jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Derek Mendez | Robert Bolotovsky | Asmit Bhowmick | Aaron S. Brewster | Jan Kern | Junko Yano | James M. Holton | Nicholas K. Sauter
Source: IUCrJ (article, 2020-10-23)
Field: Materials Science — Materials Chemistry

Beyond integration: modeling every pixel to obtain better structure factors from stills Most crystallographic data processing methods use pixel integration. In serial femtosecond crystallography (SFX), the intricate interaction between the reciprocal lattice point and the Ewald sphere is integrated out by averaging symmetrically equivalent observations recorded across a large number (10<sup>4</sup>-10<sup>6</sup>) of exposures. Although sufficient for generating biological insights, this approach converges slowly, and using it to accurately measure anomalous differences has proved difficult. This report presents a novel approach for increasing the accuracy of structure factors obtained from SFX data. A physical model describing all observed pixels is defined to a degree of complexity such that it can decouple the various contributions to the pixel intensities. Model dependencies include lattice orientation, unit-cell dimensions, mosaic structure, incident photon spectra and structure factor amplitudes. Maximum likelihood estimation is used to optimize all model parameters. The application of prior knowledge that structure factor amplitudes are positive quantities is included in the form of a reparameterization. The method is tested using a synthesized SFX dataset of ytterbium(III) lysozyme, where each X-ray laser pulse energy is centered at 9034 eV. This energy is 100 eV above the Yb<sup>3+</sup> <i>L</i>-III absorption edge, so the anomalous difference signal is stable at 10 electrons despite the inherent energy jitter of each femtosecond X-ray laser pulse. This work demonstrates that this approach allows the determination of anomalous structure factors with very high accuracy while requiring an order-of-magnitude fewer shots than conventional integration-based methods would require to achieve similar results. Pixel ; Amplitude ; Femtosecond ; Physics ; Computer science ; Lattice (music) ; Structure factor ; Laser ; Algorithm ; Optics ; Computational physics Enzyme Structure and Function ; Advanced X-ray Imaging Techniques ; Advanced Electron Microscopy Techniques and Applications
Authors: Kevin Yang | Wengong Jin | Kyle Swanson | Regina Barzilay | Tommi Jaakkola
Source: ChemRxiv (article, 2020-02-12)
Field: Materials Science — Materials Chemistry

Improving Molecular Design by Stochastic Iterative Target Augmentation Generative models in molecular design tend to be richly parameterized, data-hungry neural models, as they must create complex structured objects as outputs. Estimating such models from data may be challenging due to the lack of sufficient training data. In this paper, we propose a surprisingly effective self-training approach for iteratively creating additional molecular targets. We first pre-train the generative model together with a simple property predictor. The property predictor is then used as a likelihood model for filtering candidate structures from the generative model. Additional targets are iteratively produced and used in the course of stochastic EM iterations to maximize the log-likelihood that the candidate structures are accepted. A simple rejection (re-weighting) sampler suffices to draw posterior samples since the generative model is already reasonable after pre-training. We demonstrate significant gains over strong baselines for both unconditional and conditional molecular design. In particular, our approach outperforms the previous state-of-the-art in conditional molecular design by over 10% in absolute gain. Computer science ; Generative model ; Generative grammar ; Simple (philosophy) ; Parameterized complexity ; Weighting ; Machine learning ; Property (philosophy) ; Artificial intelligence ; Sequential analysis ; Training set ; Generative Design ; Algorithm ; Data mining ; Mathematics ; Statistics ; Engineering Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Chemical Synthesis and Analysis
Authors: Zhang Yingzhe | Yudao Chen | Juan Li | Wei Li | Ding Chen | Qingdong Qin
Source: Materials (article, 2020-01-30)
Field: Chemistry — Organic Chemistry

