jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Paul D. Veith | Dhana G. Gorasia | Eric C. Reynolds
Source: Journal of Bacteriology (article, 2023-05-10)
Field: Chemistry — Spectroscopy

Characterization of the <i>O</i> -Glycoproteome of Flavobacterium johnsoniae Flavobacterium johnsoniae is a free-living member of the <i>Bacteroidota</i> phylum that is found in soil and water. It is frequently used as a model species for studying a type of gliding motility dependent on the type IX secretion system (T9SS). <i>O</i>-Glycosylation has been reported in several <i>Bacteroidota</i> species, and the <i>O</i>-glycosylation of S-layer proteins in Tannerella forsythia was shown to be important for certain virulence features. In this study, we characterized the <i>O</i>-glycoproteome of F. johnsoniae and identified 325 <i>O</i>-glycosylation sites within 226 glycoproteins. The structure of the major glycan was found to be a hexasaccharide with the sequence Hex-(Me-dHex)-Me-HexA-Pent-HexA-Me-HexNAcA. Bioinformatic localization of the glycoproteins predicted 68 inner membrane proteins, 60 periplasmic proteins, 26 outer membrane proteins, 57 lipoproteins, and 9 proteins secreted by the T9SS. The glycosylated sites were predominantly located in the periplasm, where they are postulated to be beneficial for protein folding/stability. Six proteins associated with gliding motility or the T9SS were demonstrated to be <i>O</i>-glycosylated. <b>IMPORTANCE</b> Flavobacterium johnsoniae is a Gram-negative bacterium that is found in soil and water. It is frequently used as a model species for studying gliding motility and the T9SS. In this study, we characterized the <i>O</i>-glycoproteome of F. johnsoniae and identified 325 <i>O</i>-glycosylation sites within 226 glycoproteins. The glycosylated domains were mainly localized to the periplasm. The function of <i>O</i>-glycosylation is likely related to protein folding and stability; therefore, the finding of the glycosylation sites has relevance for studies involving expression of the proteins. Six proteins associated with gliding motility or the T9SS were demonstrated to be <i>O</i>-glycosylated, which may impact the structure and function of these components. Biology ; Flavobacterium ; Microbiology ; Bacteria ; Genetics ; Pseudomonas Advanced Proteomics Techniques and Applications ; Glycosylation and Glycoproteins Research ; Genomics and Phylogenetic Studies
Authors: Marta Monti | Giorgia Brancolini | Emanuele Coccia | Daniele Toffoli | Alessandro Fortunelli | Stefano Corni | Massimiliano Aschi | Mauro Stener
Source: The Journal of Physical Chemistry Letters (article, 2023-02-14)
Field: Materials Science — Materials Chemistry

The Conformational Dynamics of the Ligands Determines the Electronic Circular Dichroism of the Chiral Au<sub>38</sub>(SC<sub>2</sub>H<sub>4</sub>Ph)<sub>24</sub> Cluster Effects of the conformational dynamics of 2-PET protective ligands on the electronic circular dichroism (ECD) of the chiral Au<sub>38</sub>(SC<sub>2</sub>H<sub>4</sub>Ph)<sub>24</sub> cluster are investigated. We adopt a computational protocol in which ECD spectra are calculated via the first principle polTDDFT approach on a series of conformations extracted from MD simulations by using Essential Dynamics (ED) analysis, and then properly weighted to predict the final spectrum. We find that the experimental spectral features are well reproduced, whereas significant discrepancies arise when the spectrum is calculated using the experimental X-ray structure. This result unambiguously demonstrates the need to account for the conformational effects in the ECD modeling of chiral nanoclusters. The present procedure proved to be able of capturing the essential conformational features of the dynamic Au<sub>38</sub>(SC<sub>2</sub>H<sub>4</sub>Ph)<sub>24</sub> system, opening the possibility to model the ECD of soluble chiral nanoclusters in a realistic way. Nanoclusters ; Circular dichroism ; Cluster (spacecraft) ; Molecular dynamics ; Chemistry ; Dynamics (music) ; Chemical physics ; Spectrum (functional analysis) ; Crystallography ; Spectral line ; Computational chemistry ; Physics ; Computer science ; Quantum mechanics Nanocluster Synthesis and Applications ; Molecular spectroscopy and chirality ; Random Matrices and Applications
Authors: Arpan Biswas | Rama K. Vasudevan | Maxim Ziatdinov | Sergei V. Kalinin
Source: Machine Learning Science and Technology (article, 2023-01-13)
Field: Materials Science — Materials Chemistry

Optimizing training trajectories in variational autoencoders via latent Bayesian optimization approach <sup>*</sup> Abstract Unsupervised and semi-supervised ML methods such as variational autoencoders (VAE) have become widely adopted across multiple areas of physics, chemistry, and materials sciences due to their capability in disentangling representations and ability to find latent manifolds for classification and/or regression of complex experimental data. Like other ML problems, VAEs require hyperparameter tuning, e.g. balancing the Kullback–Leibler and reconstruction terms. However, the training process and resulting manifold topology and connectivity depend not only on hyperparameters, but also their evolution during training. Because of the inefficiency of exhaustive search in a high-dimensional hyperparameter space for the expensive-to-train models, here we have explored a latent Bayesian optimization (zBO) approach for the hyperparameter trajectory optimization for the unsupervised and semi-supervised ML and demonstrated for joint-VAE with rotational invariances. We have demonstrated an application of this method for finding joint discrete and continuous rotationally invariant representations for modified national institute of standards and technology database (MNIST) and experimental data of a plasmonic nanoparticles material system. The performance of the proposed approach has been discussed extensively, where it allows for any high dimensional hyperparameter trajectory optimization of other ML models. Hyperparameter ; Bayesian optimization ; Hyperparameter optimization ; MNIST database ; Artificial intelligence ; Computer science ; Machine learning ; Bayesian inference ; Autoencoder ; Bayesian probability ; Deep learning ; Support vector machine Machine Learning in Materials Science ; Advanced Multi-Objective Optimization Algorithms ; Machine Learning and Data Classification
Authors: Yu‐Jia Chen | Jun-Yen Uan
Source: Nanomaterials (article, 2023-04-26)
Field: Materials Science — Materials Chemistry

The Effect of Lithium Ion Leaching from Calcined Li–Al Hydrotalcite on the Rapid Removal of Ni2+/Cu2+ from Contaminated Aqueous Solutions A layered double hydroxide (LDH) calcined-framework adsorbent was investigated for the rapid removal of heavy metal cations from plating wastewater. Li-Al-CO<sub>3</sub> LDH was synthesized on an aluminum lathe waste frame surface to prepare the sorbent. The calcination treatment modified the LDH surface properties, such as the hydrophilicity and the surface pH. The change in surface functional groups and the leaching of lithium ions affected the surface properties and the adsorption capacity of the heavy metal cations. A zeta potential analysis confirmed that the 400 °C calcination changed the LDH surface from positively charged (+10 mV) to negatively charged (-17 mV). This negatively charged surface contributed to the sorbent instantly bonding with heavy metal cations in large quantities, as occurs during contact with wastewater. The adsorption isotherms could be fitted using the Freundlich model. The pseudo-second-order model and the rate-controlled liquid-film diffusion model successfully simulated the adsorption kinetics, suggesting that the critical adsorption step was a heterogeneous surface reaction. This study also confirmed that the recovered nickel and/or copper species could be converted into supported metal nanoparticles with a high-temperature hydrogen reduction treatment, which could be reused as catalysts. Adsorption ; Calcination ; Hydrotalcite ; Hydroxide ; Inorganic chemistry ; Aqueous solution ; Sorbent ; Metal hydroxide ; Freundlich equation ; Chemistry ; Metal ions in aqueous solution ; Copper ; Metal ; Leaching (pedology) ; Materials science ; Metallurgy ; Catalysis Layered Double Hydroxides Synthesis and Applications ; Supercapacitor Materials and Fabrication ; Advanced Battery Materials and Technologies
Authors: Nikoletta Solomakou | Aikaterini M. Drosaki | Georgios Zamvrakidis | Athanasia M. Goula
Source: Biomass Conversion and Biorefinery (article, 2023-03-25)
Field: Chemistry — Organic Chemistry

Adsorption of phenolic compounds from olive mill wastewaters on spent coffee grounds: isotherms, kinetics, and pure phenol adsorption Adsorption ; Chemistry ; Hydroxytyrosol ; Sorption ; Phenol ; Aqueous solution ; Tyrosol ; Langmuir adsorption model ; Partition coefficient ; Phenols ; Chromatography ; Oleuropein ; Langmuir ; Organic chemistry ; Nuclear chemistry ; Polyphenol Edible Oils Quality and Analysis ; Dye analysis and toxicity ; Coffee research and impacts
Authors: Freddy L. Figueira | Pablo Reyes | Mariya Edeleva | Yoshi W. Marien | Yi‐Yang Wu | Yin‐Ning Zhou | Zheng‐Hong Luo | Paul Van Steenberge | Dagmar D’hooge
Source: Chemical Engineering Journal (article, 2023-12-25)
Field: Materials Science — Polymers and Plastics

Combining ternary phase diagrams and multiphase coupled matrix-based Monte Carlo to model phase dependent compositional and molar mass variations in high impact polystyrene synthesis Polystyrene ; Phase (matter) ; Ternary operation ; Yield (engineering) ; Phase diagram ; Materials science ; Molar mass ; Monte Carlo method ; Copolymer ; Thermodynamics ; Chemistry ; Organic chemistry ; Composite material ; Mathematics ; Physics ; Polymer ; Computer science Polymer crystallization and properties ; biodegradable polymer synthesis and properties ; Advanced Polymer Synthesis and Characterization
Authors: Krishnakumar Melethil | M. Sathish Kumar | Chun‐Ming Wu | Hsin‐Hui Shen | Balaraman Vedhanarayanan | Tsung‐Wu Lin
Source: Nanomaterials (review, 2023-04-02)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Recent Progress of 2D Layered Materials in Water-in-Salt/Deep Eutectic Solvent-Based Liquid Electrolytes for Supercapacitors Supercapacitors are candidates with the greatest potential for use in sustainable energy resources. Extensive research is being carried out to improve the performances of state-of-art supercapacitors to meet our increased energy demands because of huge technological innovations in various fields. The development of high-performing materials for supercapacitor components such as electrodes, electrolytes, current collectors, and separators is inevitable. To boost research in materials design and production toward supercapacitors, the up-to-date collection of recent advancements is necessary for the benefit of active researchers. This review summarizes the most recent developments of water-in-salt (WIS) and deep eutectic solvents (DES), which are considered significant electrolyte systems to advance the energy density of supercapacitors, with a focus on two-dimensional layered nanomaterials. It provides a comprehensive survey of 2D materials (graphene, MXenes, and transition-metal oxides/dichalcogenides/sulfides) employed in supercapacitors using WIS/DES electrolytes. The synthesis and characterization of various 2D materials along with their electrochemical performances in WIS and DES electrolyte systems are described. In addition, the challenges and opportunities for the next-generation supercapacitor devices are summarily discussed. Supercapacitor ; Electrolyte ; Materials science ; Nanotechnology ; Battery (electricity) ; Energy storage ; Deep eutectic solvent ; Eutectic system ; Electrochemistry ; Electrode ; Chemistry ; Metallurgy ; Physics Supercapacitor Materials and Fabrication ; MXene and MAX Phase Materials ; Advancements in Battery Materials
Authors: Adel Hamed
Source: Egyptian journal of phycology (article, 2023-08-15)
Field: Materials Science — Biomaterials

A brief and general overview on diatoms and their applications Diatoms are single-celled, photosynthetic eukaryotic algae, known as Bacillariophyceae, that are important in the ocean's cycle of nutrients and organic matter. There are possibly more than 150,000 varieties of them spread across fresh, brackish, and marine aquatic ecosystems, and they can be found in almost all aquatic habitats. Diatoms also have value to be used in industrial applications because their glass cell wall fossils are sold as diatomite or diatomaceous earth. Diatom silica, is regarded as an important usable biomaterial for energy storage e.g. (Lithium Ion battery, super capacitor, hydrogen and thermal storage ) and energy conversion e.g. (solar cells). In addition, diatomite exhibits substantial specified area of surface, thermal stability, and affordability, which provide tremendous benefits and prospects for application as filler in the paper, rubber, ceramic, pharmaceutical industries as well as abrasive material and soil amendment. In the field of water treatment, diatomite is considered as an eco-environmental functional material and effective adsorbent in the treatment of heavy metal-contaminated water because of its high porosity, low density and high specific surface area. In biomedical applications, mesoporous silica has recently demonstrated promising results in drug delivery systems because of its special chemical and physical characteristics, including excellent drug loading capacity, biocompatibility, and large surface area. Currently, basic and applied researchers are still interested in the use of diatoms in nanotechnology functions. History ; Oceanography ; Computer science ; Geology Diatoms and Algae Research
Authors: Huijuan Tong | Qiao Liu | Nong Xu | Qing Wang | Long Fan | Qiang Dong | Aiqin Ding
Source: Membranes (article, 2023-04-13)
Field: Materials Science — Materials Chemistry

Efficient Pervaporation for Ethanol Dehydration: Ultrasonic Spraying Preparation of Polyvinyl Alcohol (PVA)/Ti3C2Tx Nanosheet Mixed Matrix Membranes Polyvinyl alcohol (PVA) pervaporation (PV) membranes have been extensively studied in the field of ethanol dehydration. The incorporation of two-dimensional (2D) nanomaterials into the PVA matrix can greatly improve the hydrophilicity of the PVA polymer matrix, thereby enhancing its PV performance. In this work, self-made MXene (Ti<sub>3</sub>C<sub>2</sub>T<sub>x</sub>-based) nanosheets were dispersed in the PVA polymer matrix, and the composite membranes were fabricated by homemade ultrasonic spraying equipment with poly(tetrafluoroethylene) (PTFE) electrospun nanofibrous membrane as support. Due to the gentle coating of ultrasonic spraying and following continuous steps of drying and thermal crosslinking, a thin (~1.5 μm), homogenous and defect-free PVA-based separation layer was fabricated on the PTFE support. The prepared rolls of the PVA composite membranes were investigated systematically. The PV performance of the membrane was significantly improved by increasing the solubility and diffusion rate of the membranes to the water molecules through the hydrophilic channels constructed by the MXene nanosheets in the membrane matrix. The water flux and separation factor of the PVA/MXene mixed matrix membrane (MMM) were dramatically increased to 1.21 kg·m<sup>-2</sup>·h<sup>-1</sup> and 1126.8, respectively. With high mechanical strength and structural stability, the prepared PGM-0 membrane suffered 300 h of the PV test without any performance degradation. Considering the promising results, it is likely that the membrane would improve the efficiency of the PV process and reduce energy consumption in the ethanol dehydration. Pervaporation ; Membrane ; Polyvinyl alcohol ; Materials science ; Nanosheet ; Chemical engineering ; Polymer ; Thermal stability ; Composite material ; Coating ; Permeation ; Nanotechnology ; Chemistry MXene and MAX Phase Materials ; Graphene research and applications ; Membrane Separation and Gas Transport
Authors: Osman Uygun | Ayşenur Murat | Gaye Ö. Çakal
Source: Clay Minerals (article, 2023-08-25)
Field: Materials Science — Biomaterials

Magnetic sepiolite/iron(III) oxide composite for the adsorption of lead(II) ions from aqueous solutions Abstract Clay minerals are effective adsorbents used for the remediation of toxic heavy metals from wastewater due to their large surface areas and great cation-exchange capacities. In this study, the removal of lead ions from aqueous solutions via adsorption was investigated using raw and iron-modified Turkish sepiolite. The aim of this study was to examine the effects of modification and environmental conditions on the sorptive properties of sepiolite samples. Initially, the raw sepiolite (Sep) and magnetic sepiolite/Fe 2 O 3 composite (MagSep) prepared using the co-precipitation method were characterized via mineralogical and petrographical means and the physicochemical properties were determined. Then, the batch adsorption of lead (Pb 2+ ) ions on the sepiolite samples was examined under various conditions (solution pH, adsorbent dosage, contact time, initial Pb 2+ ion concentration, temperature, shaking rate). The adsorption capacity of MagSep was found to be greater than that of Sep under all experimental conditions. The results showed that the adsorption process followed a pseudo-second-order kinetic model, and the Langmuir isotherm best correlated with the experimental data. The maximum adsorption capacities were found to be 60.6 and 90.1 mg g –1 for Sep and MagSep, respectively. The characterization of the Pb-adsorbed sepiolite samples showed that lead formed covalent bonds with the sepiolite samples and attached to the sepiolite surface mainly through ion exchange. MagSep can be used efficiently in the field of wastewater treatment for the removal of Pb 2+ ions as it does not release any toxic pollutants and can be separated easily with the use of a magnetic field. Sepiolite ; Adsorption ; Aqueous solution ; Chemistry ; Ion exchange ; Langmuir adsorption model ; Inorganic chemistry ; Chemical engineering ; Ion ; Raw material ; Organic chemistry Clay minerals and soil interactions ; Adsorption and biosorption for pollutant removal ; Heavy metals in environment
Authors: Bulat Gizatullin | Carlos Mattea | Siegfried Stapf
Source: Magnetic Resonance Letters (article, 2023-04-07)
Field: Chemistry — Spectroscopy

