jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Hirokazu Shoji | N. Boku | Jun Adachi
Source: Cancer Science (article, 2026-01-22)
Field: Chemistry — Spectroscopy

Clinical Applications of Phosphoproteomics: Illuminating Cancer Signaling and Enabling Rational Therapeutic Strategies Protein phosphorylation is a central post-translational modification regulating cellular signaling, frequently dysregulated in cancer. Mass spectrometry (MS)-based phosphoproteomics has emerged as a powerful approach to systematically profile phosphorylation events, thereby revealing aberrant kinase activity and therapeutic vulnerabilities that are not captured by genomic or transcriptomic analyses. Recent advances across the workflow-including optimized sample preparation and phosphopeptide enrichment, isotope- or label-free quantitative strategies, high-resolution mass spectrometry platforms, specialized algorithms for site identification and quantification, and integrative informatics analyses-have enabled the detection of tens of thousands of phosphorylation sites even from small clinical specimens. These developments have facilitated the characterization of signaling pathways across diverse cancer types, leading to the identification of targetable kinases and informing therapeutic strategies. In this review, we highlight studies that employed phosphoproteomic analyses of clinical specimens or patient-derived cancer cells to delineate signaling characteristics and to propose and validate therapeutic targets. Collectively, MS-based phosphoproteomics is poised to become a cornerstone of precision oncology. By enabling comprehensive and quantitative mapping of phosphorylation events, this technology allows mechanistic dissection of cancer signaling pathways and uncovers therapeutic vulnerabilities that may be exploited with targeted agents. Phosphoproteomics ; Phosphorylation ; Signal transduction ; Identification (biology) ; Kinase ; Cancer ; Proteomics ; Protein phosphorylation Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Cell Image Analysis Techniques
Authors: Amirmahdi Salehi | Behrang Mohajer | Mohamad Kheradmandkeysomi | Amirjalal Jalali | Markus Bussmann | Chul B. Park
Source: Thermal Science and Applications (article, 2026-03-04)
Field: Materials Science — Polymers and Plastics

Choice of the Mathematical Models in the Simulation of Elongational Flow-Induced Crystallization (FIC) During Polymer Processing: A Review This review examines mathematical models of elongational Flow-Induced Crystallization (FIC) from a computational modeling perspective, emphasizing their practical integration within transport-based simulation frameworks. The work targets researchers in computational fluid dynamics (CFD) who model the cooling stages of polymer processing operations such as melt spinning and injection molding. Rather than reiterating the extensive physics of FIC, the review focuses on the choice of mathematical formulation best suited for a given simulation objective. Existing approaches are classified into four model types distinguished by their complexity, required input data, and computational cost: Type 1 models introduce empirical crystallization terms within simplified rheological frameworks; Type 2 combine the Avrami formulation with correlations that account for flow-induced effects; Type 3 embed crystallization kinetics directly into constitutive equations through stress or strain tensors; and Type 4 represent molecular or atomistic simulations that resolve chain dynamics in detail. Each model type is critically evaluated in terms of predictive accuracy, implementation practicality, and suitability for different process scales. Comparative tables summarize these attributes, guiding the selection of an appropriate correlation strategy consistent with available data and computational resources. The review concludes by identifying current challenges—including polymer blends, non-isothermal effects, and anisotropic morphologies—and outlining promising directions for future research. Overall, this work serves as a concise reference for CFD practitioners seeking reliable FIC formulations that balance fidelity, efficiency, and applicability across polymer-processing simulations. Mathematical model ; Computational model ; Computational fluid dynamics ; Rheology ; Work (physics) ; Process (computing) ; Crystallization ; Type (biology) ; Spinning Polymer crystallization and properties ; Rheology and Fluid Dynamics Studies ; Polymer Foaming and Composites
Authors: Xiaolong Cui | Liwei Chen | Zhuo Li
Source: Coatings (article, 2026-03-10)
Field: Materials Science — Materials Chemistry

