jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Ralf Gabriels | Arthur Declercq | Robbin Bouwmeester | Sven Degroeve | Lennart Martens
Source: ChemRxiv (preprint, 2022-10-02)
Field: Chemistry — Spectroscopy

psm_utils: A high level Python API for parsing and handling peptide-spectrum-matches and proteomics search results A plethora of proteomics search engine output file formats are in circulation. This lack of standardized output files greatly complicates generic downstream processing of peptide-spectrum matches (PSMs) and PSM files. While standards exist to solve this problem, these are far from universally supported by search engines. Moreover, software libraries are available to read a selection of PSM file formats, but a light-weight package to parse PSM files into a unified data structure has been missing. Here, we present psm_utils, a Python package to read and write various PSM file formats and to handle peptidoforms, PSMs, and PSM lists in a unified and user-friendly Python-, command line-, and web-interface. psm_utils was developed with pragmatism and maintainability in mind, adhering to community standards and relying on existing packages where possible. The Python API and command line interface greatly facilitate handling various PSM file formats. Moreover, a user-friendly web application was built using psm_utils that allows anyone to interconvert PSM files and retrieve basic PSM statistics. psm_utils is freely available under the permissive Apache2 license at https://github.com/compomics/psm_utils. Python (programming language) ; Computer science ; Parsing ; File format ; Programming language ; Operating system ; Software ; Usability ; Maintainability ; Database ; World Wide Web ; Software engineering Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Chemical Synthesis and Analysis
Authors: Lilian R. Heil | Philip M. Remes | Jesse D. Canterbury | Ping Yip | William D. Barshop | Christine C. Wu | Michael J. MacCoss
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2022-12-02)
Field: Chemistry — Spectroscopy

Dynamic Data Independent Acquisition Mass Spectrometry with Real-Time Retrospective Alignment Abstract We report a data independent acquisition (DIA) strategy that dynamically adjusts the tandem mass spectrometry (MS/MS) windows during the chromatographic separation. The method focuses MS/MS acquisition on the most relevant mass range at each point in time – improving the quantitative sensitivity by increasing the time spent on each DIA window. We demonstrate an improved lower limit of quantification, on average, without sacrificing the number of peptides detected. Mass spectrometry ; Data acquisition ; Tandem mass spectrometry ; Computer science ; Dynamic range ; Chromatography ; Chemistry ; Analytical Chemistry (journal) Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Mingchao Wang | Shuang Weng | Zesong Li | Ying Jiang | Xiaohong Qian | Ping Xu | Wantao Ying
Source: Scientific Data (article, 2022-11-29)
Field: Chemistry — Spectroscopy

Proteomic overview of hepatocellular carcinoma cell lines and generation of the spectral library Cell lines are extensively used tools, therefore a comprehensive proteomic overview of hepatocellular carcinoma (HCC) cell lines and an extensive spectral library for data independent acquisition (DIA) quantification are necessary. Here, we present the proteome of nine commonly used HCC cell lines covering 9,208 protein groups, and the HCC spectral library containing 253,921 precursors, 168,811 peptides and 10,098 protein groups. The proteomic overview reveals the heterogeneity between different cell lines, and the similarity in proliferation and metastasis characteristics and drug targets-expression with tumour tissues. The HCC spectral library generating consumed 108 hours' runtime for data dependent acquisition (DDA) of 48 runs, 24 hours' runtime for database searching by MaxQuant version 2.0.3.0, and 1 hour' runtime for processing by Spectronaut<sup>TM</sup> version 15.2. The HCC spectral library supports quantification of 7,637 protein groups of triples 2-hour DIA analysis of HepG2 and discovering biological alteration. This study provides valuable resources for HCC cell lines and efficient DIA quantification on LC-Orbitrap platform, further help to explore the molecular mechanism and candidate therapeutic targets. Hepatocellular carcinoma ; Proteome ; Cell culture ; Computational biology ; Cell growth ; Metastasis ; Orbitrap ; Sorafenib ; Cell ; Computer science ; Biology ; Cancer research ; Bioinformatics ; Database ; Chemistry ; Cancer ; Mass spectrometry ; Biochemistry ; Genetics Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Genomics and Phylogenetic Studies
Authors: Elizabeth Nurmiyati Tamatjita | Rouly Doharma Sihite
Source: Information Engineering Express (article, 2022-01-01)
Field: Chemistry — Analytical Chemistry

