jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Dmitry V. Makhov | Adam Kirrander | Dmitrii V. Shalashilin
Source: arXiv (Cornell University) (preprint, 2024-02-15)
Field: Materials Science — Surfaces, Coatings and Films

Ultrafast electron diffraction of photoexcited gas-phase cyclobutanone predicted by ab initio multiple cloning simulations We present the result of our calculations of ultrafast electron diffraction (UED) for cyclobutanone excited into $S_2$ electronic state, which are based on the non-adiabatic dynamics simulations with \textit{Ab Initio} Multiple Cloning (AIMC) method with the electronic structure calculated at the SA(3)-CASSCF(12,12)/aug-cc-pVDZ level of theory. The key features in the UED pattern were identified that can be used to distinguish between the reaction pathways observed in the AIMC dynamics, although there is a significant overlap between representative signals due to structural similarity of the products. The calculated UED pattern can be compared with experiment. Ultrafast electron diffraction ; Ab initio ; Diffraction ; Ultrashort pulse ; Electron diffraction ; Phase (matter) ; Physics ; Gas phase ; Electron ; Excited state ; Atomic physics ; Molecular physics ; Materials science ; Optics ; Quantum mechanics ; Laser Electron and X-Ray Spectroscopy Techniques ; Advanced Chemical Physics Studies ; Mass Spectrometry Techniques and Applications
Authors: Haotian Ma | Zhigang Liu | C. C. Pei | Tianyou Song | Zhifei Zhao | Shuhan Wang
Source: Research Square (preprint, 2024-09-11)
Field: Chemistry — Organic Chemistry

Lightweight Salix Cheilophila Recognition Method Based on Improved YOLOv8n Computer science ; Artificial intelligence ; Pattern recognition (psychology) ; Agricultural engineering ; Environmental science ; Engineering Wood and Agarwood Research
Authors: Alka Zade | Aarti Shastri
Source: Journal of Internal Medicine and Pharmacology (JIMP) (article, 2024-10-29)
Field: Materials Science — Biomaterials

Nanoparticle-Based Drug Delivery: Enhancing Bioavailability and Therapeutic Efficacy in Pharmaceutical Applications Nanoparticle-based drug delivery systems have emerged as a transformative approach to enhance drug bioavailability and therapeutic efficacy in various pharmaceutical applications. These systems exploit the unique properties of nanoparticles, including high surface-to-volume ratios, targeted delivery capabilities, and controlled release profiles, to optimize drug administration. This review explores the types of nanoparticles utilized in drug delivery, such as polymeric nanoparticles, liposomes, dendrimers, and metallic nanoparticles, with an emphasis on their role in enhancing drug bioavailability and efficacy. Current advancements in nanotechnology have facilitated the development of nanoparticles capable of overcoming biological barriers, thereby improving drug localization at the desired sites. We further discuss the mechanisms of drug loading and release, as well as the challenges related to stability, scalability, and safety. This article aims to provide a comprehensive overview of the applications and advantages of nanoparticle-based drug delivery systems, as well as to outline future directions for research and clinical implementation. Through this, we highlight the potential of nanoparticles to revolutionize pharmaceutical science and contribute to more effective, personalized medicine Bioavailability ; Drug delivery ; Pharmaceutical sciences ; Drug ; Pharmacology ; Nanotechnology ; Nanoparticle ; Medicine ; Materials science Nanoparticle-Based Drug Delivery ; Nigella sativa pharmacological applications ; Cancer Research and Treatment
Authors: Emma Paull
Source: The Plymouth student scientist (article, 2024-12-20)
Field: Chemistry — Spectroscopy