Optimization of In Situ CO2 Oxidation Temperature for Hydrogen-Resistant ZrO2 Films on Zirconium Hydride Zirconium hydride is susceptible to dehydrogenation at elevated temperatures. In this study, zirconium hydride was oxidized by in situ oxidation in a CO2 atmosphere at temperatures ranging from 550 to 700 °C for 10 h. The morphology, elemental distribution, phase structure, and hydrogen barrier performance of the resulting oxide films were systematically characterized using SEM, EDS, XRD, film adhesion and microhardness tests, and dehydrogenation experiments. At 550–600 °C, the formed oxide films are thin and non-uniform, containing numerous micropores and cracks, which results in limited hydrogen barrier performance. When the oxidation temperature is increased to 650 °C, a better balance between the oxidation reaction and diffusion processes is achieved. This leads to the formation of a dense, continuous, and uniform ZrO2 film with strong adhesion to the substrate. As a result, the initial dehydrogenation temperature increases to 660 °C, while both the dehydrogenation rate and cumulative hydrogen release are significantly reduced, indicating the best overall hydrogen resistance. However, further increasing the oxidation temperature to 700 °C causes an excessively high oxidation rate, which introduces large growth and thermal stresses. These stresses promote the formation of microcracks in the oxide film, weaken the interfacial bonding strength, and consequently reduce the hydrogen barrier performance. The results demonstrate that the hydrogen permeation resistance of the oxide film is mainly governed by film compactness, defect evolution, and interfacial integrity. Based on these findings, 650 °C is identified as the optimal processing temperature for producing a high-quality hydrogen-resistant ZrO2 film on zirconium hydride under a CO2 atmosphere. Dehydrogenation ; Hydrogen ; Oxide ; Hydride ; Zirconium ; Zirconium hydride ; Thermal oxidation ; Permeation Nuclear Materials and Properties ; Hydrogen Storage and Materials ; Catalysts for Methane Reforming
Authors: Umasankar Dolai
Source: Research Square (preprint, 2026-02-18)
Field: Chemistry — Inorganic Chemistry

An Alternative Theoretical Framework of S-state Mechanism in PS II Manganese ; Mechanism (biology) ; Molecule ; Ion ; Substrate (aquarium) ; Oxygen ; Oxygen evolution Metal-Catalyzed Oxygenation Mechanisms ; Photosynthetic Processes and Mechanisms ; Spectroscopy and Quantum Chemical Studies
Authors: J. Howard | Akshaya Narayanasamy | Steffen Lindert
Source: bioRxiv (Cold Spring Harbor Laboratory) (article, 2026-02-10)
Field: Chemistry — Spectroscopy

Improving Protein Structure Prediction Using Integrative Cryo-EM and Ion Mobility Mass Spectrometry Modeling Proteins perform essential roles across nearly all cellular processes, and accurate three-dimensional structures remain critical for elucidating structure-function relationships and studies on drug discovery. Cryo-electron microscopy (cryo-EM), X-ray crystallography, and nuclear magnetic resonance can provide detailed structural information. However, for many proteins, structural information is available only as lower-resolution experimental data or sparse data. Such information is more difficult to translate into accurate atomic coordinates; a common example is low-resolution cryo-EM density maps. In parallel, mass spectrometry-based methods, including ion mobility (IM-MS), offer rapid, broadly applicable structural descriptors such as collisional cross section (CCS), a global measure of molecular shape and size, but CCS values also do not provide atomistic detail. Here we present CRIM (cryo-EM + IM-MS), an integrative Rosetta scoring function that combines low-resolution cryo-EM density information with IM-MS derived CCS as restraints to improve monomeric protein structure prediction. CRIM incorporates the Rosetta REF2015 (RS) energy with a CCS agreement penalty (computed via PARCS) and an electron-density agreement term (elec_dens_fast). We tested CRIM on an ideal dataset of 60 monomeric proteins using simulated CCS values and density maps. Across the ideal dataset, the CRIM score function improved or maintained prediction quality for many targets, reducing the mean RMSD from 3.65 Å (RS) to 2.90 Å and increasing the mean TM-score from 0.88 to 0.90. Furthermore, an experimental benchmark dataset of 54 proteins was curated to include either experimental cryo-EM maps or published CCS values. On the experimental dataset, CRIM similarly improved model selection, lowering the mean RMSD from 6.65 Å to 4.38 Å and raising the mean TM-score from 0.73 to 0.79. In comparison to AlphaFold3 predictions, CRIM frequently yielded competitive predictions and was able to substantially outperform AlphaFold3 for select difficult targets where sparse experimental restraints provide strong discriminatory power. The CRIM score function is freely available within the Rosetta software suite and provides a practical framework for leveraging complementary IM-MS and cryo-EM data to improve monomeric protein structure prediction. Benchmark (surveying) ; Measure (data warehouse) ; Function (biology) ; Protein structure ; Ideal (ethics) ; Protein structure prediction ; Experimental data ; Term (time) Mass Spectrometry Techniques and Applications ; Protein Structure and Dynamics ; Enzyme Structure and Function
Authors: Dandan Mao | Miaomiao Duan | Peiyou Li | Qingwei Luo
Source: Materials Research Express (article, 2026-03-17)
Field: Materials Science — Materials Chemistry

