jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Amanda S. Barnard | Baichuan Sun | George Opletal
Source:  (article, 2018-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Platinum Nanoparticle Data Set This is a set of 1300 platinum (Pt) nanoparticle FINAL CONFIGURATIONS, for use in data-driven studies. These structures have been optimized (fully relaxed) using molecular dynamics with an embedded atom (EAM) interatomic potential, at various temperatures and growth rates. All files are in XYZ format, and the naming convention is defined in the accompanying csv file that lists all of the structural features and property indicators (see Supporting Attachments). Sizes range from 54 atoms to 15837 atoms, with both crystalline and non-crystalline configurations and regions. Each nanoparticle has been characterised using a variety of topological features, including size, lattice structure, surface curvature and a number of order parameters. The final five columns in the accompanying csv file are target labels, providing the concentration of classes of surface structures responsible for different types of catalytic reactions, the total energy and the excess formtion energy. Links to publications describing these property labels are provided in the meta data. Platinum ; Data set ; Set (abstract data type) ; Computer science ; Chemistry ; Artificial intelligence ; Programming language Gold and Silver Nanoparticles Synthesis and Applications ; Laser-Ablation Synthesis of Nanoparticles ; History and advancements in chemistry
Authors: Vladimir Polužanski | Uroš Kovačević | Boško Nikolić
Source: FME Transaction (article, 2018-01-01)
Field: Materials Science — Materials Chemistry

Algorithm for calculating influence of power transformer oil temperature change on the accuracy of allacoustic non-iterative partial discharge localization This article investigates the all-acoustic method for partial discharge localization in a power transformer. This method is based on mathematical model that uses multilateration with Time Difference of Arrival (TDOA) principle and non-itterative mathematical algorithm. In this model, it is assumed that acoustic signal propagates only through transformer oil and that the velocity of acoustic signal is constant. Acoustic signal velocity is largely dependent on transformer oil temperature meaning that oil temperature is also considered to be constant. In reality if we look from the perspective of physics, thermo dynamics of fluids, transformer construction etc. this approximation is enormous. Therefore, influence of power transformer oil temperature change (velocity of acoustic signal change) on the accuracy of this method is investigated. For that purpose special algorithm is designed and implemented in Visual C# programming language. Based on conducted simulations, further knowledge is gained about interaction between transformer oil temperature and placement of acoustic sensors. This interaction produced significant disparity in noniterative algorithm's accuracy for different sensor positions with oil temperature change. In order to fully take advantage of noticed interaction, certain steps for further research and development are proposed. Multilateration ; Transformer ; Transformer oil ; Acoustics ; Computer science ; Algorithm ; Electronic engineering ; Engineering ; Electrical engineering ; Physics ; Voltage High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Electrical and Bioimpedance Tomography
Authors: Xin Bian | Mingge Deng null | George Em Karniadakis
Source: Communications in Computational Physics (article, 2018-06-01)
Field: Materials Science — Materials Chemistry

Analytical and Computational Studies of Correlations of Hydrodynamic Fluctuations in Shear Flow We study correlations of hydrodynamic fluctuations in shear flow analytically and also by dissipative particle dynamics (DPD) simulations. The hydrodynamic equations are linearized around the macroscopic velocity field and then solved by a perturbation method in Fourier-transformed space. The autocorrelation functions (ACFs) from the analytical method are compared with results obtained from DPD simulations under the same shear-flow conditions. Up to a moderate shear rate, various ACFs from the two approaches agree with each other well. At large shear rates, discrepancies between the two methods are observed, hence revealing strong additional coupling between different fluctuating variables, which is not considered in the analytical approach. In addition, the results at low and moderate shear rates can serve as benchmarks for developing multiscale algorithms for coupling of heterogeneous solvers, such as a hybrid simulation of molecular dynamics and fluctuating hydrodynamics solver, where thermal fluctuations are indispensable. Autocorrelation ; Dissipative particle dynamics ; Shear (geology) ; Shear flow ; Dissipative system ; Perturbation (astronomy) ; Coupling (piping) ; Thermal fluctuations Block Copolymer Self-Assembly ; Nanopore and Nanochannel Transport Studies ; Lattice Boltzmann Simulation Studies
Authors: Tiannan Guo | Li Li | Qing Zhong | Niels J. Rupp | Konstantina Charmpi | Christie E Wong | Ulrich Wagner | Jan H. Rueschoff | Wolfram Jochum | Christian D. Fankhauser | Karim Saba | Cédric Poyet | Peter J. Wild | Ruedi Aebersold | Andreas Beyer
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2018-01-18)
Field: Chemistry — Spectroscopy

Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers Abstract Many tumors are characterized by large genomic heterogeneity and it remains unclear to what extent this impacts on protein biomarker discovery. Here, we quantified proteome intra-tissue heterogeneity (ITH) based on a multi-region analysis of 30 biopsy-scale prostate tissues using pressure cycling technology and SWATH mass spectrometry. We quantified 8,248 proteins and analyzed the ITH of 3,700 proteins. The level of ITH varied significantly depending on proteins and tissue types. Benign tissues exhibited generally more complex ITH patterns than malignant tissues. Spatial variability of ten prostate biomarkers was further validated by immunohistochemistry in an independent cohort (n=83) using tissue microarrays. PSA was preferentially variable in benign prostatic hyperplasia, while GDF15 substantially varied in prostate adenocarcinomas. Further, we found that DNA repair pathways exhibited a high degree of variability in tumorous tissues, which may contribute to the genetic heterogeneity of tumors. This study conceptually adds a new perspective to protein biomarker discovery by quantifying spatial proteome variation and it demonstrates the feasibility by exploiting recent technological progress. Biomarker discovery ; Proteome ; Prostate ; Biomarker ; Prostate cancer ; Tissue microarray ; Computational biology ; Biology ; Hyperplasia ; Proteomics ; Biopsy ; Pathology ; Immunohistochemistry ; Bioinformatics ; Medicine ; Cancer ; Genetics ; Gene ; Endocrinology ; Immunology Advanced Proteomics Techniques and Applications ; Prostate Cancer Treatment and Research ; Molecular Biology Techniques and Applications
Authors: Chuleeporn Thanomsilp
Source: SHILAP Revista de lepidopterología (article, 2018-01-01)
Field: Chemistry — Physical and Theoretical Chemistry

STEM teaching in a chemistry laboratory "How to build a simple battery in the laboratory" Active learning, especially STEM education, has been proven to help students develop their learning skills. Most teachers are encouraged to create activities and environments that help students to learn not only about theories involved in each lesson, but also help them to develop skills required in the 21st century. The STEM approach is used in a laboratory in a Chemistry for Engineers course at Mae Fah Luang University on the topic of electrochemistry. The battery is used as a real world application of electrochemistry. The lesson plan of a 2.5-hour laboratory session based on STEM is presented in this article. Starting with concept engagement on the subject of batteries, students use their inquiry skills to search for information about batteries. The following activities are hands-on experiences in using batteries to power light bulbs, construct galvanic cells and create a functioning battery to power a light bulb using galvanic cells. The final challenge was to create a battery from galvanic cells to produce the brightest light bulb. After class, students’ self-evaluations showed that the activities helped them to understand the scientific concepts involved in electrochemistry, as well as concepts of current, voltage and electricity. They also thought that the activities helped to improve their critical thinking and team-working skills. Simple (philosophy) ; Chemical laboratory ; Medical laboratory ; Battery (electricity) ; Computer science ; Engineering ; Biochemical engineering ; Medicine ; Physics ; Epistemology ; Pathology ; Thermodynamics Various Chemistry Research Topics
Authors: Reese E. Jones | D. K. Ward
Source: Physical review. B./Physical review. B (article, 2018-02-08)
Field: Materials Science — Materials Chemistry

Influence of defects on the thermal conductivity of compressed LiF Defect formation in LiF, which is used as an observation window in ramp and shock experiments, has significant effects on its transmission properties. Given the extreme conditions of the experiments it is hard to measure the change in transmission directly. Using molecular dynamics, we estimate the change in conductivity as a function of the concentration of likely point and extended defects using a Green-Kubo technique with careful treatment of size effects. With this data, we form a model of the mean behavior and its estimated error; then, we use this model to predict the conductivity of a large sample of defective LiF resulting from a direct simulation of ramp compression as a demonstration of the accuracy of its predictions. Given estimates of defect densities in a LiF window used in an experiment, the model can be used to correct the observations of thermal energy through the window. In addition, the methodology we develop is extensible to modeling, with quantified uncertainty, the effects of a variety of defects on the thermal conductivity of solid materials. Thermal conductivity ; Materials science ; Conductivity ; Compression (physics) ; Measure (data warehouse) ; Shock (circulatory) ; Biological system ; Window (computing) ; Thermal ; Statistical physics ; Computational physics ; Mechanics ; Thermodynamics ; Composite material ; Computer science ; Physics Thermal properties of materials ; Electronic Packaging and Soldering Technologies ; Silicon Carbide Semiconductor Technologies
Authors: Jean-Claude Krapez
Source: Journal of the Optical Society of America A (article, 2018-05-29)
Field: Materials Science — Surfaces, Coatings and Films

