jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Eduardo Rolim de Oliveira | Pedro H. Bugatti | Priscila T. M. Saito
Source: PLoS ONE (article, 2023-08-25)
Field: Chemistry — Analytical Chemistry

Assessment of clustering techniques to support the analyses of soybean seed vigor Soy is the main product of Brazilian agriculture and the fourth most cultivated bean globally. Since soy cultivation tends to increase and due to this large market, the guarantee of product quality is an indispensable factor for enterprises to stay competitive. Industries perform vigor tests to acquire information and evaluate the quality of soy planting. The tetrazolium test, for example, provides information about moisture damage, bedbugs, or mechanical damage. However, the verification of the damage reason and its severity are done by an analyst, one by one. Since this is massive and exhausting work, it is susceptible to mistakes. Proposals involving different supervised learning approaches, including active learning strategies, have already been used, and have brought significant results. Therefore, this paper analyzes the performance of non-supervised techniques for classifying soybeans. An extensive experimental evaluation was performed, considering (9) different clustering algorithms (partitional, hierarchical, and density-based) applied to 5 image datasets of soybean seeds submitted to the tetrazolium test, including different damages and/or their levels. To describe those images, we considered 18 extractors of traditional features. We also considered four metrics (accuracy, FOWLKES, DAVIES, and CALINSKI) and two-dimensionality reduction techniques (principal component analysis and t-distributed stochastic neighbor embedding) for validation. Results show that this paper presents essential contributions since it makes it possible to identify descriptors and clustering algorithms that shall be used as preprocessing in other learning processes, accelerating and improving the classification process of key agricultural problems. Cluster analysis ; Computer science ; Machine learning ; Artificial intelligence ; Principal component analysis ; Quality (philosophy) ; Preprocessor ; Product (mathematics) ; Data mining ; Pattern recognition (psychology) ; Mathematics Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI
Authors: Yaping Hou | Jianyong Mao | Tianlun Li | Yunfan Xu | Weitao Jiang | Yanpeng Zhang | Lei Zhang
Source: Journal of Physics D Applied Physics (article, 2023-02-17)
Field: Materials Science — Electronic, Optical and Magnetic Materials

All-optical polarization tuning based on an intensity-dependent nonlinear metasurface Abstract Active control of light polarization at the nanoscale is essential for integrated photonic devices. Here, an all-optical approach is proposed to tune the polarization state of near-infrared light using a nonlinear metasurface. Based on the large intensity-dependent refractive index change of epsilon-near-zero (ENZ) materials, a phase difference between two orthogonal electric fields at ENZ wavelength can be continuously tuned in a range larger than 0.61 π by varying the incident light power. The polarization state of the reflected light can thus be actively tuned from linear to circular state via an all-optical approach. Notably, abundant polarization states can be obtained by altering the polarization angle of incident light. The proposed all-optical approach is promising for tunable photonic functionalities of practical applications. Polarization (electrochemistry) ; Optics ; Photonics ; Ray ; Optoelectronics ; Wavelength ; Refractive index ; Polarization rotator ; Materials science ; Physics ; Birefringence Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Photonic Crystals and Applications
Authors: David Bouyssié | Pınar Altıner | Salvador Capella-Gutiérrez | José M. Fernández | Yanick Hagemeijer | Péter Horvatovich | Martin Hubálek | Fredrik Levander | Pierluigi Mauri | Magnus Palmblad | Wolfgang Raffelsberger | Laura Rodríguez‐Navas | Dario Di Silvestre | Balázs Kunkli | Julian Uszkoreit | Yves Vandenbrouck | Juan Antonio Vizcaíno | Dirk Winkelhardt | Veit Schwämmle
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2023-10-03)
Field: Chemistry — Spectroscopy

