jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Rie Nygaard | Chris L. B. Graham | Meagan Belcher Dufrisne | Jonathan D. Colburn | Joseph G. Pepe | Molly Hydorn | Silvia Corradi | Chelsea M. Brown | Khuram U. Ashraf | Owen N. Vickery | Nicholas S. Briggs | John J. Deering | Brian Kloss | Bruno Botta | Oliver B. Clarke | Linda Columbus | Jonathan Dworkin | Phillip J. Stansfeld | David I. Roper | Filippo Mancia
Source: Nature Communications (article, 2023-08-24)
Field: Materials Science — Materials Chemistry

Structural basis of peptidoglycan synthesis by E. coli RodA-PBP2 complex Peptidoglycan (PG) is an essential structural component of the bacterial cell wall that is synthetized during cell division and elongation. PG forms an extracellular polymer crucial for cellular viability, the synthesis of which is the target of many antibiotics. PG assembly requires a glycosyltransferase (GT) to generate a glycan polymer using a Lipid II substrate, which is then crosslinked to the existing PG via a transpeptidase (TP) reaction. A Shape, Elongation, Division and Sporulation (SEDS) GT enzyme and a Class B Penicillin Binding Protein (PBP) form the core of the multi-protein complex required for PG assembly. Here we used single particle cryo-electron microscopy to determine the structure of a cell elongation-specific E. coli RodA-PBP2 complex. We combine this information with biochemical, genetic, spectroscopic, and computational analyses to identify the Lipid II binding sites and propose a mechanism for Lipid II polymerization. Our data suggest a hypothesis for the movement of the glycan strand from the Lipid II polymerization site of RodA towards the TP site of PBP2, functionally linking these two central enzymatic activities required for cell wall peptidoglycan biosynthesis. Peptidoglycan ; Biology ; Computational biology ; Microbiology ; Chemistry ; Cell wall ; Genetics Enzyme Structure and Function ; Protein Structure and Dynamics ; Bacterial Genetics and Biotechnology
Authors: Jiahang Zhou | Ruiyang Li | Tengfei Luo
Source: npj Computational Materials (article, 2023-11-24)
Field: Materials Science — Materials Chemistry

Physics-informed neural networks for solving time-dependent mode-resolved phonon Boltzmann transport equation Abstract The phonon Boltzmann transport equation (BTE) is a powerful tool for modeling and understanding micro-/nanoscale thermal transport in solids, where Fourier’s law can fail due to non-diffusive effect when the characteristic length/time is comparable to the phonon mean free path/relaxation time. However, numerically solving phonon BTE can be computationally costly due to its high dimensionality, especially when considering mode-resolved phonon properties and time dependency. In this work, we demonstrate the effectiveness of physics-informed neural networks (PINNs) in solving time-dependent mode-resolved phonon BTE. The PINNs are trained by minimizing the residual of the governing equations, and boundary/initial conditions to predict phonon energy distributions, without the need for any labeled training data. The results obtained using the PINN framework demonstrate excellent agreement with analytical and numerical solutions. Moreover, after offline training, the PINNs can be utilized for online evaluation of transient heat conduction, providing instantaneous results, such as temperature distribution. It is worth noting that the training can be carried out in a parametric setting, allowing the trained model to predict phonon transport in arbitrary values in the parameter space, such as the characteristic length. This efficient and accurate method makes it a promising tool for practical applications such as the thermal management design of microelectronics. Phonon ; Boltzmann equation ; Statistical physics ; Thermal conduction ; Curse of dimensionality ; Relaxation (psychology) ; Physics ; Mean free path ; Artificial neural network ; Computer science ; Artificial intelligence ; Scattering ; Optics ; Quantum mechanics Thermal properties of materials ; Model Reduction and Neural Networks ; Heat Transfer and Optimization
Authors: Magdalena Błachnio | Krzysztof Kuśmierek | Andrzej Świątkowski | Anna Deryło‐Marczewska
Source: Molecules (review, 2023-07-14)
Field: Chemistry — Analytical Chemistry

Adsorption of Phenoxyacetic Herbicides from Water on Carbonaceous and Non-Carbonaceous Adsorbents The increasing consumption of phenoxyacetic acid-derived herbicides is becoming a major public health and environmental concern, posing a serious challenge to existing conventional water treatment systems. Among the various physicochemical and biological purification processes, adsorption is considered one of the most efficient and popular techniques due to its high removal efficiency, ease of operation, and cost effectiveness. This review article provides extensive literature information on the adsorption of phenoxyacetic herbicides by various adsorbents. The purpose of this article is to organize the scattered information on the currently used adsorbents for herbicide removal from the water, such as activated carbons, carbon and silica adsorbents, metal oxides, and numerous natural and industrial waste materials known as low-cost adsorbents. The adsorption capacity of these adsorbents was compared for the two most popular phenoxyacetic herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D) and 2-methyl-4-chlorophenoxyacetic acid (MCPA). The application of various kinetic models and adsorption isotherms in describing the removal of these herbicides by the adsorbents was also presented and discussed. At the beginning of this review paper, the most important information on phenoxyacetic herbicides has been collected, including their classification, physicochemical properties, and occurrence in the environment. Adsorption ; MCPA ; Chemistry ; Activated carbon ; Environmental chemistry ; Environmental science ; Organic chemistry ; Pesticide Analytical chemistry methods development ; Pesticide and Herbicide Environmental Studies ; Electrochemical sensors and biosensors
Authors: Tiandong Zhang | Zhuangzhuang Shi | Chao Yin | Changhai Zhang | Yue Zhang | Yongquan Zhang | Qingguo Chen | Qingguo Chi
Source: Journal of Advanced Ceramics (article, 2023-02-17)
Field: Materials Science — Materials Chemistry

Tunable polarization-drived superior energy storage performance in PbZrO <sub>3</sub> thin films Antiferroelectric PbZrO<sub>3</sub> films have great potential to be used as the energy storage dielectrics due to the unique electric field-induced phase transition character. But the phase transition process always accompanies polarization hysteresis effect that induces large energy loss and lowers the breakdown strength, leading to inferior energy storage density as well as low efficiency. In this work, the synergistical strategies by doping smaller ions of Li<sup>+</sup>-Al<sup>3+</sup> to substitute Pb<sup>2+</sup> and lowering the annealing temperature from 700℃ to 550℃ are proposed to change the microstructure and tune the polarization character of PbZrO<sub>3</sub> films, excepting to dramatically improve the energy storage performances. The prepared Pb<sub>(1-x)</sub>(Li<sub>0.5</sub>Al<sub>0.5</sub>)<sub>x</sub>ZrO<sub>3 </sub>(abbreviated as P<sub>(1-x)</sub>(L<sub>0.5</sub>A<sub>0.5</sub>)<sub>x</sub>ZO) films exhibit ferroelectric-like (<em>FE</em>) rather than antiferroelectric (<em>AFE</em>) character once the doping content of Li<sup>+</sup>-Al<sup>3+</sup> ions reaches 6 mol%, accompanying a significant improvement of energy storage density of 49.09 J/cm<sup>3</sup>,<sup> </sup>but energy storage efficiency is only 47.94% due to the long-correlation of ferroelectric domains. Accordingly, the low-temperature annealing is carried out to reduce the crystalline degree and the polarization loss. P<sub>0.94</sub>(L<sub>0.5</sub>A<sub>0.5</sub>)<sub>0.06</sub>ZO films annealed at 550℃ deliver a linear-like polarization rather than ferroelectric-like behavior annealed at 700℃, the lowered remanent polarization as well as improved breakdown strength (4814 kV/cm) result in the superior energy storage density of 58.7 J/cm<sup>3</sup> and efficiency of 79.16%, simultaneously possessing excellent frequency and temperature stability, and good electric fatigue tolerance. Ferroelectricity ; Annealing (glass) ; Materials science ; Analytical Chemistry (journal) ; Doping ; Dielectric ; Thin film ; Crystallography ; Mineralogy ; Chemistry ; Nanotechnology ; Optoelectronics ; Metallurgy Ferroelectric and Piezoelectric Materials ; Multiferroics and related materials ; Transition Metal Oxide Nanomaterials
Authors: Ryan D. Cohen | Jared S. Wood | Yu‐hong Lam | Alexei V. Buevich | Edward C. Sherer | Mikhail Reibarkh | R. Thomas Williamson | Gary E. Martin
Source: Molecules (article, 2023-03-07)
Field: Chemistry — Spectroscopy

DELTA50: A Highly Accurate Database of Experimental 1H and 13C NMR Chemical Shifts Applied to DFT Benchmarking Density functional theory (DFT) benchmark studies of <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured <sup>1</sup>H and <sup>13</sup>C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for <sup>1</sup>H and <sup>13</sup>C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for <sup>1</sup>H and 0.5 to 2.9 for <sup>13</sup>C. Maximum deviations were less than 0.5 and 6.5 ppm for <sup>1</sup>H and <sup>13</sup>C, respectively. Chemical shift ; Polarizable continuum model ; Carbon-13 NMR ; Density functional theory ; Chemistry ; Basis set ; Atomic orbital ; Molecule ; Computational chemistry ; Solvent effects ; Solvent ; Physical chemistry ; Physics ; Organic chemistry ; Quantum mechanics Molecular spectroscopy and chirality ; Computational Drug Discovery Methods ; Metabolomics and Mass Spectrometry Studies
Authors: Rongqin Chen | Fei Liu | Chu Zhang | Wei Wang | Rui Yang | Yiying Zhao | Jiyu Peng | Wenwen Kong | Jing Huang
Source: Frontiers in Plant Science (review, 2023-03-21)
Field: Chemistry — Analytical Chemistry

Trends in digital detection for the quality and safety of herbs using infrared and Raman spectroscopy Herbs have been used as natural remedies for disease treatment, prevention, and health care. Some herbs with functional properties are also used as food or food additives for culinary purposes. The quality and safety inspection of herbs are influenced by various factors, which need to be assessed in each operation across the whole process of herb production. Traditional analysis methods are time-consuming and laborious, without quick response, which limits industry development and digital detection. Considering the efficiency and accuracy, faster, cheaper, and more environment-friendly techniques are highly needed to complement or replace the conventional chemical analysis methods. Infrared (IR) and Raman spectroscopy techniques have been applied to the quality control and safety inspection of herbs during the last several decades. In this paper, we generalize the current application using IR and Raman spectroscopy techniques across the whole process, from raw materials to patent herbal products. The challenges and remarks were proposed in the end, which serve as references for improving herb detection based on IR and Raman spectroscopy techniques. Meanwhile, make a path to driving intelligence and automation of herb products factories. Herb ; Computer science ; Quality (philosophy) ; Raman spectroscopy ; Biochemical engineering ; Process engineering ; Medicinal herbs ; Process (computing) ; Risk analysis (engineering) ; Traditional medicine ; Engineering ; Business ; Medicine ; Physics Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Identification and Quantification in Food
Authors: Daniel Wines | Kamal Choudhary | Francesca Tavazza
Source: The Journal of Physical Chemistry C (article, 2023-01-09)
Field: Materials Science — Materials Chemistry

Systematic DFT+U and Quantum Monte Carlo Benchmark of Magnetic Two-Dimensional (2D) CrX<sub>3</sub> (X = I, Br, Cl, F) The search for two-dimensional (2D) magnetic materials has attracted a great deal of attention because of the experimental synthesis of 2D CrI<sub>3</sub>, which has a measured Curie temperature of 45 K. Often times, these monolayers have a higher degree of electron correlation and require more sophisticated methods beyond density functional theory (DFT). Diffusion Monte Carlo (DMC) is a correlated electronic structure method that has been demonstrated to be successful for calculating the electronic and magnetic properties of a wide variety of 2D and bulk systems, since it has a weaker dependence on the Hubbard parameter (<i>U</i>) and density functional. In this study, we designed a workflow that combines DFT +U and DMC in order to treat 2D correlated magnetic systems. We chose monolayer CrX<sub>3</sub> (X = I, Br, Cl, F), with a stronger focus on CrI<sub>3</sub> and CrBr<sub>3</sub>, as a case study due to the fact that they have been experimentally realized and have a finite critical temperature. With this DFT+U and DMC workflow and the analytical method of Torelli and Olsen, we estimated a maximum value of 43.56 K for the <i>T<sub>c</sub></i> of CrI<sub>3</sub> and 20.78 K for the <i>T<sub>c</sub></i> of CrBr<sub>3</sub>, in addition to analyzing the spin densities and magnetic properties with DMC and DFT+U. We expect that running this workflow for a well-known material class will aid in the future discovery and characterization of lesser known and more complex correlated 2D magnetic materials. Density functional theory ; Quantum Monte Carlo ; Monolayer ; Condensed matter physics ; Workflow ; Monte Carlo method ; Curie temperature ; Hubbard model ; Materials science ; Electronic structure ; Chemistry ; Physics ; Ferromagnetism ; Computational chemistry ; Computer science ; Nanotechnology ; Mathematics 2D Materials and Applications ; Machine Learning in Materials Science ; Heusler alloys: electronic and magnetic properties
Authors: Paul Seibert | Alexander Raßloff | Karl A. Kalina | Joachim Gussone | Katrin Bugelnig | Martin Diehl | Markus Kästner
Source: Computer Methods in Applied Mechanics and Engineering (article, 2023-05-15)
Field: Materials Science — Materials Chemistry