Multipurpose S-shaped solvable profiles of the refractive index: application to modeling of antireflection layers and quasi-crystals A class of four-parameter solvable profiles of the electromagnetic admittance has recently been discovered by applying the newly developed Property & Field Darboux Transformation method (PROFIDT). These profiles are highly flexible. In addition, the related electromagnetic field solutions are exact, in closed form, and involve only elementary functions. In this paper, we focus on those that are S-shaped, and we provide all of the tools needed for easy implementation. These analytical bricks can be used for high-level modeling of lightwave propagation in photonic devices presenting a piecewise-sigmoidal refractive index profile, such as, for example, antireflection layers, rugate filters, chirped filters, and photonic crystals. For small amplitudes of the index modulation, these elementary profiles are very close to a cosine profile. They can therefore be considered as valuable surrogates for computing the scattering properties of components like Bragg filters and reflectors as well. In this paper we present an application for antireflection layers and another for 1D quasi-crystals (QC). The proposed S-shaped profiles can be easily manipulated for exploring the optical properties of smooth QC, a class of photonic devices that adds to the classical binary-level QC. Refractive index ; Piecewise ; Photonic crystal ; Binary number ; Field (mathematics) ; Photonics ; Optics ; Electromagnetic field ; Trigonometric functions ; Transformation (genetics) ; Materials science ; Optoelectronics ; Computer science ; Physics ; Mathematics ; Mathematical analysis ; Geometry Optical Coatings and Gratings ; Photonic Crystals and Applications ; Photonic and Optical Devices
Authors: Osama Shekhah | Valeriya Chernikova | Youssef Belmabkhout | Mohamed Eddaoudi
Source: Preprints.org (preprint, 2018-09-03)
Field: Chemistry — Inorganic Chemistry

Metal&amp;ndash;Organic Framework Membranes: From Fabrica-Tion to Application in Gas Separation Gas membrane-based separation is considered one of the furthermost effective technology to address energy efficiency and large footprint challenges. Various classes of advanced materials including polymers, zeolites, porous carbons and metal&amp;ndash;organic frameworks (MOFs) were attempted as membranes for gas separation. MOFs, among other porous materials, possess uniquely tunable nature, in which the pore size and environment can be controlled by connecting metal ions (or metal ion clusters) with organic linkers with various functionalities. This feature makes them attractive for thin membrane fabrication, as both diffusion and solubility components of permeability can be altered. It is interesting to notice that numerous reports have addressed the synthesis of different MOFs, fabrication of their corresponding thin films and their applications, nonetheless, relatively limited studies addressed their gas separation application as membranes. In this review, we provide a synopsis of the various MOF-based membranes that were fabricated in the last decade. In this review we propose a short introduction touching on the gas separation membrane technology and we shed light on (i) the various techniques developed for the fabrication of MOF as membranes and (ii) challenges and application for MOF thin film membranes in various important gas separation applications. Membrane ; Gas separation ; Fabrication ; Materials science ; Metal-organic framework ; Nanotechnology ; Polymer ; Porosity ; Synthetic membrane ; Chemical engineering ; Chemistry ; Adsorption ; Engineering ; Organic chemistry ; Composite material Metal-Organic Frameworks: Synthesis and Applications ; Membrane Separation and Gas Transport ; Zeolite Catalysis and Synthesis
Authors: Liangli Yang | Qiuping Gao | Junjun Dai | Guozhen Yuan | Lei Wang | Cen Qian | Baojian Zhu | Chao-Liang Liu | Guoqing Wei
Source: PLoS ONE (article, 2018-05-31)
Field: Materials Science — Biomaterials

