jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Yuxi Chen | Yongchang Ding | Haowen Yu | Xueyan Li
Source: Photonics (article, 2024-03-11)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Design of an Achromatic Graphene Oxide Metalens with Multi-Wavelength for Visible Light Dispersion control is a critical aspect in nano-optical systems. Moreover, chromatic aberration significantly impacts image quality. Despite metasurfaces being a novel approach to tackle chromatic aberration in diffractive lenses, numerous challenges hinder their practical implementation due to the complexity of 3D fabrication techniques and high manufacturing costs. In contrast, ultra-thin graphene oxide lenses are simpler and less expensive to manufacture. The optical performance of graphene oxide lenses, such as high focusing efficiency, large depth of field, wide bandwidth, and zooming capability, depends on the design of the positional arrangement of reduced graphene oxide regions. In this study, we utilized the self-constructed datasets to train machine learning models based on the structure of the graphene oxide lens and combined it with intelligent optimization algorithms. This approach facilitated the design of the graphene oxide achromatic lens in multi-wavelengths with high-performance. Experimental results substantiate that the designed ultra-thin graphene oxide lens, with a thickness of ~200 nm, effectively controls dispersion across multiple incident wavelengths (450, 550, and 650 nm) and achieves super resolution with consistent intensity at the focal point. Our graphene oxide lens holds the potential for integration into micro-optical systems that demand dispersion control, providing broad applications in optical imaging, optical communication, the biomedical field, and beyond. Achromatic lens ; Graphene ; Wavelength ; Optics ; Visible spectrum ; Optoelectronics ; Materials science ; Oxide ; Physics ; Nanotechnology Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Thermal Radiation and Cooling Technologies
Authors: Hande Yılmaz-Düzyaman | Raúl de la Rosa | Leonardo Velasco | Nieves Núñez-Sánchez | Lorenzo León
Source: Agriculture (article, 2024-05-02)
Field: Chemistry — Analytical Chemistry

Oil Quality Prediction in Olive Oil by Near-Infrared Spectroscopy: Applications in Olive Breeding The oxidative stability index (OSI) and fatty acid (FA) composition of extra virgin olive oils (EVOOs) are key parameters in the characterization of new varieties in breeding programs. Their determination through traditional methods (Rancimat and gas chromatography, respectively) is expensive and time-consuming. Therefore, there is a need to develop rapid and cost-effective analytical procedures. This study aimed to evaluate the potential use of near-infrared spectroscopy (NIRS) for analyzing OSI and FA composition in EVOOs. A total of 318 samples sourced from different origins were evaluated using both FT-NIR MPA and MicroNIR instruments in transmittance mode, with wavelengths ranging from 1100 to 2500 nm and 908 to 1676 nm, respectively. Different accuracies were obtained in the models developed for the different evaluated traits, with simpler models (using a lower number of latent variables) for the MPA analyzer in all cases. Additionally, consistent results between instruments for the partitioning of the variance and heritability estimation, and the reliable ranking of genotypes were obtained from one of the sample sets tested. In summary, models derived from PLS regression using spectroscopic data of both instruments demonstrated promising results in determining these EVOO traits, facilitating their evaluation and selection of genotypes, particularly in breeding programs. Olive oil ; Quality (philosophy) ; Environmental science ; Biology ; Botany ; Food science ; Physics Spectroscopy and Chemometric Analyses ; Edible Oils Quality and Analysis ; Essential Oils and Antimicrobial Activity
Authors: Andrea Iadarola | Raffaele Ciardiello | Davide Salvatore Paolino
Source: Polymer Engineering and Science (article, 2024-05-30)
Field: Materials Science — Polymers and Plastics

