jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Mohamed Khaled | Abden Sami Zain El
Source: Zastita materijala (article, 2022-12-15)
Field: Materials Science — Materials Chemistry

Mechanical characteristics of AL-1050 and Al-6061 alloys deformed using equal channel angular rolling process One of the effective severe plastic deformations (SPD) techniques is Equal channel angular rolling (ECAR) process which can lead to proper ultra-fine grained (UFG) structures of material, the main objective of this work is to study the improvement in mechanical properties within 1050 and 6061 aluminum alloy sheets. There are more attempts to investigate the microstructure and mechanical properties of strips material, the influence of process parameters such as number of equal channel angular rolling passes, routes (A&amp;C) and annealing temperature after each passes on deformation behavior of 6061 and 1050 Aluminum alloys were investigated experimentally .Results was indicated that for AL-6061 without annealing process at first pass it was the higher stress than the passes after annealing process and also the grains was fine in the first pass ,For AL-1050 it was indicated that with ambient temperature at six pass the mechanical properties was improved and its recorded the higher stress with more passes at six pass for rout C and also the fine grains of microstructure was obtained in the six pass with compared to the material with annealing process which becomes more ductility with more passes. Annealing (glass) ; Materials science ; Microstructure ; Aluminium ; Alloy ; Metallurgy ; Severe plastic deformation ; Composite material Microstructure and mechanical properties ; Metallurgy and Material Forming ; Metal Alloys Wear and Properties
Authors: Preeti Choudhary | Stephen Anyango | John M. Berrisford | Mihály Váradi | James Tolchard | Sameer Velankar
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-08-13)
Field: Materials Science — Materials Chemistry

Unified access to up-to-date residue-level annotations from UniProt and other biological databases for PDB data via PDBx/mmCIF files Abstract More than 58,000 proteins have up-to-date correspondence between their amino acid sequence (UniProtKB) and their 3D structures (PDB), enabled by the Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource. In addition to this fundamental mapping, SIFTS incorporates residue-level annotations from other biological resources such as Pfam, InterPro, SCOP, SCOP2, CATH, IntEnz, GO, PubMed, Ensembl, NCBI taxonomy database and Homologene. The SIFTS data is exported in XML format per individual PDB entry and is also accessible via the PDBe REST API. These mappings have always been maintained separately from the structure data (PDBx/mmCIF file) in the PDB archive. In this current work, taking advantage of the extensibility of the core PDBx/mmCIF framework, we extended the wwPDB PDBx/mmCIF data dictionary with additional categories to accommodate SIFTS data and added the UniProt, Pfam, SCOP2, and CATH mapping information directly into the PDBx/mmCIF files from the PDB archive. The integration of mapping data in the PDBx/mmCIF files provides consistent numbering of residues in different PDB entries allowing easy comparison of structure models. The extended PDBx/mmCIF format yields a more consistent, standardised metadata description without altering the core PDB information. This development enables up-to-date cross-reference information at residue level resulting in better data interoperability, supporting improved data analysis and visualisation. Availability and implementation We expanded the PDBe release pipeline with a process that adds SIFTS annotations to the PDBx/mmCIF files for individual structures in the PDB archive. The scientific community can download these updated PDBx/mmCIF files from the PDBe entry pages ( https://pdbe.org/7dr0 ) and through direct URLs ( https://www.ebi.ac.uk/pdbe/static/entry/7o9f_updated.cif ), using the PDBe download service ( https://www.ebi.ac.uk/pdbe/download/api ) or from the EMBL-EBI FTP area ( https://ftp.ebi.ac.uk/pub/databases/msd/updated_mmcif/ ). UniProt ; Protein Data Bank (RCSB PDB) ; Computer science ; Metadata ; Database ; Ensembl ; XML ; Information retrieval ; Biological database ; Protein Data Bank ; Data curation ; World Wide Web ; Bioinformatics ; Biology ; Protein structure ; Genome Enzyme Structure and Function ; Protein Structure and Dynamics ; RNA and protein synthesis mechanisms
Authors: Debdas Dhabal | Subramanian K. R. S. Sankaranarayanan | Valeria Molinero
Source: ChemRxiv (preprint, 2022-11-03)
Field: Materials Science — Materials Chemistry

