jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Petr Pylov | Roman Maitak | Elizaveta Georgievna Zaitseva
Source: Proceedings of the Institute for System Programming of RAS (article, 2023-01-01)
Field: Chemistry — Analytical Chemistry

Application of a Multimodal Transformer to the Prediction of the Yield of Saturated Hydrocarbon Compounds from Heavy Crude Oil in the Presence of Catalysts Heavy oil fields are a promising energy source in the future due to the depletion of natural sources of light oil. However, extraction, transportation and refining of heavy oil is significantly more complicated than light oil - difficulties arise at almost all technological stages. One of such stages is laboratory analytics of heavy oil and selection of the most optimal catalyst for extraction of required fractions from crude oil sample. Different catalysts are actively used in petrochemical laboratories, but special attention is paid to those of them, the basis of which is metal. In this study, catalysts based on six different metals namely zinc, nickel, copper, manganese, lead and sodium were analyzed. In order to analyze the yield ratios of the required components from the crude heavy oil composition, it is necessary to test different types of catalysts sequentially on a base sample. The yield of different hydrocarbons on a small volume of oil can be reliably estimated by chromatographic study, which takes about 68 minutes for both the base oil sample and the different catalysts. Since testing 6 different catalysts would require almost 7 hours of chromatographic analysis, a rational solution would be to apply data mining techniques to this task. A multimodal transformer model was proposed to solve this problem. It takes as input two modalities: a chromatogram of a sample of pure crude oil presented as graphical data and accompanying tabular data, which are also generated by the chromatograph and consist of text and numbers. At the output, the model produces predictive tabular data that formalize the redistributed group composition of the oil and describe both the names of the newly produced hydrocarbons and their two qualitative characteristics: time and yield area. Obtaining the prediction makes it possible to significantly reduce the time, hardware and human resources required to select the right type of catalyst in petrochemical laboratories. In the process of the study, it was found that training of the intellectual model on the data of one field allows to perform further similar forecast with acceptable accuracy for the data of another heavy oil field. The magnitude of the prediction error of the intelligent model satisfies the requirements set by the petrochemical laboratory for practical application of the multimodal transformer. Hydrocarbon ; Crude oil ; Transformer oil ; Yield (engineering) ; Transformer ; Petroleum engineering ; Catalysis ; Chemistry ; Environmental science ; Pulp and paper industry ; Organic chemistry ; Materials science ; Geology ; Metallurgy ; Engineering ; Electrical engineering Petroleum Processing and Analysis ; Advanced Data Processing Techniques
Authors: Puneet Pareek | Shivani Chaudhary | Sonu Singh | Aiswarya Thattaru Thodikayil | Dinesh Kalyanasundaram | Sachin Kumar
Source: Research Square (preprint, 2023-02-28)
Field: Materials Science — Biomaterials

Dual Architecture and Bioenergetics of Cellulose-Graphene Oxide-Arginine Aerogel Supports Stem Cell Bioactivity for Cartilage Regeneration Abstract The avascular nature of cartilage tissue limits the self-regeneration ability of the tissue to counter any damage and this has become a substantial burden to health of individuals. As a result, there is a high demand to repair and regenerate cartilage; several methods have been developed, primarily based on tissue-engineering techniques. So far, emphasis has been given to modifying the scaffold’s surface chemistry, crosslinking, and porosity to induce stem cell differentiation into chondrocytes to deposit thick cartilage extracellular matrix (ECM). However, most of these studies produced either microporous or nano-fibrous scaffolds to regenerate cartilage, but they lack biomimetic dual architecture of microporous construct with nano-fibrous interconnected structure like the native cartilage. Over the years, researchers have designed scaffolds to mimic tissue microenvironment with key metabolic components to promote efficient regeneration of tissue. Thus, scaffolds with dual architecture of microporous construct comprising of a nano-fibrous interconnected networks like native cartilage embedded with metabolite sources are necessary for a successful engineering of cartilage regeneration. Hence, in the present work, we have developed a biomimetic elastic, micro porous construct with nano-fibrous interconnection network of cellulose aerogel reinforced with arginine amino acid-functionalized graphene oxide for cartilage regeneration. The designed dual architectured aerogel loaded with bioenergetics provided multifunctionality via biomimetic morphology, enhanced mechanical stability, and cellular energetics to address the need for regeneration of cartilage tissues. Cartilage ; Regeneration (biology) ; Materials science ; Aerogel ; Scaffold ; Tissue engineering ; Chondrogenesis ; Extracellular matrix ; Nanotechnology ; Chemistry ; Biomedical engineering ; Cell biology ; Anatomy ; Biochemistry ; Biology ; Medicine Electrospun Nanofibers in Biomedical Applications ; Osteoarthritis Treatment and Mechanisms ; Tissue Engineering and Regenerative Medicine
Source: Biointerface Research in Applied Chemistry (article, 2023-10-15)
Field: Chemistry — Spectroscopy