A new effective phenomenological constitutive model for semi‐crystalline and amorphous polymers Abstract A new phenomenological constitutive model is proposed for the prediction of the tensile and compressive behavior of semi‐crystalline and amorphous polymers. The new model modifies the phenomenological model previously proposed by Zhou and Mallick (ZM model) to correctly predict the complex behavior of thermoplastic materials including the linear viscoelastic deformation, the non‐linear viscoelastic deformation, the yielding, the post‐yield strain softening and the post‐yield strain hardening. A validation activity based on literature data has been carried out for polyether‐ether‐ketone (PEEK) and polycarbonate (PC) materials. The new model proved effective in fitting with high accuracy all the phases of the flow stress behavior for the considered materials, across a wide range of strain rates and temperature conditions. Finally, the comparison with Zhu et al., Duan et al., Nasraoui et al., Mulliken‐Boyce and Zhou‐Mallick models showed the better fitting performance of the proposed phenomenological model. Highlights Formulation of a new phenomenological model. Validation on mechanical test of semi‐crystalline and amorphous thermoplastics. Comparison with different phenomenological models present in the literature. Superior prediction results achieved compared to previously developed models. Amorphous solid ; Phenomenological model ; Materials science ; Polymer ; Constitutive equation ; Statistical physics ; Physics ; Thermodynamics ; Condensed matter physics ; Composite material ; Crystallography ; Chemistry ; Finite element method Polymer crystallization and properties ; Polymer Foaming and Composites ; Polymer Nanocomposites and Properties
Authors: Stefka Atanassova | Dimitar Yorgov | Deyan Stratev | Petya Veleva | T. Stoyanchev
Source: Sensors (article, 2024-06-04)
Field: Chemistry — Analytical Chemistry

Near-Infrared Spectroscopy for Rapid Differentiation of Fresh and Frozen–Thawed Common Carp (Cyprinus carpio) This study aimed to investigate near-infrared spectroscopy (NIRS) in combination with classification methods for the discrimination of fresh and once- or twice-freeze-thawed fish. An experiment was carried out with common carp (<i>Cyprinus carpio</i>). From each fish, test pieces were cut from the dorsal and ventral regions and measured from the skin side as fresh, after single freezing at minus 18 °C for 15 ÷ 28 days and 15 ÷ 21 days for the second freezing after the freeze-thawing cycle. NIRS measurements were performed via a NIRQuest 512 spectrometer at the region of 900-1700 nm in Reflection mode. The Pirouette 4.5 software was used for data processing. SIMCA and PLS-DA models were developed for classification, and their performance was estimated using the F1 score and total accuracy. The predictive power of each model was evaluated for fish samples in the fresh, single-freezing, and second-freezing classes. Additionally, aquagrams were calculated. Differences in the spectra between fresh and frozen samples were observed. They might be assigned mainly to the O-H and N-H bands. The aquagrams confirmed changes in water organization in the fish samples due to freezing-thawing. The total accuracy of the SIMCA models for the dorsal samples was 98.23% for the calibration set and 90.55% for the validation set. For the ventral samples, respective values were 99.28 and 79.70%. Similar accuracy was found for the PLS-PA models. The NIR spectroscopy and tested classification methods have a potential for nondestructively discriminating fresh from frozen-thawed fish in as methods to protect against fish meat food fraud. Cyprinus ; Common carp ; Dorsum ; Fish <Actinopterygii> ; Chemistry ; Near-infrared spectroscopy ; Animal science ; Analytical Chemistry (journal) ; Chromatography ; Biology ; Anatomy ; Fishery Spectroscopy and Chemometric Analyses ; Meat and Animal Product Quality ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Kou Takubo | Atsushi Ono | Shunsuke Ueno | Samiran Banu | Hongwu Yu | Kaito En-ya | Ryota Nishimori | Makoto Kuwahara | Toru Asaka | Kei Maeda | Daiki Ono | Keita Ozawa | T. Itoh | Kei Shigematsu | Masaki Azuma | T. Ishikawa | Y. Okimoto | Masaki Hada | Shin‐ya Koshihara
Source: Communications Materials (article, 2024-12-04)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Photocontrol of ferroelectricity in multiferroic BiFeO3 via structural modification coupled with photocarrier Abstract Ultrafast control of ferroelectricity and magnetism by light is essential for future development in multiple functioning devices. Here, we demonstrate that the intense and ultrafast photo-modulation of the electric dipole can be realized by photocarrier injection into a multiferroic BiFeO 3 thin film using optical pump-probe and second harmonic generation measurements. Results of ultrafast electron diffraction with &lt;100 fs time resolution and theoretical study reveal that the localized photocarrier strongly couples with the lattice structure and becomes the origin for the observed sudden change in the electric dipole. In addition, the subsequent structural dynamics involve a strong oscillation with a frequency of ~3.3 THz despite a poor structural symmetry change. Based on a theoretical calculation, this oscillation can be attributed to an unexpectedly softened new phonon mode generated by mixing essential two phonon modes governing the multiferroic (ferroelectric and antiferromagnetic) nature of BiFeO 3 in the ground state due to strong coupling with a localized photocarrier. The comprehensive study shows that injection of the localized photocarrier strongly coupled with the lattice vibration mode can simultaneously realize the ultrafast switching of electric dipoles and magnetic interaction at once, even at room temperature, without modifying the long-range lattice structure. Ferroelectricity ; Multiferroics ; Condensed matter physics ; Ultrashort pulse ; Materials science ; Magnetism ; Dipole ; Phonon ; Electric field ; Optoelectronics ; Optics ; Laser ; Chemistry ; Physics ; Dielectric Multiferroics and related materials ; Ferroelectric and Piezoelectric Materials ; Dielectric properties of ceramics
Authors: Hanim Zuhrotul Amanah | Evia Zunita D. Pratiwi | Diah N. Rahmi | Muhammad Fahri Reza Pahlawan | Rudiati Evi Masithoh
Source: Food Research (article, 2024-03-30)
Field: Chemistry — Analytical Chemistry