Comparative transcriptome analysis of silkworm, Bombyx mori colleterial gland suggests their functional role in mucous secretion Colleterial glands (CG) present in the body of adult female of Bombyx mori, which can help adhere eggs on the surface of the host plants. Although this organ has been known for centuries, only morphology and its secretions have been studied. Their gene expression profiles and physiological roles remain largely unknown. Aided by high-throughput next generation sequencing (NGS), we reported the comparative transcriptome analysis of CG isolated from the H9 and the P50 strains of Bombyx mori. A total of 19,896,957 and 20,446,366 clean reads were obtained from CG of H9 and the P50 strains, respectively; then differential expression analysis was performed, and 1,509 differentially expressed genes (DEGs) were identified. Among them, 1,001 genes are up-regulated and 508 genes are down-regulated in P50 individuals compared with H9 individuals. The enrichment of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) of DEGs confirmed that many DEGs were associated with "Amino acid transport and metabolism", "Nucleotide transport and metabolism", and "Inorganic ion transport and metabolism", 25 of the DEGs related to the "ECM-receptor interaction passway", "sphingolipid metabolism passway", and "amino sugar and nucleotide sugar metabolism passway" were potentially involved in the process of CG development and mucus secretion. According to these data, we hypothesized that CG play an important role in providing favorable physiological environment for the glue secretion formation. In addition, GO enrichment and differential expression analysis of the DEGs in the CG indicate that this gland may be involved in the transporting of small solutes such as sugars, ions, amino acids and nucleotide sugar to the CG. Our findings lay the foundation for further research on CG function. KEGG ; Biology ; Transcriptome ; Bombyx mori ; Gene ; Gene expression profiling ; Bombyx ; Gene expression ; Secretion ; Nucleotide sugar ; Genetics ; Cell biology ; Biochemistry ; Nucleotide Silk-based biomaterials and applications ; Neurobiology and Insect Physiology Research ; Silkworms and Sericulture Research
Authors: Haiming Fan | Po Li | Wěi Li | Hui Li | Xiaonan Huang
Source: Molecules (article, 2018-07-27)
Field: Chemistry — Organic Chemistry

Ultrasensitive (Co)polymers Based on Poly(methacrylamide) Structure with Fining-Tunable pH Responsive Value Novel pH responsive copolymers with tertiary amine groups were prepared by free radical polymerization with 2-(dialkylamino)ethyl methacrylate monomers. These polymers were pH sensitive with the ability to be responsively fine-tuned in aqueous solution, which was proven through titration, transmittance measurements, and proton nuclear magnetic resonance spectroscopy. The polymers were soluble in water at low pH values, induced by electrostatic repulsion between amine groups, and aggregated above their p<i>K</i><sub>a</sub> value due to the hydrophobic effect of the alkyls. The pH responsive values were precisely tuned from 7.4 to 4.8 by increasing the hydrophobic monomer ratio. Our work provides a novel approach for the development of ultrasensitive pH-responsive polymers for application in biomedical materials. Methacrylamide ; Polymer ; Methacrylate ; Chemistry ; Monomer ; Polymer chemistry ; Aqueous solution ; Polymerization ; Copolymer ; Amine gas treating ; Radical polymerization ; Titration ; Chemical engineering ; Organic chemistry ; Acrylamide Advanced Polymer Synthesis and Characterization ; Analytical Chemistry and Sensors ; Hydrogels: synthesis, properties, applications
Authors: Chang Sub Kim | Harry L. Tuller
Source: Solid State Ionics (article, 2018-03-18)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Fine-tuning of oxygen vacancy and interstitial concentrations in La1.85Ce0.15CuO4+δ by electrical bias Oxygen ; Vacancy defect ; Materials science ; Chemistry ; Chemical physics ; Inorganic chemistry ; Condensed matter physics ; Crystallography ; Physics Magnetic and transport properties of perovskites and related materials ; Advancements in Solid Oxide Fuel Cells ; Electronic and Structural Properties of Oxides
Authors: F. Dalier | Galina V. Dubacheva | Marie Coniel | D. Zanchi | Anouk Galtayries | Matthieu Piel | Emmanuelle Marie | Christophe Tribet
Source: ACS Applied Materials & Interfaces (article, 2018-01-09)
Field: Materials Science — Surfaces, Coatings and Films