Microstructure and mechanical properties of novel Ti-Cu-Co-Zr complex concentrated alloys Abstract Obtaining new high-strength and high toughness complex concentrated alloys has important practical value in engineering applications. Based on this goal, this paper adopts a mixed method of intermetallic compounds (Ti 2 Cu ) and eutectic units (Co 64 Zr 36 ) to design the new Ti–Cu–Co–Zr complex concentrated alloys. The microstructure of the new alloy was observed and its mechanical properties were tested using x-ray diffractometer, optical microscope, electron scanning microscope, energy spectrum scanner, and electron universal testing machine. The experimental results show that the microstructures of three Ti–Cu–Co–Zr alloys consist of TiCo matrix phase and Ti 2 Co phase. The Ti 32 Cu 16 Co 33.28 Zr 18.72 alloy has the higher true yield strength (1945 MPa) and fracture strength (2489 MPa), which are larger than those of Ti 28 Cu 14 Co 37.12 Zr 20.88 (1778 MPa) and Ti 30 Cu 15 Co 35.2 Zr 19.8 (1843 MPa) alloys, respectively. The Ti 32 Cu 16 Co 33.28 Zr 18.72 alloy has the high quasi-static toughness. This paper provide a reference value for the composition design and their engineering applications of complex concentrated alloy with high strength. Eutectic system ; Microstructure ; Alloy ; Intermetallic ; Fracture toughness ; Toughness ; Phase (matter) Titanium Alloys Microstructure and Properties ; Intermetallics and Advanced Alloy Properties ; Advanced Welding Techniques Analysis
Authors: Anina Dufter | Sabrina Weber | Orkun Furat | Johannes Schubert | René Rekers | Maximilian Luczak | Erik Glatt | Andreas Wiegmann | Anja Bielefeld | Volker Jürgen Schmidt
Source: ArXiv.org (article, 2026-03-24)
Field: Materials Science — Materials Chemistry