Developing a method to identify tyre particles by detecting benzothiazole via GC-MS Tyre particles are a dominant source of microplastic pollution in our environment. However, their chemical and physical properties are poorly understood and no standardised methods for identifying and quantifying them exist. This study looked to develop a method to identify tyre particles using two tyre samples of differing particle sizes, fine (62 - 125 µm) and coarse (250 – 500 µm). Both samples underwent ultrasound-assisted extraction before being analysed via gas chromatography-mass spectrometry (GC-MS) in both full scan and SIM mode, using benzothiazole as a marker. Both samples were also analysed via particle size analysis, scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) in order to determine their chemical and physical properties. Particle size analysis was found to be inaccurate with greater particle size ranges than those expected being reported. SEM showed that the particles were elongated in shape with visible mineral encrustations containing a range of elements. The FTIR spectrum for each sample showed characteristic peaks for natural rubber and the polymers styrene-butadiene rubber (SBR) and ethylene propylene diene monomer (EPDM). The method successfully extracted benzothiazole from the tyre samples but only SIM mode was able to detect benzothiazole in both samples. Other issues with the method were discovered, including the method being determined semi-quantitative, a low recovery being achieved (27%) and the peak shape being suboptimal with visible tailing being present. Benzothiazole was found to be present in a significantly greater quantity in the coarse sample (0.00180 ± 0.000220 mg g-1) than in the fine sample (0.00102 ± 0.000238 mg g-1). With tyre particles being present in the environment at sizes less than 250/300 µm, these results suggest that the need for sensitive analytical techniques is a potential challenge for identifying and quantifying tyre particles in the environment. Overall, this straightforward method shows promise. The application of some simple adaptations should allow this method to become more accurate and fully quantitative, and it should help to fill the gap that exists of a lack of suitable analytical techniques currently available to detect and quantify tyre particles in the environment. This method could thus provide a greater understanding of the issue of environmental tyre particle pollution and its impacts, which could be used to inform policy and regulations on tyre particles and microplastics. Benzothiazole ; Gas chromatography–mass spectrometry ; Chromatography ; Computer science ; Chemistry ; Mass spectrometry ; Organic chemistry Analytical Chemistry and Chromatography ; Analytical Methods in Pharmaceuticals ; Pesticide Residue Analysis and Safety
Authors: Kliment Olechnovič | Sergei Grudinin
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-02-05)
Field: Materials Science — Materials Chemistry

Voronota-LT: efficient, flexible and solvent-aware tessellation-based analysis of atomic interactions Abstract Motivation In the fields of structural biology and bioinformatics, understanding molecular interactions is paramount. However, existing advanced geometric methods for describing interatomic contacts considering full structural context have typically demanded substantial computational resources, hindering their practical application. Given the ever-growing volume of structural data, there is an urgent need for more efficient tools for interaction analysis. Results We present Voronota-LT, a new efficient method tailored for computing Voronoi tessellation-based atom-atom contacts within the solvent-accessible surface of molecular structures. Voronota-LT constructs every interatomic contact surface directly, without pre-computing the global Voronoi diagram or Delaunay triangulation. This approach results in a method that is not only fast, but also parallelizable and capable of selectively targeting specific interface areas within molecular complexes. While offering high execution speed, Voronota-LT provides a comprehensive description of every interatomic interaction, taking full account of the relevant structural context. Availability and Implementation Voronota-LT software is freely available as both a standalone application and a C++ header-only library at https://kliment-olechnovic.github.io/voronota/expansion_lt/ . Tessellation (computer graphics) ; Solvent ; Computer science ; Chemistry ; Computer graphics (images) ; Organic chemistry Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Protein Structure and Dynamics
Authors: Andrius Merkys | Antanas Vaitkus | Eva Sidlauskaite | M. Urbonaitė | A. Grybauskas | S. Gražulis
Source: Acta Crystallographica Section A Foundations and Advances (article, 2024-08-26)
Field: Chemistry — Physical and Theoretical Chemistry

Quality control of the chemical information in the Crystallography Open Database Database ; Quality (philosophy) ; Computer science ; Control (management) ; Information retrieval ; Artificial intelligence ; Physics History and advancements in chemistry ; Semantic Web and Ontologies ; Rough Sets and Fuzzy Logic
Authors: V V
Source: African Journal of Biomedical Research (article, 2024-09-20)
Field: Chemistry — Analytical Chemistry

