jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Zhen-Wei Wu
Source: Chinese Physics B (article, 2026-01-04)
Field: Materials Science — Materials Chemistry

A Kinetic Criterion for Stokes–Einstein Relation Breakdown Based on Effective Collisional Geometry Abstract Here we propose a kinetic framework for interpreting the Stokes–Einstein (SE) relation breakdown in supercooled liquids by introducing an effective collision diameter, d eff , derived from transport data. Numerical simulation of a model CuZr alloy reveal that d eff increases upon cooling but saturates near the first peak of the radial distribution function just before SE breakdown. This saturation defines a geometric upper bound for the collisional cross-section beyond which further slowdown is governed by cooperative, heterogeneous motion rather than local collisional transport. Our analysis yields a compact criterion for SE breakdown in a mean-field perspective and provides physically interpretable inputs for future data-driven models of glassy dynamics. Kinetic energy ; Collision ; Supercooling ; Saturation (graph theory) ; Function (biology) ; Distribution function ; Distribution (mathematics) ; Slowdown Material Dynamics and Properties ; Solidification and crystal growth phenomena ; Theoretical and Computational Physics
Authors: Katarina Davalieva | Vanja Ralić | Gjorgji Bozhinovski | Branislava Gemović | Maja D. Nešić | Lela Korićanac | Tanja Dučić | Manuel Algarra | Iva Popović | Milutin Stepić | Miloš Petković
Source: Current Issues in Molecular Biology (article, 2026-03-26)
Field: Materials Science — Materials Chemistry

S-Doped Carbon Dot Treatment Alters RNA Processing, Translation, and Protein Degradation Pathways in HeLa Cells Carbon dots offer excellent physico-chemical properties and biocompatibility for cancer theranostics systems, either as therapeutic agents themselves, or as potential drug carriers. It is, however, postulated that the drug carrier affects the mechanism of action and intracellular target molecules of a drug. Therefore, in the present study, we systematically evaluated protein alterations in HeLa cervical cancer cells after treatment with sulfur-doped carbon dots (S-CDs). Synchrotron Radiation μFTIR spectroscopy and label-free LC–MS/MS proteomics integrated with bioinformatics were used to assess molecular changes. μFTIR revealed a shift and increased intensity of α-helices, indicating structural changes in proteins as a result of the interaction between S-CDs and cells. Proteomic analysis identified 122 statistically significant (p ≤ 0.05) proteins with increased abundance and 61 with decreased abundance following S-CD exposure, many of which possess high α-helix content, consistent with μFTIR findings. Functional analyses showed that up-regulated proteins were enriched in molecular adaptor, transporter, and transcription regulator activities, particularly those involved in RNA metabolism and translation. Down-regulated proteins were dominated by protein-modifying enzymes and cytoskeletal components. Pathway enrichment analysis indicated alterations in mRNA processing, ribosomal pathways, translation factors, aminoacyl-tRNA biosynthesis, and proteasome degradation. Key hub proteins included ribosomal proteins and translation initiation factors. S-CD treatment led to opposite regulation of many proteins compared to their regulation in untreated HeLa cells including down-regulation of ribosomal proteins (RPS27L, RPS19, and RPS5), aminoacyl-tRNA biosynthesis proteins (IARS1, LARS1, and MARS1), and proteasome degradation proteins (PSMD2, PSMD3, and PSMD11), which aligns with the observed cytotoxic effect of S-CDs on cervical cancer cells. Overall, these results highlight significant proteomic and structural protein changes induced by S-CDs and support their potential for cervical cancer treatment, warranting further investigation of this nanomaterial’s biological applications. HeLa ; Ribosomal protein ; Proteasome ; Protein biosynthesis ; Protein degradation ; Proteomics ; Translation (biology) ; Ribosome ; RNA Carbon and Quantum Dots Applications ; Electrochemical sensors and biosensors ; Advanced Nanomaterials in Catalysis
Authors: Jürgen Bartel | Philipp T. Kaulich | Borja Ferrero-Bordera | Rick Gelhausen | Rolf Backofen | Andreas Tholey | Sandra Maaß
Source: microLife (article, 2026-01-01)
Field: Chemistry — Spectroscopy

CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins In proteome studies, the application of alternative proteases, exclusively or in addition to trypsin, often increases protein sequence or proteome coverage. It has recently been shown that, in particular, the analysis of small proteins benefits from such multi-protease approaches. However, selecting the most optimal combination of proteases either requires laboursome experiments or the decision of an experienced user, which might be biased. In this manuscript, we present a protease score that enables the objective comparison of multiple-protease digestions and a Python-based tool named CoMPaseD (Comparison of Multiple Protease Digestions), which utilizes Monte-Carlo simulations to predict this score for a user-defined set of proteases and any combination of these. By analysis of the small proteomes of the two model organisms <i>Bacillus subtilis</i> and <i>Methanosarcina mazei</i> with five proteases and different experimental setups, we demonstrate a good correlation between experimentally derived and predicted scores. This highlights the broad applicability of CoMPaseD, which can effectively guide the selection of proteases to enhance the characterization of specific subsets of the proteome, e.g. based on factors such as protein size, localization or isoelectric point. CoMPaseD is freely available at <i>https://github.com/MicrobialProteomics/CoMPaseD</i>. Proteases ; Proteome ; Protease ; Selection (genetic algorithm) ; Proteomics ; Set (abstract data type) Advanced Proteomics Techniques and Applications ; Enzyme Production and Characterization ; vaccines and immunoinformatics approaches
Authors: Ajay Shankar
Source: RSC Advances (article, 2026-01-01)
Field: Chemistry — Organic Chemistry

Hydration-induced modulation of aromaticity and reactivity in anthocyanidins: a quantum mechanical study This study explores the hydration effects on aromaticity, orbital delocalization, and local and global reactivity descriptors of anthocyanidins. Using the Harmonic Oscillator Model of Aromaticity (HOMA) and <i>para</i>-delocalization index (PDI), the quantitative assessment of the aromaticity of the three rings in anthocyanidins is performed. It revealed that the hydration generally increases their aromaticity, though the extent of change varies across different rings in the skeletal structure. The HOMA and PDI indices show consistent trends in aromaticity, with ring B exhibiting the highest aromaticity, followed by fused rings, <i>i.e.</i>, ring A and ring C. The study also highlights the role of orbital delocalization indices (ODI) in understanding the hydration effects on the electronic structure of anthocyanidins. A significant increase in the delocalization of electrons in the HOMO post-hydration is observed. The global reactivity descriptors computed under conceptual density functional theory (CDFT) show that the hydration of anthocyanidins affects their reactivity towards electron-rich species. The acidic forms of anthocyanidins are characterized as superelectrophiles whose nature is retained while the electrophilic strength decreases slightly upon hydration. The decrease in global chemical hardness (<i>η</i>), increase in global nucleophilicity (NI), and changes in vertical ionization potential (VIP) and vertical electron affinity (VEA) indicate the differences in reactivity arising from the hydration of anhydrous forms of anthocyanidins. This should have implications for their antioxidant properties and potential applications in food packaging and smart sensors for quality monitoring of protein-rich foods such as meat and fish, which are perishable in nature. The atomic level attribution over the 2D chemical structures created a heatmap, which assisted the local reactivity analysis using condensed dual descriptors (CDDs). The heatmap overlapped with 2D chemical structures highlighted the specific sites, mostly in the fused ring C, suggesting it to be more favourable for nucleophilic attack after hydration. This observation reinforces the alteration in reactivity as predicted from the several global descriptors of the anthocyanidin molecules. Overall, this comprehensive analysis provides a deeper understanding of the hydration effects on the chemical behaviour of anthocyanidins, offering valuable insights into their applications. Aromaticity ; Delocalized electron ; Reactivity (psychology) ; Anthocyanidins ; Ionization energy ; Hyperpolarizability ; Ring (chemistry) ; Density functional theory Synthesis and Properties of Aromatic Compounds ; Free Radicals and Antioxidants ; Crystallography and molecular interactions
Authors: Yulia Rachmawati | Amellia Dwi Rizkyana | Lulus Mualimin | Fawait Afnani | Deyla Prajna
Source: Springer Link (Chiba Institute of Technology) (article, 2026-01-15)
Field: Materials Science — Biomaterials