Stability and Metastability of Liquid water in a Machine-learned Coarse-grained Model with Short-range Interactions Coarse-grained water models are ~100 times more efficient than all-atom models, enabling simulations of supercooled water and crystallization. The machine-learned monatomic model ML-BOP reproduces the experimental equation of state (EOS) and ice-liquid thermodynamics at 0.1 MPa on par with all-atom TIP4P/2005 and TIP4/Ice. These all-atom models were parameterized using high-pressure experimental data, and are either accurate for water’s EOS (TIP4P/2005) or ice-liquid equilibrium (TIP4P/Ice). ML-BOP was parameter-ized from temperature-dependent ice and liquid experimental densities and melting data at 0.1 MPa; its only pressure training is from com-pression of TIP4P/2005 ice at 0 K. Here we investigate whether ML-BOP replicates the experimental EOS and ice-water thermodynamics along all pressures of ice I. We find that ML-BOP reproduce the temperature, enthalpy, entropy and volume of melting of hexagonal ice up to 400 MPa and the EOS of water along the melting line with accuracy that rivals both TIP4P/2005 and TIP4P/Ice. We interpret that the accu-racy of ML-BOP originates from its ability to capture the shift between compact and open local structures to changes in pressure and temper-ature. ML-BOP reproduces the sharpening of the tetrahedral peak of the pair distribution function of water upon supercooling, and its pres-sure dependence. We characterize the region of metastability of liquid ML-BOP with respect to crystallization and cavitation. The accessibil-ity of ice crystallization to simulations of ML-BOP, together with its accurate representation of the thermodynamics of water, makes it prom-ising for investigating the interplay between anomalies, glass transition, and crystallization under conditions challenging to access through experiments. Supercooling ; Thermodynamics ; Metastability ; Water model ; Chemistry ; Materials science ; Molecular dynamics ; Physics Machine Learning in Materials Science ; Theoretical and Computational Physics ; Arctic and Antarctic ice dynamics
Authors: John Lewis | Hollie L. Cockings | Daniel J.C. Stewart | James E. Russell | Matthew H. Thomas | Mark Greenslade
Source: Ironmaking & Steelmaking Processes Products and Applications (article, 2022-10-30)
Field: Materials Science — Materials Chemistry

Investigating carbon type differentiation techniques for blast furnace dust Coal char presence in blast furnace dust, indicates the inefficiency of combustion in the raceway. A retroactive approach has been applied by investigating the presence of carbon sources in blast furnace dust via carbon type differentiation methodologies. The current state of the art in carbon type differentiation for similar applications consists of thermogravimetric analysis, however this technique does not allow for samples to be analysed in line with the ever-changing conditions of the blast furnace. Here, the TGA method has been trialled for use with blast furnace dust, with improvements offered to the heating profile, allowing for faster analysis. Moreover, alternative techniques have been trialled, in combination with characterisation methods such as XRD, SEM/EDS, total carbon and ICP-OES. The ‘Winkler Method’ originally designed to quantify charcoal in soil sediment, has been successfully optimised for carbon type differentiation in blast furnace dust, showing good correlation with the original benchmark technique. Blast furnace ; Raceway ; Combustion ; Carbon fibers ; Char ; Charcoal ; Thermogravimetric analysis ; Coal ; Environmental science ; Waste management ; Metallurgy ; Materials science ; Chemistry ; Chemical engineering ; Engineering ; Composite material Thermal and Kinetic Analysis ; Thermochemical Biomass Conversion Processes ; Radioactive element chemistry and processing
Authors: M. N. Hamdan | W. Mansor | A. R. M. Radzol | İlhan Umut | A. R. Mahmud | Suhaili Beeran Kutty
Source: International Journal of Emerging Technology and Advanced Engineering (article, 2022-08-02)
Field: Chemistry — Analytical Chemistry

Principal Component Analysis of SERS-Based Chicken, Beef and Pork Fats The issues of non-halal ingredients in food products make it important to investigate the technique to cluster the animal fats. Combination of Surface Enhanced Raman Spectroscopy (SERS) and Principal Components Analysis (PCA) has not been investigated in differentiating chicken, beef and pork fats. This paper describes the analysis of SERS based chicken, beef and pork fats in the form of solid and liquid using PCA. The Raman spectra of raw fats, dried fats and oil data were acquired using SERS, filtered using a high-pass filter and then normalized. The features of the chicken, beef and pork fats were selected using three PCA selection criteria. It was found that the data dimension of these fat samples can be reduced up to 99.75% and the cluster of the chicken, beef and pork fats can be observed clearly in the oil compared to the raw and dried fats. Food science ; Principal component analysis ; Animal fat ; Chemistry ; Mathematics Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Identification and Quantification in Food
Authors: S. Kasri | Lazhar Herous | K. Smili | Mohamed Tahar Kimour | Azzeddine Dekhane
Source: Latvian Journal of Physics and Technical Sciences (article, 2022-10-01)
Field: Materials Science — Materials Chemistry

