jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Zahars Selivanovs | Vitaly Panchuk | Dmitry Kirsanov
Source: Applied Sciences (article, 2023-04-26)
Field: Chemistry — Analytical Chemistry

On the Possibility of Universal Chemometric Calibration in X-ray Fluorescence Spectrometry: Case Study with Ore and Steel Samples The accuracy of X-ray fluorescence spectrometry in quantitative element analysis depends on the particular sample composition (so-called matrix effects). Counteracting these effects requires a large number of calibration samples similar in composition to those under analysis. Application of the model constructed for a particular type of samples is not possible for the analysis of samples having a different matrix composition. A possible solution for this problem can be found in the construction of universal calibration models. We propose the development of these universal models using chemometric tools: influence coefficients—partial least squares regression (IC-PLS) and nonlinear kernel regularized least squares regression. We hypothesize that the application of these methods for constructing calibration models would allow embracing the samples of different types in the framework of a single model. We explored this approach for the case of two substantially different types of samples: ores and steels. The performance of these methods was compared with the fundamental parameters (FP) method, which takes into account matrix effects using theoretical equations and allows handling samples of different elemental composition. IC-PLS significantly outperforms traditional FP in terms of accuracy for predicting the content of Al (root mean squared error of prediction 0.96% vs. 3.87%) and Ti (0.05% vs. 0.09%) and yields comparable results for Si and Mn quantification in ores and steels. Partial least squares regression ; Calibration ; Matrix (chemical analysis) ; Biological system ; Kernel (algebra) ; Mathematics ; Analytical Chemistry (journal) ; Chemistry ; Statistics ; Chromatography Spectroscopy and Chemometric Analyses ; Geochemistry and Geologic Mapping ; Mineral Processing and Grinding
Authors: Frédéric Guyon | Gautier Moroy
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-08-03)
Field: Chemistry — Spectroscopy

Non-sequential alignment of binding sites for fast peptide screening Abstract Motivation Peptides are molecules involved in many essential biological activities by interacting with proteins in the body. They can also be used as therapeutic molecules, particularly to disrupt protein-protein interactions involved in disease. However, it is difficult to identify potential therapeutic peptides if the structure of the protein-protein complex to be inhibited has not been solved. Results The PepIT program was developed to propose peptides that can interact with a given protein. PepIT is based on a non-sequential alignment algorithm to identify peptide binding sites that share geometrical and physicochemical properties with a surface region of the target protein. PepIT compares the entire surface of the target protein with the peptide binding sites of the Propedia dataset, which contains more than 19,000 high-resolution protein-peptide structures. Once a peptide binding site similar to a portion of the protein surface is found, the peptide bound to the binding site is repositioned on the corresponding portion of the protein surface. Availability and implementation The PepIT source code is freely available at https://github.com/DSIMB/pepit Supplementary information Supplementary data are available online. Peptide ; Surface protein ; Computational biology ; Binding site ; Small molecule ; Chemistry ; Plasma protein binding ; Protein structure ; Protein–protein interaction ; Biophysics ; Computer science ; Combinatorial chemistry ; Biochemistry ; Biology Advanced Proteomics Techniques and Applications ; Chemical Synthesis and Analysis ; Peptidase Inhibition and Analysis
Authors: Carsten Speckmann | Julia Lang | Jacob Madsen | Mohammad Reza Ahmadpour Monazam | Georg Zagler | Gregor Leuthner | Niall McEvoy | Clemens Mangler | Toma Susi | Jani Kotakoski
Source: arXiv (Cornell University) (preprint, 2023-02-21)
Field: Materials Science — Surfaces, Coatings and Films