Non-destructive determination of water content in fruits using Vis-NIRspectroscopy Visible near-infrared (Vis-NIR) spectroscopy is less accurate for detecting -OH molecules, therefore, the use of Vis-NIR spectroscopy is challenging for samples containing high water content, such as fruits. However, as Vis-NIR spectroscopy is a portable and economical instrument, it can be used in the field by small-scale farmers. This study aimed to evaluate Vis-NIR spectra to measure water content in fruits. Four fruits were used in this study, including dragon fruit, guava, sapodilla and banana (100 pieces each). All fruits were randomly divided into a calibration set (two-thirds of the samples) and a prediction set (one-third of the samples). Water content was predicted using partial least square regression (PLSR) analysis. The PLSR calibration model had a coefficient of determination (R²) of 0.29 for dragon fruit, 0.63 for guava, 0.62 for sapodilla and 0.80 for banana. The prediction model had an R² of 0.11 for dragon fruit, 0.63 for guava, 0.52 for sapodilla and 0.75 for banana. These results show that Vis-NIR spectroscopy has the potential to predict water content in relatively low water-content fruits, such as bananas. Spectroscopy ; Water content ; Near-infrared spectroscopy ; Materials science ; Content (measure theory) ; Analytical Chemistry (journal) ; Environmental science ; Environmental chemistry ; Chemistry ; Optics ; Geology ; Mathematics ; Physics Spectroscopy and Chemometric Analyses ; Water Quality Monitoring and Analysis ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Anthony J. Schaefer | Daniel H. Ess
Source: Physical Chemistry Chemical Physics (article, 2024-01-01)
Field: Chemistry — Organic Chemistry

Vibrational synchronization and its reaction pathway influence from an entropic intermediate in a dirhodium catalyzed allylic C–H activation/Cope rearrangement reaction In reactions with consecutive transition states without an intermediate, and an energy surface bifurcation, atomic motion generally determines product selectivity. Understanding this dynamic-based selectivity can be straightforward if there is extremely fast descent from the first transition state to a product. However, in cases where a nonstatistical roaming/entropic intermediate occurs prior to product formation the motion that influences selectivity can be difficult to identify. Here we report quasiclassical direct dynamics trajectories for the dirhodium catalyzed reaction between styryldiazoacetate and 1,4-cyclohexadiene and prior experiments by Davies showed competitive allylic C-H insertion and Cope products. Trajectories confirmed the proposed energy surface bifurcation and revealed that dirhodium vinylcarbenoid when reacting with 1,4-cyclohexadiene can induce either a dynamically concerted pathway or a dynamically stepwise pathway with a nonstatistical entropic tight ion-pair intermediate. In the dynamically stepwise reaction pathway C-H insertion <i>versus</i> Cope selectivity is highly influenced by whether or not vibrational synchronization occurs in the nonstatistical entropic intermediate. This vibrational synchronization highlights the possible need for an entropic intermediate to have organized transition state-like motion to proceed to a product. Allylic rearrangement ; Selectivity ; Chemistry ; Catalysis ; Transition state ; Potential energy surface ; Cope rearrangement ; Photochemistry ; Chemical physics ; Computational chemistry ; Stereochemistry ; Molecule ; Organic chemistry Cyclopropane Reaction Mechanisms ; Asymmetric Synthesis and Catalysis ; Ionic liquids properties and applications
Authors: Ivo Fierro-Monti | Klemens Fröhlich | Christian Schori | Alexander Schmidt
Source: Proteomes (article, 2024-11-06)
Field: Chemistry — Spectroscopy