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows Abstract Proteomics research encompasses a wide array of experimental designs, resulting in diverse datasets varying in structure and properties. This diversity has led to a considerable variety of software solutions for data analysis, each of them using multiple tools with different algorithms for operations like peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. Computational workflows combine these algorithms to facilitate end-to-end analysis, spanning from raw data to detecting differentially regulated proteins. We introduce WOMBAT-P, a versatile platform designed for the automatic benchmarking and comparison of bottom-up label-free proteomics workflows. By standardizing software parameterization and workflow outputs, WOMBAT-P empowers an objective comparison of four commonly utilized data analysis workflows. Furthermore, WOMBAT-P streamlines the processing of public data based on the provided metadata, with an optional specification of 30 parameters. Wombat-P can use Sample and Data Relationship Format for Proteomics (SDRF-Proteomics) as the file input to simply process annotated local or ProteomeXchange deposited datasets. This feature offers a shortcut for data analysis and facilitates comparisons among diverse outputs. Through an examination of experimental ground truth data and a realistic biological dataset, we unveil significant disparities and a low overlap between identified and quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of four workflows (on the same dataset) using a wide range of benchmarking metrics but also provides insights into the capabilities of different software solutions. These metrics support researchers in selecting the most suitable workflow for their specific dataset. The modular architecture of WOMBAT-P promotes extensibility and customization, making it an ideal platform for testing newly developed software tools within a realistic data analysis context. Computer science ; Workflow ; Benchmarking ; Software ; Data mining ; Pipeline (software) ; Proteomics ; Shotgun proteomics ; Database ; Programming language Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Chunyan Zhang | Xinxing Li
Source: Journal of Food Process Engineering (article, 2023-07-12)
Field: Chemistry — Analytical Chemistry

De‐noising method of aquatic product image with foreign matters based on improved wavelet transform and bilateral filter Abstract Aiming at the strong spot noise caused by the reflection of meat slices in fish image with foreign matters that collected by ordinary camera or Single Lens Reflex (SLR) camera, we proposed an improved wavelet transform and bilateral filtering algorithm to reduce the noise of image. In this paper, our algorithm absorbed the advantages of wavelet threshold de‐noising algorithm and bilateral filtering algorithm, the wavelet threshold de‐noising algorithm being used for high frequency components and bilateral filtering being used for low frequency components, which not only achieved the effect of eliminating noise and weakening light spot, but also protected the details of the image. In the experiment, in order to verify the effectiveness of the proposed algorithm, we used the traditional bilateral filtering, Gaussian filtering and median filtering algorithms to process 500 salmon fish images which had residual fishbone, respectively. Since the original image itself was a noisy image, it was impossible to evaluate the noise reduction effect by using an algorithm that requires a noiseless image as a reference image, so we used five methods to evaluate the quality of the image processed by each algorithm, which were Blind/Referenceless Image Spatial QUality Evaluator (BRISQE), Cumulative Probability of Blur Detection (CPBD), variance, image entropy, and operation speed. Among them, BRISQE and CPBD could quantitatively reflect the overall quality of the image, the lower the BRISQE score or the higher the CPBD score, the better the quality of the image. Compared with other algorithms, the BRISQE score and CPBD score of the image processed by our algorithm were the best, with the average scores reaching 20.65 and .8421, respectively. Experimental results showed that the improved algorithm in this paper can effectively eliminate this kind of strong spot noise. The processed image has achieved better visual effect in both subjective and objective level. Artificial intelligence ; Median filter ; Computer vision ; Bilateral filter ; Computer science ; Image quality ; Noise (video) ; Pattern recognition (psychology) ; Wavelet ; Discrete wavelet transform ; Mathematics ; Wavelet transform ; Image (mathematics) ; Image processing Spectroscopy and Chemometric Analyses ; Advanced Image Fusion Techniques ; Image Enhancement Techniques
Authors: Anthony Sementilli | Rolando F. Rengifo | Wei Li | Andrew M. Stewart | Katie L. Stewart | Umar T. Twahir | Youngsun Kim | Jipeng Yue | Anil Mehta | Jason Shearer | Kurt Warncke | David G. Lynn
Source: Inorganic Chemistry (article, 2023-12-21)
Field: Chemistry — Electrochemistry