Combined electronic excitation and knock-on damage in monolayer MoS2 Electron irradiation-induced damage is often the limiting factor in imaging materials prone to ionization or electronic excitations due to inelastic electron scattering. Quantifying the related processes at the atomic scale has only become possible with the advent of aberration-corrected (scanning) transmission electron microscopes and two-dimensional materials that allow imaging each lattice atom. While it has been shown for graphene that pure knock-on damage arising from elastic scattering is sufficient to describe the observed damage, the situation is more complicated with two-dimensional semiconducting materials such as MoS2. Here, we measure the displacement cross section for sulfur atoms in MoS2 with primary beam energies between 55 and 90 keV, and correlate the results with existing measurements and theoretical models. Our experimental data suggests that the displacement process can occur from the ground state, or with single or multiple excitations, all caused by the same impinging electron. The results bring light to reports in the recent literature, and add necessary experimental data for a comprehensive description of electron irradiation damage in a two-dimensional semiconducting material. Specifically, the results agree with a combined inelastic and elastic damage mechanism at intermediate energies, in addition to a pure elastic mechanism that dominates above 80 keV. When the inelastic contribution is assumed to arise through impact ionization, the associated excitation lifetime is on the order of picoseconds, on par with expected excitation lifetimes in MoS2, whereas it drops to some tens of femtoseconds when direct valence excitation is considered. Picosecond ; Excitation ; Inelastic scattering ; Atomic physics ; Ionization ; Electron ; Femtosecond ; Valence electron ; Materials science ; Scattering ; Valence (chemistry) ; Elastic scattering ; Molecular physics ; Physics ; Optics ; Nuclear physics Electron and X-Ray Spectroscopy Techniques ; Ion-surface interactions and analysis ; Ga2O3 and related materials
Authors: Andreas Kapshammer | Matei Constantin Miron | Lukas Dangl | Zoltán Major
Source: Polymers (article, 2023-02-14)
Field: Materials Science — Polymers and Plastics

Interface Characterization of Consolidated PPGF Tapes on PPGF Mat Material Laminated composites with thermoset matrices are already well established in major engineering fields like automotive and aviation. The primary drawbacks of such thermoset-based composites are the high cycle times required during manufacturing and their limited potential for recycling. Providing an alternative to thermoset-based composites, thermoplastic matrix materials gained more and more momentum by addressing these previously mentioned drawbacks. The preferred manufacturing technique for these materials employs fiber-reinforced thermoplastic tapes consolidated and formed together with a compatible substrate. The most critical aspect for all these applications is the stress or load transfer between the thermoplastic tapes and the substrate. If the interface is too weak and fails prior to the substrate or tape, a high amount of theoretical mechanical performance is lost. The presented research investigates the influence of variations in manufacturing parameters, within the industrially relevant process window, on the interface strength of the final composite. The investigated composite material consists of PPGF UD tapes consolidated on a PPGF mat substrate. In particular, the influence of the consolidation parameters of pressure, temperature, and time are of special interest. The results of this work reveal a 400% increase in the measured mean strain energy release rate upon increasing the consolidation time from 60 s to 120 s at a consolidation temperature of 230 °C and a pressure of one bar. In contrast to this, an increase in the consolidation pressure, at constant temperature and time, leads to a minor improvement in the <i>G<sub>C</sub></i> value of 20%. For testing and characterizing the corresponding interface properties, a mandrel peel testing setup was employed. Thermosetting polymer ; Materials science ; Composite material ; Thermoplastic ; Consolidation (business) ; Composite number ; Epoxy Natural Fiber Reinforced Composites ; Mechanical Behavior of Composites ; Fiber-reinforced polymer composites
Authors: Romuald Kilianski | Robert Bennett
Source: Physical Review Research (article, 2023-08-03)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Inverse design of arbitrary optical helicity patterns Superposing multiple plane waves can generate helicity lattices in which the optical helicity varies regularly in space. Here we propose an inverse design method for constructing arbitrary helicity structures based on placing a digital object consisting of dielectric inclusions in three-dimensional space. We apply the method to design structures that reproduce two-dimensional lattices embedded within a three-dimensional region using only a single plane wave as an input. In order to demonstrate the power and flexibility of our method, we go beyond the paradigm of a regular lattice and propose structures which can create arbitrary images consisting of regions of varying helicity, again using only a single plane wave as an input. Helicity ; Lattice (music) ; Inverse ; Physics ; Optics ; Topology (electrical circuits) ; Geometry ; Mathematics ; Quantum mechanics ; Acoustics ; Combinatorics Metamaterials and Metasurfaces Applications ; Photonic Crystals and Applications ; Advanced Optical Imaging Technologies
Authors: Bruno Simões de Almeida | Lyndon Emsley
Source: CHIMIA International Journal for Chemistry (article, 2023-04-26)
Field: Chemistry — Spectroscopy

