jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Cheng‐Wei Lee | Andriy Zakutayev | Vladan Stevanović
Source: arXiv (Cornell University) (preprint, 2023-12-18)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Computational insights into phase equilibria between wide-gap semiconductors and contact materials Novel wide-band-gap semiconductors are needed for next-generation power electronic but there is a gap between a promising material and a functional device. Finding stable contacts is one of the major challenges, which is currently dealt with mainly via trial and error. Herein, we computationally investigate the thermochemistry and phase co-existence at the junction between three wide gap semiconductors, $β$-Ga$_{2}$O$_{3}$, GeO$_2$, and GaN, and possible contact materials. The pool of possible contacts includes 47 elemental metals and 4 common $n$-type transparent conducting oxides (ZnO, TiO$_2$, SnO$_2$, and In$_2$O$_3$). We use first-principles thermodynamics to model the Gibbs free energies of chemical reactions as a function of the gas pressure (p$_{\mathrm{O}_2}$/p$_{\mathrm{N}_2}$) and equilibrium temperature. We deduce whether a semiconductor/contact interface will be stable at relevant conditions, possibly influencing the long-term reliability and performance of devices. We generally find that most elemental metals tend to oxidize or nitridize and form various interface oxide/nitride layers. Exceptions include select late- and post-transition metals, and in case of GaN also the alkali metals, which are predicted to exhibit stable coexistence, although in many cases at relatively low gas partial pressures. Similar is true for the transparent conducting oxides, for which in most cases we predict a preference toward forming ternary oxides when in contact with $β$-Ga$_{2}$O$_{3}$ and GeO$_{2}$. The only exception is SnO$_2$, which can form stable contacts with both oxides. Finally, we show how the same approach can be used to predict gas partial pressure vs. temperature phase diagrams to help direct synthesis of ternary compounds. We believe these results provide a valuable guidance in selecting contact materials to wide-gap semiconductors and suitable growth conditions. Ternary operation ; Semiconductor ; Thermochemistry ; Band gap ; Materials science ; Oxide ; Gibbs free energy ; Phase (matter) ; Condensed matter physics ; Thermodynamics ; Nanotechnology ; Chemical physics ; Chemistry ; Optoelectronics ; Physics ; Computer science ; Metallurgy Ga2O3 and related materials ; ZnO doping and properties ; Electronic and Structural Properties of Oxides
Authors: Sungjun Cho | Dae-Woong Jeong | Sung Moon Ko | Jinwoo Kim | Sehui Han | Seunghoon Hong | Honglak Lee | Moontae Lee
Source: arXiv (Cornell University) (preprint, 2023-09-08)
Field: Materials Science — Materials Chemistry

3D Denoisers are Good 2D Teachers: Molecular Pretraining via Denoising and Cross-Modal Distillation Pretraining molecular representations from large unlabeled data is essential for molecular property prediction due to the high cost of obtaining ground-truth labels. While there exist various 2D graph-based molecular pretraining approaches, these methods struggle to show statistically significant gains in predictive performance. Recent work have thus instead proposed 3D conformer-based pretraining under the task of denoising, which led to promising results. During downstream finetuning, however, models trained with 3D conformers require accurate atom-coordinates of previously unseen molecules, which are computationally expensive to acquire at scale. In light of this limitation, we propose D&amp;D, a self-supervised molecular representation learning framework that pretrains a 2D graph encoder by distilling representations from a 3D denoiser. With denoising followed by cross-modal knowledge distillation, our approach enjoys use of knowledge obtained from denoising as well as painless application to downstream tasks with no access to accurate conformers. Experiments on real-world molecular property prediction datasets show that the graph encoder trained via D&amp;D can infer 3D information based on the 2D graph and shows superior performance and label-efficiency against other baselines. Computer science ; Graph ; Modal ; Encoder ; Conformational isomerism ; Noise reduction ; Artificial intelligence ; Distillation ; Molecular graph ; Pattern recognition (psychology) ; Machine learning ; Algorithm ; Theoretical computer science ; Chemistry ; Molecule Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Various Chemistry Research Topics
Authors: Safa Q. Hussien | Mohamed M. El-Defrawy | Esam A. Gomaa | Marwa G. Elghalban
Source: Bulletin of the Chemical Society of Ethiopia (article, 2023-11-29)
Field: Chemistry — Electrochemistry

