jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Aaron Wacholder | Eric W. Deutsch | Leron W. Kok | Jip T. van Dinter | Jiwon Lee | James C. Wright | Sébastien Leblanc | Ayodya H Jayatissa | Kevin Jiang | Ihor Arefiev | Kevin Cao | Francis Bourassa | Félix-Antoine Trifiro | Michal Bassani‐Sternberg | Pavel V. Baranov | Annelies Bogaert | Sonia Chothani | Ivo Fierro-Monti | Daria Fijalkowska | Kris Gevaert | Norbert Hubner | Jonathan M. Mudge | Jorge Ruiz‐Orera | Jana Schulz | Juan Antonio Vizcaíno | John R. Prensner | Marie A. Brunet | Thomas F. Martínez | Sarah A. Slavoff | Xavier ROUCOU | Jyoti S. Choudhary | Sebastiaan van Heesch | Robert L. Moritz | Anne‐Ruxandra Carvunis
Source: Nature Communications (article, 2026-01-21)
Field: Chemistry — Spectroscopy

Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins. We find that studies vary by three orders of magnitude in the number of unannotated proteins they report. Of nearly 10,000 reported sORF-encoded peptides, 96% were unique to a single study, and 12% mapped to annotated proteins or proteoforms. Manual curation of a benchmark dataset of 406 manually evaluated spectra from 204 sORF-encoded proteins revealed large variation in peptide-spectrum match (PSM) quality between studies, with immunopeptidomics studies generally reporting higher quality PSMs than conventional enzymatic digests of whole cell lysates. We estimate that 65% of predicted sORF-encoded protein detections in immunopeptidomics studies were supported by high-quality PSMs versus 7.8% in non-immunopeptidomics datasets. Our work stresses the need for standardized protocols and analysis workflows to guide future advancements in microprotein detection by MS towards uncovering how many human microproteins exist. Proteomics ; Benchmarking ; Workflow ; Benchmark (surveying) ; Quantitative proteomics ; Protein methods Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications ; Biotin and Related Studies
Authors: Takuya Hosokai | Wataru Ota | Kenshiro Matsuda | Hikaru Ishii | Amane Niwa | Yasuo Nakayama | Keisuke Nakamura | Daiki Asakawa | Emiko Fujiwara | Tohru Sato | Ken Albrecht
Source: Advanced Optical Materials (article, 2026-01-30)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Mechanistic Origin of Photodegradation and Impurity Effects in Donor–Acceptor Luminescent Radicals Abstract Organic luminescent radicals have emerged as promising open‐shell emitters for advanced optoelectronic and sensing applications. Among them, the carbazole‐substituted tris(2,4,6‐trichlorophenyl)methyl radical (Cz‐TTM) exhibits remarkable photostability and emission efficiency compared with the parent TTM radical. Nevertheless, Cz‐TTM can be visibly degraded by indoor light irradiation and its photodegradation mechanism is poorly understood. Here, the study systematically investigates the photochemical behavior of Cz‐TTM in solutions, together with the influence of impurities on the photophysical properties of the compound. It is found that emissive and non‐emissive impurities are introduced depending on the purification methods and the light irradiation conditions. Impurities cause underestimation of photoluminescence quantum yield through competitive absorption. Photodegradation under continuous irradiation undergoes a multi‐step reaction via metastable intermediates, which react with dissolved oxygen upon local excitation of the TTM radical moiety. Quantum‐chemical calculations indicate a ring‐closure followed by dechlorination within the TTM moiety as the key degradation pathway. The superior photostability of Cz‐TTM to TTM originates from its stabilized first excited doublet energy level, which increases the activation energy for ring‐closure reaction in Cz‐TTM. These combined experimental and theoretical insights reveal the fundamental factors governing the photostability of TTM‐type luminescent radicals and offer design principles for next‐generation organic luminescent materials. Radical ; Photodegradation ; Luminescence ; Impurity ; Photoluminescence ; Excited state ; Quantum yield ; Moiety Magnetism in coordination complexes ; Organic and Molecular Conductors Research ; Organic Light-Emitting Diodes Research
Authors: Baocheng Zhou | Tu Hu | Guo Lin | Shixing Wang | Hongying Xia | Libo Zhang | Chen WANG
Source: Coordination Chemistry Reviews (article, 2026-01-03)
Field: Chemistry — Inorganic Chemistry