Improvements in Resolution of 1H NMR of solids Magic angle spinning (MAS) in 1H NMR has allowed progress from featureless spectra in static samples to linewidths of a few hundreds of Hertz for powdered solids at the fastest spinning rates available today (100-150 kHz). While this is a remarkable improvement, this level of resolution is still limiting to the widespread use of 1H NMR for complex systems. This review will discuss two recent alternative strategies that have significantly improved 1H resolution, when combined with fast MAS. The first is based on anti-z-COSY, a 2D experiment originally used for J decoupling in liquids, which removes residual broadening due to splittings caused by imperfect coherent averaging of MAS. The second strategy is to obtain pure isotropic proton (PIP) spectra in solids, by parametrically mapping any residual broadening due to imperfect averaging into a second dimension of a multidimensional correlation spectrum. Spinning ; Residual ; Decoupling (probability) ; Resolution (logic) ; Limiting ; Spectral line ; Isotropy ; NMR spectra database ; Proton NMR ; Imperfect ; Magic angle spinning ; Analytical Chemistry (journal) ; Chemistry ; Computational physics ; Materials science ; Nuclear magnetic resonance spectroscopy ; Nuclear magnetic resonance ; Physics ; Mathematics ; Optics ; Algorithm ; Computer science ; Chromatography Advanced NMR Techniques and Applications ; NMR spectroscopy and applications ; Quantum, superfluid, helium dynamics
Authors: Muhathir Muhathir | Reydo Trisno Pangestu | Ira Safira | Melisah Melisah
Source: Journal of Computer Science Information Technology and Telecommunication Engineering (article, 2023-03-04)
Field: Chemistry — Inorganic Chemistry

Performance Comparison of Boosting Algorithms in Spices Classification Using Histogram of Oriented Gradient Feature Extraction Spice classification is an important task in the food industry to ensure food safety and quality. This study focuses on the classification of spices using the HoG feature extraction method and boosting algorithms. The objective of this research is to compare the performance of four different models of boosting algorithms, namely Adaboost Classifier, Gradient Boosting Classifier, XGB Classifier, and Light GBM Classifier, in classifying spices. The evaluation metrics used in this research are Precision, Recall, F1-Score, F2-Score, Jaccard Score, and Accuracy. The results show that the XGB Classifier model achieved the best performance, with a precision of 0.811, recall of 0.809, and F1-score of 0.809, while the Adaboost Classifier model had the lowest performance, with a precision of 0.709, recall of 0.689, and F1-score of 0.682. Overall, the results indicate a fairly good success rate in classifying spices using the HoG feature extraction method and boosting algorithms. However, further evaluation is needed to improve the accuracy of the classification results, such as increasing the number of training data or considering the use of other feature extraction methods Boosting (machine learning) ; Artificial intelligence ; Classifier (UML) ; AdaBoost ; Pattern recognition (psychology) ; Computer science ; Gradient boosting ; Feature extraction ; F1 score ; Precision and recall ; Machine learning ; Random forest Coconut Research and Applications ; Identification and Quantification in Food ; Agricultural and Environmental Management
Authors: Khaled Belhouchet | Lyamine Ouchen | Abdelhafid Bayadi | Nadjim Alti
Source: Research Square (preprint, 2023-05-16)
Field: Materials Science — Materials Chemistry

