jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Lennard Roscher-Ehrig | Sven E. Weber | Amine Abbadi | Milka Malenica | Stefan Abel | Reinhard Hemker | Rod J. Snowdon | Benjamin Wittkop | Andreas Stahl
Source: Plant Phenomics (article, 2024-01-01)
Field: Chemistry — Analytical Chemistry

Phenomic Selection for Hybrid Rapeseed Breeding Phenomic selection is a recent approach suggested as a low-cost, high-throughput alternative to genomic selection. Instead of using genetic markers, it employs spectral data to predict complex traits using equivalent statistical models. Phenomic selection has been shown to outperform genomic selection when using spectral data that was obtained within the same generation as the traits that were predicted. However, for hybrid breeding, the key question is whether spectral data from parental genotypes can be used to effectively predict traits in the hybrid generation. Here, we aimed to evaluate the potential of phenomic selection for hybrid rapeseed breeding. We performed predictions for various traits in a structured population of 410 test hybrids, grown in multiple environments, using near-infrared spectroscopy data obtained from harvested seeds of both the hybrids and their parental lines with different linear and nonlinear models. We found that phenomic selection within the hybrid generation outperformed genomic selection for seed yield and plant height, even when spectral data was collected at single locations, while being less affected by population structure. Furthermore, we demonstrate that phenomic prediction across generations is feasible, and selecting hybrids based on spectral data obtained from parental genotypes is competitive with genomic selection. We conclude that phenomic selection is a promising approach for rapeseed breeding that can be easily implemented without any additional costs or efforts as near-infrared spectroscopy is routinely assessed in rapeseed breeding. Rapeseed ; Selection (genetic algorithm) ; Genomic selection ; Hybrid ; Biology ; Population ; Biotechnology ; Computer science ; Agronomy ; Machine learning ; Genotype ; Genetics ; Demography ; Gene Spectroscopy and Chemometric Analyses ; Genetic and phenotypic traits in livestock ; Genetics and Plant Breeding
Authors: Capucine Laprais | Clément Zrounba | Julien Bouvier | Nicholas Blanchard | Matthieu Bugnet | Alban Gassenq | Yael Gutiérrez | Saúl Vázquez-Miranda | Shirly Espinoza | Peter Thiesen | Romain Bourrellier | Aziz Benamrouche | Nicolas Baboux | Guillaume Saint‐Girons | Lotfi Berguiga | Sébastien Cueff
Source: Advanced Optical Materials (article, 2024-08-27)
Field: Materials Science — Materials Chemistry

Reversible Single‐Pulse Laser‐Induced Phase Change of Sb<sub>2</sub>S<sub>3</sub> Thin Films: Multi‐Physics Modeling and Experimental Demonstrations Abstract Phase change materials (PCMs) have gained a tremendous interest as a means to actively tune nanophotonic devices through the large optical modulation produced by their amorphous to crystalline reversible transition. Recently, materials such as Sb 2 S 3 emerged as particularly promising low loss PCMs, with both large refractive index modulations and transparency in the visible and near‐infrared. Controlling the local and reversible phase transition in this material is of major importance for future applications, and an appealing method to do so is to exploit pulsed lasers. Yet, the physics and limits involved in the optical switching of Sb 2 S 3 are not yet well understood. Here, the reversible laser‐induced phase transition of Sb 2 S 3 is investigated, focusing specifically on the mechanisms that drive the optically induced amorphization, with multi‐physics considerations including the optical and thermal properties of the PCM and its environment. The laser energy threshold for reversibly changing the phase of the PCM is determined through both theoretical analysis and experimental investigation, not only between fully amorphous and crystalline states but also between partially recrystallized states. Then, the non‐negligible impact of the material's polycrystallinity and anisotropy on the power thresholds for optical switching is revealed. Finally, the challenges related to laser amorphization of thick Sb 2 S 3 layers are addressed, as well as strategies to overcome them. These results enable a qualitative and quantitative understanding of the physics behind the optically‐induced reversible change of phase in Sb 2 S 3 layers. Materials science ; Amorphous solid ; Laser ; Phase transition ; Refractive index ; Optoelectronics ; Nanophotonics ; Anisotropy ; Phase (matter) ; Thermal ; Optics ; Condensed matter physics ; Physics ; Thermodynamics ; Crystallography Phase-change materials and chalcogenides ; Chalcogenide Semiconductor Thin Films ; Nonlinear Optical Materials Studies
Authors: Ioannis Malounas | Wout Vierbergen | Sezer Kutluk | Manuela Zude-Sasse | Kai Yang | Ming Zhao | Dimitrios Argyropoulos | Jonathan Van Beek | Eva Ampe | Spyros Fountas
Source: Data in Brief (article, 2024-01-11)
Field: Chemistry — Analytical Chemistry

