jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Franziska Elsässer | Roberta Florea | Felix Räsch | Mostafa Zedan | Nesli-Ece Şen | Tim Pflästerer | Tatjana Kleele | Robbie Loewith | Karsten Weis | Natalie de Souza | Paola Picotti
Source: Molecular Systems Biology (article, 2026-01-12)
Field: Chemistry — Spectroscopy

Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells The function of a protein is determined by its structure, which may change dynamically in response to post-translational modifications, interaction with other molecules, or environmental factors like temperature. Limited proteolysis-coupled mass spectrometry (LiP-MS) captures such structural alterations on a proteome-wide scale via the detection of altered protease susceptibility patterns of proteins. However, this technique has so far required cell lysis, which exposes proteins to non-native conditions and can disrupt labile interactions such as those occurring within biomolecular condensates. To study protein structures directly within cells, we developed in-cell LiP-MS. We optimized conditions for introduction of proteinase K into human cells using electroporation and validated that intracellular cleavage occurs. In-cell LiP-MS captured the known binding of rapamycin to FKBP1A within the cell. Moreover, it detected global protein structural alterations upon sodium arsenite treatment and captured the structural dynamics of hundreds of proteins from biomolecular condensates with peptide level resolution and within live human cells. The data allowed monitoring of structural alterations of individual sites on the involved proteins, such as known RNA-binding and intrinsically-disordered regions, and dissected the timing of the different events. We detected known (G3BP1) and novel structural alterations of proteins from stress granules as well as from nuclear speckles and validated alteration of nuclear speckles by fluorescence microscopy and of the protein SERBP1 by polysome profiling. Our dataset further provides a resource describing the structural changes of human proteins in response to a cellular stress leading to biomolecular condensation and pinpoints structurally altered regions. Comparison of LiP-based structural fingerprints before and after cell lysis revealed which human proteins are susceptible to structural change upon cell lysis, therefore guiding the design of future experiments requiring native protein structures. Lysis ; Cytosol ; Structural biology ; Intracellular ; Cell ; Protein structure ; Protein–protein interaction ; Protease ; Function (biology) ; Protein dynamics Advanced Proteomics Techniques and Applications ; Biotin and Related Studies ; Mass Spectrometry Techniques and Applications
Authors: Mariantonietta Pizzella | Valéria Gomes | Enrico Gallo | Sérgio Veloso | Célio Fernandes | A. Accardo | Carlo Diaferia
Source: Gels (article, 2026-01-24)
Field: Materials Science — Biomaterials

β-Hairpin-Based Peptide Hydrogels: The Case of MAX1 This review explores the advancements and applications of β-hairpin peptide hydrogels, starting from the paradigmatic case of MAX1 and its highly versatile analogue MAX8. MAX1 (H-VKVKVKVKV<sup>D</sup>PPTKVKVKVKV-NH<sub>2</sub>) has been identified as the first synthetic β-hairpin peptide for the preparation of stimuli-responsive peptide-based hydrogels. At low ionic strength or neutral pH, MAX1 remains unfolded and soluble. However, under physiological conditions, it folds into a β-hairpin structure, then producing a self-supporting matrix within minutes. The formed gel is shear-thinning and self-healing, making it suitable for injectable therapies. To explore MAX1 molecular space and enhance its practical clinical use, the primary sequence was engineered via chemical modification, with specific single amino acid substitution and relative net charge alteration. This approach generates MAX1 analogues, differing in gelation kinetics, mechanical response and biological performances. The β-hairpin peptide hydrogels are categorized into five different groups: MAX1, MAX1 analogues, MAX8, MAX8 analogues and non-MAX peptides sequences. Collectively, the review outcomes demonstrate the use of β-hairpin peptide matrices as tunable platforms for the development of predictable and stable biomaterials for advanced tissue engineering and drug delivery applications. Peptide ; Self-healing hydrogels ; Peptide sequence ; Drug delivery ; Amino acid ; Click chemistry ; Ionic strength ; Oligopeptide Supramolecular Self-Assembly in Materials ; Hydrogels: synthesis, properties, applications ; Dendrimers and Hyperbranched Polymers
Authors: Mengchen Wang | Zengshuo Huang | Feng Li | Yebao Chen | Fangfang Ban | Hua Yang | Siming Zhu | Junlin Wu
Source: Foods (article, 2026-02-03)
Field: Materials Science — Biomaterials

Investigating the Shelf-Life Extension of Shrimp Surimi Using a Polysaccharide-Based Film from Alpinia oxyphylla To investigate the effect of a polysaccharide-based composite film (ASC) composed of <i>Alpinia oxyphylla</i> polysaccharide (its molecular weight was approximately 4.07 kDa, and the monosaccharide composition was predominantly glucose and galacturonic acid), sodium alginate, and calcium chloride on the storage quality of shrimp surimi, this study compared the preservation efficacy of the ASC film with that of treatments using chitosan, potassium sorbate, ascorbic acid, sodium alginate, <i>Alpinia oxyphylla</i> polysaccharide, and distilled water. