 4-fold increase in FunFams with structural information. UniProt ; Protein Data Bank (RCSB PDB) ; Biology ; Protein Data Bank ; Structural Classification of Proteins database ; Homology (biology) ; KEGG ; Computational biology ; SUPERFAMILY ; Computer science ; Bioinformatics ; Protein structure ; Genetics Advanced Proteomics Techniques and Applications ; Enzyme Structure and Function ; Protein Structure and Dynamics
Authors: YinBo Zhu | ZhouYu Fang | ZhongTing Zhang | HengAn Wu
Source: National Science Review (article, 2024-02-06)
Field: Materials Science — Materials Chemistry

Discontinuous phase diagram of amorphous carbons The short-range order and medium-range order of amorphous carbons demonstrated in experiments allow us to rethink whether there exist intrinsic properties hidden by atomic disordering. Here we presented six representative phases of amorphous carbons (0.1-3.4 g/cm<sup>3</sup>), namely, disordered graphene network (DGN), high-density amorphous carbon (HDAC), amorphous diaphite (a-DG), amorphous diamond (a-D), paracrystalline diamond (p-D), and nano-polycrystalline diamond (NPD), respectively, classified by their topological features and microstructural characterizations that are comparable with experiments. To achieve a comprehensive physical landscape for amorphous carbons, a phase diagram was plotted in the sp<sup>3</sup>/sp<sup>2</sup> versus density plane, in which the counterintuitive discontinuity originates from the inherent difference in topological microstructures, further guiding us to discover a variety of phase transitions among different amorphous carbons. Intriguingly, the power law, log(sp<sup>3</sup>/sp<sup>2</sup>) ∝ <i>ρ</i><sup>n</sup>, hints at intrinsic topology and hidden order in amorphous carbons, providing an insightful perspective to reacquaint atomic disorder in non-crystalline carbons. Phase diagram ; Amorphous solid ; Diagram ; Materials science ; Phase (matter) ; Physics ; Mathematics ; Chemistry ; Crystallography ; Statistics ; Quantum mechanics Diamond and Carbon-based Materials Research ; Carbon Nanotubes in Composites ; Fullerene Chemistry and Applications
Authors: Thy Truong | Ryan Kelly
Source: Current Opinion in Biotechnology (review, 2024-02-14)
Field: Chemistry — Spectroscopy

What’s new in single-cell proteomics Proteomics ; Computational biology ; Computer science ; Biomarker discovery ; Nanotechnology ; Biology ; Data science Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Single-cell and spatial transcriptomics
Authors: Denys Oliinyk | Andreas Will | Felix R Schneidmadel | Maximilian Böhme | Jenny Rinke | Andreas Hochhaus | Thomas Ernst | Nina Hahn | Christian Geis | Markus Lubeck | Oliver Raether | Sean J. Humphrey | Florian Meier
Source: Molecular Systems Biology (article, 2024-06-21)
Field: Chemistry — Spectroscopy

µPhos: a scalable and sensitive platform for high-dimensional phosphoproteomics Mass spectrometry has revolutionized cell signaling research by vastly simplifying the analysis of many thousands of phosphorylation sites in the human proteome. Defining the cellular response to perturbations is crucial for further illuminating the functionality of the phosphoproteome. Here we describe µPhos ('microPhos'), an accessible phosphoproteomics platform that permits phosphopeptide enrichment from 96-well cell culture and small tissue amounts in <8 h total processing time. By greatly minimizing transfer steps and liquid volumes, we demonstrate increased sensitivity, >90% selectivity, and excellent quantitative reproducibility. Employing highly sensitive trapped ion mobility mass spectrometry, we quantify ~17,000 Class I phosphosites in a human cancer cell line using 20 µg starting material, and confidently localize ~6200 phosphosites from 1 µg. This depth covers key signaling pathways, rendering sample-limited applications and perturbation experiments with hundreds of samples viable. We employ µPhos to study drug- and time-dependent response signatures in a leukemia cell line, and by quantifying 30,000 Class I phosphosites in the mouse brain we reveal distinct spatial kinase activities in subregions of the hippocampal formation. Phosphoproteomics ; Biology ; Computational biology ; Phos ; Cell biology ; Biochemistry ; Phosphorylation Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Cell Image Analysis Techniques
Authors: Tianshu Chu | Ze Zhou | Pengfei Tian | Tingting Yu | Cheng Lian | Bowei Zhang | Fu‐Zhen Xuan
Source: Nature Communications (article, 2024-08-26)
Field: Materials Science — Materials Chemistry

Nanofluidic sensing inspired by the anomalous water dynamics in electrical angstrom-scale channels Manipulation of confined water dynamics by voltage keeps great importance for diverse applications. However, limitations on the membrane functions, voltage-control range, and unclear dynamics need to be addressed. Herein, we report an anomalous electrically controlled gating phenomenon on cation-intercalated multi-layer Ti<sub>3</sub>C<sub>2</sub> membranes and reveal the confined water dynamics. The water permeation rate was improved rapidly following the application and rise of voltage and finally reached a maximum rate at 0.9 V. The permeation rate starts to decrease from 0.9 V. Below 0.9 V, the electric field affects the charge and polarity of water molecules and then leads to ordered and denser rearrangement in the two-dimensional (2D) channel to accelerate the permeation rate. Above 0.9 V, with the assistance of metal cations, the surge in current induced aggregation of water molecules into clusters, thereby limiting the water mobility. Based on these findings, a high-performance humidity sensor was developed by simultaneously optimizing the response and recovery speeds through electric manipulation. This work provides flexible strategies in intelligent membrane design and nanofluidic sensing. Permeation ; Chemical physics ; Gating ; Materials science ; Electric field ; Membrane ; Nanotechnology ; Voltage ; Molecular dynamics ; Water transport ; Molecule ; Chemistry ; Water flow ; Physics ; Biophysics ; Environmental science ; Computational chemistry MXene and MAX Phase Materials ; Ferroelectric and Negative Capacitance Devices ; Nanopore and Nanochannel Transport Studies
Authors: Matias Davis Cortina | Manuel Romero de Terreros Aramburu | A.M. Neves | Lourdes Hurtado | Julian Jepsen | Ulrich Ulmer
Source: Inorganics (review, 2024-12-03)
Field: Materials Science — Materials Chemistry

The Integration of Thermal Energy Storage Within Metal Hydride Systems: A Comprehensive Review Hydrogen storage technologies are key enablers for the development of low-emission, sustainable energy supply chains, primarily due to the versatility of hydrogen as a clean energy carrier. Hydrogen can be utilized in both stationary and mobile power applications, and as a low-environmental-impact energy source for various industrial sectors, provided it is produced from renewable resources. However, efficient hydrogen storage remains a significant technical challenge. Conventional storage methods, such as compressed and liquefied hydrogen, suffer from energy losses and limited gravimetric and volumetric energy densities, highlighting the need for innovative storage solutions. One promising approach is hydrogen storage in metal hydrides, which offers advantages such as high storage capacities and flexibility in the temperature and pressure conditions required for hydrogen uptake and release, depending on the chosen material. However, these systems necessitate the careful management of the heat generated and absorbed during hydrogen absorption and desorption processes. Thermal energy storage (TES) systems provide a means to enhance the energy efficiency and cost-effectiveness of metal hydride-based storage by effectively coupling thermal management with hydrogen storage processes. This review introduces metal hydride materials for hydrogen storage, focusing on their thermophysical, thermodynamic, and kinetic properties. Additionally, it explores TES materials, including sensible, latent, and thermochemical energy storage options, with emphasis on those that operate at temperatures compatible with widely studied hydride systems. A detailed analysis of notable metal hydride–TES coupled systems from the literature is provided. Finally, the review assesses potential future developments in the field, offering guidance for researchers and engineers in advancing innovative and efficient hydrogen energy systems. Hydrogen storage ; Hydride ; Energy storage ; Thermal energy storage ; Renewable energy ; Process engineering ; Energy carrier ; Hydrogen technologies ; Hydrogen ; Hydrogen economy ; Hydrogen fuel ; Materials science ; Environmental science ; Chemistry ; Engineering ; Thermodynamics ; Electrical engineering ; Power (physics) Hydrogen Storage and Materials ; Ammonia Synthesis and Nitrogen Reduction ; Carbon dioxide utilization in catalysis