Determination of calcium in water samples by using Au-electrode in HCl solution in the absence and presence of a crystal violet and environmental studies The hydrochloric acid (HCl 0.1 M) supporting electrolyte was used in the electrochemical estimation cyclic voltammetry for CaCl2 concentrations also using crystal violet dye or (hexamethyl pararosaniline) as ligand. For oxidation and reduction waves, the potential range is 0.5 V, -0.5 V. The interaction of calcium ions with crystal violet was examined using several analytical estimates, and kinetic and thermodynamic parameters. The analytical concentration for calcium ions in different samples especially in Nile River were estimated in the range from 1.6 to 14.3 mmol. The estimation of calcium ion concentrations was achieved up to 11.49 mmol in waste water in Mansoura University. Applications were made for calcium estimation of different water samples and molecular docking of the calcium-crystal violet complex against the Hepatitis C viral proteins (4i33, 4KTC), roving strong bonds of interaction were observed. And anti-bacterial effect on calcium complex with crystal violet and face mask N-95 tissue.&#x0D; KEY WORDS: Calcium ions, Thermodynamic properties, Solvation parameters, Nile water samples, Anti-bacterial, Molecular docking&#x0D; Bull. Chem. Soc. Ethiop. 2024, 38(1), 43-54. DOI: https://dx.doi.org/10.4314/bcse.v38i1.4 Crystal violet ; Chemistry ; Calcium ; Nile blue ; Hydrochloric acid ; Solvation ; Crystal structure ; Electrolyte ; Inorganic chemistry ; Ion ; Crystal (programming language) ; Electrochemistry ; Nuclear chemistry ; Electrode ; Crystallography ; Physical chemistry ; Organic chemistry Electrochemical Analysis and Applications
Authors: Jakub Rydzewski | Ming Chen | Ómar Valsson
Source: arXiv (Cornell University) (review, 2023-03-15)
Field: Materials Science — Materials Chemistry

Manifold Learning in Atomistic Simulations: A Conceptual Review Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. Such practice is needed in atomistic simulations of complex systems where even thousands of degrees of freedom are sampled. An abundance of such data makes gaining insight into a specific physical problem strenuous. Our primary aim in this review is to focus on unsupervised machine learning methods that can be used on simulation data to find a low-dimensional manifold providing a collective and informative characterization of the studied process. Such manifolds can be used for sampling long-timescale processes and free-energy estimation. We describe methods that can work on datasets from standard and enhanced sampling atomistic simulations. Unlike recent reviews on manifold learning for atomistic simulations, we consider only methods that construct low-dimensional manifolds based on Markov transition probabilities between high-dimensional samples. We discuss these techniques from a conceptual point of view, including their underlying theoretical frameworks and possible limitations. Nonlinear dimensionality reduction ; Computer science ; Curse of dimensionality ; Dimensionality reduction ; Manifold (fluid mechanics) ; Sampling (signal processing) ; Statistical physics ; Degrees of freedom (physics and chemistry) ; Focus (optics) ; Process (computing) ; Machine learning ; Artificial intelligence ; Theoretical computer science ; Physics Machine Learning in Materials Science ; Protein Structure and Dynamics ; Theoretical and Computational Physics
Authors: Ekaterina Babich | Sergey Scherbak | Demid A. Kirilenko | Valeriy M. Kondratev | Daniil D. Stupin | A. A. Lipovskiĭ
Source: Journal of Physics D Applied Physics (article, 2023-12-06)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Glasses with biocompatible Au/Ag NPs of governed composition Abstract Silver-gold alloy nanoparticles were grown using heat treatment of soda-lime glass slides with depercolated gold film subjected to silver-to-sodium ion exchange. Varying the regime of the heat treatment allows one to control the proportion of silver in the nanoparticles and adjust the spectral position of their local surface plasmon resonance (LSPR) in the spectral range between the resonances of gold and silver nanoparticles. The position of LSPR in gold nanoparticles can be shifted by 15% via their dilution by silver in 50 wt % concentration. This shift is accompanied by only a 3% decrease in HeLa cell viability on the slides with alloy nanoparticles on the surface and by a slight decrease in the cell functionality/adhesion (FA) that show the biocompatibility of these nanoparticles. On the contrary, a notable decrease in the viability and ∼100% drop of FA were registered for the slides with purely silver nanoparticles. Surface plasmon resonance ; Nanoparticle ; Materials science ; Colloidal gold ; Biocompatibility ; Silver nanoparticle ; Alloy ; Adhesion ; Chemical engineering ; Nanotechnology ; Nuclear chemistry ; Chemistry ; Metallurgy ; Composite material Gold and Silver Nanoparticles Synthesis and Applications ; Laser-Ablation Synthesis of Nanoparticles ; Nanoparticles: synthesis and applications
Authors: Liuyan Li | Lingyu Wan | Changtai Xia | Qinglin Sai | Devki N. Talwar | Zhe Chuan Feng | Haoyue Liu | Jiang Jiang | Ping Li
Source: Materials (article, 2023-06-08)
Field: Materials Science — Electronic, Optical and Magnetic Materials