Optimization of extraction and characterization of cellulose from edamame pod waste for active biofilm applications Edamame pod waste, a by-product of soybean processing, represents a promising lignocellulosic biomass source for biopolymer development. This study aimed to optimize cellulose extraction from edamame pod waste using Response Surface Methodology (RSM) with a Box–Behnken Design (BBD) and to characterize the extracted cellulose for potential biofilm applications. Four independent factors—particle size (40– 80 mesh), extraction temperature (60–90 °C), extraction time (1–3 h), and NaOH concentration (5–10%, w/v)—were investigated, with cellulose yield (%) and whiteness index (WI) as responses. The optimized conditions (80 mesh, 75°C, 1 h, 7.5% NaOH) produced cellulose with a yield of 54.5% and a WI of 70%. Subsequent alkaline hydrogen peroxide (AHP) washing enhanced cellulose purity, increasing cellulose content from 41.25% to 65.14% and reducing hemicellulose and lignin to 19.07% and 9.21%, respectively. FTIR analysis confirmed successful delignification through the disappearance of lignin-associated peaks (1508–1512 cm⁻¹) and the presence of characteristic β-1,4-glycosidic linkages. Thermal characterization using Thermogravimetric Analysis (TGA) and Derivative Thermogravimetry (DTG) showed a single-step degradation pattern with Tonset ≈ 275 °C, Tmax ≈ 350 °C, and ~13% residue at 600 °C, indicating high thermal stability and purity comparable to commercial cellulose. These findings demonstrate that edamame pod waste can be efficiently converted into high-purity, thermally stable cellulose through an eco-friendly alkaline extraction process, providing a sustainable raw material for the development of biodegradable biopolymers and active biofilms as alternatives to synthetic plastics. Cellulose ; Hemicellulose ; Extraction (chemistry) ; Lignin ; Biopolymer ; Thermogravimetric analysis ; Thermal stability ; Response surface methodology ; Thermogravimetry Advanced Cellulose Research Studies ; Biofuel production and bioconversion ; Polysaccharides and Plant Cell Walls
Authors: Haven I. Blair | Rayna E. Nemcek | Hallie G. McKinnie | Sarah Saleh | Madison L. Walker | Justin M. Miller | Deon T. Miles
Source: ACS Omega (article, 2026-03-11)
Field: Materials Science — Materials Chemistry

Mercury Ion Sensing Using Mercaptosuccinic Acid-Derived Carbon Quantum Dots Carbon quantum dots, prepared from mercaptosuccinic acid (MSA), were used to sense metal ions in aqueous solutions. Two fractions of nanoparticles were obtained after several purification steps, designated blue and green based on their color under UV illumination. We monitored the photoluminescence of the carbon nanoparticles upon the addition of metal ions. Stern-Volmer plots were made to determine whether photoluminescence quenching of the nanoparticles in solution occurred. Photoluminescence quenching was observed with adding Hg<sup>2+</sup>, Fe<sup>3+</sup>, Cr<sup>3+</sup>, Co<sup>2+</sup>, Ag<sup>+</sup>, Fe<sup>2+</sup>, Cu<sup>2+</sup>, and Ni<sup>2+</sup>. Most of these metal ions have partially filled d orbitals, contributing to the transfer of electrons from the photoexcited nanoparticles to the available empty orbitals of the metal ions. The detection limits for sensing the metal ions were calculated. The lowest detection limits observed were for Hg<sup>2+</sup>, with values of 4.1 and 1.4 ppm using the blue and green MSA-CQDs, respectively. Changes in the excitation wavelength and pH had a moderate impact on the spectral properties of the nanoparticles. Quantum dot ; Carbon quantum dots ; Mercury (programming language) ; Ion ; Carbon fibers Carbon and Quantum Dots Applications ; Molecular Sensors and Ion Detection ; Polydiacetylene-based materials and applications
Authors: Shuo Zhang | Yangming Zhou | Qi Zhang | Juanjuan Xue | Ruijie Li | Tao Liu | Qianqian Duan | Shengbo Sang
Source: Nanomaterials (article, 2026-01-26)
Field: Materials Science — Materials Chemistry