Virtual materials testing of ASSB cathodes combining AI-based stochastic 3D modeling and numerical simulations The performance of all-solid-state battery (ASSB) cathodes strongly depends on their microstructure. Optimizing the cathode morphology can therefore enhance effective macroscopic properties such as ionic and electronic conductivity. The search for optimized microstructures can be facilitated by virtual materials testing: By integrating image analysis and stochastic microstructure modeling to generate a wide range of realistic 3D microstructures and evaluate their effective macroscopic properties by means of numerical simulations, thereby reducing the need for extensive physical experiments. This approach allows for the investigation of structure-property relationships through parametric regression models that incorporate relevant geometrical descriptors of microstructures such as volume fractions, mean geodesic tortuosities, specific surface areas, and constrictivities. By linking these geometrical descriptors to macroscopic properties, virtual materials testing provides quantitative insight into how microstructure influences material performance. In the present paper, this framework is applied for ASSB cathodes. In addition, by systematically varying model parameters, a broad range of 3D microstructures can be generated, which remain close to the original cathode morphology while inducing targeted changes in selected geometrical descriptors. The resulting database enables the calibration of regression models whose predictive performance is assessed by comparing predicted and simulated effective properties such as the ionic and electronic conductivity, thereby quantifying how accurately combinations of geometrical descriptors can explain and predict variations in effective macroscopic properties. Microstructure ; Parametric statistics ; Range (aeronautics) ; Cathode ; Stochastic geometry ; Stochastic modelling ; Calibration ; Material properties Machine Learning in Materials Science ; Advancements in Battery Materials ; Advanced Neural Network Applications
Authors: Hamadi Zineb | Bendahma Fatima | Bessaha Fatiha | Mana Abdirahman Mohamed | Mika Sillanpää | Saleh Al-Farraj | Dinesh C. Gupta
Source: Scientific Reports (article, 2026-03-23)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Study of half-metallic ferromagnet RhHfVGa for spintronic and thermoelectric applications This study presents a comprehensive first-principles investigation of the newly proposed quaternary Heusler compound RhHfVGa, focusing on its structural, electronic, magnetic, thermodynamic, and thermoelectric properties. Density functional theory (DFT) with GGA-PBE96, supplemented by GGA + U and the modified Becke-Johnson potential (mBJ), was employed to ensure accurate band gap characterization. This compound crystallizes in the Type 1 structure, with the optimized lattice constant of 6.354 Å. RhHfVGa exhibits half-metallic ferromagnet (HMF) behavior, with a 100% spin-polarization and a total magnetic moment of 3.00 µB, consistent with the Slater-Pauling rule (M<sub>tot</sub> = Z<sub>tot</sub> - 18). The results suggest that RhHfVGa is well-suited for spintronic applications. Thermodynamic parameters were successfully calculated, which enhances the credibility of the findings. The heat capacity (Cv = 99.68 Jmol<sup>- 1</sup>K<sup>- 1</sup>) approaches the Dulong-Petit limit, a phenomenon common to all solids. The narrow band gaps (approximately 0.98 to 1.26 eV), high n-type electrical conductivities (3.35 × 10<sup>19</sup> (Ω.m.s)<sup>-1</sup> in GGA + U and 8.43 × 10<sup>19</sup> (Ω m s)<sup>-1</sup> in mBJ), and a dimensionless figure of merit (ZT) ranging from 0.82 to 1.65 across various temperatures indicate strong potential for thermoelectric applications. Spintronics ; Ferromagnetism ; Thermoelectric effect ; Dimensionless quantity ; Lattice constant ; Figure of merit ; Density functional theory ; Magnetic moment Heusler alloys: electronic and magnetic properties ; Advanced Thermoelectric Materials and Devices ; 2D Materials and Applications
Authors: Marwa M. A. Abdallah | Reham F. El-kased | Ghadir S. El-Housseiny | Khaled M. Aboshanab
Source: Applied Microbiology and Biotechnology (article, 2026-03-23)
Field: Materials Science — Materials Chemistry