The Spatial Correlation and Anisotropy of β-(AlxGa1−x)2O3 Single Crystal The long-range crystallographic order and anisotropy in β-(Al<sub>x</sub>Ga<sub>1-x</sub>)<sub>2</sub>O<sub>3</sub> (x = 0.0, 0.06, 0.11, 0.17, 0.26) crystals, prepared by optical floating zone method with different Al composition, is systematically studied by spatial correlation model and using an angle-resolved polarized Raman spectroscopy. Alloying with aluminum is seen as causing Raman peaks to blue shift while their full widths at half maxima broadened. As x increased, the correlation length (CL) of the Raman modes decreased. By changing x, the CL is more strongly affected for low-frequency phonons than the modes in the high-frequency region. For each Raman mode, the CL is decreased by increasing temperature. The results of angle-resolved polarized Raman spectroscopy have revealed that the intensities of β-(Al<sub>x</sub>Ga<sub>1-x</sub>)<sub>2</sub>O<sub>3</sub> peaks are highly polarization dependent, with significant effects on the anisotropy with alloying. As the Al composition increased, the anisotropy of Raman tensor elements was enhanced for the two strongest phonon modes in the low-frequency range, while the anisotropy of the sharpest Raman phonon modes in the high-frequency region decreased. Our comprehensive study has provided meaningful results for comprehending the long-range orderliness and anisotropy in technologically important β-(Al<sub>x</sub>Ga<sub>1-x</sub>)<sub>2</sub>O<sub>3</sub> crystals. Anisotropy ; Single crystal ; Materials science ; Spatial correlation ; Correlation ; Crystal (programming language) ; Crystallography ; Condensed matter physics ; Optics ; Physics ; Chemistry ; Geometry ; Mathematics ; Computer science ; Statistics Ga2O3 and related materials ; ZnO doping and properties ; Microwave Dielectric Ceramics Synthesis
Authors: Dane R. Letourneau | Dennis D. August | Dietrich A. Volmer
Source: Journal of Cheminformatics (article, 2023-01-18)
Field: Chemistry — Spectroscopy

New algorithms demonstrate untargeted detection of chemically meaningful changing units and formula assignment for HRMS data of polymeric mixtures in the open-source constellation web application The field of high-resolution mass spectrometry (HRMS) and ancillary hyphenated techniques comprise a rapidly expanding and evolving area. As popularity of HRMS instruments grows, there is a concurrent need for tools and solutions to simplify and automate the processing of the large and complex datasets that result from these analyses. Constellation is one such of these tools, developed by our group over the last two years to perform unsupervised trend detection for repeating, polymeric units in HRMS data of complex mixtures such as natural organic matter, oil, or lignin. In this work, we develop two new unsupervised algorithms for finding chemically-meaningful changing units in HRMS data, and incorporate a molecular-formula-finding algorithm from the open-source CoreMS software package, both demonstrated here in the Constellation software environment. These algorithms are evaluated on a collection of open-source HRMS datasets containing polymeric analytes (PEG 400 and NIST standard reference material 1950, both metabolites in human plasma, as well as a swab extract containing polymers), and are able to successfully identify all known changing units in the data, including assigning the correct formulas. Through these new developments, we are excited to add to a growing body of open-source software specialized in extracting useful information from complex datasets without the high costs, technical knowledge, and processor-demand typically associated with such tools. Computer science ; Constellation ; Open source ; Data mining ; Algorithm ; Combinatorial chemistry ; Chemistry ; Information retrieval ; Software Analytical Chemistry and Chromatography ; Metabolomics and Mass Spectrometry Studies ; Advanced Chemical Sensor Technologies
Authors: K. S. Bejoymohandas | A. Ashish | Chithra H. Sharma | Sunil SeethaLekshmi | Mangalampalli S. R. N. Kiran | Indira S. Divya | Madhu Thalakulam | Filippo Monti | Rajesh V. Nair | Sunil Varughese
Source: ChemRxiv (preprint, 2023-06-28)
Field: Materials Science — Materials Chemistry