SpectroFood dataset: A comprehensive fruit and vegetable hyperspectral meta-dataset for dry matter estimation In the dataset presented in this article, samples belonging to one of the following crops, apple, broccoli, leek, and mushroom, were measured by hyperspectral cameras in the visible/near-infrared spectral domain (430-900 nm). The dataset was compiled by putting together measurements from different calibrated hyperspectral imaging cameras and crops to facilitate the training of artificial intelligence models, helping to overcome the generalization problem of hyperspectral models. In particular, this dataset focuses on estimating dry matter content across various crops by a single model in a non-destructive way using hyperspectral measurements. This dataset contains extracted mean reflectance spectra for each sample (n=1028) and their respective dry matter content (%). Hyperspectral imaging ; Dry matter ; Computer science ; Remote sensing ; Artificial intelligence ; Reflectivity ; Environmental science ; Pattern recognition (psychology) ; Agronomy ; Geography ; Biology Spectroscopy and Chemometric Analyses ; Remote Sensing in Agriculture ; Smart Agriculture and AI
Authors: Jacopo Pelini | Stefano Dello Russo | Iñaki López | Mariaconcetta Canino | Alberto Roncaglia | Pablo Cancio Pastor | Iacopo Galli | Wei Ren | Paolo De Natale | Zhen Wang | Simone Borri | Mario Siciliani de Cumis
Source: Photoacoustics (article, 2024-05-21)
Field: Chemistry — Spectroscopy

New silicon-based micro-electro-mechanical systems for photo-acoustic trace-gas detection The achievable sensitivity level of photo-acoustic trace-gas sensors essentially depends on the performances of the acoustic transducer. In this work, the mechanical response of different silicon-based micro-electro-mechanical systems (MEMS) is characterized, aiming at investigating both their mechanical properties, namely the resonance frequency and the quality factor, and the minimum detection limit (MDL) achievable when they are exploited as an acoustic-to-voltage transducer in a trace-gas photoacoustic setup. For this purpose, a 4.56 µm Continuous-Wave (CW) quantum cascade laser (QCL) is used to excite a strong N<sub>2</sub>O roto-vibrational transition with a line strength of 2.14 × 10<sup>-19</sup> cm/molecule, and the detection of MEMS oscillations is performed via an interferometric readout. As a general trend, the minimum detection limit decreases when the resonance frequency investigated increases, achieving a value of 15 parts per billion with a 3 dB cut-off lock-in bandwidth equal to 100 mHz, around 10 kHz. Trace gas ; TRACE (psycholinguistics) ; Silicon ; Materials science ; Optoelectronics ; Environmental science ; Nanotechnology ; Physics ; Meteorology Spectroscopy and Laser Applications ; Gas Sensing Nanomaterials and Sensors ; Advanced Chemical Sensor Technologies
Authors: Zhao Qi Jiang | Wenjia Li | Zhi Xu | Hua Wei Tang | Meng Wang | Jie Chang | Hui Feng | Yu Xiang Li | Zheng Zhu | Chun Guan | Shuang Zhang | Jin Hui Shi
Source: Laser & Photonics Review (article, 2024-04-09)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Photonic Spin‐Hall Logic Devices Based on Programmable Spoof Plasmonic Metamaterial Abstract The entanglement of the momentum of light with its spin at interfaces or inside structured media, known as the photonic spin‐Hall effect, holds great promise for various applications, such as beam splitting, focusing, and polarization detection. However, the photonic spin‐Hall effect remains unexplored in the field of logic operation. In this work, the photonic spin‐Hall effect of spoof surface plasmon polaritons (SSPPs) in programmable metamaterial is demonstrated. Moreover, photonic spin‐Hall logic devices based on programmable spoof plasmonic metamaterial are designed, enabling the control of energy flow through the utilization of both spin and digital coding, with examples including SSPPs logic gates such as the “AND” gate, the “NIMPLY” gate (A AND NOT B), the “OR” gate, and the “NOT” gate. The findings introduce the combination of digital coding metamaterial with the photonic spin Hall effect, which offers a powerful and flexible platform for controlling electromagnetic waves in information processing. Metamaterial ; Plasmon ; Optoelectronics ; Photonics ; Physics ; Optics Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Neural Networks and Reservoir Computing
Authors: A. Codolini | Shuai Chen | G.D. Lawrence | L.T. Harper | M.P.F. Sutcliffe
Source: Composites Part B Engineering (article, 2024-05-22)
Field: Materials Science — Polymers and Plastics