Banana Ripeness Classification using HSV Colour Space and Nearest Centroid Classifier Banana is a common fruit which is found throughout Southeast Asia and are beneficial both as delicacy and as a dessert which is good for health. Although quite common and easy to obtain, many people today find it difficult to identify the correct ripeness stage of banana, especially when purchasing from traditional vendors, where varying degree of ripeness are available. This research sought for a possibility to classify banana ripeness by its peel colour with HSV colour space as the feature and classified using Nearest Centroid Classifier (NCC). 'Ambon Lumut', 'Kepok' and 'Raja' bananas are used as examples for the research as they are among the most common types of banana available for many use in Indonesia, and its ripeness is divided into 4 classes according to different usage of the banana: unripe, almost ripe, ripe, and overripe. Photographic images of 'Ambon Lumut', 'Kepok' and 'Raja' bananas are used as training and test data. The experiment is conducted using cleaned images which have the background removed, and this experiment also resulting in 73.33% recognition. The recognition results for each class respectively are: Green = 93.33%; Almost Ripe=80%; Ripe=66.67% and Overripe=53.33%. Ripeness ; Artificial intelligence ; Pattern recognition (psychology) ; HSL and HSV ; Classifier (UML) ; Mathematics ; Centroid ; Computer science ; Horticulture ; Ripening ; Biology Spectroscopy and Chemometric Analyses ; Banana Cultivation and Research ; Smart Agriculture and AI
Authors: Kajetan Koperwas | F. Kaśkosz | Frédéric Affouard | A. Grzybowski | Marian Paluch
Source: Scientific Reports (article, 2022-06-10)
Field: Materials Science — Materials Chemistry

The role of the diffusion in the predictions of the classical nucleation theory for quasi-real systems differ in dipole moment value Abstract In this paper, we examine the crystallization tendency for two quasi-real systems, which differ exclusively in the dipole moment's value. The main advantage of the studied system is the fact that despite that their structures are entirely identical, they exhibit different physical properties. Hence, the results obtained for one of the proposed model systems cannot be scaled to reproduce the results for another corresponding system, as it can be done for simple model systems, where structural differences are modeled by the different parameters of the intermolecular interactions. Our results show that both examined systems exhibit similar stability behavior below the melting temperature. This finding is contrary to the predictions of the classical nucleation theory, which suggests a significantly higher crystallization tendency for a more polar system. Our studies indicate that the noted discrepancies are caused by the kinetic aspect of the classical nucleation theory, which overestimates the role of diffusion in the nucleation process. Moment (physics) ; Dipole ; Nucleation ; Diffusion ; Value (mathematics) ; Statistical physics ; Classical nucleation theory ; Diffusion theory ; Mathematics ; Physics ; Classical mechanics ; Statistics ; Thermodynamics ; Quantum mechanics Material Dynamics and Properties ; nanoparticles nucleation surface interactions ; Theoretical and Computational Physics
Authors: V. Pavan Laxmipathy | Fei Wang | Michael Selzer | Britta Nestler
Source: Metals (article, 2022-02-22)
Field: Materials Science — Materials Chemistry

A Two-Dimensional Phase-Field Investigation on Unidirectionally Solidified Tip-Splitting Microstructures The onset of morphological instabilities along a solidifying interface has a tendency to influence the microstructural characteristics of cast alloys. In the present study, the initiation as well as the mechanism of microstructural pattern formation is investigated by a quantitative phase-field approach. For energetically isotropic interfaces, we show that the presence of grain boundary grooves promotes the initiation of morphological instabilities, and with progressive solidification, they subsequently amplify into tip-splitting microstructures. We also demonstrate that the grain boundary groove shape influences the amplification of the ridge-shaped instability near the pit region. The structural transition of tip splitting to dendritic microstructures is showcased through the effect of interfacial anisotropy. In addition, the prediction of the tip-splitting position is discussed through an analytical criterion, wherein the sign of the surface Laplacian of interfacial curvature dictates the formation of crest and trough positions in a tip-splitting pattern. In complete agreement with the sharp-interface theory, our phase-field simulations validate the analytically obtained tip-splitting position and suggest that the two tips evolve symmetrically on either side of the hindered concave region. Furthermore, the role of lattice anisotropy on the tip-splitting phenomenon is also discussed in detail. Materials science ; Microstructure ; Instability ; Faceting ; Curvature ; Perpendicular ; Isotropy ; Grain boundary ; Condensed matter physics ; Anisotropy ; Lattice (music) ; Geometry ; Mechanics ; Optics ; Composite material ; Physics Solidification and crystal growth phenomena ; Aluminum Alloy Microstructure Properties ; Fluid Dynamics and Thin Films
Authors: Ling Shi | Songzhe Xu | Heyu Lu | Chaoyue Chen | Sansan Shuai | Tao Hu | Andrew Kao | Jiang Wang | Zhongming Ren
Source: ISIJ International (article, 2022-08-15)
Field: Materials Science — Materials Chemistry