Ultrasonic synthesis of metal-organic frameworks: mechanistic insights, structural modulation, and industrial prospects The widespread industrial adoption of metal-organic frameworks (MOFs) is hindered by limitations inherent to conventional syntheses, such as high energy demands, reliance on toxic solvents, and poor scalability. This comprehensive review establishes ultrasonic synthesis (US) as a green and efficient alternative, systematically analyzing the fundamental mechanisms by which ultrasonic cavitation governs MOFs nucleation and growth kinetics, enabling rapid reactions, reduced crystal dimensions, and tailored defect densities. Critical advances in structural control strategies are examined, particle size/morphology optimization through US parameters; defect engineering for active site/pore functionality enhancement; and crystal facet regulation synergized with surface engineering. Breakthrough applications of US-synthesized MOFs are highlighted across domains: enhanced catalysis (electro-, photo-, enzyme); superior molecular recognition (gas adsorption/separation, water purification); high-capacity electrodes (supercapacitors, batteries); and targeted drug delivery/biosensing. Prospects for industrial scale-up of US-synthesized MOFs are analyzed. Persistent challenges in acoustic field uniformity and defect-property predictability are noted. Future perspectives emphasize in situ characterization and AI-guided optimization to unlock MOFs potential. By linking fundamental insights with practical applications, this review guides the development of high-performance MOFs for industry. We underscore US synthesis as a transformative platform for MOFs industrialization, aligning with UN Sustainable Development Goals through sustainable, cost-effective manufacturing. • Acoustic cavitation mechanisms and parameter effects on MOF nucleation, growth, and defects. • Ultrasonic control of MOF morphology, porosity, and defect density. • Enhanced performance in catalysis, gas storage, sensing, and energy storage. • Green advantages: rapid, energy-efficient, reduced solvent usage. • Industrial scale-up challenges, opportunities, and future directions. Ultrasonic sensor ; Nucleation ; Transformative learning ; Cavitation ; Characterization (materials science) ; Sonochemistry ; Low energy ; Metal-organic framework ; Facet (psychology) Metal-Organic Frameworks: Synthesis and Applications ; Magnesium Oxide Properties and Applications ; Copper-based nanomaterials and applications
Authors: Siwen Zhang | Jing Li | Jiawei Liu | Milad Abolhasani | Lijun Hou
Source: Chemical Engineering Journal (article, 2026-01-30)
Field: Materials Science — Materials Chemistry

Microfluidic synthesis of quantum dots: Design, mechanism, properties and applications Microfluidics ; Quantum dot ; Scalability ; Personalization ; Microfluidic chip Quantum Dots Synthesis And Properties ; Innovative Microfluidic and Catalytic Techniques Innovation ; Carbon and Quantum Dots Applications
Authors: Mingna Li | Yi Du | Juan Zhao | Yongli Jiang | Yifeng Zhang | Junjie Yi
Source: Food Packaging and Shelf Life (article, 2026-01-01)
Field: Materials Science — Materials Chemistry

Carbon quantum dot-enhanced stimulus-responsive hydrogels for smart food packaging: Sensing, preservation, and AI-enabled predictive quality management Commercialization ; Sustainability ; Active packaging ; Food safety ; Food packaging ; Food spoilage ; Internet of Things Carbon and Quantum Dots Applications ; Nanocomposite Films for Food Packaging ; Advanced Cellulose Research Studies
Authors: Sabrina Weber | Benedikt Prifling | R. K. Jeela | Andreas Prahs | Daniel Schneider | Britta Nestler | V. Hugo Schmidt
Source: Computational Materials Science (article, 2026-01-12)
Field: Materials Science — Materials Chemistry

