jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Dmytro Antypov | Christopher M. Collins | Andrij Vasylenko | Vladimir V. Gusev | Michael W. Gaultois | George R. Darling | Matthew S. Dyer | Matthew J. Rosseinsky
Source: ChemRxiv (preprint, 2023-10-16)
Field: Materials Science — Materials Chemistry

Statistically derived proxy potentials accelerate geometry optimisation of crystal structures Geometry optimisation is a ubiquitous task in computational materials science, but the number of systems for which fast and reliable force field models have been developed is limited. This leaves local energy minimisation using computationally expensive density functional theory (DFT) as the only reliable route to structure optimisation. At the same time, the available crystal structures of known materials contain the information about the interatomic interactions that produced these stable compounds, expressed as the interatomic distances between all the constituent atoms. We use this relationship to statistically learn the effective interatomic interactions in crystalline inorganic solids from their structures. By analysing pairwise interatomic distances in the reported crystallographic data for inorganic materials, we have constructed statistically derived proxy potentials (SPPs) that can be used for structure optimisation. We apply such optimisation step to markedly improve the quality of the input crystal structures for DFT calculations and demonstrate that the SPPs accelerate geometry optimisation for three systems relevant to battery materials. As this approach is chemistry-agnostic and can be used at scale, we produced a database of all possible pair potentials in a tabulated form ready to use. Pairwise comparison ; Interatomic potential ; Crystal structure ; Energy minimization ; Crystal structure prediction ; Density functional theory ; Computer science ; Force field (fiction) ; Statistical physics ; Chemistry ; Algorithm ; Crystallography ; Computational chemistry ; Molecular dynamics ; Physics ; Artificial intelligence Machine Learning in Materials Science ; X-ray Diffraction in Crystallography ; Crystallography and molecular interactions
Authors: Siti Mariatul Hazwa Mohd Huzir | Anis Hazirah ‘Izzati Hasnu Al-Hadi | Amir Hussairi Zaidi | Nurlaila Ismail | Zakiah Mohd Yusoff | Mohamad Hushni Haron | Ali Abd Almisreb | Mohd Nasir Taib
Source: Bulletin of Electrical Engineering and Informatics (article, 2023-12-13)
Field: Chemistry — Organic Chemistry

Pre-processing technique of Aquilaria species from Malaysia for four different qualities The paper interprets data distribution by using boxplot pre-processing in classify the quality of Agarwood oil for eleven chemical substances into four different qualities. The varieties usage of Agarwood oil makes it considered as an expensive and valuable product on the essential oil market. Perfumes, fragrances, incense, aromatherapy, and traditional medicine are the most popular Agarwood oil applications. However, the classification of Agarwood oil grades does not yet have standard grading method. This because it has been graded manually into different qualities by using human sensory evaluation. Boxplot analysis involving eleven chemical subtances that will be focusing in this study by concerned the quality for low, medium low, medium high and high. ɤ-eudesmol, ar-curcumene, β-dihydro agarofuran, ϒ-cadinene, α-agarofuran, allo aromadendrene epoxide, valerianol, α-guaiene, 10-epi-ɤ-eudesmol, β-agarofuran, and dihydrocollumellarin compounds are the selected significant compounds that represent the input for boxplot. Agarwood oil consist 660 data samples from low, medium low, medium high, and high quality. The result in this study showed that the four selected significant compounds (ɤ-eudesmol, 10-epi-ɤ-eudesmol, β-agarofuran, and dihydrocollumellarin) are important as a marker for Agarwood oil quality classification. The identification of chemical substances on high quality done as reference for future research studies. Agarwood ; Mathematics ; Incense ; Geography Wood and Agarwood Research ; Cultural Heritage Materials Analysis ; Biological Stains and Phytochemicals
Authors: Gianmaria Viciconte | Paolo Guida | Tadd Truscott | William L. Roberts
Source: arXiv (Cornell University) (preprint, 2023-11-22)
Field: Materials Science — Materials Chemistry