Formation of Cu2O Solid Solution via High-Frequency Electromagnetic Field-Assisted Ball Milling: The Reaction Mechanism The contamination of environmental water with organic pollutants poses significant challenges for society, and much effort has been directed toward the development of catalysts and methods that can decompose these pollutants. While effort has been directed toward the fabrication of Cu<sub>2</sub>O catalysts by ball milling, this technique can involve long preparation times and provide low yields. In this study, we synthesized a solid solution of Cu<sub>2</sub>O in 22 h by high-frequency electric-field-assisted ball milling below 40 °C in only one step under aqueous conditions. We investigated the catalytic activities of the produced Cu<sub>2</sub>O solid solution in the microwave-assisted degradation of dyes, namely rhodamine B, phenol red and methyl orange. The prepared Cu<sub>2</sub>O solid solution was very catalytically active and completely degraded the above-mentioned dyes within 2 min. The one-dimensional diffusion model and the phase boundary (planar) model were found to describe the kinetics well. Synergism between ball milling and the high-frequency electromagnetic field plays a key role in the preparation of Cu<sub>2</sub>O solid solution nanoparticles. Ball milling facilitates the relaxation of the Cu<sub>2</sub>O lattice and high-frequency electromagnetic radiation accelerates the diffusion of Fe atoms into the Cu<sub>2</sub>O crystal along the (111) crystal plane, quickly leading to the formation of a Cu<sub>2</sub>O solid solution. Materials science ; Solid solution ; Aqueous solution ; Ball mill ; Methyl orange ; Rhodamine B ; Catalysis ; Phenol ; Chemical engineering ; Photocatalysis ; Chemistry ; Composite material ; Metallurgy ; Organic chemistry Nanomaterials for catalytic reactions ; Copper-based nanomaterials and applications ; Advanced materials and composites
Authors: Mansouri Taki Eddine Mohammed | Djamel Nibou | Trari Mohamed | Samira Amokrane
Source: Water Science & Technology (article, 2020-11-27)
Field: Chemistry — Inorganic Chemistry

Study of the adsorption of an organic pollutant onto a microporous metal organic framework In this study, the microporous metal organic framework-5 (MOF-5) has been synthesized to be used to remove methyl orange by adsorption. The adsorption experiments exhibit a good adsorption capacity at a catalyst dose of 0.1 g L<sup>-1</sup> and for an initial concentration of 200 mg L<sup>-1</sup>, whereas the performance is stable over a wide pH range. The equilibrium adsorption data showed a sigmoidal course, which is well fitted by the Dubinin-Astakhov model applicable for physical adsorption processes (E = 0.055 kJ mol<sup>-1</sup>) onto heterogeneous surfaces and a more homogeneous pore structure (n = 9.9), with a maximum adsorption capacity of 1248.35 mg g<sup>-1</sup>. As can be observed from the evaluation of the kinetic data, the surface of the adsorbent is heterogeneous with different active sites for methyl orange (MO) adsorption. Moreover, based on the rate constant, it can be suggested that there is a specific interaction like electrostatic interaction between MO and the adsorbent for rapid and high uptake of the dye, whereas the adsorption phenomenon is reversible. According to the adsorption mechanisms, intra-particle and film diffusion models simultaneously controlled the rate sorption, which was confirmed by the calculated intra-particle diffusion and the film diffusion coefficients. The evaluation of the thermodynamic parameters revealed that the MO adsorption is spontaneous, endothermic and the randomness increases with the adsorption of MO. Adsorption ; Microporous material ; Endothermic process ; Sorption ; Chemistry ; Diffusion ; Metal-organic framework ; Methyl orange ; Chemical engineering ; Inorganic chemistry ; Thermodynamics ; Catalysis ; Organic chemistry Metal-Organic Frameworks: Synthesis and Applications ; Adsorption and biosorption for pollutant removal ; Dendrimers and Hyperbranched Polymers
Authors: Changdong Yin | Jianjun Chen | Dongdong Ye | Zhou Xu | Jiahao Ge | Haiting Zhou
Source: Materials (article, 2020-05-14)
Field: Materials Science — Metals and Alloys