In silico study of selected lignins as COX-2 inhibitors Natural products present in medicinal plants play an important role in several biological processes, many of which alleviate and control inflammation-related diseases. These have been linked to an action involving direct inhibitory binding, especially on COX-2 protein. The present study reports the in-silico study of selected lignins for COX-2 inhibition and its correlation with its anti-inflammatory activities. We aim to understand lignin's structural and conformational features for inhibitory capability and illustrate their binding mode in the COX-2 active site. For this purpose, six lignins, namely pinoresinol, syringaresinol, 1-acetoxypinoresinol, berchemol, 8-Hydroxypinoresinol, and (-)-Olivil have been analyzed through ADME (absorption, distribution, metabolism, excretion) prediction, molecular docking study, molecular dynamic simulation, and binding free energy analysis. ADME study supports the potential biological activity of all selected lignins. At the same time, the described docking scores, the interaction profile, and the obtained conformations suggested berchemol as the best inhibitor for COX-2 protein, followed by 8-Hydroxypinoresinol and pinoresinol. 50 ns of the molecular dynamic simulation was then used to evaluate the stability of docked protein-ligand complexes and to estimate the conformational changes occurring during protein-ligand interaction. From the RMSD, RMSF, the number of hydrogen bonds, SASA, and MM/PBSA binding free energy score analysis, we have found that syringaresinol showed a good binding free energy score of -154.06±15.08 kJ/mol and displayed excellent pharmacological and structural properties to be drug candidate for the anti-inflammatory disease. In addition, MD results indicated shows that syringaresinol established more favorable interactions than rofecoxib. It is fixed in the COX-2 active site by the key residue Tyr-355 and stabilized by Ser-530. In silico ; Chemistry ; Computational chemistry ; Computational biology ; Biochemistry ; Biology ; Gene Analytical Chemistry and Chromatography ; Synthesis and Reactions of Organic Compounds
Authors: A. V. Pashkevich | А.К. Fedotov | Eugen N. Poddenezhny | L. A. Bliznyuk | Vladimir Khovaylo | В. В. Федотова | A. A. Kharchenko
Source: Modern Electronic Materials (article, 2023-07-05)
Field: Materials Science — Materials Chemistry

Thermal and thermoelectric properties of metal-doped zinc oxide ceramics The thermal, electrical and thermoelectric properties of ZnO– Me x O y ceramics with 1 ≤ x , y ≤ 3, where Me = Al, Co, Fe, Ni, Ti, have been studied. The specimens have been synthesized using the ceramic sintering technology from two or more oxides in an open atmosphere with annealing temperature and time variation. The structural and phase data on the ceramics have shown that post-synthesis addition of Me x O y doping powders to wurtzite-structured ZnO powder causes Zn x ( Mе ) y O 4 spinel-like second phase precipitation and a 4-fold growth of ceramics porosity. Room temperature heat conductivity studies have testified to predominant lattice contribution. A decrease in the heat conductivity upon doping proves to be caused by phonon scattering intensification due to the following factors: size factor upon zinc ion substitution in the ZnO lattice (wurtzite) by Me x O y doping oxide metal ions; defect formation, i.e., point defects, grain boundaries (microstructure refinement); porosity growth (density decline); secondary phase particle nucleation (Zn x ( Mе ) y O 4 spinel-like ones). The above listed factors entailed by zinc ion substitution for metal ions (Co, Al, Ti, Ni, Fe) increase the figure-of-merit ZT by four orders of magnitude (due to a decrease in the electrical resistivity and heat conductivity coupled with a moderate thermo-emf decline). The decrease in the electrical resistivity originates from a more homogeneous distribution of doping metal ions in the wurtzite lattice upon longer annealing which increases the number of donor centers. Materials science ; Wurtzite crystal structure ; Electrical resistivity and conductivity ; Thermoelectric effect ; Spinel ; Grain growth ; Doping ; Annealing (glass) ; Ceramic ; Nucleation ; Mineralogy ; Sintering ; Grain size ; Zinc ; Metallurgy ; Analytical Chemistry (journal) ; Thermodynamics ; Chemistry Advanced Thermoelectric Materials and Devices ; Gas Sensing Nanomaterials and Sensors ; ZnO doping and properties
Authors: D. A. Malcolm | Laia Vilà‐Nadal
Source: ACS Organic & Inorganic Au (article, 2023-07-22)
Field: Materials Science — Materials Chemistry

