jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Pavol Skubák
Source: Acta Crystallographica Section D Structural Biology (article, 2024-06-11)
Field: Materials Science — Materials Chemistry

Deep-learning map segmentation for protein X-ray crystallographic structure determination When solving a structure of a protein from single-wavelength anomalous diffraction X-ray data, the initial phases obtained by phasing from an anomalously scattering substructure usually need to be improved by an iterated electron-density modification. In this manuscript, the use of convolutional neural networks (CNNs) for segmentation of the initial experimental phasing electron-density maps is proposed. The results reported demonstrate that a CNN with U-net architecture, trained on several thousands of electron-density maps generated mainly using X-ray data from the Protein Data Bank in a supervised learning, can improve current density-modification methods. Substructure ; Iterated function ; Phaser ; Segmentation ; Convolutional neural network ; Electron density ; Protein Data Bank ; Artificial intelligence ; Computer science ; Net (polyhedron) ; Pattern recognition (psychology) ; X-ray ; Scattering ; Crystallography ; Physics ; Protein structure ; Electron ; Mathematics ; Optics ; Chemistry ; Geometry ; Nuclear magnetic resonance ; Mathematical analysis ; Engineering Enzyme Structure and Function ; Protein Structure and Dynamics ; Advanced Electron Microscopy Techniques and Applications
Authors: Diego González‐García | Florian Pohl | Felix Marxer | Stepan Petrovich Krasheninnikov | Renat Almeev | François Holtz
Source: European Journal of Mineralogy (article, 2024-08-23)
Field: Materials Science — Ceramics and Composites

Chemical interdiffusion between Na-series tephritic and phonolitic melts with different H<sub>2</sub>O content, temperature, and oxygen fugacity values Abstract. The diffusive exchange of major elements in Na-series tephrite–phonolite diffusion couples with compositions relevant to the Canary Islands magmatism was determined at 300 MPa and variable H2O concentrations (0.3 wt % to 3.3 wt %), temperatures (1150 to 1300 °C), and fO2 levels (NNO−1.5 to NNO+1.7). Composition-dependent effective binary diffusion coefficients were determined from concentration–distance profiles. Results show a wide range of diffusivities for different cations, consistently following the sequence Na ≫ Al ≫ K ≥ Mg = Fe = Ca &gt; Si &gt; Ti, with a mild diffusivity contrast (0.2–0.8 log units) between tephritic and phonolitic melts. Na is the fastest component, with diffusivities falling ∼1.0 log units above those of Si for any given condition. An anomalously fast Al diffusion is observed, with DAl falling ∼0.4 log units above Si and ∼0.6 log units below Na, suggesting a prevalence of Al–alkali coupling across our range of run conditions. The relationships between log D and H2O content in melt for all cations in an intermediate composition are strongly nonlinear and can be fitted using an exponential function with a convergence in diffusion coefficients for different temperatures with increasing H2O content. Thus, Arrhenius analyses result in a decrease in activation energies from 222–293 kJ mol−1 at 1.7 wt % H2O to 48–112 kJ mol−1 at 3.0 wt % H2O. These results provide new data on chemical interdiffusion in highly alkaline Na-rich melts and suggest that H2O content plays a key role in increasing the chemical efficiency of magma mixing at low temperatures. The obtained dataset is used to test chemical controls of magma mixing in the El Abrigo ignimbrite, Tenerife, where banded pumices involving basanitic–tephritic to phonolitic magmas are common in several compositionally bimodal ignimbrite units. Mineral redox buffer ; Fugacity ; Oxygen ; Mineralogy ; Series (stratigraphy) ; Analytical Chemistry (journal) ; Content (measure theory) ; Chemistry ; Geology ; Thermodynamics ; Environmental chemistry ; Physical chemistry ; Physics ; Organic chemistry ; Mathematics Glass properties and applications ; Solid-state spectroscopy and crystallography ; Mineralogy and Gemology Studies
Authors: Shahid Iqbal | Aamir Hussain | Syed Furqan Qadri | Abdul Razzaq | Muhammad Talha Jahangir
Source: Journal of agriculture and biology. (article, 2024-11-06)
Field: Chemistry — Analytical Chemistry