Hydrogen Concentration Distribution in 2.25Cr-1Mo-0.25V Steel under the Electrochemical Hydrogen Charging and Its Influence on the Mechanical Properties The deterioration of the mechanical properties of metal induced by hydrogen absorption threatens the safety of the equipment serviced in hydrogen environments. In this study, the hydrogen concentration distribution in 2.25Cr-1Mo-0.25V steel after hydrogen charging was analyzed following the hydrogen permeation and diffusion model. The diffusible hydrogen content in the 1-mm-thick specimen and its influence on the mechanical properties of the material were investigated by glycerol gas collecting test, static hydrogen charging tensile test, scanning electron microscopy (SEM) test, and microhardness test. The results indicate that the content of diffusible hydrogen tends to be the saturation state when the hydrogen charging time reaches 48 h. The simulation results suggest that the hydrogen concentration distribution can be effectively simulated by ABAQUS and the method can be used to analyze the hydrogen concentration in the material with complex structures or containing multiple microstructures. The influence of hydrogen on the mechanical properties is that the elongation of this material is reduced and the diffusible hydrogen will cause a decrease in the fracture toughness of the material, and thus hydrogen embrittlement (HE) will occur. Moreover, the Young's modulus E and microhardness are increased due to hydrogen absorption, and the variation value is related to the hydrogen concentration introduced into the specimen. Hydrogen ; Hydrogen embrittlement ; Materials science ; Elongation ; Indentation hardness ; Electrochemistry ; Composite material ; Tensile testing ; Ultimate tensile strength ; Microstructure ; Metallurgy ; Corrosion ; Chemistry ; Electrode Hydrogen embrittlement and corrosion behaviors in metals ; Corrosion Behavior and Inhibition ; Non-Destructive Testing Techniques
Authors: Margarita Kostré | Christof Schütte | Frank Noé | Mauricio J. del Razo
Source: arXiv (Cornell University) (article, 2020-05-29)
Field: Materials Science — Materials Chemistry

Coupling particle-based reaction-diffusion simulations with reservoirs mediated by reaction-diffusion PDEs Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small to be relevant for life processes. Alternatively, particle-based reaction-diffusion models are currently the most accurate and computationally feasible approach at these scales. Their efficiency lies in modeling entire molecules as particles that can diffuse and interact with each other. In this work, we develop modeling and numerical schemes for particle-based reaction-diffusion in an open setting, where the reservoirs are mediated by reaction-diffusion PDEs. We derive two important theoretical results. The first one is the mean-field for open systems of diffusing particles; the second one is the mean-field for a particle-based reaction-diffusion system with second-order reactions. We employ these two results to develop a numerical scheme that consistently couples particle-based reaction-diffusion processes with reaction-diffusion PDEs. This allows modeling open biochemical systems in contact with reservoirs that are time-dependent and spatially inhomogeneous, as in many relevant real-world applications. Reaction–diffusion system ; Diffusion ; Coupling (piping) ; Particle (ecology) ; Particle method ; Coupling reaction ; Statistical physics ; Physics ; Mechanics ; Materials science ; Chemistry ; Thermodynamics ; Nuclear physics ; Geology ; Catalysis Block Copolymer Self-Assembly ; Advanced Mathematical Modeling in Engineering ; Nanopore and Nanochannel Transport Studies
Authors: Chenlin Li | Xiaogeng Tian | Tianhu He
Source: Archive of Applied Mechanics (article, 2020-04-24)
Field: Materials Science — Materials Chemistry

Size-dependent buckling analysis of Euler–Bernoulli nanobeam under non-uniform concentration Buckling ; Materials science ; Eigenvalues and eigenvectors ; Euler's formula ; Bernoulli's principle ; Elasticity (physics) ; Mechanics ; Work (physics) ; Timoshenko beam theory ; Mathematical analysis ; Mathematics ; Physics ; Vibration ; Composite material ; Thermodynamics ; Acoustics Nonlocal and gradient elasticity in micro/nano structures ; Thermoelastic and Magnetoelastic Phenomena ; Composite Structure Analysis and Optimization
Authors: Giuseppe Cavallaro | Leonardo Chiappisi | Michael Gradzielski | Giuseppe Lazzara
Source: Physical Chemistry Chemical Physics (article, 2020-01-01)
Field: Materials Science — Biomaterials