A High-efficiency Virtual Submesh Cellular Automata Method for Solidification Simulation with Low Mesh Anisotropy The cellular automata (CA) method has been widely used in microstructure simulation during solidification, but it is time-consuming when used for multiple orientations and large-scale computation. In this work, a novel high-efficiency virtual submesh cellular automata (VISCA) method is proposed to reduce the mesh-induced artificial anisotropy. This method conceptually divides the mesh into a series of submeshes by giving a unique index to each CA cell. The proposed VISCA method results in a good accuracy in all orientations using uniform mesh, while an aggressive time stepping can be used. Compared with the previous CA models, the VISCA method exhibits a significant reduction in computational cost and improvement in computational efficiency. The nucleation is simulated based on a continuous nucleation model, and the Kurz-Giovanola-Trivedi (KGT) model is used to simulate the growth of the grains nucleated in the bulk material. The proposed VISCA method is comprehensively validated using an analytical solution, a casting simulation, and a directional solidification experiment. A quantitative comparison with the experiment in the directional solidification example shows that the difference in position of Columnar-to-Equiaxed Transition (CET) between the simulation and the experiment is within 1 mm while the length of directional solidification is 60 mm. Cellular automaton ; Equiaxed crystals ; Nucleation ; Directional solidification ; Anisotropy ; Computer science ; Computation ; Materials science ; Work (physics) ; Reduction (mathematics) ; Computational science ; Mechanics ; Algorithm ; Parallel computing ; Biological system ; Microstructure ; Mathematics ; Geometry ; Thermodynamics ; Composite material ; Physics Solidification and crystal growth phenomena ; Aluminum Alloy Microstructure Properties ; Metallurgy and Material Forming
Authors: Matteo Manica | Jannis Born | Joris Cadow | Dimitrios Christofidellis | Ashish Dave | Dean Clarke | Yves Gaëtan Nana Teukam | Giorgio Giannone | Samuel C. Hoffman | Matthew J. Buchan | Vijil Chenthamarakshan | Timothy P. Donovan | Hsiang Han Hsu | Federico Zipoli | Oliver Schilter | Akihiro Kishimoto | Lisa Hamada | Inkit Padhi | Karl Wehden | Lauren McHugh | Alexy Khrabrov | Payel Das | Seiji Takeda | John R. Smith
Source: arXiv (Cornell University) (preprint, 2022-07-08)
Field: Materials Science — Materials Chemistry

Accelerating Material Design with the Generative Toolkit for Scientific Discovery With the growing availability of data within various scientific domains, generative models hold enormous potential to accelerate scientific discovery. They harness powerful representations learned from datasets to speed up the formulation of novel hypotheses with the potential to impact material discovery broadly. We present the Generative Toolkit for Scientific Discovery (GT4SD). This extensible open-source library enables scientists, developers, and researchers to train and use state-of-the-art generative models to accelerate scientific discovery focused on material design. Scientific discovery ; Generative grammar ; Computer science ; Data science ; Generative model ; Generative Design ; Scientific literature ; Artificial intelligence ; Engineering ; Cognitive science Machine Learning in Materials Science ; Scientific Computing and Data Management ; Data Visualization and Analytics
Authors: Nisha Thanua | Ganesh B. Kumbhar
Source: IEEE Transactions on Plasma Science (article, 2022-12-29)
Field: Materials Science — Materials Chemistry