Radicals on the silica surface: probes for studying dynamics by means of fast field cycling relaxometry and dynamic nuclear polarization Determining the dynamics of adsorbed liquids on nanoporous materials is crucial for a detailed understanding of interactions and processes on the solid-liquid interface in many materials and porous systems. Knowledge of the influence of the presence of paramagnetic species on the surface or within the porous matrices is essential for fundamental studies and industrial processes such as catalysts. Magnetic resonance methods, such as electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR) and dynamic nuclear polarization (DNP), are powerful tools to address these questions and to quantify dynamics, electron-nuclear interaction features and their relation to the physical-chemical parameters of the system. This paper presents an NMR study of the dynamics of polar and nonpolar adsorbed liquids, represented by water, n-decane, deuterated water and nonane-d20, on the native silica surface as well as silica modified with vanadyl porphyrins. The analysis of the frequency dependence of the nuclear spin-lattice relaxation time is carried out by separating the intra- and intermolecular contributions, which were analyzed using reorientations mediated by translational displacements (RMTD) and force-free-hard-sphere (FFHS) models, respectively. Electron paramagnetic resonance ; Relaxometry ; Chemical physics ; Chemistry ; Adsorption ; Polarization (electrochemistry) ; Intermolecular force ; Paramagnetism ; Molecular dynamics ; Relaxation (psychology) ; Nuclear magnetic resonance ; Materials science ; Physical chemistry ; Spin echo ; Computational chemistry ; Condensed matter physics ; Organic chemistry ; Molecule ; Magnetic resonance imaging ; Physics Advanced NMR Techniques and Applications ; NMR spectroscopy and applications ; Molecular spectroscopy and chirality
Authors: Feng Xiong | Yanyan Hao | Helin Xu | Xueqin Li | Yu Sun | Jiaxing Liu | Xi Chen | Zhong Wei
Source: Macromolecular Chemistry and Physics (article, 2023-02-20)
Field: Materials Science — Materials Chemistry

High‐Affinity Adsorbent with Honeycomb Structure for Efficient Acteoside Separation Abstract In this study, a series of adsorbents with honeycomb structure that hyperbranched polyethyleneimine (PEI) functionalized carboxymethyl chitosan (CMC/PEI) are successfully designed for acteoside (ACT) separation. The microstructures of adsorbents are adjusted to optimum by changing the molecular weight and addition amount of PEI. The scanning electron microscope (SEM) and N 2 adsorption‐desorption experiment results show that CMC/PEI‐70000‐4.5g presents the honeycomb structure with the highest specific surface area and the largest pore volume. The honeycomb structure has the multiple internal cavities, which provide sufficient space for accommodating and adsorbing ACT molecules, improving the adsorption capacity. Furthermore, this work introduces PEI on the inner and outer surface of pores and forms an amino layer, which has high‐affinity for ACT molecules and realizes the excellent selectivity. Therefore, CMC/PEI‐70000‐4.5g shows the highest adsorption capacity of 125.67 mg g −1 and selectivity of 5.38. The adsorption process of ACT can be fitted by pseudo‐second‐order kinetics, intraparticle diffusion, and Langmuir isotherm models. High‐affinity (hydrogen bond, hydrophilic attraction, and Van der Waals force) is proposed as the main driving forces for adsorption between CMC/PEI‐70000‐4.5g and ACT. This work provides a strategy to synthesize the adsorbents with honeycomb structure for bioactive components separation from natural products. Adsorption ; Chemical engineering ; Chemistry ; Selectivity ; Honeycomb ; Langmuir adsorption model ; Desorption ; Molecule ; Hydrogen bond ; van der Waals force ; Monolayer ; Polymer chemistry ; Organic chemistry ; Materials science ; Composite material ; Catalysis Mesoporous Materials and Catalysis ; Surfactants and Colloidal Systems ; Pickering emulsions and particle stabilization