Fine-Tuning Positive-Surface-Charge Carbon Dots for High-Efficiency and Low-Cytotoxicity Gene Delivery Carbon dots (CDs) have emerged as a promising non-viral gene delivery vector due to their excellent biocompatibility and tunable surface properties. In this study, four CDs with gradient-positive zeta potentials (7.23 mV, 16.7 mV, 25.3 mV, 34.5 mV) were synthesized via a hydrothermal method. Among these, CDs-3 with an optimal zeta potential of 25.3 mV stood out, exhibiting ultra-low cytotoxicity (cell viability > 80% even at 50 μg/mL) and a transfection efficiency of nearly 100% (for GFP plasmid delivery), significantly outperforming commercial vectors Lipo2000 and PEI. A stable CDs-3/siIhh delivery system was constructed at a mass ratio of 2:1. In vitro evaluations confirmed that CDs-3/siIhh could efficiently regulate the Indian Hedgehog (Ihh) signaling pathway and osteoarthritis (OA)-related markers in both normal and IL-1β-induced inflammatory ATDC5 chondrocytes. Its regulatory effect was significantly superior to that of the commercial Lipo2000/siIhh and PEI/siIhh systems. This consistent "transcription-translation" regulation, combined with the carrier's safety and excellent cellular internalization capacity in chondrocytes, highlights its potential for OA gene therapy. Collectively, our work develops a novel, safe, and efficient positive-potential CD-based gene delivery vector, providing a promising gene regulatory capacity by leveraging optimized surface charge engineering. Zeta potential ; Gene delivery ; Transfection ; Biocompatibility ; Internalization ; Cytotoxicity ; Viability assay ; In vitro ; Surface charge Carbon and Quantum Dots Applications ; Graphene and Nanomaterials Applications ; RNA Interference and Gene Delivery
Authors: Jutta Geier | Chiara Barretta | Mario Messiha | Katarina Marković | Márton Bredács | Florian Arbeiter | Eric Helfer | L. Meinhart | Gernot Oreski
Source: Österreichische Wasser- und Abfallwirtschaft (article, 2026-01-26)
Field: Chemistry — Analytical Chemistry

Alt oder wertvoll? – Detektion von gealtertem Polyethylen mittels NIR-Hyperspektraltechnik für hochwertiges Kunststoffrecycling Zusammenfassung Die Qualität von Polyethylen (PE-)-Rezyklaten ist entscheidend für deren Einsatz in neuen Anwendungen. Der Eintrag gealterter PE-Produkte in den Recyclingstrom kann diese Qualität jedoch mindern. Um den Bedarf an Neumaterial oder zusätzlichen Stabilisatoren zur Kompensation dieser Qualitätsminderung zu reduzieren, ist eine zuverlässige Identifikation und Aussortierung stark gealterter Materialien erforderlich, um die Qualität von PE-Rezyklaten nachhaltig zu verbessern. In dieser Studie wurde das Potenzial der Alterungs- bzw. Degradationserkennung von PE mittels Nahinfrarot (NIR)-Hyperspektraltechnik untersucht. Hierfür wurden PE-Proben künstlich durch UV-Bestrahlung gealtert. Die Degradation wurde durch mechanische Prüfungen erfasst, wobei die Bruchdehnung als Kriterium zur Einteilung in die gewählten Degradationsklassen diente. Die NIR-Hyperspektraldaten wurden an einem NIR-Labor-Setup aufgenommen. Die Trennbarkeit wurde anhand von Klassifikationsmodellen bewertet, wobei sowohl multivariate Datenanalyse (Partial Least Squares Discriminant Analysis) als auch ein Verfahren des maschinellen Lernens (Support Vector Machine) eingesetzt und anschließend miteinander verglichen wurden. Die Ergebnisse zeigen, dass unter Verwendung von maschinellem Lernen hochgradig und weniger gealterte PE-Proben mit hoher Genauigkeit getrennt werden können. Damit eröffnet sich die Möglichkeit, bereits etablierte NIR-Sortiersysteme nicht nur zur Identifizierung von Polymertypen, sondern auch gezielt zur Degradationserkennung einzusetzen, was ein wichtiger Schritt hin zu qualitativ hochwertigeren Rezyklaten sowie Ressourcenschonung ist. Gas analysis ; L-Lactate dehydrogenase ; Qualitative analysis Spectroscopy and Chemometric Analyses ; Microplastics and Plastic Pollution ; biodegradable polymer synthesis and properties
Authors: Penglin Wang | Huibin Ke | Yunfei Xue
Source: Scientific Data (article, 2026-02-16)
Field: Materials Science — General Materials Science

An integrated database of combustion properties of metallic materials Metal combustion, which is fundamentally a rapid exothermic redox reaction with oxygen, governs critical applications from aerospace propulsion to structural fire safety. Understanding key combustion metrics including combustion enthalpy, ignition temperature, ignition delay time, combustion rate, and threshold pressure is essential for designing fire-resistant alloys or high-energy propellants. This work establishes a comprehensive database of 725 curated data points extracted from 45 publications, mainly encompassing pure metals, Al-based, Ti-based, Mg-based, Fe-based alloys and multi-component alloys. Each data entry integrates combustion metrics with alloy composition and critical experimental metadata, such as sample geometry, oxygen partial pressure and test method. By integrating scattered literature data into a unified framework with standardized parameters, this work provides a foundation for data-driven discovery of next-generation materials with tailored combustion performance. Combustion ; Ignition system ; Exothermic reaction ; Work (physics) ; Aerospace ; Energetic material ; Autoignition temperature ; Sample (material) Engineering and Material Science Research ; Energetic Materials and Combustion ; Rocket and propulsion systems research
Authors: Narayan Achale | Pranay Guru
Source: International Journal of Chemical Studies (article, 2026-02-01)
Field: Materials Science — Ceramics and Composites