Two-stage 2D-to-3D reconstruction of realistic microstructures: Implementation and numerical validation by effective properties Microscale chemistry ; Computer science ; Microstructure ; Algorithm ; Tomography ; Smoothness ; Computational science ; Artificial intelligence ; Mathematics ; Materials science ; Mathematical analysis ; Physics Machine Learning in Materials Science ; Hydrocarbon exploration and reservoir analysis ; Enhanced Oil Recovery Techniques
Authors: Alfredo Fiorentino | Paolo Pegolo | Stefano Baroni
Source: npj Computational Materials (article, 2023-08-26)
Field: Materials Science — Materials Chemistry

Hydrodynamic finite-size scaling of the thermal conductivity in glasses Abstract In the past few years, the theory of thermal transport in amorphous solids has been substantially extended beyond the Allen-Feldman model. The resulting formulation, based on the Green-Kubo linear response or the Wigner-transport equation, bridges this model for glasses with the traditional Boltzmann kinetic approach for crystals. The computational effort required by these methods usually scales as the cube of the number of atoms, thus severely limiting the size range of computationally affordable glass models. Leveraging hydrodynamic arguments, we show how this issue can be overcome through a simple formula to extrapolate a reliable estimate of the bulk thermal conductivity of glasses from finite models of moderate size. We showcase our findings for realistic models of paradigmatic glassy materials. Thermal conductivity ; Statistical physics ; Scaling ; Limiting ; Range (aeronautics) ; Simple (philosophy) ; Thermal ; Boltzmann equation ; Boltzmann constant ; Kinetic energy ; Amorphous solid ; Cube (algebra) ; Kinetic theory ; Physics ; Materials science ; Mathematics ; Thermodynamics ; Classical mechanics ; Chemistry ; Geometry Material Dynamics and Properties ; Glass properties and applications ; Theoretical and Computational Physics
Authors: Tony Collins | Georges Feller
Source: Essays in Biochemistry (article, 2023-04-06)
Field: Materials Science — Materials Chemistry

Psychrophilic enzymes: strategies for cold-adaptation Psychrophilic organisms thriving at near-zero temperatures synthesize cold-adapted enzymes to sustain cell metabolism. These enzymes have overcome the reduced molecular kinetic energy and increased viscosity inherent to their environment and maintained high catalytic rates by development of a diverse range of structural solutions. Most commonly, they are characterized by a high flexibility coupled with an intrinsic structural instability and reduced substrate affinity. However, this paradigm for cold-adaptation is not universal as some cold-active enzymes with high stability and/or high substrate affinity and/or even an unaltered flexibility have been reported, pointing to alternative adaptation strategies. Indeed, cold-adaptation can involve any of a number of a diverse range of structural modifications, or combinations of modifications, depending on the enzyme involved, its function, structure, stability, and evolutionary history. This paper presents the challenges, properties, and adaptation strategies of these enzymes. Psychrophile ; Adaptation (eye) ; Flexibility (engineering) ; Enzyme ; Substrate (aquarium) ; Thriving ; Biology ; Biochemistry ; Biophysics ; Ecology Enzyme Structure and Function ; Metalloenzymes and iron-sulfur proteins ; Enzyme function and inhibition
Authors: Carl E. Krill | Elizabeth A. Holm | Jules M. Dake | Ryan Cohn | Karolína Holíková | Fabian Andorfer
Source: Annual Review of Materials Research (article, 2023-05-01)
Field: Materials Science — Materials Chemistry