Computational Study into the Effects of Countercations on the [P<sub>8</sub>W<sub>48</sub>O<sub>184</sub>]<sup>40–</sup> Polyoxometalate Wheel Porous metal oxide materials have been obtained from a ring-shaped macrocyclic polyoxometalate (POM) structural building unit, [P<sub>8</sub>W<sub>48</sub>O<sub>184</sub>]<sup>40-</sup>. This is a tungsten oxide building block with an integrated "pore" of 1 nm in diameter, which, when connected with transition metal linkers, can assemble frameworks across a range of dimensions and which are generally referred to as POMzites. Our investigation proposes to gain a better understanding into the basic chemistry of this POM, specifically local electron densities and locations of countercations within and without the aforementioned pore. Through a rigorous benchmarking process, we discovered that 8 potassium cations, located within the pore, provided us with the most accurate model in terms of mimicking empirical properties to a sufficient degree of accuracy while also requiring a relatively small number of computer cores and hours to successfully complete a calculation. Additionally, we analyzed two other similar POMs from the literature, [As<sub>8</sub>W<sub>48</sub>O<sub>184</sub>]<sup>40-</sup> and [Se<sub>8</sub>W<sub>48</sub>O<sub>176</sub>]<sup>32-</sup>, in the hopes of determining whether they could be similarly incorporated into a POMzite network; given their close semblance in terms of local electron densities and interaction with potassium cations, we judge these POMs to be theoretically suitable as POMzite building blocks. Finally, we experimented with substituting different cations into the [P<sub>8</sub>W<sub>48</sub>O<sub>184</sub>]<sup>40-</sup> pore to observe the effect on pore dimensions and overall reactivity; we observed that the monocationic structures, particularly the Li<sub>8</sub>[P<sub>8</sub>W<sub>48</sub>O<sub>184</sub>]<sup>32-</sup> framework, yielded the least polarized structures. This correlates with the literature, validating our methodology for determining general POM characteristics and properties moving forward. Polyoxometalate ; Block (permutation group theory) ; Reactivity (psychology) ; Oxide ; Benchmarking ; Potassium ; Chemistry ; Transition metal ; Crystallography ; Materials science ; Nanotechnology ; Mathematics ; Combinatorics ; Organic chemistry ; Catalysis Polyoxometalates: Synthesis and Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Advanced Nanomaterials in Catalysis
Authors: Elena A. Korznikova | V. A. Bryzgalov | Andrey A. Kistanov
Source: Applied Sciences (article, 2023-01-06)
Field: Materials Science — Materials Chemistry

First-Principles Prediction of Structure and Properties of the Cu2TeO6 Monolayer In this work, first-principles calculations have been utilized to predict the existence of a new Cu2TeO6 monolayer. It is shown that the predicted material is dynamically and thermally stable. The Cu2TeO6 monolayer is also found to be a narrow band gap semiconductor with a band gap size of 0.20 eV. Considering the obtained properties of the Cu2TeO6 monolayer, it is proposed for applications in various nanodevices in electronics and straintronics. Monolayer ; Materials science ; Band gap ; Semiconductor ; Electronics ; Engineering physics ; Nanotechnology ; Condensed matter physics ; Optoelectronics ; Physics ; Chemistry ; Physical chemistry ZnO doping and properties ; Copper-based nanomaterials and applications ; Electronic and Structural Properties of Oxides
Authors: Yiming Wang | Yuxuan Song | Minkai Xu | Rui Wang | Hao Zhou | Wei‐Ying Ma
Source: arXiv (Cornell University) (preprint, 2023-11-23)
Field: Materials Science — Materials Chemistry