Recent Advances in Dy³⁺-Doped Glasses: A Review of Spectroscopic Behavior and White Light Emission for Photonic Technologies Dy³?-doped glass systems have garnered considerable interest as potential materials for white light-emitting diodes (W-LEDs), solid-state lasers, optical thermometry, and multifunctional photonic devices. This literature review thoroughly examines significant research on Dy³?-doped glasses with diverse host compositions, such as phosphate, borate, tellurite, lead phosphate, aluminofluoroborophosphate, oxyfluoro-borophosphate, boro-tellurite, and multicomponent borate matrices. The spectroscopic characteristics were primarily examined by Judd-Ofelt theory, which indicated elevated ?? values, signifying pronounced asymmetry and covalent bonding around Dy³? ions in the majority of hosts. Characteristic emissions at around 480 nm (blue: ?F?/? ? ?H??/?) and 575 nm (yellow: ?F?/? ? ?H??/?) were regularly recorded, with the yellow-to-blue intensity ratio (Y/B) adjustable via glass composition, modifier cations, co-dopants (e.g., Eu³?), and Dy³? concentration. Numerous studies achieved near-optimal white light output with CIE coordinates around (0.33, 0.33) and linked colour temperatures appropriate for indoor and display illumination. Methods include fluoride inclusion, heavy metal oxide addition, and co-doping significantly decreased phonon energy, inhibited non-radiative relaxation, and improved radiative transition probabilities. In addition to illumination, some research revealed other capabilities such as thermoluminescence for dosimetry, gamma radiation attenuation, optical thermometry via fluorescence intensity ratio, and prospective laser gain medium attributed to elevated stimulated emission cross-sections. The examined literature underscores the adaptability of Dy³?-activated glassy hosts, providing economical, stable, and efficient substitutes for traditional phosphor systems. These materials have significant potential for next-generation solid-state illumination, multifunctional photonic devices, and enhanced sensing technologies. Photonics ; Emission intensity ; Laser ; Phosphor ; White light ; Optical materials ; Diode ; Fluorescence ; Boron Glass properties and applications ; Luminescence Properties of Advanced Materials ; Lanthanide and Transition Metal Complexes
Authors: Imelda L. Lazcano-Carrasco | Carlos Z. Gómez‐Castro | Luis Ángel Zárate-Hernández | Rosa Luz Camacho | Simplicio Gonzalez-Montiel | Marco Franco-Perez | Julián Cruz‐Borbolla
Source: Organic & Biomolecular Chemistry (article, 2026-01-01)
Field: Chemistry — Organic Chemistry

Molecular interactions of cinnamyl and quinoxaline derivatives with Bcl-2 antiapoptotic proteins: a computational study Antiapoptotic proteins represent a major obstacle to the success of anticancer therapies, as they promote the survival of malignant cells and contribute to treatment resistance. Among these, Bcl-2 and Bcl-xl are frequently overexpressed in pancreatic cancer, making them important therapeutic targets. In this work, we present a systematic computational study aimed at identifying the molecular features that enable selected cinnamyl and quinoxaline derivatives to inhibit the oligomerization of these proteins. Using a combination of molecular docking and molecular dynamics simulations, we characterized the most plausible binding modes and assessed the stability of the resulting complexes. Key intermolecular interactions responsible for binding were analyzed using the Quantum Theory of Atoms in Molecules (QTAIM), while reactivity descriptors derived from temperature-dependent chemical reactivity theory were employed to rationalize trends in affinity and stability. Our results reveal consistent structural and electronic patterns that govern the effective inhibition of Bcl-2 and Bcl-xl, providing mechanistic insight into their molecular recognition processes. Beyond improving the understanding of antiapoptotic protein inhibition, this study offers practical guidelines for the rational design of new small-molecule inhibitors with potential anticancer activity. Quinoxaline ; Molecular dynamics ; Rational design ; Docking (animal) ; Reactivity (psychology) ; Intermolecular force ; Protein–protein interaction ; Molecular model ; Molecule Synthesis and Biological Evaluation ; Cell death mechanisms and regulation ; Toxin Mechanisms and Immunotoxins