Engineering Synthetic Electron Transfer Chains from Metallopeptide Membranes The energetic and geometric features enabling redox chemistry across the copper cupredoxin fold contain key components of electron transfer chains (ETC), which have been extended here by templating the cross-β bilayer assembly of a synthetic nonapeptide, HHQALVFFA-NH<sub>2</sub> (K16A), with copper ions. Similar to ETC cupredoxin plastocyanin, these assemblies contain copper sites with blue-shifted (<i>λ</i><sub><i>max</i></sub> 573 nm) electronic transitions and strongly oxidizing reduction potentials. Electron spin echo envelope modulation and X-ray absorption spectroscopies define square planar Cu(II) sites containing a single His ligand. Restrained molecular dynamics of the cross-β peptide bilayer architecture support metal ion coordination stabilizing the leaflet interface and indicate that the relatively high reduction potential is not simply the result of distorted coordination geometry (entasis). Cyclic voltammetry (CV) supports a charge-hopping mechanism across multiple copper centers placed 10-12 Å apart within the assembled peptide leaflet interface. This metal-templated scaffold accordingly captures the electron shuttle and cupredoxin functionality in a peptide membrane-localized electron transport chain. Chemistry ; Electron transfer ; Crystallography ; Copper ; Plastocyanin ; Bilayer ; Electron transport chain ; Redox ; Membrane ; Cyclic voltammetry ; Chemical physics ; Electrochemistry ; Inorganic chemistry ; Photochemistry ; Physical chemistry ; Electrode ; Organic chemistry Electrochemical Analysis and Applications ; Porphyrin and Phthalocyanine Chemistry ; Molecular Sensors and Ion Detection
Authors: Long Zhang | Anton Kozhevnikov | T. C. Schulthess | S. B. Trickey | Hai‐Ping Cheng
Source: The Journal of Chemical Physics (article, 2023-06-16)
Field: Materials Science — Electronic, Optical and Magnetic Materials

All-electron APW+<i>lo</i> calculation of magnetic molecules with the SIRIUS domain-specific package We report APW+lo (augmented plane wave plus local orbital) density functional theory (DFT) calculations of large molecular systems using the domain specific SIRIUS multi-functional DFT package. The APW and FLAPW (full potential linearized APW) task and data parallelism options and the advanced eigen-system solver provided by SIRIUS can be exploited for performance gains in ground state Kohn-Sham calculations on large systems. This approach is distinct from our prior use of SIRIUS as a library backend to another APW+lo or FLAPW code. We benchmark the code and demonstrate performance on several magnetic molecule and metal organic framework systems. We show that the SIRIUS package in itself is capable of handling systems as large as a several hundred atoms in the unit cell without having to make technical choices that result in the loss of accuracy with respect to that needed for the study of magnetic systems. Benchmark (surveying) ; Density functional theory ; Solver ; Sirius ; Physics ; Domain (mathematical analysis) ; Code (set theory) ; Computational science ; Computer science ; Computational physics ; Quantum mechanics ; Mathematics ; Mathematical analysis ; Set (abstract data type) Magnetism in coordination complexes ; Advanced NMR Techniques and Applications ; Advanced Chemical Physics Studies
Authors: Ambroise de Izarra | François‐Xavier Coudert | Alain H. Fuchs | Anne Boutin
Source: ChemRxiv (preprint, 2023-09-01)
Field: Chemistry — Inorganic Chemistry

Predictive Thermodynamic Model for Intrusion of Electrolyte Aqueous Solutions in Nanoporous Materials We performed Monte Carlo simulations in the osmotic ensemble in three representative hypothetical pure-silica zeolites that are silicalite-1, chabazite and faujasite for which adsorption isotherm of water has been calculated from grand canonical Monte Carlo simulations. Monte Carlo moves in the osmotic ensemble to insert electrolyte reveal that ions do not penetrate the zeosils at water intrusion pressure because they are better solvated in the bulk for low-diameter pore zeosils, which is associated to a lower ion solvation. Then, Chemical potential of water in electrolyte solutions has been calculated and highlight the same dependency in pressure as the chemical potential of pure water. From these conclusions, we propose a thermodynamic model that revisit the law of osmotic pressure in order to predict the intrusion pressure in zeosils taking account of the nature of electrolytes in solution. Electrolyte ; Monte Carlo method ; Solvation ; Thermodynamics ; Osmotic coefficient ; Aqueous solution ; Nanoporous ; Chemistry ; Water model ; Materials science ; Ion ; Molecular dynamics ; Activity coefficient ; Physical chemistry ; Physics ; Computational chemistry ; Mathematics Zeolite Catalysis and Synthesis ; Nanopore and Nanochannel Transport Studies ; Spectroscopy and Quantum Chemical Studies
Authors: Rita Cimino | Emanuela Gatto | Marta De Zotti | Fernando Formaggio | Claudio Toniolo | Micaela Giannetti | Antonio Palleschi | Carlos Serpa | Mariano Venanzi
Source: Journal of Photochemistry and Photobiology (article, 2023-06-12)
Field: Materials Science — Materials Chemistry