A Novel Application of Artificial intelligence technology for Outdoor High-Voltage Composite Insulators Corona ring ; Corona (planetary geology) ; Insulator (electricity) ; Finite element method ; Electric field ; Transmission line ; Corona discharge ; Voltage ; Installation ; High voltage ; Materials science ; Electrical engineering ; Electronic engineering ; Computer science ; Engineering ; Mechanical engineering ; Structural engineering ; Physics High voltage insulation and dielectric phenomena ; Aerosol Filtration and Electrostatic Precipitation ; Thermal Analysis in Power Transmission
Authors: Teemu Härkönen | Emma Hannula | Matthew T. Moores | Erik M. Vartiainen∥ | Lassi Roininen
Source: Foundations of Data Science (article, 2023-01-01)
Field: Chemistry — Analytical Chemistry

A log-Gaussian Cox process with sequential Monte Carlo for line narrowing in spectroscopy We propose a statistical model for narrowing line shapes in spectroscopy that are well approximated as linear combinations of Lorentzian or Voigt functions. We introduce a log-Gaussian Cox process to represent the peak locations thereby providing uncertainty quantification for the line narrowing. Bayesian formulation of the method allows for robust and explicit inclusion of prior information as probability distributions for parameters of the model. Estimation of the signal and its parameters is performed using a sequential Monte Carlo algorithm followed by an optimization step to determine the peak locations. Our method is validated using a simulation study and applied to a mineralogical Raman spectrum. Monte Carlo method ; Gaussian process ; Algorithm ; Gaussian ; Statistical physics ; Line (geometry) ; Bayesian probability ; Markov chain Monte Carlo ; Voigt profile ; Mathematics ; Computer science ; Applied mathematics ; Mathematical optimization ; Biological system ; Statistics ; Physics ; Spectral line Spectroscopy and Chemometric Analyses ; Advanced Statistical Methods and Models ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Xinpei Yi | Bo Wen | Shuyi Ji | Alex Saltzman | Eric J. Jaehnig | Jonathan T. Lei | Qiang Gao | Bing Zhang
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-01-12)
Field: Chemistry — Spectroscopy

Deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification Shotgun phosphoproteomics enables high-throughput analysis of phosphopeptides in biological samples, but low phosphopeptide identification rate in data analysis limits the potential of this technology. Here we present DeepRescore2, a computational workflow that leverages deep learning-based retention time and fragment ion intensity predictions to improve phosphopeptide identification and phosphosite localization. Using a state-of-the-art computational workflow as a benchmark, DeepRescore2 increases the number of correctly identified peptide-spectrum matches by 17% in a synthetic dataset and identifies 19%-46% more phosphopeptides in biological datasets. In a liver cancer dataset, 30% of the significantly altered phosphosites between tumor and normal tissues and 60% of the prognosis-associated phosphosites identified from DeepRescore2-processed data could not be identified based on the state-of-the-art workflow. Notably, DeepRescore2-processed data uniquely identifies EGFR hyperactivation as a new target in poor-prognosis liver cancer, which is validated experimentally. Integration of deep learning prediction in DeepRescore2 improves phosphopeptide identification and facilitates biological discoveries. Phosphoproteomics ; Phosphopeptide ; Computer science ; Workflow ; Identification (biology) ; Benchmark (surveying) ; Computational biology ; Artificial intelligence ; Chemistry ; Biology ; Peptide ; Database ; Biochemistry ; Phosphorylation Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Molecular Biology Techniques and Applications
Authors: Katherine Do | Subina Mehta | Reid Wagner | Dechen Bhuming | Andrew T. Rajczewski | Amy P.N. Skubitz | James E. Johnson | Timothy J. Griffin | Pratik Jagtap
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-11-22)
Field: Chemistry — Spectroscopy