RetroDiff: Retrosynthesis as Multi-stage Distribution Interpolation Retrosynthesis poses a fundamental challenge in biopharmaceuticals, aiming to aid chemists in finding appropriate reactant molecules and synthetic pathways given determined product molecules. With the reactant and product represented as 2D graphs, retrosynthesis constitutes a conditional graph-to-graph generative task. Inspired by the recent advancements in discrete diffusion models for graph generation, we introduce Retrosynthesis Diffusion (RetroDiff), a novel diffusion-based method designed to address this problem. However, integrating a diffusion-based graph-to-graph framework while retaining essential chemical reaction template information presents a notable challenge. Our key innovation is to develop a multi-stage diffusion process. In this method, we decompose the retrosynthesis procedure to first sample external groups from the dummy distribution given products and then generate the external bonds to connect the products and generated groups. Interestingly, such a generation process is exactly the reverse of the widely adapted semi-template retrosynthesis procedure, i.e. from reaction center identification to synthon completion, which significantly reduces the error accumulation. Experimental results on the benchmark have demonstrated the superiority of our method over all other semi-template methods. Retrosynthetic analysis ; Computer science ; Graph ; Benchmark (surveying) ; Process (computing) ; Artificial intelligence ; Data mining ; Algorithm ; Theoretical computer science ; Geography ; Programming language Machine Learning in Materials Science ; Gene expression and cancer classification ; Asymmetric Hydrogenation and Catalysis
Authors: Prescott E. Evans | Yang Wang | Peter V. Sushko | Zdenek Dohnálek
Source: PNAS Nexus (article, 2023-06-28)
Field: Materials Science — Materials Chemistry

Understanding palladium–tellurium cluster formation on WTe2: From a kinetically hindered distribution to thermodynamically controlled monodispersity A fundamental understanding of the transition metal dichalcogenide (TMDC)-metal interface is critical for their utilization in a broad range of applications. We investigate how the deposition of palladium (Pd), as a model metal, on WTe<sub>2</sub>(001), leads to the assembly of Pd into clusters and nanoparticles. Using X-ray photoemission spectroscopy, scanning tunneling microscopy imaging, and ab initio simulations, we find that Pd nucleation is driven by the interaction with and the availability of mobile excess tellurium (Te) leading to the formation of Pd-Te clusters at room temperature. Surprisingly, the nucleation of Pd-Te clusters is not affected by intrinsic surface defects, even at elevated temperatures. Upon annealing, the Pd-Te nanoclusters adopt an identical nanostructure and are stable up to ∼523 K. Density functional theory calculations provide a foundation for our understanding of the mobility of Pd and Te atoms, preferential nucleation of Pd-Te clusters, and the origin of their annealing-induced monodispersity. These results highlight the role the excess chalcogenide atoms may play in the metal deposition process. More broadly, the discoveries of synthetic pathways yielding thermally robust monodispersed nanostructures on TMDCs are critical to the manufacturing of novel quantum and microelectronics devices and catalytically active nano-alloy centers. Nanoclusters ; Nucleation ; Materials science ; Palladium ; Tellurium ; Scanning tunneling microscope ; Nanostructure ; Annealing (glass) ; Density functional theory ; Chemical physics ; Nanotechnology ; Chalcogenide ; Cluster (spacecraft) ; Transition metal ; Computational chemistry ; Chemistry ; Optoelectronics ; Metallurgy Quantum Dots Synthesis And Properties ; 2D Materials and Applications ; Advanced Photocatalysis Techniques
Authors: Stella Kavokina | Anton Osipov | Vlad Samyshkin | А. Абрамов | N. N. Rozhkova | V. V. Kononenko | В. И. Конов | A. O. Kucherik
Source: Condensed Matter (article, 2023-11-14)
Field: Materials Science — Materials Chemistry