Towards a general description of the cavitation threshold in acoustic systems Traditionally, the occurrence of cavitation has been related to the ratio between flow velocity and pressure gradient in the case of hydrodynamic cavitation, or some combination of vapor pressure and surface tension. However, both formulations present a large discrepancy with experimental data for cases in which cavitation is induced by acoustic waves. The present study aims to identify a more suitable cavitation threshold for such cases. The methodology adopted in this work consists of a combination of visualization with high-speed cameras and direct measurements using a hydrophone. The data collected confirmed that the vapor pressure is not a proper indicator of cavitation occurrence for an acoustic system characterized by high frequencies. The main reason behind the inability of vapor pressure to predict incipient cavitation in acoustic systems is that they evolve very quickly toward strong gradients in pressure, and the quasi-static assumptions used by traditional models are not valid. Instead, the system evolves towards a metastable state [Brennen, 2013], where the liquid exhibits an elastic behavior and can withstand negative pressures. A new cavitation number accounting for the tensile strength of the liquid was defined. An acoustic analogy is also proposed for the description, with the same framework, of an impulsive cavitation phenomenon. Cavitation ; Acoustics ; Mechanics ; Hydrophone ; Materials science ; Work (physics) ; Vapor pressure ; Surface tension ; Tension (geology) ; Flow (mathematics) ; Ultimate tensile strength ; Thermodynamics ; Physics ; Composite material Ultrasound and Cavitation Phenomena ; Acoustic Wave Phenomena Research ; Cavitation Phenomena in Pumps
Authors: Jiani Zhu | Youwei Ma | Guoqing Ding | Manhua Liu | Xin Chen
Source: Sensors (article, 2023-07-31)
Field: Materials Science — Polymers and Plastics

Extraction of the Microstructure of Wool Fabrics Based on Structure Tensor The trends of "fashionalization", "personalization" and "customization" of wool fabrics have prompted the textile industry to change the original processing design based on the experience of engineers and trial production. In order to adapt to the promotion of intelligent production, the microstructure of wool fabrics is introduced into the finishing process. This article presents an automated method to extract the microstructure from the micro-CT data of woven wool fabrics. Firstly, image processing was performed on the 3D micro-CT images of the fabric. The raw grayscale data were converted into eigenvectors of the structure tensor to segment the individual yarns. These data were then used to calculate the three parameters of diameter, spacing and the path of the center points of the yarn for the microstructure. The experimental results showed that the proposed method was quite accurate and robust on woven single-ply tweed fabrics. Wool ; Microstructure ; Textile ; Materials science ; Grayscale ; Yarn ; Tensor (intrinsic definition) ; Composite material ; Computer science ; Engineering drawing ; Computer vision ; Pixel ; Engineering ; Mathematics ; Geometry Textile materials and evaluations ; Industrial Vision Systems and Defect Detection ; Optical measurement and interference techniques
Authors: Matthew J. Carlo | Amanda L. Patrick
Source: Journal of Mass Spectrometry (article, 2023-11-21)
Field: Chemistry — Spectroscopy

Further exploration of the collision‐induced dissociation of select beta blockers: Acebutolol, atenolol, bisoprolol, carteolol, and labetalol Beta blockers are a class of drugs commonly used to treat heart-related diseases; they are also regulated under the World Anti-Doping Agency. Tandem mass spectrometry is often used in the pharmaceutical industry, clinical analysis laboratory, and antidoping laboratory for detection and characterization of drugs and their metabolites. A deeper chemical understanding of dissociation pathways may eventually lead to an improved ability to predict tandem mass spectra of compounds based strictly on their chemical structure (or vice versa), which is especially important for characterization of unknowns such as emerging designer drugs or novel metabolites. In addition to providing insights into dissociation pathways, the use of energy-resolved breakdown curves can produce improved selectivity and lend insights into optimal fragmentation conditions for liquid chromatography-tandem mass spectrometry LC-MS/MS workflows. Here, we perform energy-resolved collision cell and multistage ion trap collision-induced dissociation-mass spectrometry (CID-MS) experiments, along with complementary density functional theory calculations, on five beta blockers (acebutolol, atenolol, bisoprolol, carteolol, and labetalol), to better understand the details of the pathways giving rise to the observed MS/MS patterns. Results from this work are contextualized within previously reported literature on these compounds. New insights into the formation of the characteristic product ion m/z 116 and the pathway leading to characteristic loss of 77 u are highlighted. We also present comparisons of breakdown curves obtained via qToF, quadrupole ion trap, and in-source CID, allowing for differences between the data to be noted and providing a step toward allowing for improved selectivity of breakdown curves to be realized on simple instruments such as single quadrupoles or ion traps. Chemistry ; Bisoprolol ; Collision-induced dissociation ; Atenolol ; Tandem mass spectrometry ; Acebutolol ; Mass spectrometry ; Dissociation (chemistry) ; Selectivity ; Analytical Chemistry (journal) ; Chromatography ; Organic chemistry Mass Spectrometry Techniques and Applications ; Pesticide Residue Analysis and Safety ; Analytical Chemistry and Chromatography
Authors: Qian Liu
Source: Research Square (preprint, 2023-04-17)
Field: Chemistry — Inorganic Chemistry