Plasma Dynamics-Based Modeling and Analysis of Partial Discharge in Voids Inside Insulation of Power Transformer Partial discharge (PD) modeling in voids is being studied; earlier, however, most studies considered a simplified model with many adjustable parameters. In this article, a comprehensive comparative study is being done with possible void shapes in transformer insulation using a modified drift-diffusion model with single adjustable free parameter of the electron generation rate and considering the secondary ionization process. In simulation studies, plasma-dynamics-based models are used to better understand PD activity inside voids. A drift-diffusion model is used for investigating the PD phenomena inside air-filled voids of commonly found geometries, namely, cylindrical, spherical, and ellipsoidal, bounded by different insulating materials in power transformers. The model is applicable for all void shapes and material of insulation. PD inception field, residual field, space charge density, and other electrical properties are obtained, and all the possible parameters are incorporated in the model thus improving its accuracy. In this article, the effect of void shape and insulation material on the PD activity is obtained. The inception electric field at which the discharge initiates is found to be lowest in case of spherical void resulting in easy formation of plasma discharge. This study thus uncovers the physical mechanism of PD inside insulation thus helping in maintenance and optimum design of transformer insulation. Partial discharge ; Insulation system ; Materials science ; Void (composites) ; Mechanics ; Transformer ; Plasma ; Electric field ; Porosity ; Composite material ; Voltage ; Electrical engineering ; Physics ; Engineering High voltage insulation and dielectric phenomena ; Power Transformer Diagnostics and Insulation ; Lightning and Electromagnetic Phenomena
Authors: Alexey Zhokh | T. G. Serebrii | P. E. Strizhak
Source: Chemical Physics Letters (article, 2022-08-04)
Field: Materials Science — Materials Chemistry

Diffusion-controlled adsorption–desorption of C6 hydrocarbons by multiwall carbon nanotubes The adsorption–desorption of n-hexane, cyclohexane, and benzene on multiwall carbon nanotubes is investigated using the quartz crystal microbalance technique. Desorption kinetics is found to be diffusion-controlled. The standard Fickian diffusion models for short and long times have been applied to quantify the desorption kinetics. Considering surface diffusion as a rate-limiting step of desorption, the estimated surface diffusion coefficients for all hydrocarbons are of order 10-14 m2/s. This is an order of magnitude lower compared to surface diffusion coefficient on various carbon materials. The surface diffusion coefficient increases with an increase in surface loading. Desorption ; Diffusion ; Adsorption ; Quartz crystal microbalance ; Surface diffusion ; Carbon nanotube ; Kinetics ; Chemistry ; Cyclohexane ; Analytical Chemistry (journal) ; Fick's laws of diffusion ; Materials science ; Chemical engineering ; Thermodynamics ; Physical chemistry ; Organic chemistry ; Nanotechnology Carbon Nanotubes in Composites ; Graphene research and applications ; Nanopore and Nanochannel Transport Studies
Authors: Tae-Hyun Kim | Chihyun Seo | Jaeyoung Seon | Anujin Battulga | Yuhoon Hwang
Source: International Journal of Molecular Sciences (article, 2022-10-13)
Field: Materials Science — Materials Chemistry

Granulation of Bismuth Oxide by Alginate for Efficient Removal of Iodide in Water The granulation of bismuth oxide (BO) by alginate (Alg) and the iodide adsorption efficacy of Alg-BO for different initial iodide concentrations and contact time values were examined. The optimal conditions for Alg-BO granulation were identified by controlling the weight ratio between Alg and BO. According to the batch iodide adsorption experiment, the Alg:BO weight ratio of 1:20 was appropriate, as it yielded a uniform spherical shape. According to iodide adsorption isotherm experiments and isotherm model fitting, the maximum sorption capacity (<i>q</i><sub>m</sub>) was calculated to be 111.8 mg/g based on the Langmuir isotherm, and this value did not plateau even at an initial iodide concentration of 1000 mg/L. Furthermore, iodide adsorption by Alg-BO occurred as monolayer adsorption by the chemical interaction and precipitation between bismuth and iodide, followed by physical multilayer adsorption at a very high concentration of iodide in solution. The iodide adsorption over time was fitted using the intraparticle diffusion model. The results indicated that iodide adsorption was proceeded by boundary layer diffusion during 480 min and reached the plateau from 1440 min to 5760 min by intraparticle diffusion. According to the images obtained using cross-section scanning electron microscopy assisted by energy-dispersive spectroscopy, the adsorbed iodide interacted with the BO in Alg-BO through Bi-O-I complexation. This research shows that Alg-BO is a promising iodide adsorbent owing to its high adsorption capacity, stability, convenience, and ability to prevent secondary pollution. Iodide ; Adsorption ; Chemistry ; Bismuth ; Langmuir adsorption model ; Inorganic chemistry ; Nuclear chemistry ; Physical chemistry ; Organic chemistry Covalent Organic Framework Applications ; Chemical Synthesis and Characterization ; Metal-Organic Frameworks: Synthesis and Applications
Authors: J.K. Efavi | Nathaniel Yeboah | Richard Y. Abrokwah | Emmanuel Nyankson
Source: Water Air & Soil Pollution (article, 2022-08-01)
Field: Materials Science — Biomaterials