Assessment of Data-Independent Acquisition Mass Spectrometry (DIA-MS) for the Identification of Single Amino Acid Variants Proteogenomics integrates genomic and proteomic data to elucidate cellular processes by identifying variant peptides, including single amino acid variants (SAAVs). In this study, we assessed the capability of data-independent acquisition mass spectrometry (DIA-MS) to identify SAAV peptides in HeLa cells using various search engine pipelines. We developed a customised sequence database (DB) incorporating SAAV sequences from the HeLa genome and conducted searches using DIA-NN, Spectronaut, and Fragpipe-MSFragger. Our evaluation focused on identifying true positive SAAV peptides and false positives through entrapment DBs. This study revealed that DIA-MS provides reproducible and comprehensive coverage of the proteome, identifying a substantial proportion of SAAV peptides. Notably, the DIA-MS searches maintained consistent identification of SAAV peptides despite varying sizes of the entrapment DB. A comparative analysis showed that Fragpipe-MSFragger (FP-DIA) demonstrated the most conservative and effective performance, exhibiting the lowest false discovery match ratio (FDMR). Additionally, integrating DIA and data-dependent acquisition (DDA) MS data search outputs enhanced SAAV peptide identification, with a lower false discovery rate (FDR) observed in DDA searches. The validation using stable isotope dilution and parallel reaction monitoring (SID-PRM) confirmed the SAAV peptides identified by DIA-MS and DDA-MS searches, highlighting the reliability of our approach. Our findings underscore the effectiveness of DIA-MS in proteogenomic workflows for identifying SAAV peptides, offering insights into optimising search engine pipelines and DB construction for accurate proteomics analysis. These methodologies advance the understanding of proteome variability, contributing to cancer research and the identification of novel proteoform therapeutic targets. Proteome ; Computational biology ; False discovery rate ; Proteogenomics ; Proteomics ; False positive paradox ; Shotgun ; Database search engine ; Identification (biology) ; Mass spectrometry ; Shotgun proteomics ; Computer science ; Chemistry ; Data mining ; Bioinformatics ; Biology ; Genome ; Search engine ; Genomics ; Chromatography ; Artificial intelligence ; Biochemistry ; Gene ; Information retrieval Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Machine Learning in Bioinformatics
Authors: Shihua Yu | Huoqing Zheng | Xiaogang Ye | Xiangping Dai | Xinqiu Wang | Shuo Zhao | Xiaoyan Dai | Boxiong Zhong
Source: Frontiers in Bioengineering and Biotechnology (article, 2024-05-20)
Field: Materials Science — Biomaterials

TALEN-mediated homologous-recombination-based fibroin light chain in-fusion expression system in Bombyx mori Silkworm was the first domesticated insect and has important economic value. It has also become an ideal model organism with applications in genetic and expression studies. In recent years, the use of transgenic strategies has made the silkworm silk gland an attractive bioreactor for the production of recombinant proteins, in particular, <i>piggyBac</i>-mediated transgenes. However, owing to differences in regulatory elements such as promoters, the expression levels of exogenous proteins have not reached expectations. Here, we used targeted gene editing to achieve site-specific integration of exogenous genes on genomic DNA and established the fibroin light chain (FibL) in-fusion expression system by TALEN-mediated homology-directed recombination. First, the histidine-rich cuticular protein (CP) was successfully site-directed inserted into the native FibL, and the FibL-CP fusion gene was correctly transcribed and expressed in the posterior silk gland under the control of the endogenous FibL promoter, with a protein expression level comparable with that of the native FibL protein. Moreover, we showed based on molecular docking that the fusion of FibL with cuticular protein may have a negative effect on disulfide bond formation between the C-terminal domain of fibroin heavy chain (FibH) and FibL-CP, resulting in abnormal spinning and cocoon in homozygotes, indicating a significant role of FibL in silk protein formation and secretion. Our results demonstrate the feasibility of using the FibL fusion system to express exogenous proteins in silkworm. We expect that this bioreactor system will be used to produce more proteins of interest, expanding the application value of the silk gland bioreactor. Fibroin ; Bombyx mori ; Homologous recombination ; Immunoglobulin light chain ; Chain (unit) ; Fusion ; Recombination ; Homologous chromosome ; Cell biology ; Expression (computer science) ; Chemistry ; Genetics ; Biology ; Computer science ; Physics ; Gene ; SILK ; Programming language Silk-based biomaterials and applications ; Invertebrate Immune Response Mechanisms ; Viral Infectious Diseases and Gene Expression in Insects
Authors: Nenglong Yang | Zhenmin Zou | Constantinos Soutis | Prasad Potluri | K.B. Katnam
Source: Composites Part A Applied Science and Manufacturing (article, 2024-11-01)
Field: Materials Science — Polymers and Plastics