Characterisation of process-induced variability in wrinkle defects during double diaphragm forming of non-crimp fabric Experiments and numerical simulations are employed to determine the critical process variables that affect the quality of a two-layer biaxial non-crimp fabric (NCF) preformed using the double diaphragm forming (DDF) process. To prevent wrinkling defects, the process variables must be controlled, including the vacuum pressure, diaphragm tension, and ply-tool alignment. Inter-ply friction plays a critical role in the deformation mechanism, while the frictional interaction between the diaphragm and tool has a limited impact. The study also reveals that geometrical features have an impact on the variability induced by the forming process. Preforms deformed to tools with geometrical features of higher asymmetry or Gaussian curvatures reduce the uncertainty of the forming process by maintaining the same preform quality despite changes in forming variables. Crimp ; Wrinkle ; Diaphragm (acoustics) ; Materials science ; Process (computing) ; Structural engineering ; Composite material ; Computer science ; Engineering ; Vibration ; Acoustics ; Physics Textile materials and evaluations ; Mechanical Behavior of Composites ; Additive Manufacturing and 3D Printing Technologies
Authors: Jeff Guo | Philippe Schwaller
Source: JACS Au (article, 2024-04-10)
Field: Materials Science — Materials Chemistry

Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning Sample efficiency is a fundamental challenge in <i>de novo</i> molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparent when using oracles that can provide increased predictive accuracy but impose significant computational cost. Consequently, designing molecules that are optimized for such oracles cannot be achieved under a practical computational budget. Molecular generative models based on simplified molecular-input line-entry system (SMILES) have shown remarkable sample efficiency when coupled with reinforcement learning, as demonstrated in the practical molecular optimization (PMO) benchmark. Here, we first show that experience replay drastically improves the performance of multiple previously proposed algorithms. Next, we propose a novel algorithm called Augmented Memory that combines data augmentation with experience replay. We show that scores obtained from oracle calls can be reused to update the model multiple times. We compare Augmented Memory to previously proposed algorithms and show significantly enhanced sample efficiency in an exploitation task, a drug discovery case study requiring both exploration and exploitation, and a materials design case study optimizing explicitly for quantum-mechanical properties. Our method achieves a new state-of-the-art in sample-efficient <i>de novo</i> molecular design, outperforming all of the previously reported methods. The code is available at https://github.com/schwallergroup/augmented_memory. Reinforcement learning ; Generative grammar ; Sample (material) ; Computer science ; Reinforcement ; Artificial intelligence ; Psychology ; Chemistry ; Chromatography ; Social psychology Machine Learning in Materials Science ; Innovative Microfluidic and Catalytic Techniques Innovation ; Computational Drug Discovery Methods
Authors: Yun Sik Choi | Won Ki Son | H. Shaun Kwak | Jiyeun Park | Sumin Choi | D. H. Sim | Min Gyeong Kim | Hyungsuk Kimm | Hokyoung Son | Dae Hong Jeong | Seon‐Yeong Kwak
Source: Advanced Science (article, 2024-12-24)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Real‐Time Monitoring of Volatile Organic Compound‐Mediated Plant Intercommunication Using Surface‐Enhanced Raman Scattering Nanosensor Plants communicate through volatile organic compounds (VOCs), but real-time monitoring of VOCs for plant intercommunication is not practically possible yet. A nanobionic VOC sensor plant is created to study VOC-mediated plant intercommunication by incorporating surface-enhanced Raman scattering (SERS) nanosensors into a living plant. This sensor allows real-time monitoring of VOC with a sensitivity down to the parts per trillion level. A quantitative VOC diffusion model in plants is proposed to describe this extreme sensitivity. The sensor plant is paired with a customized portable Raman device, demonstrating its ability to detect multiple VOCs on-field. The sensor demonstrated that plants collect VOCs emitted from neighboring plants and hazardous volatile chemicals in the air at a certain distance. As a feasibility study, this nanobionic VOC sensor plant successfully monitored the early stages of fungal infection in strawberry fruits. This result suggests that interfacing nanosensors with plants offers an innovative approach to studying interplant communication and can be used as a compelling tool for monitoring VOC occurrence. Nanosensor ; Interfacing ; Volatile organic compound ; Environmental science ; Raman scattering ; Environmental chemistry ; Materials science ; Remote sensing ; Nanotechnology ; Raman spectroscopy ; Chemistry ; Computer science ; Computer hardware Gold and Silver Nanoparticles Synthesis and Applications ; Insect and Arachnid Ecology and Behavior ; Insect and Pesticide Research
Authors: Zaixi Zhang | Wan Xiang Shen | Qi Liu | Marinka Žitnik
Source: Nature Machine Intelligence (article, 2024-11-15)
Field: Chemistry — Spectroscopy