Technological Innovation in the Recognition Process of Yaozhou Kiln Ware Patterns Based on Image Classification Abstract The Chinese traditional culture embodies the wisdom and strength of the people of all ethnic groups in China. The superb and exquisite workmanship of Yaozhou kiln ceramics, as well as the decorative patterns on the surface of porcelain and the rich categories of porcelain, fully reflect the great charm of Chinese traditional culture, which also has high historical research value, artistic appreciation value, and collection value. In the process of making Yaozhou Kiln ceramics, craftsmen selected raw materials according to local characteristics, and studied the rich and varied patterns of porcelain in terms of porcelain molding methods, decoration techniques and baking temperatures. In the process of the development of computer vision technology, image classification is the main content to improve the level of technology development, and it is also related to the efficiency of pattern recognition. Yaozhou's porcelain design method not only endows porcelain with material value, but also expresses people's spiritual sustenance by using the patterns on the porcelain surface. Decorations can not only become an important element of porcelain decoration, but also link national culture together and promote cultural transmission. The main principle of image classification is to automatically classify an image according to the visual characteristics, so that the image has a unique classification mark, which is convenient for the system to recognize. This paper uses image classification technology to extract and analyze the characteristics of Yaozhou kiln ceramics, mainly from the shape of porcelain, the type of ornamentation and inscriptions of its three features for image recognition and classification, and discusses the use of advanced technology to replace traditional experts to identify porcelain ornamentation. Kiln ; Sustenance ; Value (mathematics) ; Workmanship ; Process (computing) ; Aesthetic value ; Computer science ; Artificial intelligence ; Visual arts ; Engineering ; Engineering drawing ; Aesthetics ; Art Pigment Synthesis and Properties ; Digital Media and Visual Art
Authors: Robin Löffler | Stephan Tremmel | Rüdiger Hornfeck
Source: Preprints.org (preprint, 2023-02-22)
Field: Materials Science — Materials Chemistry

Owl Neck Spine inspired, Additively Manufactured, Joint Assemblies with Shape Memory Alloy Wire Actuators Nature provides plenty of good examples for simple and very efficient joint assemblies. One example is the enormously flexible cervical spine of American barn owls, which consists of 14 cervical vertebrae. Each pair of vertebrae produces a comparatively small individual movement in order to provide a large overall movement of the entire cervical spine. The biomimetic replication of such joints is difficult due to the delicate and geometric unrestricted joint shapes as well as the muscles that have to be mimicked. Using X-ray as well as micro computed tomography images and with the utilisation of additive manufacturing, it is possible to produce the owl neck vertebrae in scaled-up form, to analyse them and then to transfer them into technically usable joint assemblies. The muscle substitution of these joints is realised by smart materials actuators in the form of shape memory alloy wire actuators. This actuator technology is outstanding for its muscle-like movement and for its enormous energy density [1,2]. The disadvantage of this wire actuator technology is the low rate of contraction, which means that a large length of wire has to be installed to generate adequate movement. For this reason, the actuator wires are integrated into additively manufactured carrier components to mimic the biological joints. This results in joint designs that compensate for the disadvantages of the small contraction of the actuators by intelligently installing large wire lengths on comparatively small installation spaces, while also providing a sufficient force output. With the help of a test rig, the developed technical joint variants are examined and evaluated. This demonstrates the technical applicability of this bionic joints. Actuator ; Shape-memory alloy ; Joint (building) ; USable ; Mechanical engineering ; Computer science ; Structural engineering ; Engineering ; Artificial intelligence Shape Memory Alloy Transformations ; Anatomy and Medical Technology
Authors: Jonathan P. Antle | Michael A. LaRock | Zackary Falls | Carla A. Ng | Ekin Atilla-Gokcumen | Diana S. Aga | Scott Simpson
Source: ChemRxiv (preprint, 2023-10-04)
Field: Materials Science — Polymers and Plastics