A time-continuous approach to analyzing anode aging in solid-oxide fuel cells via stochastic 3D microstructure modeling and physics-based simulations Solid-oxide fuel cells (SOFCs) are a promising energy conversion technology, offering a low environmental impact, low costs and high flexibility regarding the choice of the fuel. However, electrochemical performance of SOFCs decreases with time as a result of complex structural aging mechanisms of their anodes that are not yet fully understood. An option to quantitatively investigate this aging behavior could be tomographic imaging of the 3D microstructure of SOFC anodes for different aging durations, which is expensive and time-consuming. To overcome this issue, physics-based aging simulations resolving the 3D microstructural evolution can be exploited, which use tomographic image data of pristine SOFC anodes consisting of nickel, gadolinium-doped ceria (GDC) and pore space, as initial state. This microstructure simulation method is based on a grand-chemical potential multi-phase-field approach including surface diffusion. Computations conducted with the simulation framework are capable to predict the coarsening of the multiphase polycrystalline electrode. A promising approach to further accelerate the quantitative investigation of SOFC degradation is to combine physics-based aging simulation with data-driven stochastic 3D microstructure modeling, which is typically less computationally intensive compared to phase-field simulations. More precisely, an excursion set model based on Gaussian random fields is used to characterize the 3D microstructure of SOFC anodes by means of a small number of interpretable model parameters. Moreover, the evolution of the parameter vector of the calibrated stochastic 3D model over time is modeled by analytical functions that make fast predictive simulations possible. The prediction robustness is investigated by first assuming that the evolution of the 3D microstructure is known up to a certain point in time. Then, in a second step, the 3D microstructure of SOFC anodes is predicted for further future points in time and, through geometrical descriptors, compared with the results of physics-based aging simulation. • Combining multi-phase field simulations with stochastic modeling to quantitatively analyze the aging behavior of SOFC anodes. • Time-continuous stochastic 3D model based on excursion sets of random fields for SOFC anodes. • Predictive microstructure simulations by interpolation of model parameters. • Analytical regression formulas to investigate the relationship between model parameters and geometrical descriptors. Microstructure ; Anode ; Robustness (evolution) ; Solid oxide fuel cell ; Computation ; Gaussian ; Stochastic modelling ; Context (archaeology) Advancements in Solid Oxide Fuel Cells ; Fuel Cells and Related Materials ; Electrocatalysts for Energy Conversion
Authors: Abdalrahman M. Rayan | Mehawed M. Ahmed | H. A. A. Saadallah | A. A. Azab | Kh. Roumaih | A. M. Abdel Hakeem
Source: Scientific Reports (article, 2026-01-11)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Structure and physical property correlation in magnesium doped LaFeO3 nano perovskites synthesized by the green method In this work, La<sub>1 - x</sub>MgₓFeO₃ (0.0 ≤ x ≤ 0.20) perovskite nanoparticles were successfully synthesized using a green synthesis route assisted by Moringa oleifera leaf extract. The influence of Mg²⁺ substitution on the structural, dielectric, and magnetic properties of LaFeO₃ was systematically investigated. X-ray diffraction and Rietveld refinement revealed a clear phase transition from cubic (Pm-3 m) to orthorhombic (Pnma) symmetry at x ≥ 0.17. Low Mg doping (x = 0.05, 0.10) induced a slight lattice expansion due to oxygen vacancy formation and Fe³⁺ → Fe²⁺ reduction, while higher doping levels led to lattice contraction from ionic size mismatch and structural distortion. Dielectric measurements demonstrated a significant enhancement in dielectric constant and suppression of dielectric loss up to x = 0.15, attributed to improved interfacial polarization and defect-induced conduction. Magnetic analysis via Vibrating Sample Magnetometer (VSM) and electron spin resonance (ESR) confirmed a transition from weak ferromagnetic to strong ferromagnetic behavior with increased Mg content, peaking at x = 0.17 due to enhanced Fe³⁺/Fe⁴⁺ exchange interactions and surface spin effects. These findings highlight the potential of Mg-doped LaFeO₃ nanoparticles for multifunctional applications in energy storage, sensing, and spintronic devices, while emphasizing the environmental and economic advantages of green synthesis approaches. Rietveld refinement ; Ferromagnetism ; Dielectric ; Orthorhombic crystal system ; Doping ; Nanoparticle ; Spintronics ; Magnetization ; Electron paramagnetic resonance Multiferroics and related materials ; Dielectric properties of ceramics ; Magnetic Properties and Synthesis of Ferrites
Authors: Mitradeep Sarkar | Michael T. Enders | Mehrdad Shokooh‐Saremi | Kenji Watanabe | Takashi Taniguchi | Hanan Herzig Sheinfux | Frank H. L. Koppens | Georgia T. Papadakis
Source: npj Nanophotonics (preprint, 2026-02-21)
Field: Materials Science — Materials Chemistry