Dimorphs of a Benzothiophene-quinoline Derivative with Distinct Mechanical, Optical, Photophysical and Conducting Properties Because of distinct molecular conformations, packing modes, interaction types, and consequently their physicochemical properties, polymorphic forms of organic conjugated small molecules are intrinsically ideal for elucidating the relationship between their microstructures and the transcribed properties. Ethyl-2‐(1‐benzothiophene‐2‐yl)quinoline‐4‐carboxylate (BZQ) exists as dimorphs with distinct crystal habits―blocks (BZB) and needles (BZN). The crystal forms differ in their molecular arrangements―BZB has a slip-stacked column-like structure in contrast to a zig-zag crystal packing with limited π–overlap in BZN―and their photophysical and conducting properties. The BZB crystals characterized by extended π-stacking along [100] demonstrated semiconductor behavior, whereas the BZN, with its zig-zag crystal packing and limited stacking characteristics, was reckoned as an insulator. Monotropically related crystal forms also differ in their nanomechanical properties, with BZB crystals being considerably softer than BZN crystals. This discrepancy in mechanical behavior can be attributed to the distinct molecular arrangements adopted by each crystal form, resulting in unique mechanisms to relieve the strain generated during nanoindentation experiments. Waveguiding experiments on the acicular crystals of BZN revealed the passive waveguiding properties of the crystals. Excitation of these crystals using a 532 nm laser confirmed the propagation of elastically scattered photons (green) and the subsequent generation of inelastically scattered (orange) photons by the crystals. Further, the dimorphs display dissimilar photoluminescence properties; they are both blue-emissive, but BZN displays twice the quantum yield of BZB. This study underscores the integral role of polymorphism in modulating the mechanical, photophysical, and conducting properties of functional molecular materials. Importantly, our findings reveal the existence of light-emitting crystal polymorphs with varying electric conductivity, a relatively scarce phenomenon in the literature. Stacking ; Crystal (programming language) ; Crystallography ; Quantum yield ; Photoluminescence ; Materials science ; Benzothiophene ; Crystal structure ; Chemistry ; Molecule ; Chemical physics ; Optics ; Organic chemistry ; Optoelectronics ; Fluorescence ; Physics Luminescence and Fluorescent Materials ; Crystallography and molecular interactions ; Force Microscopy Techniques and Applications
Authors: Cyril Li | Christophe Ducottet | Sylvain Desroziers | Maxime Moreaud
Source:  (article, 2023-01-01)
Field: Materials Science — Surfaces, Coatings and Films

Toward Few Pixel Annotations for 3D Segmentation of Material from Electron Tomography International audience Segmentation ; Volume (thermodynamics) ; Artificial intelligence ; Computer science ; Scale-space segmentation ; Image segmentation ; Pixel ; Computer vision ; Electron tomography ; Pattern recognition (psychology) ; Computed tomography ; Tomography ; Task (project management) ; Engineering ; Optics ; Physics ; Medicine ; Radiology Electron and X-Ray Spectroscopy Techniques ; Non-Destructive Testing Techniques ; Advanced Electron Microscopy Techniques and Applications
Authors: Weiguang Yang | Danyang Luo | Guanrong Li | Qiaoli Luo | Martin G. Banwell | Lanmei Chen
Source: Molecules (article, 2023-09-08)
Field: Chemistry — Organic Chemistry