Advanced Crop Health Monitoring: Leveraging Specim Iq Hyperspectral Imaging And Residual Neural Networks (Resnet-50 And Resnet-101) For Accurate Detection Of Corn Or Maize Leaf Diseases Plant diseases significantly impact agricultural yields and food security worldwide. Accurate and timely disease detection is essential for effective crop management. This research explores an advanced approach to plant leaf disease detection, focusing on corn or maize leaves, through the integration of Specim IQ hyperspectral imaging and Residual Neural Networks (ResNet-50 and ResNet-101). The Specim IQ sensor is employed for data acquisition, providing high-resolution hyperspectral imagery. The methodology involves preprocessing techniques tailored to the Specim IQ sensor, customization of ResNet architectures for hyperspectral data, and comprehensive training and validation processes. This research involves dataset acquisition, pre-processing, and training the models with spectral information. Results indicate a notable improvement in disease detection accuracy, showcasing the potential of ResNet architectures and spectral imaging in plant pathology. The study evaluates the model performance using metrics such as accuracy, precision, recall, and F1 score. A specific case study on corn or maize leaves unveils insights into the potential of hyperspectral imaging for precise disease identification. This research contributes to the advancement of plant disease detection methodologies, showcasing the synergy between cutting-edge hyperspectral imaging technology and powerful deep learning architectures. Residual neural network ; Hyperspectral imaging ; Residual ; Crop ; Agronomy ; Environmental science ; Remote sensing ; Computer science ; Artificial intelligence ; Biology ; Geography ; Algorithm Spectroscopy and Chemometric Analyses
Authors: Juan Caravaca
Source: Preprints.org (preprint, 2024-10-31)
Field: Chemistry — Analytical Chemistry

Comparison of Machine Learning Techniques to Classify Dry Beans Using Computer Vision This study explores the classification of seven registered dry bean species using a dataset of 13,611 grain samples characterized by 16 features, including both dimensional and shape measurements. The primary objective was to develop robust Machine Learning models to accurately identify species while addressing challenges related to class imbalance and feature redundancy. A series of classification algorithms, including Decision Trees (DT), Random Forests (RF), k-Nearest Neighbors (KNN), Support Vector Machines (SVM), and Multi-Layer Perceptrons (MLP), were applied to evaluate their performance under various data conditions. Notably, the MLP model exhibited superior performance due to its capacity to capture complex patterns in high-dimensional data, achieving the highest classification accuracy. Random Forest models showed resilience to class imbalance, though misclassifications between similar species highlighted the need for improved feature selection. The results indicate that effective feature engineering and careful model tuning are crucial for enhancing classification accuracy in agricultural applications. The study concludes that future work should aim to expand the dataset and explore advanced data augmentation techniques to further improve model robustness and applicability in food security contexts. All code to recapitulate the analysis is available along with documentation of pipeline usage at https://github.com/jesusch10/beans_classification. Artificial intelligence ; Computer science ; Computer vision ; Pattern recognition (psychology) ; Machine learning Spectroscopy and Chemometric Analyses ; Smart Agriculture and AI
Authors: Hao Shen | Eric M. Lynch | Chenyang Shi | Joseph L. Watson | Yulai Liu | Ke‐Jia Wu | Hua Bai | Chan Johng Kim | William Sheffler | Emmanuel Derivery | James J De Yoreo | Justin M. Kollman | David Baker
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2024-09-21)
Field: Materials Science — Materials Chemistry

Nucleation limited assembly and polarized growth of a <i>de novo</i> -designed allosterically modulatable protein filament The design of inducibly assembling protein nanomaterials is an outstanding challenge. Here, we describe the computational design of a protein filament formed from a monomeric subunit that binds a peptide ligand. The cryoEM structure of the micron-scale fibers is very close to the computational design model. The ligand acts as a tunable allosteric modulator: while not part of the fiber subunit-subunit interfaces, the assembly of the filament is dependent on ligand addition, with longer peptides having more extensive interaction surfaces with the monomer, promoting more rapid growth. Seeded growth and capping experiments reveal that the filaments grow primarily from one end. We show that designed nucleators that present 12 copies of the peptide ligand promote fiber assembly at concentrations where otherwise assembly occurs very slowly, likely by generating critical local concentrations of monomer in the assembly competent conformation. Following filament assembly, the peptide ligand can be exchanged with free peptide in solution fused to any functional protein of interest, opening the door to a wide variety of tunable engineered materials. Nucleation ; Protein filament ; Biophysics ; Chemistry ; Cell biology ; Biology ; Biochemistry Enzyme Structure and Function ; Biochemical and Molecular Research ; Protein Structure and Dynamics
Authors: Nina Girotto Erhardt | Aloïs Castellano | J. P. Alvarinhas Batista | Raffaello Bianco | Ivor Lončarić | Matthieu J. Verstraete | Dino Novko
Source: arXiv (Cornell University) (preprint, 2024-10-31)
Field: Materials Science — Materials Chemistry