Far-field extraction of the dielectric function of exfoliated flakes near phonon resonances The lateral dimensions of mechanically exfoliated flakes of emerging van der Waals (vdW) materials rarely exceed a few tens of micrometers. This limits the experimental determination of their complex dielectric function (ϵ(ω)) at mid-infrared (IR) frequencies, as the IR beam in conventional angle-resolved spectroscopic ellipsometry is typically larger than a flake. To overcome this, previous methods mapped the dispersion of surface phonon polaritons using near-field probes, but these require costly instrumentation, are sensitive to external factors, demand extensive numerical fitting, and become cumbersome for anisotropic or dispersive materials. Here, we introduce a simple empirical method to extract the in-plane dielectric tensor components of small flakes using conventional Fourier Transform Infrared (FTIR) micro-spectrometry. By identifying reflectance minima near phonon resonances, we determine ϵ per frequency without model fitting. Applying this approach to flakes of varying thicknesses enables reconstruction of ϵ(ω) over a broad spectral range. van der Waals force ; Dielectric ; Materials science ; Permittivity ; Maxima and minima ; Optics ; Ellipsometry ; Boron nitride ; Molecular physics ; Nanotechnology ; Optoelectronics ; Physics ; Thin film Graphene research and applications ; 2D Materials and Applications ; Thermal properties of materials
Authors: Eric C.-Y. Yuan | Yunsheng Liu | Junmin Chen | Peichen Zhong | Sanjeev Raja | Tobias Kreiman | Santiago Vargas | Wenbin Xu | Martin Head‐Gordon | Chao Yang | Samuel M. Blau | Bingqing Cheng | Aditi S. Krishnapriyan | Teresa Head‐Gordon
Source: Nature Reviews Chemistry (article, 2026-02-11)
Field: Materials Science — Materials Chemistry

Foundation models for atomistic simulation of chemistry and materials Scaling ; Foundation (evidence) ; Observable ; Variety (cybernetics) ; Forcing (mathematics) ; Field (mathematics) Machine Learning in Materials Science ; Block Copolymer Self-Assembly ; Inorganic Chemistry and Materials
Authors: Sicheng Fan | Zerui Yan | Binhao Wang | Yuting Song | Dafu Tang | Huan Liu | Yimei Ouyang | Kun Lan | Zhangquan Peng | Guiming Zhong | Dong-Liang Peng | Qiulong Wei
Source: Nature Communications (article, 2026-01-09)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Unlocking limited electric double-layer capacity via electrochemically-driven continuous partial desolvations in carbon nanopores Electrochemical capacitors are primarily limited by the low electric double-layer storage capacity and narrow operating window that avoids the formation of solid electrolyte interface layers. Herein, we demonstrate that electric double-layer adsorption of solvated Na<sup>+</sup> in carbon nanopores is achievable under a large offset potential of -2.95 V vs. potential of zero charge in diethylene-glycol-dimethyl-ether electrolyte, even accompanying with the as-formed solid electrolyte interface layers. The largely enlarged offset potential in situ drives the continued partial desolvations in carbon nanopores, which largely reduces the average solvation numbers from 2.1 to 0.6, leading to a high electric double-layer capacitance of 172 F g<sup>-1</sup>, a high capacity of 508 C g<sup>-1</sup> and high initial coulombic efficiency of 92.2% at 0.1 A g<sup>-1</sup> (0.5 mA cm<sup>-2</sup>), together with high-rate capability and long-term cycling stability. Thereby, such increased electric double-layer charge storage enables the redesign and assembly of sodium-ion capacitor pouch cells that display a high specific density of 40 Wh kg<sup>-1</sup> (on cell level) and 30,000 cycles at a fast (dis)charging rate of 51 C (20 mA cm<sup>-2</sup>). Such sodium-ion capacitors are assembled without any pretreatments that are beneficial for scale-up fabrications in industry. Nanopore ; Electrolyte ; Capacitor ; Capacitance ; Faraday efficiency ; Electric double-layer capacitor ; Electrochemistry ; Porosity ; Electrochemical window Supercapacitor Materials and Fabrication ; Advancements in Battery Materials ; Advanced Battery Materials and Technologies
Authors: Antonia Albers | Max Masthoff | Gustavo Fernández
Source: Angewandte Chemie International Edition (article, 2026-01-19)
Field: Materials Science — Materials Chemistry

Self‐Assembled (Aza)BODIPY Dyes for Biomedical in Vivo Imaging 4,4-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) and their N-containing analogs (aza-BODIPYs) are highly versatile organic dyes that combine excellent photophysical, electronic, and supramolecular properties with high chemical stability. These features have enabled their use in diverse applications such as bioimaging, targeted drug delivery, and functional self-assembled materials. Their broad structural modularity allows different stacking modes with controlled exciton coupling during self-assembly, resulting in supramolecular materials with tunable spectroscopic and morphological properties. This is particularly relevant in aqueous media, where tunable near-infrared (NIR) absorption and emission are essential for advanced contrast agents (CAs) in biomedical imaging. Besides meso-heteroatom modification, J-aggregation stands out as especially advantageous for achieving red-shifted absorption and emission, thereby improving tissue penetration and reducing autofluorescence and light scattering. Of particular promise is the concept of pathway complexity, whereby a single (aza)BODIPY scaffold can access multiple aggregated states with distinct photophysical signatures, enabling stimuli-responsive and multifunctional imaging behavior. Hence, understanding the interplay between (aza)BODIPY molecular design, exciton coupling in aqueous media and their resulting supramolecular and bioimaging properties is of utmost importance. This minireview discusses recent advances in (aza)BODIPY-based self-assembled structures used as CA platforms for in vivo biomedical imaging and highlights the structure-property relationships that govern their performance. Supramolecular chemistry ; Stacking ; Autofluorescence ; Optical imaging ; Scaffold ; Absorption (acoustics) ; Aqueous medium ; Modularity (biology) Luminescence and Fluorescent Materials ; Supramolecular Chemistry and Complexes ; Supramolecular Self-Assembly in Materials
Authors: Dheanda Absharina | Csilla Veres | Alfonz Kedves | Zoltán Kónya | Balázs P. Szabó | Csaba Vágvölgyi
Source: Applied Microbiology and Biotechnology (article, 2026-01-29)
Field: Materials Science — Biomaterials