Automated Identification of Citrus Fruits Nutrients Through Non-destructive Analysis The development of digital technology has played a significant role in digitizing this world. This technology has enabled the storage, processing, and analysis of data using a cloud-based platform that benefits farmers. Image processing is a technique that involves performing specific tasks on an image to extract useful information. Citrus fruits such as mandarins, lemons, grapefruits, and oranges are the most widely grown fruits in the world. Citrus is a large plant cultivated primarily in the world's tropical regions due to its abundance of vitamin C, Total Soluble Solids (TSS), Titratable Acidity (TA), and pH. To find out these nutrients, we need to consult with a horticulturist. The traditional approach is costly, complex, and time-consuming for a common farmer. The study aims to provide an efficient and cost-effective solution to achieve the same goal. This work trains an efficient deep learning-based system to process data more efficiently and precisely. A framework is developed to automate the system for classifying and detecting nutritional values from images of different citrus fruits. The system is trained using the Transform Learning Approach (TLA) and Single Shot Detection (SSD) V2 to process the custom dataset. Results obtained from the experiments show that the accuracy achieved with our proposed methodology approaches 97%. This non-destructive predictive analysis of citrus fruit will pave the path for prescriptive analytics to enhance the qualitative productivity of the fruit. Identification (biology) ; Nutrient ; Horticulture ; Citrus fruit ; Biology ; Agronomy ; Botany ; Ecology Spectroscopy and Chemometric Analyses ; Advanced Chemical Sensor Technologies ; Identification and Quantification in Food
Authors: 泰英 望月 | Yasuhide Mochizuki | 楓 永松 | Kaede Nagamatsu | 宏喜 小磯 | Hiroki Koiso | 敏宏 磯部 | Toshihiro Isobe | 章 中島 | Akira Nakajima
Source: Institutional Repositories DataBase (IRDB) (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Mechanism of Negative Thermal Expansion in Monoclinic Cu2P2O7 from First Principles Negative thermal expansion (NTE) materials generally have high-symmetry space groups, large average atomic volumes, and corner-sharing octahedral and tetrahedral coordination structures.By contrast, monoclinic -Cu 2 P 2 O 7 , which has a small average atomic volume and edge-sharing structure, has been reported to exhibit NTE, the detailed mechanism of which is unclear.In this study, we investigate the A 2 B 2 O 7 polymorphs and analyze the NTE behavior of -Cu 2 P 2 O 7 using first-principles lattice-dynamics calculations.From the polymorphism investigation in 20 A 2 B 2 O 7 compounds using 6 representative crystal structures, small A and B cationic radii are found to stabilize the -Cu 2 P 2 O 7 -type structure.We then analyze the NTE behavior of -Cu 2 P 2 O 7 using quasi-harmonic approximation.Our calculated thermal expansion coefficients and anisotropic atomic displacement parameters were in good agreement with those of the experimental reports at low temperatures.From the mode-Gruneisen parameter distribution plotted over the entire first-Brillouin zone, we found that the phonon contributing most significantly to NTE emerges not into the special points but between them.In this phonon mode, the O connecting two PO 4 tetrahedra rotates, and the Cu and O vibrate perpendicular to the bottom of the CuO 5 pyramidal unit, which folds the ac lattice plane.This vibration behavior can explain the experimentally reported anisotropic NTE behavior of -Cu 2 P 2 O 7 .Our results demonstrate that the most negative mode-Gruneisen parameter contributing to NTE behavior is not always located on high-symmetry special points, indicating the importance of lattice vibration analyses for the entire first-Brillouin zone. Monoclinic crystal system ; Thermal expansion ; Mechanism (biology) ; Negative thermal expansion ; Thermal Thermal Expansion and Ionic Conductivity ; High-pressure geophysics and materials ; Thermal and Kinetic Analysis
Authors: Suriani Mat Jusoh | Mohammad Fakhratul Ridwan Zulkifli | Samsuri Abdullah | Ayu Rafiqah Shafi | Mohd Fadzhel Mohd Nasir | Ummi Nurashira Maulana | Fathin Sakinah Mohd Radzi | Syakir Hakimi Zainulabidin
Source: Pertanika journal of science & technology (article, 2024-10-29)
Field: Materials Science — Polymers and Plastics