Mixed Copolymer Adlayers Allowing Reversible Thermal Control of Single Cell Aspect Ratio Dynamic guidance of living cells is achieved by fine-tuning and spatiotemporal modulation on artificial polymer layers enabling reversible peptide display. Adjustment of surface composition and interactions is obtained by coadsorption of mixed poly(lysine) derivatives, grafted with either repellent PEG, RGD adhesion peptides, or T-responsive poly(N-isopropylacrylamide) strands. Deposition of mixed adlayers provides a straightforward mean to optimize complex substrates, which is here implemented to achieve (1) thermal control of ligand accessibility and (2) adjustment of relative adhesiveness between adjacent micropatterns, while preserving cell attachment during thermal cycles. The reversible polarization of HeLa cells along orthogonal stripes mimics guidance along natural matrices. Materials science ; Copolymer ; Thermal ; Adhesion ; Polymer ; Chemical engineering ; Polarization (electrochemistry) ; Peptide ; HeLa ; Cell adhesion ; Nanotechnology ; Cell ; Chemistry ; Physical chemistry ; Composite material Polymer Surface Interaction Studies ; 3D Printing in Biomedical Research ; Nanofabrication and Lithography Techniques
Authors: Muhammed Açıkgöz | Czesław Rudowicz
Source: Polyhedron (article, 2018-05-03)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Temperature and pressure dependence of local structural changes around Gd 3+ centers in RAl 3 (BO 3 ) 4 crystals: Modeling zero-field splitting parameters Electron paramagnetic resonance ; Chemistry ; Zero field splitting ; Ion ; Superposition principle ; Paramagnetism ; Molecular physics ; Field (mathematics) ; Electron ; Condensed matter physics ; Nuclear magnetic resonance ; Spin polarization ; Physics Magnetism in coordination complexes ; Crystal Structures and Properties ; Lanthanide and Transition Metal Complexes
Authors: Ricardo F. Mendes | Ana D. G. Firmino | João P. C. Tomé | Filipe A. Almeida Paz
Source: Acta Crystallographica Section C Structural Chemistry (article, 2018-05-30)
Field: Chemistry — Inorganic Chemistry

Metal–organic framework assembled from erbium and a tetrapodal polyphosphonic acid organic linker A three-dimensional metal-organic framework (MOF), poly[[μ<sub>6</sub>-5'-pentahydrogen [1,1'-biphenyl]-3,3',5,5'-tetrayltetrakis(phosphonato)]erbium(III)] 2.5-hydrate], formulated as [Er(C<sub>12</sub>H<sub>11</sub>O<sub>12</sub>P<sub>4</sub>)]·2.5H<sub>2</sub>O or [Er(H<sub>5</sub>btp)]·2.5H<sub>2</sub>O (I) and isotypical with a Y<sup>3+</sup>-based MOF reported previously by our research group [Firmino et al. (2017b). Inorg. Chem. 56, 1193-1208], was constructed based solely on Er<sup>3+</sup> and on the polyphosphonic organic linker [1,1'-biphenyl]-3,3',5,5'-tetrakis(phosphonic acid) (H<sub>8</sub>btp). The present work describes our efforts to introduce lanthanide cations into the flexible network, demonstrating that, on the one hand, the compound can be obtained using three distinct experimental methods, i.e. hydro(solvo)thermal (Hy), microwave-assisted (MW) and one-pot (Op), and, on the other hand, that crystallite size can be approximately fine-tuned according to the method employed. MOF I contains hexacoordinated Er<sup>3+</sup> cations which are distributed in a zigzag inorganic chain running parallel to the [100] direction of the unit cell. The chains are, in turn, bridged by the anionic organic linker to form a three-dimensional 6,6-connected binodal network. This connectivity leads to the existence of one-dimensional channels (also running parallel to the [100] direction) filled with disordered and partially occupied water molecules of crystalization which are engaged in O-H...O hydrogen-bonding interactions with the [Er(H<sub>5</sub>btp)] framework. Additional weak π-π interactions [intercentroid distance = 3.957 (7) Å] exist between aromatic rings, which help to maintain the structural integrity of the network. Linker ; Lanthanide ; Biphenyl ; Chemistry ; Metal-organic framework ; Zigzag ; Hydrogen bond ; Binodal ; Metal ; Molecule ; Crystallography ; Crystallite ; Hydrate ; Ion ; Organic chemistry ; Phase (matter) ; Computer science Metal-Organic Frameworks: Synthesis and Applications ; Chemical Synthesis and Characterization ; Lanthanide and Transition Metal Complexes