Electron-mediated anharmonicity and its role in the Raman spectrum of graphene The Raman active G mode in graphene exhibits strong coupling to electrons, yet the comprehensive treatment of this interaction in the calculation of its temperature-dependent Raman spectrum remains incomplete. In this study, we calculate the temperature dependence of the G mode frequency and linewidth, and successfully explain the experimental trend, by accounting for the contributions arising from the first-order electron-phonon coupling, electron-mediated phonon-phonon coupling, and standard lattice anharmonicity. The generality of our approach enables its broad applicability to study phonon dynamics in materials where both electron-phonon coupling and anharmonicity are important. Anharmonicity ; Graphene ; Raman spectroscopy ; Electron ; Physics ; Spectrum (functional analysis) ; Condensed matter physics ; Quantum mechanics Graphene research and applications ; Carbon Nanotubes in Composites ; Diamond and Carbon-based Materials Research
Authors: J. Nobre | Dayane Fonseca Soares | Roberto Lima de Albuquerque | José Milton Ferreira Júnior
Source: Revista E-Tech Tecnologias para Competitividade Industrial - ISSN - 1983-1838 (article, 2024-07-23)
Field: Chemistry — Analytical Chemistry

EVALUATION OF ADSORPTION ISOTHERMS OF BANANA PRATA PEEL (MUSA PARADISIACA) IN THE REMOVAL OF METYLENE BLUE TEXTILE DYE: A SUSTENTAINABLE APPROACH In the textile industry, the processing of fibers and the application of dyes require high water consumption, producing high rates of industrial waste. Dyes, in turn, have great stability, which can result in highly contaminated effluents. If disposed of incorrectly, this waste can cause serious problems to the environment and human health. In this sense, it is essential to decontaminate these effluents before releasing them into water bodies. To this end, the adsorption process has proven to be very effective in removing dyes from wastewater in the textile sector. Aiming at the optimization and economic viability of this process, this investigation focuses on the use of an agro-industrial residue, the silver banana peel (Musa paradisiaca), as an alternative biosorbent. Based on an experimental and applied methodology, tests to determine pH were applied in order to determine the most suitable pH for the procedure. Variations in adsorbent concentrations were also evaluated to obtain the best use of the material in removing the methylene blue dye. The results obtained in the biosorption tests indicated 99.5% removal, demonstrating high efficiency in the process. In this way, the silver banana peel (Musa paradisiaca) presented itself as an efficient biosorbent in the adsorption of methylene blue dye, becoming a sustainable and low-cost alternative. Musa × paradisiaca ; Banana peel ; Adsorption ; Textile ; Pulp and paper industry ; Chemistry ; Sorption isotherm ; Horticulture ; Chromatography ; Materials science ; Food science ; Composite material ; Biology ; Organic chemistry ; Engineering Dye analysis and toxicity
Authors: Jerson González-Hernández | Jairo Garcia-Céspedes
Source: Revista de Química (article, 2024-10-16)
Field: Chemistry — Electrochemistry

Voltamperometría: fundamentos electroquímicos y aplicaciones La voltamperometría es una técnica electroquímica con un amplio campo de aplicación en la determinación cuantitativa de analitos, en el análisis de caracterización y en el estudio de procesos de difusión, adsorción, reducción y oxidación. La capacidad de adaptación de esta herramienta analítica se atribuye, principalmente, a la integración de diversas modificaciones en su metodología, impulsadas por los avances tecnológicos que han mejorado y evolucionado los equipos y los sistemas electródicos. En esta revisión se abordan los principios fundamentales de la voltamperometría que incluyen las bases de la instrumentación, de la termodinámica y de la cinética de los procesos electroquímicos, así como un repaso por las técnicas voltamperométricas y algunas aplicaciones relevantes en distintos campos, tales como el análisis ambiental, la industria alimenticia y las ciencias forenses. Los múltiples estudios interdisciplinarios que se basan en la voltamperometría evidencian un uso significativo y una aplicabilidad reconocida de la técnica electroquímica. Philosophy Electrochemical Analysis and Applications ; Advanced Chemical Sensor Technologies
Authors: Mayara Karla dos Santos Nunes | Aleson Pereira de Sousa | Abrahão Alves de Oliveira Filho | José Venâncio Chaves Júnior | Fábio Santos de Souza | Margareth de Fátima Formiga Melo Diniz | Hilzeth de Luna Freire Pêssoa | Rita de Cássia da Silveira e Sá
Source: OBSERVATÓRIO DE LA ECONOMÍA LATINOAMERICANA (article, 2024-12-02)
Field: Materials Science — Materials Chemistry