Laser Fabrication of Gold–sp-Carbon Films We develop a method for the laser synthesis and deposition of carbon–gold films formed by a net of linear sp-carbon chains and stabilized by gold nanoparticles. The originality of the method is in the simultaneous production of carbon chains and gold nanoparticles due to the laser fragmentation of the amorphous carbon and hydrogen tetrachloroaurate (III) or chloroauric acid. We study how surface resistivity alters the effect of the obtained films via the illumination in the visible spectral range. Chloroauric acid ; Materials science ; Amorphous carbon ; Carbon fibers ; Colloidal gold ; Carbon film ; Fabrication ; Laser ablation ; Nanotechnology ; Laser ; Hydrogen ; Nanoparticle ; Chemical engineering ; Thin film ; Amorphous solid ; Chemistry ; Optics ; Composite material ; Composite number ; Crystallography ; Organic chemistry Diamond and Carbon-based Materials Research ; Laser-Ablation Synthesis of Nanoparticles ; Carbon Nanotubes in Composites
Authors: Nasser A Al-Tayyar | Abdulaziz Radhi S ALjohni | Fayez Hadhram ALsehli | Mohammed Abdulrahman Alsaedi
Source: ACTA SCIENTIFIC MICROBIOLOGY (article, 2023-05-01)
Field: Materials Science — Biomaterials

Metal/Metal Oxide Nanoparticles for Enhancing the Antimicrobial Activity of Food Packaging and Reducing Food-Borne Disease One of the main challenges of creating food packaging is preventing the products from deteriorating, but still keeping their quality during handling and storage.One factor that decreases shelf life is a lack of antimicrobial packaging films.These normally prevent microbial contamination, but without them might be decreases shelf life of food products.The best packaging films have great mechanical properties and also the permeability of water vapor or oxygen, for example.Because consumers often prefer products that are high quality and fresh, they buy food without additives.This creates issues for manufacturers that need the additives to maintain freshness.In this review, the development of innovative packaging materials using nanotechnology was addressed.Polysaccharides such as chitosan, carboxymethyl cellulose, and starch are biodegradable and nontoxic, so they do not pose environmental threats; however, they have poor antimicrobial activity, mechanical properties, and low water resistance.Therefore, nanomaterials can be employed to improve antimicrobial activity, thermal, mechanical, and gas barrier properties of food packaging.Bionanocomposites technologies are novel, high-performance, lightweight, and ecofriendly materials that can replace traditional nonbiodegradable plastic packaging. Food packaging ; Metal ; Antimicrobial ; Materials science ; Nanoparticle ; Food science ; Nanotechnology ; Metallurgy ; Chemistry Nanocomposite Films for Food Packaging
Authors: Arne Schobert | Jan Berges | Erik G. C. P. van Loon | Michael A. Sentef | Sergey Brener | Mariana Rossi | Tim O. Wehling
Source: arXiv (Cornell University) (preprint, 2023-03-13)
Field: Materials Science — Materials Chemistry

Ab initio electron-lattice downfolding: potential energy landscapes, anharmonicity, and molecular dynamics in charge density wave materials The interplay of electronic and nuclear degrees of freedom presents an outstanding problem in condensed matter physics and chemistry. Computational challenges arise especially for large systems, long time scales, in nonequilibrium, or in systems with strong correlations. In this work, we show how downfolding approaches facilitate complexity reduction on the electronic side and thereby boost the simulation of electronic properties and nuclear motion - in particular molecular dynamics (MD) simulations. Three different downfolding strategies based on constraining, unscreening, and combinations thereof are benchmarked against full density functional calculations for selected charge density wave (CDW) systems, namely 1H-TaS$_2$, 1T-TiSe$_2$, 1H-NbS$_2$, and a one-dimensional carbon chain. We find that the downfolded models can reproduce potential energy surfaces on supercells accurately and facilitate computational speedup in MD simulations by about five orders of magnitude in comparison to purely ab initio calculations. For monolayer 1H-TaS$_2$ we report classical replica exchange and quantum path integral MD simulations, revealing the impact of thermal and quantum fluctuations on the CDW transition. Anharmonicity ; Physics ; Electronic structure ; Ab initio ; Molecular dynamics ; Quantum ; Charge density wave ; Statistical physics ; Electron ; Lattice (music) ; Condensed matter physics ; Quantum mechanics Machine Learning in Materials Science ; 2D Materials and Applications ; Molecular Junctions and Nanostructures