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, which are usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification and prioritization of microbial and host proteins, enabling targeted assay development to investigate host-microbe dynamics in disease. The bioinformatics tools are implemented in the Galaxy ecosystem, offering the development and dissemination of complex bioinformatic workflows. The modular workflow integrates MetaNovo (to generate a reduced protein database), SearchGUI/PeptideShaker and MaxQuant (to generate peptide-spectral matches (PSMs) and quantification), PepQuery2 (to verify the quality of PSMs), and Unipept and MSstatsTMT (for taxonomy and functional annotation). We have utilized this workflow in diverse clinical samples, from the characterization of nasopharyngeal swab samples to bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness via analysis of residual fluid from cervical swabs. The complete workflow, including training data and documentation, is available via the Galaxy Training Network, empowering non-expert researchers to utilize these powerful tools in their clinical studies. Workflow ; Metaproteomics ; Computer science ; Computational biology ; Metagenomics ; Proteomics ; Microbiome ; Identification (biology) ; Bioinformatics ; Biology ; Database Advanced Proteomics Techniques and Applications ; Genomics and Phylogenetic Studies ; Microbial Community Ecology and Physiology
Authors: Zhuo Zhang | Yandong Gong | Kai Pang
Source: Microwave and Optical Technology Letters (article, 2023-06-23)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Terahertz wideband wave plates designed by stacking multilayered metasurface with different geometries Abstract The use of metamaterials in terahertz (THz) polarization wave plates is widespread. Metallic metamaterials, however, typically operate within a constrained bandwidth and have a large ohmic loss. All‐dielectric metamaterials could address these issues. To achieve an ultrawide‐band at THz frequencies, a multilayered silicon metasurface with elliptical or rectangular pillars has been employed. According to simulations, the achromatic relative bandwidth of the dielectric metamaterial can remain flat within a broadband with the appropriate structural parameters. Additionally, a scoring system with error analysis is added to help with choosing the geometry of terahertz polarization wave plates with various layers of metasurface. Due to its flexible polarization control capability, the proposed multilayer metasurface may open the door for arbitrary phase delays of incident waves. Metamaterial ; Terahertz radiation ; Broadband ; Optics ; Wideband ; Polarization (electrochemistry) ; Materials science ; Bandwidth (computing) ; Achromatic lens ; Dielectric ; Optoelectronics ; Physics ; Computer science ; Telecommunications Metamaterials and Metasurfaces Applications ; Millimeter-Wave Propagation and Modeling ; Advanced Antenna and Metasurface Technologies
Authors: Jingxiao Xu | Martin D. B. Charlton
Source:  (article, 2023-03-10)
Field: Materials Science — Surfaces, Coatings and Films

Speed efficiency optimization for GPU accelerated rigorous coupled-wave analysis program Rigorous Coupled Wave Analysis (RCWA) method is highly efficient for the simulation of diffraction efficiency and field distribution patterns in periodic structures and textured optoelectronic devices such as VCSELs, LEDs, and DOEs. RCWA provides exact solutions provided the Fourier expansion has infinite order. In practice, the Fourier expansion must be truncated due to computer memory limitations. Researchers are trying to utilize fast convergence algorithms such as the ‘normal vector method’ and ‘Li’s rule’ which could obtain accurate TM mode results with fewer Fourier orders. However, to thoroughly investigating the behavior of a structure usually requires thousand and even millions of RCWA simulations which may last hours and days. GPU is highly suitable for solutions of complex systems allowing large-scale multi-threaded parallel programming (&lt; 1000 / low-end GPU, &lt;5k / high-end GPU) to speed up matrix computations significantly. In this paper, we present a high-speed RCWA program utilizing optimized CUDA-GPU code and MAGMA libraries. It achieves 2-6 X speedup compared to conventional multithreaded CPU-based code utilizing the Intel MKL library running on IRIDIS 5 super-computer (1 NVIDIA v100 GPU, 40 Intel Xeon Gold 6138 2.0GHz cores CPU) Speedup ; Parallel computing ; Computer science ; CUDA ; Xeon ; Xeon Phi ; Computational science ; SIMD ; Fast Fourier transform ; Algorithm Optical Coatings and Gratings ; Photonic and Optical Devices ; Photonic Crystals and Applications