Potential Decay Simulation on Insulating Films Abstract Surface potential decay (SPD) of a corona charged polymeric material is a powerful tool to characterise electrical properties such as charge transport, trapping/detrapping and recombination. Over the years, various predictive simulation techniques have been proposed to describe charge transport within the material. Despite recent progress, it appears that there have been a few attempts to theoretically interpret the nature of the charge migration on the insulation surface. The aim of the present paper is to introduce a new technique with differential evolution algorithm (DEA) to reveal the steady state surface potential decay experimental results. Experimental measurement was carried on a thin film of polyethylene terephthalate (thickness: 0.5 mm; surface: 50 mm × 50 mm). The domains of variation of the factors used were respectively: 1000 V to 1800 V; 25 to 55 °C; 50 % to 80 %. The simulation results show that computational modelling and optimization approaches may improve the effectiveness to characterise electrical properties of polymers. More importantly, these studies demonstrate that DEA is effective and performs better than the experimental design method. Polyethylene terephthalate ; Trapping ; Polyethylene ; Materials science ; Corona (planetary geology) ; Charge (physics) ; Surface (topology) ; Surface charge ; Polymer ; Computational physics ; Chemical physics ; Statistical physics ; Composite material ; Physics ; Chemistry ; Mathematics ; Physical chemistry High voltage insulation and dielectric phenomena ; Electrostatic Discharge in Electronics ; Power Transformer Diagnostics and Insulation
Authors: Philippe Urban | Denis Pompon
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-03-21)
Field: Materials Science — Materials Chemistry

Confrontation of AlphaFold2 models with cryo-EM and crystal structures enlightens alternate geometries of the CYP102A1 multidomain protein Abstract Large range structural dynamics plays a critical role for the function of electron transfer proteins. This information is generally not available from crystallographic structures, while cryo-electron microscopy (cryo-EM) can provide some elements but frequently with a degraded spatial resolution. Recently, AlphaFold-based structural modelling was extended to the prediction of protein complexes. In this work, bacterial CYP102A1 from Priestia megaterium was used as a test case to evaluate the capability of AlphaFold2 to predict alternative structures critical for catalysis. CYP102A1 monooxygenase, a NADPH-supported fatty acid hydroxylase, works as a soluble homodimer, each monomer harboring two flavins (FAD and FMN) and one heme cofactors. Large conformational changes are required during catalytic cycle to allow successive electron transfers from FAD to FMN and finally heme iron. We used the recently released AlphaFold2_advanced notebook (AF2A), to predict the possible alternate conformations supporting electron transfers in CYP102A1 homodimer. Challenging AF2A-derived models with previously reported experimental data revealed an unforeseen domain connectivity of the diflavin reductase part of the enzyme. Intermolecular crossed complex constitutes a novel type of structural organization never previously described. The predicted formation within the dimer of a stable complex between the heme containing domains was challenged and found consistent with uninterpreted features of reported crystallographic structures and cryo-EM imaging. The particularly efficient CYP102A1 catalytic mechanism was revisited to the light of the new evidenced connectivity in which the FMN-binding domain of each monomer oscillates on themselves to alternatively receive and transfer electrons without needing large structural change in the dimer. Such model was found explanatory for previously contradictory reported biochemical data. Possibility to mimic CYP102A1 structural organization into bicomponent eukaryotic P450 systems was evaluated by designing and modeling in silico synthetic reductase domains built from composite sequence segments from P. megaterium and human origins. More generally, this work illustrates how the ability of AF2A to predict alternate complex structures can enlighten and explain conformational changes critical for bio-assemblies. Chemistry ; Electron transfer ; Flavin group ; Cryo-electron microscopy ; Flavin mononucleotide ; Oxidoreductase ; Heme ; Protein structure ; Dimer ; Flavin adenine dinucleotide ; Cofactor ; Stereochemistry ; Enzyme ; Biochemistry ; Organic chemistry Enzyme Structure and Function ; Protein Structure and Dynamics ; Pharmacogenetics and Drug Metabolism
Authors: Juncheng Li | Wei Wang | Haolin Wang
Source: Research Square (preprint, 2022-12-05)
Field: Chemistry — Organic Chemistry