Enhanced bacterial cellulose production by Komagataeibacter xylinus using agro-derived flour nitrogen sources Bacterial cellulose (BC) production is limited by the high cost of refined nitrogen sources such as yeast extract and tryptone. While carbon source substitution has been widely studied, approaches for nitrogen replacement remain underexplored. Here, we evaluated cereal and pseudo-cereal flours as low-cost nitrogen alternatives for Komagataeibacter xylinus DSMZ 2325 under static fermentation under static fermentation using two nitrogen substitution strategies: constant total nitrogen (CTN) and constant nitrogen source mass (CNSM). Thirteen flour variants were screened, with maximum BC yields of 3.40 g/L (soy), 3.17 g/L (teff), 2.74 g/L (quinoa), and 1.94 g/L (triticale) under the CTN strategy, in several cases surpassing the modified HS control. Structural analyses confirmed that flour-derived BC retained the defining characteristics of high-quality cellulose, including high crystallinity, robust fibrillar networks, and thermal stability. Soy consistently produced the highest volumetric yields, whereas triticale exhibited the greatest fold-increase compared to the control, highlighting the distinct nutritional and compositional contributions. These results demonstrate that flour-based media provide a viable strategy to reduce production costs while tailoring BC properties through substrate choice. By shifting the focus from carbon to nitrogen optimization, this study introduces a sustainable and scalable approach to bioprocessing using agro-derived raw materials. KEY POINTS: • Flour-based nitrogen sources replace costly yeast extract and tryptone in BC media • Triticale, teff, quinoa, and soy influence BC yield and cellulose fibril formation • Agro-flour substrates offer low-cost, sustainable bacterial cellulose production. Bacterial cellulose ; Nitrogen ; Cellulose ; Fermentation ; Bioprocess ; Yeast extract ; Raw material ; Yeast Advanced Cellulose Research Studies ; Biofuel production and bioconversion ; Polysaccharides and Plant Cell Walls
Authors: Ilya S. Besedin | Michael Kerschbaum | J. Knoll | Ian Hesner | Lukas Bödeker | Luis Colmenárez | Luca Hofele | Nathan Lacroix | Christoph Hellings | François Swiadek | Alexander Flasby | Mohsen Bahrami Panah | Dante Colao Zanuz | Markus Müller | Andreas Wallraff
Source: Nature Physics (preprint, 2026-01-30)
Field: Materials Science — Materials Chemistry

Lattice surgery realized on two distance-three repetition codes with superconducting qubits Quantum error correction is needed for quantum computers to be capable of executing algorithms using hundreds of logical qubits in a fault-tolerant manner. Recent experiments have progressed towards this by demonstrating sufficiently low error rates for state preservation of a single logical qubit. However, quantum computation algorithms also require that these logical qubits can be entangled and that gate operations can be performed on them. Lattice surgery is a technique that offers a practical approach for implementing such gates, particularly in planar quantum processor layouts. Here we demonstrate lattice surgery between two distance-three repetition-code qubits by splitting a single distance-three surface-code qubit. Using a quantum circuit that is fault-tolerant for bit-flip errors, we achieve an improvement in the value of the decoded <i>Z</i> <i>Z</i> logical two-qubit observable compared with a similar non-encoded circuit. We therefore demonstrate the functional building blocks needed for lattice-surgery operations on larger-distance codes based on superconducting circuits. Repetition (rhetorical device) ; Qubit ; Superconductivity ; Superconducting quantum computing ; Lattice (music) ; Condensed matter physics ; Physics ; Theoretical physics ; Quantum mechanics ; Quantum ; Philosophy ; Acoustics ; Josephson effect ; Linguistics Nanoporous metals and alloys