Response Surface Methodology for Optimisation of Parameter on Water Absorption of Natural Fibre Hybrid Composite in Boat Construction Today, the utilisation of natural or green fibre has supplanted engineered fibre as fibreglass has become a pattern in composite boat producing and other gears because of its lightweight, excellent relative mechanical properties, and more significant elements. For example, it is eco-accommodating, has manageable materials, and has lower costs compared to fibreglass. The utilisation of fibreglass is costly and has a high effect on the natural biological system. It also gets over the area of ecological contamination, word-related well-being, and security concerns. This study used the Woven Kenaf/fibreglass as reinforcement and polyester as matric to fabricate hybrid composite coupons. Response Surface Methodology (RSM) of Box-Behnken Design (BBD) was applied to optimise fibre contents (35 to 75 wt%) and water absorption performance for the development of Woven Kenaf/fibreglass to polyester hybrid composite material based on the parameters. The BBD revealed that 45% Woven Kenaf/fibreglass to polyester performed the optimum fibre content and water absorption. Analyses of variance (ANOVA) showed that the model satisfactorily correlated the parameters. After immersion, 45% Woven Kenaf/fibreglass to polyester composite also gained 9.48% weight. Composite number ; Response surface methodology ; Natural (archaeology) ; Absorption (acoustics) ; Absorption of water ; Surface (topology) ; Composite material ; Materials science ; Environmental science ; Geology ; Chemistry ; Mathematics ; Chromatography Natural Fiber Reinforced Composites ; Material Properties and Applications ; Polymer composites and self-healing
Authors: Irakli Nakhutsrishvili | Zurab Adamia | Lasha Loria
Source: Journal of applied surface science. (article, 2024-12-30)
Field: Chemistry — Organic Chemistry

Analisys of Kinetic Curves of Mass Change During the Interaction of Active Gases with Certain Metals and Compounds with Simultaneous Evaporation of the Product of Reaction The influence of the secondary process of evaporation of the reaction product on the kinetics of interaction of gases (O2 , Cl2 , NH3 , H2 O and N2 H4 vapors) with the surface of some metals (Cr, Pb, Si, Ge) and compounds (BN, SiO2 , SiC) is discussed. Also is considered the case when the growth of the scale is preceded by the process of gas etching of the metal surface. A general equation is given that describes the scale growth-evaporation kinetic (sample mass change - time) curves during the interaction of gases with the surface of metals and compounds. Special cases of parabolic, cubic and fourth degree processes are discussed. The kinetics of nitridation of the surface of single-crystaline germanium by ammonia and hydrazine vapors was studied in detail. By evaporating the nitride formed on the germanium surface, a film of germanium oxyntride is deposited on a substrate located in the cold zone of the reactor. Kinetic energy ; Evaporation ; Chemistry ; Product (mathematics) ; Thermodynamics ; Computational chemistry ; Inorganic chemistry ; Physical chemistry ; Physics ; Mathematics ; Geometry ; Classical mechanics Chemical Thermodynamics and Molecular Structure ; Thermal and Kinetic Analysis ; Adsorption, diffusion, and thermodynamic properties of materials
Authors: Ahmad, Khairulmazmi | Bashir Kutawa, Abdulaziz | Mohd Zobir, Syazwan Afif
Source: Universiti Putra Malaysia Institutional Repository (Universiti Putra Malaysia) (article, 2024-01-01)
Field: Materials Science — Biomaterials

What it takes to control plant pathogenic fungi using Chitosan and Chitosan-based nanoparticles in the twenty-first century Chitosan ; Biosafety ; Fungicide ; Antimicrobial ; Antifungal ; Nanoparticle ; Nanotoxicology Nanocomposite Films for Food Packaging ; Polymer-Based Agricultural Enhancements ; Antimicrobial agents and applications
Authors: David Shulman | Assaf Israeli | Yael Botnaro | Ori Margalit | Oved Tamir | Shaul Naschitz | Dan Gamrasni | Ofer M. Shir | Itai Dattner
Source: arXiv (Cornell University) (preprint, 2024-03-13)
Field: Chemistry — Analytical Chemistry