In silico and in vitro toxicity assessment of ferulic acid and nicotinamide: analysis using admet tools and effects on bacteria, erythrocytes, and sun protection The study addresses the properties of ferulic acid (FA) and nicotinamide (NAM), which are widely explored due to their antioxidant and anti-inflammatory effects, beneficial for cosmetic and pharmaceutical applications. The objective was to assess the toxicity of these substances, both in silico and in vitro, to predict safety and efficacy. Using software such as Molinspiration© and admetSAR©, pharmacokinetic properties, including absorption and toxicity, were calculated. The in vitro analyses involved cytotoxicity assays in human erythrocytes and antibacterial activity tests. Results indicated that both compounds comply with Lipinski's “Rule of 5,” suggesting potential for adequate absorption. Regarding toxicity, FA and NAM showed low human toxicity, though FA exhibited considerable environmental toxicity. In vitro tests revealed that FA demonstrated bacteriostatic activity against Gram-positive bacteria and a dose-dependent effect on human erythrocytes, with higher hemolysis observed at high concentrations. Additionally, FA provided effective sun protection, reaching a sun protection factor (SPF) of 25.01 at all tested concentrations. It is concluded that FA and NAM have promising safety and efficacy profiles, with FA standing out as a potential photoprotective and antimicrobial agent, while NAM exhibits neuroprotective properties due to its permeability through the blood-brain barrier. Toxicity ; Hemolysis ; Pharmacology ; Cytotoxicity ; Chemistry ; Ferulic acid ; In silico ; Lipinski's rule of five ; In vitro toxicology ; In vitro ; Nicotinamide ; Biochemistry ; Biology ; Immunology Nanoparticles: synthesis and applications ; Phytochemicals and Medicinal Plants ; Essential Oils and Antimicrobial Activity
Authors: Fuwei Yang | Wenjiang Zhou | Zhibin Zhang | Xuanyu Huang | Jingwen Zhang | Nianjie Liang | Wujuan Yan | Yuxi Wang | Mingchao Ding | Quanlin Guo | Yu Han | Te‐Huan Liu | Kaihui Liu | Quanshui Zheng | Bai Song
Source: arXiv (Cornell University) (preprint, 2024-06-06)
Field: Materials Science — Materials Chemistry

Phonon heat conduction across slippery interfaces in twisted graphite Interlayer rotation in van der Waals (vdW) materials offers great potential for manipulating phonon dynamics and heat flow in advanced electronics with ever higher compactness and power density. However, despite extensive theoretical efforts in recent years, experimental measurements remain scarce especially due to the critical challenges of preparing single-crystalline twisted interfaces and probing interfacial thermal transport with sufficient resolution. Here, we exploited the intrinsic twisted interfaces in highly oriented pyrolytic graphite (HOPG). By developing novel experimental schemes based on microfabricated mesas, we managed to achieve simultaneous mechanical characterizations and thermal measurements. In particular, we pushed the HOPG mesas with a microprobe to identify and rotate single-crystalline intrinsic interfaces owing to their slippery nature as is well known in structural superlubricity. Remarkably, we observed over 30-fold suppression of thermal conductance for the slippery interfaces by using epitaxial graphite as a control. Nonetheless, the interfacial conductance remains around 600 $\mathrm{MWm^{-2}K^{-1}}$ which surpasses the highest values for artificially stacked vdW structures by more than five times. Further, atomic simulations revealed the predominant role of the transverse acoustic phonons. Together, our findings highlight a general physical picture that directly correlates interfacial thermal transport with sliding resistance, and lay the foundation for twist-enabled thermal management which are particularly beneficial to twistronics and slidetronics. Thermal conduction ; Graphite ; Materials science ; Phonon ; Condensed matter physics ; Composite material ; Physics Thermal properties of materials