Adsorption Potential, Kinetic, and Thermodynamic Studies of Halloysite-Based Magnetic Field-Responsive Adsorbent Adsorption ; Halloysite ; Thermogravimetric analysis ; Freundlich equation ; Aqueous solution ; Methylene blue ; Chemistry ; Fourier transform infrared spectroscopy ; Chemical engineering ; Brilliant green ; Materials science ; Nuclear chemistry ; Organic chemistry ; Composite material ; Catalysis Clay minerals and soil interactions ; Iron oxide chemistry and applications ; Layered Double Hydroxides Synthesis and Applications
Authors: Valéria V.L. Carvalho | Diana Pinto | Nina Paula Gonçalves Salau | Luiz Antônio de Almeida Pinto | Tito Roberto Sant’Anna Cadaval | Luís F.O. Silva | Toni Jefferson Lopes | Guilherme Luiz Dotto
Source: Separation and Purification Technology (article, 2022-04-11)
Field: Materials Science — Biomaterials

Modeling of anthocyanins adsorption onto chitosan films: An approach using the pore volume and surface diffusion model Adsorption ; Mass transfer ; Chitosan ; Diffusion ; Mass transfer coefficient ; Chemistry ; Biot number ; Anthocyanin ; Freundlich equation ; Particle (ecology) ; Chemical engineering ; Volume (thermodynamics) ; Red cabbage ; Chromatography ; Analytical Chemistry (journal) ; Thermodynamics ; Organic chemistry ; Food science Nanocomposite Films for Food Packaging ; Biochemical Analysis and Sensing Techniques ; Sensory Analysis and Statistical Methods
Authors: Zhiyuan Han | Rohit Vaidya | Opeyemi H. Arogundade | Liang Ma | Mohammad U. Zahid | Suresh Sarkar | Chia-Wei Kuo | Paul R. Selvin | Andrew M. Smith
Source: Chemistry of Materials (article, 2022-05-09)
Field: Materials Science — Materials Chemistry

Structural Design of Multidentate Copolymers as Compact Quantum Dot Coatings for Live-Cell Single-Particle Imaging Quantum dots (QDs) are a class of semiconductor nanocrystal used broadly as fluorescent emitters for analytical studies in the life sciences. These nanomaterials are particularly valuable for single-particle imaging and tracking applications in cells and tissues. An ongoing technological goal is to reduce the hydrodynamic size of QDs to enhance access to sterically hindered biological targets. Multidentate polymer coatings are a focus of these efforts and have resulted in compact and stable QDs with hydrodynamic diameters near 10 nm. New developments are needed to reach smaller sizes to further enhance transport through pores in cells and tissues. Here, we describe how structural characteristics of linear multidentate copolymers determine hydrodynamic size, colloidal stability, and biomolecular interactions of coated QDs. We tune copolymer composition, degree of polymerization, and hydrophilic group length, and coat polymers on CdSe and (core)shell (HgCdSe)CdZnS QDs. We find that a broad range of polymer structures and compositions yield stable colloidal dispersions; however, hydrodynamic size minimization and nonspecific binding resistance can only be simultaneously achieved within a narrow range of properties, requiring short polymers, balanced compositions, and small nanocrystals. In quantitative single-molecule imaging assays in synapses of live neurons, size reduction progressively increases labeling specificity of neurotransmitter receptors. Our findings provide a design roadmap to next-generation QDs with sizes approaching fluorescent protein labels that are the standard of many live-cell biomolecular studies. Quantum dot ; Nanotechnology ; Materials science ; Polymer ; Nanomaterials ; Nanocrystal ; Nanoparticle ; Particle size ; Polymerization ; Fluorescence ; Particle (ecology) ; Colloid ; Copolymer ; Chemical engineering ; Chemistry ; Organic chemistry Quantum Dots Synthesis And Properties ; Advanced biosensing and bioanalysis techniques ; Carbon and Quantum Dots Applications