Prediction of Thermal Modified Wood Color Change after Artificial Weathering Based on IPSO-SVM Model Abstract The support vector machine (SVM) model was applied to the prediction of the color change of heat-modified wood after artificial weathering. In order to improve the prediction performance, the improved particle swarm optimization (IPSO) algorithm was used to optimize the parameters of the SVM model, and the IPSO-SVM model was established based on the nonlinear descending weight strategy to improve the particle swarm optimization. To verify the performance of the established model, MAE, RMSE and R 2 of the test set and training set were compared with the PSO-SVM model and SVM model. According to the analysis of the results, the RMSE of the training set data of IPSO-SVM model is reduced by 49% and 72%, the MAE is reduced by 52% and 78%, and the RMSE of the test set data is reduced by 6% and 24%, and the MAE is reduced by 2% and 25%, respectively. The results show that the support vector machine optimized by the improved particle swarm optimization algorithm is more accurate in predicting the color change of the heat-modified wood after artificial weathering. Support vector machine ; Particle swarm optimization ; Mean squared error ; Artificial intelligence ; Computer science ; Test set ; Data set ; Set (abstract data type) ; Weathering ; Algorithm ; Machine learning ; Mathematics ; Statistics ; Geology Wood and Agarwood Research ; Wood Treatment and Properties ; Cultural Heritage Materials Analysis
Authors: Marko Viskić | Njara Rakotomanomana | Farid Chemat | Anet ­Režek ­Jambrak
Source: Croatica Chemica Acta (article, 2022-01-01)
Field: Chemistry — Spectroscopy

Solubility of Bioactive Compounds from Mediterranean Plants in Natural Deep Eutectic Solvents Estimated by COSMO-RS Software Natural deep eutectic solvents (NADES) represent a promising group of green solvents employed for the extraction of bioactive compounds from medicinal plants. Due to the wide range of polarities of investigated solutes, and an outstanding number of combinations of NADES components, fine tuning and selection by software for modeling and evaluation of thermodynamic properties of solvents and solutes is a necessary step preceding the extraction from real samples. In this study, four hydrophilic NADES were chosen for the prediction of solubility of 19 bioactive compounds from Mediterranean plants, which was performed by COSMO-RS software. NADES structure optimization was performed by pseudocomponent approach and individual constituent approach. Change of hydrogen bond donor components of NADES did not show a significant influence on the solubility of screened solutes. According to both approaches, the investigated systems represent promising solvents for extraction of hydrophilic and moderately lipophilic flavonoids, terpenoids, and phenylpropanoids, while being unsuitable for extraction of the most lipophilic (logkow 4) natural products and compounds lacking polar functional groups due to the absence of sites participating in hydrogen bond formation. Eutectic system ; Solubility ; Chemistry ; Mediterranean climate ; Natural (archaeology) ; Organic chemistry ; Geography ; Biology ; Ecology ; Archaeology Analytical Chemistry and Chromatography
Authors: Xue Cai | Zhangzhi Xue | Fangfang Zeng | Jun Tang | Liang Yue | Bo Wang | Weigang Ge | Yuting Xie | Zelei Miao | Wanglong Gou | Yuanqing Fu | Sainan Li | Jinlong Gao | Menglei Shuai | Ke Zhang | Fengzhe Xu | Yunyi Tian | Nan Xiang | Yan Zhou | Peng‐Fei Shan | Yi Zhu | Yu‐Ming Chen | Ju‐Sheng Zheng | Tiannan Guo
Source: medRxiv (preprint, 2022-10-22)
Field: Chemistry — Spectroscopy