Peptide-bridged bis-porphyrin compounds: A photophysical and molecular dynamics study Covalently linked peptide-porphyrin compounds are most suitable systems for fundamental studies aiming to the comprehension of the mechanisms driving photoinduced energy/electron transfer processes. Mimicking photosynthetic units, the porphyrin groups act as antenna moieties while the peptide chain is the active medium through which energy and/or electron funneling occur. In this contribution we studied the transfer of excitation between two identical tetraphenylporphyrin groups connected by short peptide chains of different length formed by non-coded conformationally constrained α-amino acids, i.e., Cα-methylvaline. The photophysical events following porphyrin photoexcitation were characterized from the microsecond to the picosecond time region by time-resolved spectroscopy techniques. Ultrafast transient absorption measurements revealed the presence of a transient species that we assign to a self-trapped exciton migrating through the peptide chain. The exciton species propagates the electronic coupling between the two porphyrin groups giving rise to a characteristic bisignate band measured by circular dichroism experiments. Molecular dynamics simulations strongly suggest that the long lifetime (hundreds of picoseconds) of the exciton species is determined by the rigidity of the Cα-methylvaline residues, that inhibited energy relaxation pathways coupled to torsional motions of the peptide chain. Porphyrin ; Ultrafast laser spectroscopy ; Photochemistry ; Picosecond ; Photoexcitation ; Chemistry ; Tetraphenylporphyrin ; Exciton ; Peptide ; Electron transfer ; Molecular dynamics ; Covalent bond ; Photoinduced electron transfer ; Spectroscopy ; Crystallography ; Computational chemistry ; Excited state ; Organic chemistry ; Atomic physics ; Physics Porphyrin and Phthalocyanine Chemistry ; Photosynthetic Processes and Mechanisms ; Photoreceptor and optogenetics research
Authors: Vladimir A. Fedorov | Sergey Sergeevich Khruschev | I. B. Kovalenko
Source: Computer Research and Modeling (article, 2023-06-01)
Field: Chemistry — Spectroscopy

Analysis of Brownian and molecular dynamics trajectories of to reveal the mechanisms of protein-protein interactions , - . f . - , 134 . , f , - . K122 Statistical physics ; Brownian dynamics ; Brownian motion ; Dynamics (music) ; Protein dynamics ; Molecular dynamics ; Physics ; Computational biology ; Biology ; Quantum mechanics Advanced Proteomics Techniques and Applications ; Genetics, Bioinformatics, and Biomedical Research ; Advanced Biosensing Techniques and Applications
Authors: Carlotta Pieroni | Eduarda Sangiogo Gil | Lea-Maria Ibele | Maurizio Persico | Giovanni Granucci | Federica Agostini
Source: ChemRxiv (preprint, 2023-09-11)
Field: Materials Science — Materials Chemistry