Effect of the supramolecular interactions on the nanostructure of halloysite/biopolymer hybrids: a comprehensive study by SANS, fluorescence correlation spectroscopy and electric birefringence The structural properties of halloysite/biopolymer aqueous mixtures were firstly investigated by means of combining different techniques, including small-angle neutron scattering (SANS), electric birefringence (EBR) and fluorescence correlation spectroscopy (FCS). Among the biopolymers, non-ionic hydroxypropylcellulose and polyelectrolytes (anionic alginate and cationic chitosan) were selected. On this basis, the specific supramolecular interactions were correlated to the structural behavior of the halloysite/biopolymer mixtures. SANS data were analyzed in order to investigate the influence of the biopolymer adsorption on the halloysite gyration radius. In addition, a morphological description of the biopolymer-coated halloysite nanotubes (HNTs) was obtained by the simulation of SANS curves. EBR experiments evidenced that the orientation dynamics of the nanotubes in the electric field is influenced by the specific interactions with the polymers. Namely, both variations of the polymer charge and/or wrapping mechanisms strongly affected the HNT alignment process and, consequently, the rotational mobility of the nanotubes. FCS measurements with fluorescently labeled biopolymers allowed us to study the aqueous dynamic behavior of ionic biopolymers after their adsorption onto the HNT surfaces. The combination of EBR and FCS results revealed that the adsorption process reduces the mobility in water of both components. These effects are strongly enhanced by HNT/polyelectrolyte electrostatic interactions and wrapping processes occurring in the halloysite/chitosan mixture. The attained findings can be useful for designing halloysite/polymer hybrids with controlled structural properties. Nanostructure ; Biopolymer ; Supramolecular chemistry ; Birefringence ; Materials science ; Halloysite ; Spectroscopy ; Fluorescence spectroscopy ; Fluorescence ; Nanoscopic scale ; Nanotechnology ; Chemical physics ; Chemistry ; Crystallography ; Optics ; Polymer ; Physics ; Composite material Clay minerals and soil interactions ; Iron oxide chemistry and applications ; Therapeutic Uses of Natural Elements
Authors: Zhimin Dong | Zhibin Zhang | Runze Zhou | Yayu Dong | Yuanyuan Wei | Zhijian Zheng | Youqun Wang | Ying Dai | Xiaohong Cao | Yunhai Liu
Source: RSC Advances (article, 2020-01-01)
Field: Chemistry — Inorganic Chemistry

Facile construction of Fe, N and P co-doped carbon spheres by carbothermal strategy for the adsorption and reduction of U(<scp>vi</scp>) In this work, nitrogen and phosphorus co-doped magnetic carbon spheres encapsulating well-dispersed active Fe nanocrystals (Fe/P-CN) were fabricated <i>via</i> a simple copolymer pyrolysis strategy. Benefiting from heteroatoms doping, Fe/P-CN could primarily adsorb soluble U(vi) ions through abundant functional groups, and subsequently, the adsorbed U(vi) could be reduced to insoluble U(iv) by Fe nanocrystals. Fe/P-CN pyrolyzed at 800 °C (Fe/P-CN-800) exhibited excellent U(vi) removal capacity of 306.76 mg g<sup>-1</sup>, surpassing nitrogen and phosphorus co-doped carbon spheres and nano zero-valent iron. In addition, the magnetic separation and thermal reactivation properties endow Fe/P-CN-800 with excellent reusability. This research, especially, provides a promising synergistic adsorption and reduction strategy to effectively remove U(vi) using heteroatom-doped composites. Heteroatom ; Adsorption ; Pyrolysis ; Carbothermic reaction ; Carbon fibers ; Chemical engineering ; Nitrogen ; Thermal decomposition ; Doping ; Inorganic chemistry ; Chemistry ; Mesoporous material ; Materials science ; Phosphorus ; Nuclear chemistry ; Catalysis ; Organic chemistry ; Composite number ; Carbide ; Composite material Radioactive element chemistry and processing ; Geochemistry and Elemental Analysis ; Nuclear Materials and Properties
Authors: Agin Vyas | Kun Wang | Qi Li | Amin M. Saleem | Maria Bylund | Rickard Andersson | Vincent Desmaris | Anderson D. Smith | Per Lundgren | Peter Enoksson
Source: RSC Advances (article, 2020-01-01)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Impact of electrode geometry and thickness on planar on-chip microsupercapacitors We report an assessment of the influence of both finger geometry and vertically-oriented carbon nanofiber lengths in planar micro-supercapacitors. Increasing the finger number leads to an up-scaling in areal power densities, which increases with scan rate. Growing the nanofibers longer, however, does not lead to a proportional growth in capacitance, proposedly related to limited ion penetration of the electrode. Planar ; Supercapacitor ; Electrode ; Capacitance ; Materials science ; Penetration (warfare) ; Horizontal scan rate ; Scaling ; Carbon nanofiber ; Optoelectronics ; Nanofiber ; Chip ; Composite material ; Nanotechnology ; Geometry ; Electrical engineering ; Carbon nanotube ; Chemistry ; Cyclic voltammetry ; Electrochemistry ; Computer science Supercapacitor Materials and Fabrication ; Advancements in Battery Materials ; Graphene research and applications
Authors: François Parmentier
Source: Comptes Rendus Chimie (article, 2020-11-10)
Field: Chemistry — Spectroscopy