Population serum proteomics uncovers prognostic protein classifier and molecular mechanisms for metabolic syndrome ABSTRACT Metabolic syndrome (MetS) is a complex metabolic disorder with a global prevalence of 20-25%. Early identification and intervention would help minimize the global burden on healthcare systems. Here, we measured over 400 proteins from ∼20,000 proteomes using data-independent acquisition mass spectrometry for 7890 serum samples from a longitudinal cohort of 3840 participants with two follow-up time points over ten years. We then built a machine learning model for predicting the risk of developing MetS within ten years. Our model, composed of 11 proteins and the age of the individuals, achieved an area under the curve of 0.784 in the discovery cohort (n=855) and 0.774 in the validation cohort (n=242). Using linear mixed models, we found that apolipoproteins, immune-related proteins, and coagulation-related proteins best correlated with MetS development. This population-scale proteomics study broadens our understanding of MetS, and may guide the development of prevention and targeted therapies for MetS. Metabolic syndrome ; Cohort ; Proteomics ; Proteome ; Population ; Medicine ; Bioinformatics ; Computational biology ; Internal medicine ; Biology ; Endocrinology ; Diabetes mellitus ; Environmental health ; Genetics Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies ; Diabetes and associated disorders
Authors: Takeshi Sato
Source: Nihon Reoroji Gakkaishi (article, 2022-02-15)
Field: Chemistry — Organic Chemistry

Modeling Techniques for the Rheology of Wormlike Micellar Solutions A short review on the rheology of entangled linear wormlike micellar solutions is presented. To date, the linear and nonlinear rheological properties of wormlike micellar solutions have been extensively studied from experimental, theoretical, and numerical perspectives. For a linear response region, there are several sophisticated models, and the rheological properties have been well reproduced by these models. On the other hand, modeling the nonlinear rheological properties is still an active and challenging topic. In this review, we summarize theoretical and numerical studies on the rheological properties of wormlike micellar solutions. Furthermore, future perspectives of related topics including associative polymers are presented. Rheology ; Materials science ; Micellar solutions ; Nonlinear system ; Polymer science ; Polymer ; Statistical physics ; Thermodynamics ; Micelle ; Composite material ; Physical chemistry ; Physics ; Aqueous solution ; Chemistry Surfactants and Colloidal Systems ; Rheology and Fluid Dynamics Studies ; Enhanced Oil Recovery Techniques
Authors: Dien Hu | Junyuan Zheng | M.W. Fu
Source: Research Square (preprint, 2022-01-14)
Field: Materials Science — Materials Chemistry

Study on Size-Related Product Quality of Multiscale Central-Punched Cups Fabricated by Compound Forming Directly Using Brass Sheet Brass ; Product (mathematics) ; Quality (philosophy) ; Materials science ; Metallurgy ; Engineering drawing ; Composite material ; Manufacturing engineering ; Engineering ; Mathematics ; Geometry ; Physics ; Copper Metallurgy and Material Science ; Metallurgy and Material Forming ; Aluminum Alloy Microstructure Properties
Authors: Megan Pitz | Margaret A. Elpers | Alexandra Nukovic | Sarah Wilde | Arica Jordan Gregory | Angela Alexander-Bryant
Source: Biomedicines (article, 2022-09-02)
Field: Materials Science — Biomaterials

De Novo Self-Assembling Peptides Mediate the Conversion of Temozolomide and Delivery of a Model Drug into Glioblastoma Multiforme Cells Glioblastoma multiforme (GBM) is the most aggressive central nervous system tumor, and standard treatment, including surgical resection, radiation, and chemotherapy, has not significantly improved patient outcomes over the last 20 years. Temozolomide (TMZ), the prodrug most commonly used to treat GBM, must pass the blood-brain barrier and requires a basic pH to convert to its active form. Due to these barriers, less than 30% of orally delivered TMZ reaches the central nervous system and becomes bioactive. In this work, we have developed a novel biomaterial delivery system to convert TMZ to its active form and that shows promise for intracellular TMZ delivery. Self-assembling peptides were characterized under several different assembly conditions and evaluated for TMZ loading and conversion. Both solvent and method of assembly were found to affect the supramolecular and secondary structure of peptide assemblies. Additionally, as peptides degraded in phosphate-buffered saline, TMZ was rapidly converted to its active form. This work demonstrates that peptide-based drug delivery systems can effectively create a local stimulus during drug delivery while remaining biocompatible. This principle could be used in many future biomedical applications in addition to cancer treatment, such as wound healing and regenerative medicine. Temozolomide ; Glioblastoma ; Cancer research ; Drug delivery ; Drug ; Medicine ; Chemistry ; Pharmacology Supramolecular Self-Assembly in Materials ; Advanced biosensing and bioanalysis techniques ; RNA Interference and Gene Delivery