Efficient generation of protein pockets with PocketGen Abstract Designing protein-binding proteins is critical for drug discovery. However, artificial-intelligence-based design of such proteins is challenging due to the complexity of protein–ligand interactions, the flexibility of ligand molecules and amino acid side chains, and sequence–structure dependencies. We introduce PocketGen, a deep generative model that produces residue sequence and atomic structure of the protein regions in which ligand interactions occur. PocketGen promotes consistency between protein sequence and structure by using a graph transformer for structural encoding and a sequence refinement module based on a protein language model. The graph transformer captures interactions at multiple scales, including atom, residue and ligand levels. For sequence refinement, PocketGen integrates a structural adapter into the protein language model, ensuring that structure-based predictions align with sequence-based predictions. PocketGen can generate high-fidelity protein pockets with enhanced binding affinity and structural validity. It operates ten times faster than physics-based methods and achieves a 97% success rate, defined as the percentage of generated pockets with higher binding affinity than reference pockets. Additionally, it attains an amino acid recovery rate exceeding 63%. Business Advanced Proteomics Techniques and Applications ; Protein Structure and Dynamics ; Genetics, Bioinformatics, and Biomedical Research
Authors: Ming Cai | Ji‐Wei Liu | Xian Zhang | Qihua Ma | Dazhong Wang | Geoffrey I. N. Waterhouse | Baozhong Sun
Source: Applied Composite Materials (article, 2024-03-03)
Field: Materials Science — Polymers and Plastics

Mechanical Stability of Carbon/Ramie Fiber Hybrid Composites Under Hygrothermal Aging Materials science ; Ramie ; Composite material ; Fiber ; Composite number Natural Fiber Reinforced Composites ; biodegradable polymer synthesis and properties ; Flame retardant materials and properties
Authors: Kristen A. Miller | Jessica Gayle | Soumyabrata Roy | Mohamed H. Abdellah | Rifan Hardian | Levente Cseri | Pedro Guerra Demingos | Hema Rajesh Nadella | Frank Lee | Manoj Tripathi | Sashikant Gupta | Galio Guo | S. P. Bhattacharyya | Xu Wang | Alan Β. Dalton | Ashish Garg | Chandra Veer Singh | Róbert Vajtai | György Székely | Pulickel M. Ajayan
Source: Small (article, 2024-04-30)
Field: Materials Science — Materials Chemistry

Tunable 2D Conjugated Porous Organic Polymer Films for Precise Molecular Nanofiltration and Optoelectronics Structural design of 2D conjugated porous organic polymer films (2D CPOPs), by tuning linkage chemistries and pore sizes, provides great adaptability for various applications, including membrane separation. Here, four free-standing 2D CPOP films of imine- or hydrazone-linked polymers (ILP/HLP) in combination with benzene (B-ILP/HLP) and triphenylbenzene (TPB-ILP/HLP) aromatic cores are synthesized. The anisotropic disordered films, composed of polymeric layered structures, can be exfoliated into ultrathin 2D-nanosheets with layer-dependent electrical properties. The bulk CPOP films exhibit structure-dependent optical properties, triboelectric nanogenerator output, and robust mechanical properties, rivaling previously reported 2D polymers and porous materials. The exfoliation energies of the 2D CPOPs and their mechanical behavior at the molecular level are investigated using density function theory (DFT) and molecular dynamics (MD) simulations, respectively. Exploiting the structural tunability, the comparative organic solvent nanofiltration (OSN) performance of six membranes having different pore sizes and linkages to yield valuable trends in molecular weight selectivity is investigated. Interestingly, the OSN performances follow the predicted transport modeling values based on theoretical pore size calculations, signifying the existence of permanent porosity in these materials. The membranes exhibit excellent stability in organic solvents at high pressures devoid of any structural deformations, revealing their potential in practical OSN applications. Materials science ; Polymer ; Nanofiltration ; Porosity ; Chemical engineering ; Membrane ; Organic electronics ; Conjugated system ; Nanotechnology ; Composite material ; Chemistry Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Membrane Separation and Gas Transport
Authors: Amal M. Alkhudaydi | Ekram Y. Danish | Mohamed Abdel Salam
Source: Molecules (article, 2024-03-19)
Field: Materials Science — Materials Chemistry