Synthesis of Pyridin-1(2H)-ylacrylates and the Effects of Different Functional Groups on Their Fluorescence While fluorescent organic materials have many potential as well as proven applications and so have attracted significant attention, pyridine-olefin conjugates remain a less studied subset of such systems. Herein, therefore, we report on the development of the straightforward syntheses of pyridin-1(2<i>H</i>)-ylacrylates and the outcomes of a study of the effects of substituents on their fluorescent properties. Such compounds were prepared using a simple, metal-free and three-component coupling reaction involving 2-aminopyridines, sulfonyl azides and propiolates. The fluorescent properties of the ensuing products are significantly affected by the positions of substituents on the cyclic framework, with those located in central positions having the greatest impact. Electron-withdrawing groups tend to induce blue shifts while electron-donating ones cause red shifts. This work highlights the capacity that the micro-modification of fluorescent materials provides for fine-tuning their properties such that they may be usefully applied to, for example, the study of luminescent materials. Fluorescence ; Pyridine ; Chemistry ; Sulfonyl ; Combinatorial chemistry ; Olefin fiber ; Conjugate ; Luminescence ; Photochemistry ; Organic chemistry ; Materials science ; Catalysis Catalytic C–H Functionalization Methods ; Catalytic Cross-Coupling Reactions ; Cyclopropane Reaction Mechanisms
Authors: Alexandre de Camargo | Ricky T. Q. Chen | Rodrigo A. Vargas–Hernández
Source: arXiv (Cornell University) (preprint, 2023-11-22)
Field: Materials Science — Materials Chemistry

Orbital-Free Density Functional Theory with Continuous Normalizing Flows Orbital-free density functional theory (OF-DFT) provides an alternative approach for calculating the molecular electronic energy, relying solely on the electron density. In OF-DFT, both the ground-state density is optimized variationally to minimize the total energy functional while satisfying the normalization constraint. In this work, we introduce a novel approach by parameterizing the electronic density with a normalizing flow ansatz, which is also optimized by minimizing the total energy functional. Our model successfully replicates the electronic density for a diverse range of chemical systems, including a one-dimensional diatomic molecule, specifically Lithium hydride with varying interatomic distances, as well as comprehensive simulations of hydrogen and water molecules, all conducted in Cartesian space. Density functional theory ; Orbital-free density functional theory ; Energy functional ; Ansatz ; Electronic structure ; Physics ; Work (physics) ; Linear scale ; Electronic density ; Statistical physics ; Hybrid functional ; Computational chemistry ; Quantum mechanics ; Chemistry Machine Learning in Materials Science ; Advanced Chemical Physics Studies ; Molecular Junctions and Nanostructures
Authors: Pan Sun | Mrinal K. Bera | Wei Bu | Binhua Lin | Mark L. Schlossman
Source: ChemRxiv (preprint, 2023-06-19)
Field: Chemistry — Spectroscopy

Confined micro-environment of micelles regulates their interaction with anions Ion interactions with supramolecular assemblies underlie their applications in the areas of drug delivery, ion recognition, and conduction. The current challenge remains in directly characterizing the interaction of ions with supramolecular assemblies at the nanoscale. Here, we demonstrate that the micro-environment of neutral polymer micelles regulates its interaction with anions by combining element-sensitive anomalous small angle X-ray scattering (ASAXS) and theoretical calculations. ASAXS and molecular dynamics simulations reveal that monovalent ReO4− is located preferentially in the outer shell of the micelle, while the more strongly hydrated divalent SeO42– is excluded from the micelle. However, DFT calculations show that the more highly charged SeO42– should have stronger affinity for an isolated polymer chain than ReO4−. These results suggest that the confined environment created by polymer self-assembly modulates the contribution of hydrophobic and electrostatic interactions to the binding of anions with polymers. The present work sheds light on the role of crowded environments in the interaction of anions with polymers in supramolecular assemblies and offers valuable insights to optimize the design of supramolecular systems. Supramolecular chemistry ; Micelle ; Polymer ; Chemical physics ; Ion ; Divalent ; Chemistry ; Supramolecular polymers ; Nanoscopic scale ; Small-angle X-ray scattering ; Static electricity ; Electrostatics ; Nanotechnology ; Non-covalent interactions ; Scattering ; Materials science ; Crystallography ; Molecule ; Hydrogen bond ; Organic chemistry ; Aqueous solution ; Physical chemistry ; Physics ; Crystal structure Molecular Sensors and Ion Detection ; Electrostatics and Colloid Interactions ; Advanced Battery Materials and Technologies