Evaluation of the biological activities of Bacillus cereus-synthesized titanium dioxide nanoparticles The emergence of multidrug-resistant pathogens and the growing burden of cancer worldwide demand novel therapeutic approaches. This study evaluated the biological activities of green-synthesized titanium dioxide nanoparticles (TiO₂ NPs) using Bacillus cereus cell-free supernatant and titanium tetra-isopropoxide precursor. Nanoparticles were analyzed and standard methods were employed to evaluate the antimicrobial, antibiofilm, and cell cytotoxicity. UV-Vis spectroscopy confirmed the synthesis of TiO₂ NPs with a characteristic peak at 360 nm. Transmission electron microscopy (TEM) revealed roughly spherical particles (8.8 ± 3 nm diameter). A Z-average hydrodynamic diameter of 328.1 nm (PDI, 0.439) was revealed by dynamic light scattering (DLS). According to the energy-dispersive X-ray spectroscopy (EDX) results, oxygen was 42.39% and titanium was 45.93%. The X-ray diffraction (XRD) measurement confirmed a crystalline anatase structure, with a prominent peak at 25.3° 2θ. Fourier transform infrared (FTIR) detected the characteristic Ti-O-Ti and vibrational band at 403.31 cm⁻<sup>1</sup>. The nanoparticles demonstrated broad-spectrum antimicrobial activity with MICs of 78 μg/mL (E. coli), 156 μg/mL (C. albicans), 625 μg/mL (E. faecalis), and 2500 μg/mL (S. aureus and P. aeruginosa). At sub-MIC concentrations, TiO₂ NPs reduced biofilm formation in S. aureus by roughly 65.72% ± 0.01, in E. faecalis by 50.91% ± 0.02, and in P. aeruginosa by 38.4% ± 0.1. Cytotoxicity investigations revealed IC₅₀ values of 212.15 μg/mL (Caco-2) and 342.96 μg/mL (Vero cells), with a selectivity index of 1.62. Strong antiviral activity against HSV-1 was observed (74.74% inhibition at 60 µg/mL, EC₅₀ = 17.41 µg/mL, selectivity index = 19.7). Biogenic synthesis using B. cereus successfully produced highly crystalline, small-sized anatase TiO₂ nanoparticles demonstrating multifunctional biological activities including antimicrobial, antibiofilm, anticancer selectivity, and antiviral properties. KEY POINTS: • Green synthesis via B. cereus yielded crystalline anatase TiO₂ NPs with nanoscale dimensions. • TiO₂ NPs demonstrated broad antimicrobial/antibiofilm effects and selective anticancer activity. • Strong antiviral potency against HSV-1 with excellent selectivity was observed. Bacillus cereus ; Dynamic light scattering ; Anatase ; Nanoparticle ; Titanium dioxide ; Transmission electron microscopy ; Titanium ; Fourier transform infrared spectroscopy ; Biofilm Nanoparticles: synthesis and applications ; TiO2 Photocatalysis and Solar Cells ; Cancer Research and Treatments
Authors: Mingfeng Xu | Di Sang | Mingbo Pu | Peng Gao | Bowen Zhao | Yuhan Zheng | Qingji Zeng | L. M. Chen | F. B. Zhang | Yu Guo | Xiong Li | X. Ma | Yunqi Fu | Xiangang Luo
Source: Light Science & Applications (article, 2026-04-03)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Full-space inverse-designed meta-optics for complex vector field shaping of intracavity landscapes The sophisticated shaping of electromagnetic field landscapes, both outside and inside optical cavities, has long been an important goal of optics and photonics, with broad applications in near-field imaging, lithography, and laser science. Despite extensive progress in far-field shaping of extracavity landscapes, achieving accurate tailoring of three-dimensional intracavity fields has remained elusive. Here, we propose full-space adjoint-enabled freeform meta-optics for complex, on-demand vector field shaping of intracavity landscapes. In contrast with conventional semi-space adjoint approaches, the full-space adjoint strategy allows for efficient full-wave optimization of vector fields at the subwavelength scale, overcoming strong multiple scattering and interference intrinsic to enclosed cavity boundaries. We experimentally demonstrate tailored plasmonic cavity landscapes with a freeform metasurface mask, realizing a fivefold enhancement in imaging fidelity without sacrificing optical super-resolution performance. Our work significantly broadens the scope of freeform meta-optics and may open new avenues for applications in nanophotonics, topological photonics, and quantum optics. Field (mathematics) ; Plasmon ; Scattering ; Nanophotonics ; Laser ; Electromagnetic field ; Fidelity ; Nonlinear optics ; Quantum optics Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Orbital Angular Momentum in Optics
Authors: Shubham Tanwar | Han-Yan Wu | C.-L. Yang | Rubén Millán‐Solsona | Simone Fabiano | Adrica Kyndiah | Gabriel Gomila
Source: ArXiv.org (article, 2026-01-08)
Field: Materials Science — Polymers and Plastics

Local Multimodal Dynamics in Mixed Ionic-Electronic Conductors and Their Fingerprints in Organic Electrochemical Transistor Operation Mixed ionic-electronic conductors host tightly coupled interactions among mobile ions, electronic charges, and the polymer matrix, giving rise to complex multimodal responses spanning electrical, mechanical, and morphological transformations. These materials underpin organic electrochemical transistors (OECTs), which translate such interactions into low-voltage signal amplification and sensing for applications in bioelectronics, neuromorphic computing, and memory. Despite their central role, OECT current-voltage transfer characteristics are often treated phenomenologically, as both the local multimodal dynamics and their connection to global device response remain unresolved. Here, we reveal that the transfer curve encodes a cascade of spatially localized electrochemical transitions, each associated with distinct changes in conductivity, stiffness, and morphology, fundamentally redefining it as a spatially resolved fingerprint of device's internal state. Using automated operando multimodal in-liquid scanning dielectric microscopy, we directly map these dynamics and identify region-specific electrochemical thresholds governing the interplay between source, channel, and drain. We found that the local tip-sample electrostatic force serves as a remarkable mechanistic observable of coupled multimodal dynamics in mixed conductors. A physically grounded model links it to general material, interfacial, and geometric parameters, enabling mechanistic interpretation and predictive insights. Our work provides a new framework for probing and understanding mixed conduction in ion-electron coupled systems. Neuromorphic engineering ; Electrical conductor ; Transistor ; Thermal conduction ; Dynamics (music) ; SIGNAL (programming language) ; Local field potential ; Observable ; Complex dynamics Conducting polymers and applications ; Advanced Memory and Neural Computing ; Advanced Sensor and Energy Harvesting Materials