Physics-Guided Inverse Regression for Crop Quality Assessment We present an innovative approach leveraging Physics-Guided Neural Networks (PGNNs) for enhancing agricultural quality assessments. Central to our methodology is the application of physics-guided inverse regression, a technique that significantly improves the model's ability to precisely predict quality metrics of crops. This approach directly addresses the challenges of scalability, speed, and practicality that traditional assessment methods face. By integrating physical principles, notably Fick`s second law of diffusion, into neural network architectures, our developed PGNN model achieves a notable advancement in enhancing both the interpretability and accuracy of assessments. Empirical validation conducted on cucumbers and mushrooms demonstrates the superior capability of our model in outperforming conventional computer vision techniques in postharvest quality evaluation. This underscores our contribution as a scalable and efficient solution to the pressing demands of global food supply challenges. Inverse ; Crop ; Regression ; Quality (philosophy) ; Quality assessment ; Econometrics ; Mathematics ; Statistics ; Physics ; Agricultural engineering ; Biology ; Agronomy ; Engineering ; Evaluation methods ; Reliability engineering Spectroscopy and Chemometric Analyses
Authors: F. Fontani
Source: arXiv (Cornell University) (preprint, 2024-07-26)
Field: Chemistry — Spectroscopy

Observations of phosphorus-bearing molecules in the interstellar medium The chemistry of phosphorus (31P) in space is particularly significant due to the key role it plays in biochemistry on Earth. Utilising radio and infrared spectroscopic observations, several key phosphorus-containing molecules have been detected in interstellar clouds, circumstellar shells, and even extragalactic sources. Among these, phosphorus nitride (PN) was the first P-bearing molecule detected in space, and still is the species detected in the largest number of sources. Phosphorus oxide (PO) and phosphine (PH3) were also crucial species due to their role both in chemical networks and in forming biogenic compounds. The still limited high-angular resolution observations performed so far are shading light on the geometrical distribution of these molecules, which represent crucial insights on their formation processes. Observations have also highlighted the challenges and complexities associated with detecting and understanding phosphorus chemistry in space, owing to the low elemental abundance of P relative to other elements. This review article provides a state-of-art picture of the observational results obtained so far on phosphorus compounds in the interstellar medium. Special attention is given to star-forming regions, and to their implications for our understanding of prebiotic chemistry and the potential for life beyond Earth. Our knowledge of the dominant formation and destruction pathways of the most abundant species has improved, but critical questions remain open, among which: what is (are) the main phosphorus carrier(s) in space? Upcoming facilities will offer new opportunities to both detect new phosphorus-bearing molecules and enlarge the number of sources in which the chemistry of P can be studied. The synergy between observations, models, laboratory experiments, and computational works is mandatory to progress in this field. Bearing (navigation) ; Interstellar medium ; Phosphorus ; Molecule ; Physics ; Astrobiology ; Chemistry ; Environmental science ; Astrophysics ; Astronomy ; Organic chemistry ; Quantum mechanics ; Galaxy Molecular Spectroscopy and Structure ; Advanced Chemical Physics Studies ; Cold Atom Physics and Bose-Einstein Condensates
Authors: Hamdy Khamees Thabet | Mohd Imran | Saleh I. Alaqel | Mohamed H. Helal | Abida Abida
Source: International Journal of Life Science and Pharma Research (article, 2024-07-03)
Field: Chemistry — Organic Chemistry

Design, Synthesis, and the Biological Evaluation of Some New Fused Thiazolotriazine Derivatives Thiazolotriazine is an essential medicinal chemistry molecule due to its biological properties, particularly antifungalactivity. Antifungal drug resistance is rising worldwide, necessitating the development of innovative, safer, and more effectiveantifungals. This study intended to uncover safer and more effective thiazolotriazine antifungals. ProTox II software was employedto forecast the toxicity of the designed thiazolotriazines. The pharmacokinetic parameters were calculated using the Swiss-ADMEdatabase. The Molecular Operating Environment software (2019.0102 version) was employed for the docking studies utilizing 14-α-demethylase protein (PDB ID: 3LD6). Compounds 4c, 4d, and 4e were prepared and evaluated for in vitro antifungal activity.The computational studies revealed compounds 4a, 4b, 5b, 5c, 6b, 6c and 6d as carcinogenic; 4a, 4b, 4c, 4d and 4e demonstratedbetter pharmacokinetic behaviour; and docking results of 4c, 4d, and 4e were superior than fluconazole (FLU). The moleculardocking studies establish 4c, 4d, and 4e as SDM inhibitors, suggesting a mechanism similar to FLU and ketoconazole (KET). Theantifungal activity evaluation revealed 4d (MIC = 6.25 μg/ml) as a more potent antifungal agent than KET (MIC = 12.5 μg/ml) andFLU (MIC = 12.5 μg/ml). Compounds 4c and 4e showed equal antifungal activity to KET (MIC = 12.5 μg/ml) and FLU (MIC = 12.5μg/ml). Compounds 4c, 4d, and 4e displayed encouraging antifungal activity with a favorable safety profile. Assessing the broadspectrum of 4c, 4d, and 4e against various pathogenic fungi, including resistant forms, is recommended. Combinatorial chemistry ; Biochemical engineering ; Computer science ; Chemistry ; Engineering Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and biological activity ; Phenothiazines and Benzothiazines Synthesis and Activities
Authors: Mingzhen Zhang | Tao Chen | Ao Zeng | Jialin Tang | Ruiqiang Guo | Puqing Jiang
Source: arXiv (Cornell University) (preprint, 2024-11-24)
Field: Materials Science — Materials Chemistry