Extreme Abnormal Grain Growth: Connecting Mechanisms to Microstructural Outcomes If variety is the spice of life, then abnormal grain growth (AGG) may be the materials processing equivalent of sriracha sauce. Abnormally growing grains can be prismatic, dendritic, or practically any shape in between. When they grow at least an order of magnitude larger than their neighbors in the matrix—a state we call extreme AGG—we can examine the abnormal/matrix interface for clues to the underlying mechanism. Simulating AGG for various formulations of the grain boundary (GB) equation of motion, we show that anisotropies in GB mobility and energy leave a characteristic fingerprint in the abnormal/matrix boundary. Except in the case of prismatic growth, the morphological signature of most reported instances of AGG is consistent with a certain degree of GB mobility variability. Open questions remain, however, concerning the mechanism by which the corresponding growth advantage is established and maintained as the GBs of abnormal grains advance through the matrix. Grain boundary ; Matrix (chemical analysis) ; Abnormal grain growth ; Materials science ; Grain growth ; Anisotropy ; Boundary (topology) ; Crystallography ; Biological system ; Microstructure ; Composite material ; Biology ; Physics ; Mathematics ; Chemistry ; Mathematical analysis ; Optics Material Dynamics and Properties ; Rheology and Fluid Dynamics Studies ; Polymer crystallization and properties
Authors: Siqi Wang | Tongqi Wen | Jian Han | David J. Srolovitz
Source: npj Computational Materials (article, 2023-12-07)
Field: Materials Science — Materials Chemistry

Coherent and semicoherent α/β interfaces in titanium: structure, thermodynamics, migration Abstract The α / β interface is central to the microstructure and mechanical properties of titanium alloys. We investigate the structure, thermodynamics and migration of the coherent and semicoherent Ti α / β interfaces as a function of temperature and misfit strain via molecular dynamics (MD) simulations, thermodynamic integration and an accurate, DFT-trained Deep Potential. The structure of an equilibrium semicoherent interface consists of an array of steps, an array of misfit dislocations, and coherent terraces. Analysis determines the dislocation and step (disconnection) array structure and habit plane. The MD simulations show the detailed interface morphology dictated by intersecting disconnection arrays. The steps are shown to facilitate α / β interface migration, while the misfit dislocations lead to interface drag; the drag mechanism is different depending on the direction of interface migration. These results are used to predict the nature of α phase nucleation on cooling through the α - β phase transition. Nucleation ; Solvent drag ; Materials science ; Dislocation ; Disconnection ; Microstructure ; Interface (matter) ; Phase (matter) ; Drag ; Titanium aluminide ; Molecular dynamics ; Titanium ; Chemical physics ; Thermodynamics ; Condensed matter physics ; Chemistry ; Physics ; Composite material ; Metallurgy ; Computational chemistry ; Intermetallic Titanium Alloys Microstructure and Properties ; Nuclear Materials and Properties ; Metal and Thin Film Mechanics
Authors: Michael Adesokan | Emmanuel Oladeji Alamu | Bolanle Otegbayo | Busie Maziya‐Dixon
Source: Applied Sciences (review, 2023-04-22)
Field: Chemistry — Analytical Chemistry

A Review of the Use of Near-Infrared Hyperspectral Imaging (NIR-HSI) Techniques for the Non-Destructive Quality Assessment of Root and Tuber Crops Hyperspectral imaging (HSI) is one of the most often used techniques for rapid quality evaluation for various applications. It is a non-destructive technique that effectively evaluates the quality attributes of root and tuber crops, including yam and cassava, and their food products. Hyperspectral imaging technology, which combines spectroscopy and imaging principles, has an advantage over conventional spectroscopy due to its ability to simultaneously evaluate the physical characteristics and chemical components of various food products and specify their spatial distributions. HSI has demonstrated significant potential for obtaining quick information regarding the chemical composition of the root and tuber, such as starch, protein, dry matter, amylose, and soluble sugars, as well as physical characteristics such as textural properties and water binding capacity. This review highlights the principles of near-infrared hyperspectral imaging (NIR-HSI) techniques combined with relevant image processing tools. It then provides cases of its application in determining crucial biochemical quality traits and textural attributes of roots and tuber crops, focusing on cassava and yam. The need for more information on using NIR-HSI in the quality evaluation of yam and cassava was underscored. It also presents the challenges and prospects of this technology. Hyperspectral imaging ; Amylose ; Chemical imaging ; Near-infrared spectroscopy ; Agricultural engineering ; Remote sensing ; Environmental science ; Starch ; Computer science ; Artificial intelligence ; Food science ; Chemistry ; Biology ; Geography ; Engineering Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Date Palm Research Studies