Investigating the photodynamics of trans-azobenzene with coupled trajectories In this work, we present the first implementation of the coupled-trajectory Tully surface hopping (CT-TSH) suitable for applications to molecular systems. We combine CT-TSH with the semiempirical Floating Occupation Molecular Orbitals-Configuration Interaction (FOMO-CI) electronic structure method to investigate the photoisomerization dynamics of trans-azobenzene. Our study shows that CT-TSH can capture correctly decoherence effects in this system, yielding consistent electronic and nuclear dynamics in agreement with (standard) decoherence-corrected TSH. Specifically, CT-TSH is derived from the exact factorization and the electronic coefficients’ evolution is directly influenced by the coupling of trajectories, resulting in the improvement of internal consistency if compared to standard TSH. Quantum decoherence ; Photoisomerization ; Azobenzene ; Surface hopping ; Factorization ; Coupling (piping) ; Atomic orbital ; Trajectory ; Consistency (knowledge bases) ; Work (physics) ; Molecular dynamics ; Physics ; Photochemistry ; Chemistry ; Quantum mechanics ; Materials science ; Computer science ; Molecule ; Isomerization ; Electron ; Catalysis ; Algorithm ; Quantum ; Artificial intelligence ; Organic chemistry Photochromic and Fluorescence Chemistry ; Photoreceptor and optogenetics research ; Spectroscopy and Quantum Chemical Studies
Authors: Raphael Schoof | Johannes Niermann | Alexander Dyck | Thomas Böhlke | Willy Dörfler
Source: arXiv (Cornell University) (preprint, 2023-10-09)
Field: Materials Science — Biomaterials

Modeling and Simulation of Chemo-Elasto-Plastically Coupled Battery Active Particles As an anode material for lithium-ion batteries, amorphous silicon offers a significantly higher energy density than the graphite anodes currently used. Alloying reactions of lithium and silicon, however, induce large deformation and lead to volume changes up to 300%. We formulate a thermodynamically consistent continuum model for the chemo-elasto-plastic diffusion-deformation behavior of amorphous silicon and it's alloy with lithium based on finite deformations. In this paper, two plasticity theories, i.e. a rate-independent theory with linear isotropic hardening and a rate-dependent one, are formulated to allow the evolution of plastic deformations and reduce occurring stresses. Using modern numerical techniques, such as higher order finite element methods as well as efficient space and time adaptive solution algorithms, the diffusion-deformation behavior resulting from both theories is compared. In order to further increase the computational efficiency, an automatic differentiation scheme is used, allowing for a significant speed up in assembling time as compared to an algorithmic linearization for the global finite element Newton scheme. Both plastic approaches lead to a more heterogeneous concentration distribution and to a change to tensile tangential Cauchy stresses at the particle surface at the end of one charging cycle. Different parameter studies show how an amplification of the plastic deformation is affected. Interestingly, an elliptical particle shows only plastic deformation at the smaller half axis. With the demonstrated efficiency of the applied methods, results after five charging cycles are also discussed and can provide indications for the performance of lithium-ion batteries in long term use. Battery (electricity) ; Materials science ; Computer science ; Physics ; Thermodynamics biodegradable polymer synthesis and properties ; Polymer Nanocomposites and Properties ; Advanced Theoretical and Applied Studies in Material Sciences and Geometry
Authors: Gaurav Kumar | Datong Zhang | Gyoko Nagayama
Source: Proceedings of International Exchange and Innovation Conference on Engineering & Sciences (IEICES) (article, 2023-10-19)
Field: Materials Science — Surfaces, Coatings and Films

OpenFOAM-based Numerical Simulation on Capillary Flow in Closed Hierarchical Microchannels Surfaces with hierarchical micro/nanoscale structures result in unique flow characteristics in nature. The validity of the classical Lucas–Washburn equation has been argued for the capillary-driven flow in open rectangular microchannels. Meanwhile, there is no guarantee that the Lucas–Washburn equation is valid for the capillary-driven flow in hierarchical microchannels. Here, we perform 3D numerical simulations using the OpenFOAM Volume-of-Fluid method to predict the capillary-driven flow of water in a closed hierarchical microchannel. It is found that the imbibition rate is increased in the hierarchical microchannel, and the mean imbibition rate shows a dependence on the height of minor channel. Consequently, an optimized hierarchical channel geometry has been proposed to improve the capillary flow in microchannels. Capillary action ; Flow (mathematics) ; Mechanics ; Computer science ; Materials science ; Physics Surface Modification and Superhydrophobicity ; Lattice Boltzmann Simulation Studies ; Heat Transfer and Optimization