Building Chemical Intuition About Physicochemical Properties of C8-Per-/Poly-fluoroalkyl Carboxylic Acids Through Computational Means We have predicted acid dissociation constants (pKa), octanol-water partition coefficients (KOW), and DPMC lipid membrane-water partition coefficients (Klipid-w) of 150 different 8-carbon containing poly-/per-fluoroalkyl carboxylic acids (C8-PFCAs) utilizing COMSO-RS theory. Different trends associated with functionalization, degree of fluorination, degree of saturation, degree of chlorination, and branching are discussed based upon the predicted values for the partition coefficients. In general, functionalization closest to the carboxylic head group had the greatest impact on the value of the predicted physicochemical properties. Partition coefficient ; Dissociation constant ; Surface modification ; Carboxylic acid ; Chemistry ; Dissociation (chemistry) ; Intuition ; Chemical modification ; Organic chemistry ; Polymer chemistry ; Physical chemistry ; Biochemistry Synthesis and properties of polymers ; Chemistry and Chemical Engineering ; Environmental Chemistry and Analysis
Authors: S. Stepanović | Gérard Hopfgartner
Source: Journal of the American Society for Mass Spectrometry (article, 2023-03-21)
Field: Chemistry — Spectroscopy

Predicting Preferences for Adduct Formation in Electrospray Ionization: The Case Study of Succinic Acid A simple theoretical approach is developed that can be used to predict the preference of ion adduct formation (with alkali Li<sup>+</sup>, Na<sup>+</sup>, K<sup>+</sup> and alkaline earth Ca<sup>2+</sup>, Mg<sup>2+</sup> metals) in electrospray ionization mass spectrometry (ESI-MS) of succinic acid, associated with several protonation/deprotonation equilibria. The applied strategy consists of using a vacuum environment as well as both implicit and explicit solvation of reactive sites and density functional theory as the method of choice. These distinct levels of theory mimic the smooth transition between the condensed environment and free ion in the gas phase. Good correlation between the Gibbs free energies for protonation/adduct formation processes with peak observation in the obtained mass spectra provide insight into the physical basis behind adduct preference and selectivity. This signifies the relationship between microscopic interactions, ionization efficiency, and types of ions that reach the detector. Chemistry ; Protonation ; Electrospray ionization ; Adduct ; Ionization ; Deprotonation ; Mass spectrometry ; Density functional theory ; Ion ; Solvation ; Computational chemistry ; Organic chemistry ; Chromatography Mass Spectrometry Techniques and Applications ; Analytical Chemistry and Chromatography ; Advanced Chemical Sensor Technologies
Authors: Aytekin Demirci | Dominik Steinberger | Markus Stricker | Nina Gunkelmann | D. Weygand | Stefan Sandfeld
Source: arXiv (Cornell University) (preprint, 2023-01-01)
Field: Materials Science — Materials Chemistry

Statistical analysis of Discrete Dislocation Dynamics simulations: initial structures, cross-slip and microstructure evolution Over the past decades, discrete dislocation dynamics simulations have been shown to reliably predict the evolution of dislocation microstructures for micrometer-sized metallic samples. Such simulations provide insight into the governing deformation mechanisms and the interplay between different physical phenomena such as dislocation reactions or cross-slip. This work is focused on a detailed analysis of the influence of the cross-slip on the evolution of dislocation systems. A tailored data mining strategy using the ``\ab*{discrete-to-continuous} framework'' allows to quantify differences and to quantitatively compare dislocation structures. We analyze the quantitative effects of the cross-slip on the microstructure in the course of a tensile test and a subsequent relaxation to present the role of cross-slip in the microstructure evolution. The precision of the extracted quantitative information using D2C strongly depends on the resolution of the domain averaging. We also analyze how the resolution of the averaging influences the distribution of total dislocation density and curvature fields of the specimen. Our analyzes are important approaches for interpreting the resulting structures calculated by dislocation dynamics simulations. Dislocation ; Slip (aerodynamics) ; Microstructure ; Materials science ; Statistical physics ; Curvature ; Molecular dynamics ; Mechanics ; Physics ; Geometry ; Mathematics ; Composite material ; Thermodynamics Microstructure and mechanical properties ; Metallurgy and Material Forming ; Microstructure and Mechanical Properties of Steels
Authors: Kejia Li | Shijie Chen | Keyun Wang | Yan Wang | Zheng Fang | Jiawen Lyu | Haiyang Zhu | Yanan Li | Ting Yu | Feng Yang | Xiaolei Zhang | Siqi Guo | Chengfei Ruan | Jiahua Zhou | Qi Wang | Cheng Luo | Mingliang Ye
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-10-19)
Field: Chemistry — Organic Chemistry