Simultaneous Measurement of Thermal Conductivity, Heat Capacity, and Interfacial Thermal Conductance by Leveraging Negative Delay-Time Data in Time-Domain Thermoreflectance Time-domain thermoreflectance (TDTR) is a widely used technique for characterizing the thermal properties of bulk and thin-film materials. Traditional TDTR analyses typically focus on positive delay time data for fitting, often requiring multiple-frequency measurements to simultaneously determine thermal conductivity and heat capacity. However, this multiple-frequency approach is cumbersome and may introduce inaccuracies due to inconsistencies across different frequency measurements. In this study, we propose a novel solution to these challenges by harnessing the often-overlooked negative delay time data in TDTR. By integrating these data points, we offer a streamlined, single-frequency method that simultaneously measures thermal conductivity, heat capacity, and interface thermal conductance for both bulk and thin-film materials, enhancing measurement efficiency and accuracy. We demonstrate the effectiveness of this method by measuring several bulk samples including sapphire, silicon, diamond, and Si0.992Ge0.008, and several thin-film samples including a 1.76-μm-thick gallium nitride (GaN) film epitaxially grown on a silicon substrate, a 320-nm-thick gallium oxide (ε-Ga2O3) film epitaxially grown on a silicon carbide substrate, and a 330-nm-thick tantalum nitride (TaN) film deposited on a sapphire substrate, all coated with an aluminum (Al) transducer layer on the surface. Our results show that the new method accurately determines the thermal conductivity and heat capacity of these samples as well as the Al/sample interface thermal conductance using a single modulation frequency, except for the Si0.992Ge0.008 sample. This study sheds light on the untapped potential of TDTR, offering a new, efficient, and accurate avenue for thermal analysis in material science. Thermal conductivity ; Time domain ; Materials science ; Heat capacity ; Thermal ; Thermal conduction ; Conductance ; Thermodynamics ; Mechanics ; Computer science ; Composite material ; Physics ; Condensed matter physics Thermal properties of materials ; Heat Transfer and Optimization ; Thermography and Photoacoustic Techniques
Authors: Daniel Haider | Martin Ehler | Péter Balázs
Source: arXiv (Cornell University) (preprint, 2024-06-22)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Injectivity of ReLU-layers: Tools from Frame Theory Injectivity is the defining property of a mapping that ensures no information is lost and any input can be perfectly reconstructed from its output. By performing hard thresholding, the ReLU function naturally interferes with this property, making the injectivity analysis of ReLU layers in neural networks a challenging yet intriguing task that has not yet been fully solved. This article establishes a frame theoretic perspective to approach this problem. The main objective is to develop a comprehensive characterization of the injectivity behavior of ReLU layers in terms of all three involved ingredients: (i) the weights, (ii) the bias, and (iii) the domain where the data is drawn from. Maintaining a focus on practical applications, we limit our attention to bounded domains and present two methods for numerically approximating a maximal bias for given weights and data domains. These methods provide sufficient conditions for the injectivity of a ReLU layer on those domains and yield a novel practical methodology for studying the information loss in ReLU layers. Finally, we derive explicit reconstruction formulas based on the duality concept from frame theory. Frame (networking) ; Computer science ; Linguistics ; Mathematics ; Geology ; Philosophy ; Telecommunications Copper Interconnects and Reliability