Magnetite/MXene (Fe3O4/Ti3C2) Nanocomposite as a Novel Adsorbent for Environmental Remediation of Malachite Green Dye In this work, a novel adsorbent called magnetite/MXene (Fe<sub>3</sub>O<sub>4</sub>/Ti<sub>3</sub>C<sub>2</sub>) nanocomposite was prepared, characterized, and applied for the removal of organic dye, malachite green dye (MG), from both real water and model solutions. Numerous techniques were used to characterize the prepared Fe<sub>3</sub>O<sub>4</sub>/Ti<sub>3</sub>C<sub>2</sub> nanocomposite: XRD, SEM, TEM, FTIR, and surface area analysis. The outcomes showed that the Al layer had been selectively etched, that the MAX phase (Ti<sub>3</sub>AlC<sub>2</sub>) had been transformed into layered Ti<sub>3</sub>C<sub>2</sub> MXene, that the cubic Fe<sub>3</sub>O<sub>4</sub> phase had been prepared, and that the prepared Fe<sub>3</sub>O<sub>4</sub> NPs had been evenly distributed on the MXene surface. Also, SEM pictures showed the successful etching of the MAX phase and the formation of the ultrathin multi-layered MXene, which the Fe<sub>3</sub>O<sub>4</sub> NPs covered upon forming the Fe<sub>3</sub>O<sub>4</sub>/Ti<sub>3</sub>C<sub>2</sub> nanocomposite at the surface and inside the ultrathin multi-layered MXene. The effect of different operational parameters affecting the removal process was explored and optimized. The MG dye was removed mostly within 60 min, with a 4.68 mg/g removal capacity using 5 mg of the Fe<sub>3</sub>O<sub>4</sub>/Ti<sub>3</sub>C<sub>2</sub> nanocomposite. The removal was examined from both kinetic and thermodynamic perspectives, and the findings demonstrated the spontaneity of the removal process as well as the applicability of fractal-like pseudo-first-order and fractal-like pseudo-second-order kinetics when compared to other kinetics models. The Fe<sub>3</sub>O<sub>4</sub>/Ti<sub>3</sub>C<sub>2</sub> nanocomposite was used to remove MG dye from real spiked environmental water samples, and the results revealed the successful remediation of the real samples from the organic dye by the Fe<sub>3</sub>O<sub>4</sub>/Ti<sub>3</sub>C<sub>2</sub> nanocomposite. Accordingly, Fe<sub>3</sub>O<sub>4</sub>/Ti<sub>3</sub>C<sub>2</sub> nanocomposite could be considered a potential adsorbent for the environmental remediation of polluted water. Malachite green ; Nanocomposite ; Materials science ; Chemical engineering ; Adsorption ; Magnetite ; Fourier transform infrared spectroscopy ; Kinetics ; Environmental remediation ; Nanotechnology ; Metallurgy ; Chemistry ; Organic chemistry ; Contamination MXene and MAX Phase Materials ; Graphene and Nanomaterials Applications ; Nanomaterials for catalytic reactions
Authors: Saba Jamil | Rabia Afzal | Shanza Rauf Khan | Mehwish Shabbir | Norah Alhokbany | Songnan Li | Muhammad Ramzan Saeed Ashraf Janjua
Source: RSC Advances (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Photocatalytic degradation of indigo carmine dye by hydrothermally synthesized graphene nanodots (GNDs): investigation of kinetics and thermodynamics All the data have been shared in the manuscript. However, the data are also available on request via email from the corresponding author. Indigo carmine ; Kinetics ; Graphene ; Chemistry ; Degradation (telecommunications) ; Materials science ; Chemical engineering ; Nuclear chemistry ; Nanotechnology ; Physics ; Computer science Carbon and Quantum Dots Applications ; Graphene and Nanomaterials Applications ; Gold and Silver Nanoparticles Synthesis and Applications