A peptide-centric local stability assay to unveil protein targets of diverse ligands ABSTRACT While tremendous progress has been made in chemical proteomics for identifying protein-ligand interactions, it remains challenging for proteome-wide identification of ligand-binding regions without modifying the ligands. Here, we discovered that “disruptive trypsinization” amplifies the readout of ligand-induced protein local stability shifts, and explored this notion in developing “peptide-centric local stability assay” (PELSA), a modification-free approach which achieves unprecedented sensitivity in proteome-wide target identification and binding-region determination. We demonstrate the versatility of PELSA by investigating the interactions across various biological contexts including drug-target interactions, metabolism, epitope mapping, metal proteomics, and post-translational modification recognition. A PELSA study of the oncometabolite R2HG revealed functional insights about its targets and pathogenic processes in both cancer and immune cells. Thus, beyond offering users unprecedented sensitivity for characterizing diverse target-ligand interactions, PELSA supports informative screening and hypothesis generation studies throughout life science. Proteome ; Computational biology ; Proteomics ; Identification (biology) ; Ligand (biochemistry) ; Protein–protein interaction ; Biology ; Peptide ; Epitope ; Posttranslational modification ; Chemistry ; Cell biology ; Bioinformatics ; Biochemistry ; Genetics ; Receptor ; Antigen ; Gene Click Chemistry and Applications ; Ubiquitin and proteasome pathways ; Microbial Natural Products and Biosynthesis
Authors: Joachim Sødequist | Thomas Olsen
Source: arXiv (Cornell University) (preprint, 2023-09-21)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Magnetic order in the computational 2D materials database (C2DB) from high throughput spin spiral calculations We report a detailed investigation of the magnetic order in 192 stable magnetic two-dimensional materials from the Computational 2D Materials Database having one magnetic atom in the unit cell. The calculations are based on a systematic workflow that employs spin spiral calculations and yields the magnetic order in terms of a two-dimensional ordering vector $\mathbf{Q}$. We then include spin-orbit coupling to extract the easy and hard axes for collinear structures and the orientation of spiral planes in non-collinear structures. Finally, for all predicted ferromagnets we compute the Dzyaloshinskii-Moriya interactions and determine whether or not these are strong enough to overcome the magnetic anisotropy and stabilise a chiral spin spiral ground state. These steps completely determines the ground state order within the spiralling ansatz. We find 58 ferromagnets, 21 collinear anti-ferromagnets, and 85 non-collinear ground states of which 15 are chiral spin spirals driven by Dzyaloshinskii-Moriya interactions. The results show that non-collinear order is in fact as common as collinear order in these materials and emphasise the need for detailed investigation of the magnetic ground state when reporting magnetic properties of new materials. Furthermore, non-collinear order typically breaks symmetries inherent to the lattice and may give rise to emergent properties such as multiferroicity, magnetoelectricity or second order optical effects that would be predicted as absent based on a collinear assumption. Physics ; Ground state ; Ferromagnetism ; Condensed matter physics ; Spin (aerodynamics) ; Ansatz ; Spiral (railway) ; Magnetic structure ; Order (exchange) ; Lattice (music) ; Antiferromagnetism ; Anisotropy ; Magnetic field ; Quantum mechanics ; Magnetization Multiferroics and related materials ; Advanced Condensed Matter Physics ; Physics of Superconductivity and Magnetism