Effect of diffusional bridging in multicapillary packing The pressure drop required by available chromatography column packings constitutes an operational drawback. Some attempts to solve this problem have been directed toward the use of packings composed of a multiplicity of capillary tubes working in parallel, as a high factor of gain on the pressure drop appears possible. Unfortunately, the small differences in dimensions among individual capillaries have made this solution unpractical. In this study we show that the superimposition of a radial diffusive term between adjacent channels efficiently eliminates this limitation. The behavior becomes that of common particulate packing, with the benefit of a pressure drop that is lower by approximately one order of magnitude for identical characteristic dimensions. The effect is quantified for long retention times by a combination of theoretical, transfer function analysis and simulation studies. The reduced partial height equivalent to a theoretical plate (HETP) of the dispersion phenomena is given quantitatively by the following formula valid for high k when the mass transfer resistance of the stationary phase is negligible: <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="block"> <mml:mrow> <mml:mi>h</mml:mi> <mml:mo>=</mml:mo> <mml:mfrac> <mml:mrow> <mml:mn>2</mml:mn> <mml:mo>·</mml:mo> <mml:msubsup> <mml:mi>σ</mml:mi> <mml:mrow> <mml:mi mathvariant="normal">rel</mml:mi> </mml:mrow> <mml:mn>2</mml:mn> </mml:msubsup> </mml:mrow> <mml:mrow> <mml:mfrac> <mml:mn>1</mml:mn> <mml:mi>u</mml:mi> </mml:mfrac> <mml:mo>+</mml:mo> <mml:mfrac> <mml:mn>1</mml:mn> <mml:mrow> <mml:mn>2</mml:mn> <mml:mo>·</mml:mo> <mml:mi>l</mml:mi> </mml:mrow> </mml:mfrac> </mml:mrow> </mml:mfrac> </mml:mrow> </mml:math> Mass transfer ; Pressure drop ; Chemistry ; Capillary action ; Physics ; Thermodynamics ; Chromatography Analytical Chemistry and Chromatography ; Microfluidic and Capillary Electrophoresis Applications ; Protein purification and stability
Authors: Akiko Ueda | Yijin Zhang | Nobuyuki Sano | Hiroshi Imamura | Yoshihiro Iwasa
Source: npj Computational Materials (article, 2020-03-20)
Field: Materials Science — Materials Chemistry

Ambipolar device simulation based on the drift-diffusion model in ion-gated transition metal dichalcogenide transistors Abstract Ionic gating is known as a powerful tool for investigation of electronic functionalities stemming from low voltage transistor operation to gate-induced electronic phase control including superconductivity. Two-dimensional (2D) material is one of the archetypal channel materials which exhibit a variety of gate-induced phenomena. Nevertheless, the device simulations on such ion-gated transistor devices have never been reported, despite its importance for the future design of device structures. In this paper, we developed a drift-diffusion (DD) model on a 2D material, WSe 2 monolayer, attached with an ionic liquid, and succeeded in simulating the transport properties, potential profile, carrier density distributions in the transistor configuration. In particular, the simulation explains the ambipolar behavior with the gate voltage comparable to the band gap energy, as well as the formation of p-n junctions in the channel reported in several experimental papers. Such peculiar behavior becomes possible by the dramatic change of the potential profiles at the Schottky barrier by the ionic gating. The present result indicates that the DD model coupled to the Poisson equation is a fascinating platform to explain and predict further functionalities of ion-gated transistors through including the spin, valley, and optical degrees of freedom. Ambipolar diffusion ; Transistor ; Materials science ; Optoelectronics ; Ionic bonding ; Schottky barrier ; Diffusion ; Ion ; Nanotechnology ; Chemical physics ; Voltage ; Chemistry ; Electrical engineering ; Physics ; Diode ; Plasma ; Engineering 2D Materials and Applications ; MXene and MAX Phase Materials ; Graphene research and applications
Authors: Sobhan Patnaik
Source: Ceramics International (review, 2020-06-29)
Field: Materials Science — Materials Chemistry

Comparative analysis of temperature dependent properties of commercial nuclear fuel pellet and surrogates undergoing cracking: A review Materials science ; Pellets ; Cracking ; Pellet ; Yttria-stabilized zirconia ; Nuclear engineering ; Combustion ; Composite material ; Cubic zirconia ; Ceramic Nuclear Materials and Properties ; Nuclear reactor physics and engineering ; Nuclear materials and radiation effects