Effect of micro-scale fibre uncertainties on the mechanical behaviour of natural/synthetic hybrid fibre composites This paper investigates how uncertainties in natural/synthetic hybrid fibre composites—specifically fibre distribution, diameter, and elastic properties—affect the lamina properties and micro-stress distributions. Using a representative volume element model and Monte Carlo simulations, the study examines unidirectional flax/E-glass/epoxy and flax/epoxy composite laminae. Flax fibre uncertainties are modelled as normal distributions with a 20% coefficient of variation. Results reveal that these uncertainties minimally influence the homogenised properties of flax/epoxy laminae. However, in flax/E-glass/epoxy laminae, E-glass fibres significantly alter homogenised properties, with fibre elastic properties uncertainties having a greater effect. These uncertainties also influence matrix stress fields in flax/epoxy laminae, primarily due to uncertainties in fibre elastic properties. Although the influence is smaller in flax/E-glass laminae, it remains significant, as hybridisation can increase von Mises stress and potentially cause early resin cracking. This stochastic approach highlights the importance of micro-scale fibre uncertainties for damage analysis despite their limited influence on homogenised properties. Materials science ; Composite material ; Synthetic fiber ; Natural fiber ; Scale (ratio) ; Composite number ; Fiber Natural Fiber Reinforced Composites ; Mechanical Engineering and Vibrations Research ; Textile materials and evaluations
Authors: Dmitri G. Fedorov
Source: ChemPhysChem (article, 2024-05-15)
Field: Chemistry — Spectroscopy

The Peptide Bond: Resonance Increases Bond Order and Complicates Fragmentation The enhancement of the peptide bond order by a resonance in the lone pair of N and the π-bond of CO is analyzed. A decomposition of the bond order in terms of localized molecular orbitals is developed and applied to the peptide bond. A combination of two rotations of hybrid orbitals is proposed to improve the boundary treatment in the fragment molecular orbital method. The developed approach is applied to peptide bonds, and it is found crucial to retain the π orbital in the variational space of both fragments across the boundary. The interaction energies between conventional amino acid residues in Trp-cage (1L2Y) are discussed. Bond order ; Peptide bond ; Chemistry ; Natural bond orbital ; Resonance (particle physics) ; Molecular orbital ; Localized molecular orbitals ; Sextuple bond ; Covalent bond ; Orbital hybridisation ; Peptide ; Computational chemistry ; Valence bond theory ; Atomic orbital ; Fragmentation (computing) ; Fragment molecular orbital ; Three-center two-electron bond ; Bond length ; Molecule ; Atomic physics ; Physics ; Quantum mechanics ; Organic chemistry ; Density functional theory Mass Spectrometry Techniques and Applications ; Chemical Synthesis and Analysis ; Crystallography and molecular interactions
Authors: Dmitri G. Fedorov
Source: Journal of Computational Chemistry (article, 2024-03-15)
Field: Chemistry — Organic Chemistry

Use of caps in the auxiliary basis set formulation of the fragment molecular orbital method An auxiliary polarization formulation of the fragment molecular orbital (FMO) method is developed, combining a basis set correction computed for capped isolated fragments with a polarization obtained from uncapped fragments. For a set of organic and inorganic test systems, it is shown that the total energy and atomic charges are accurately reproduced with respect to full unfragmented calculations. It is demonstrated that the method is accurate for computing electronic excited states. The developed approach is applied to rank the isomers of chignolin from experimental NMR data (PDB: 1UAO) according to their relative energy. Contributions of polarization and basis set effects to pair interactions between fragments are elucidated. Fragment (logic) ; Fragment molecular orbital ; Basis (linear algebra) ; Set (abstract data type) ; Basis set ; Mathematics ; Computational chemistry ; Physics ; Computer science ; Chemistry ; Algorithm ; Molecular orbital ; Molecule ; Geometry ; Quantum mechanics Chemical Thermodynamics and Molecular Structure ; Thermal and Kinetic Analysis ; Advanced Chemical Physics Studies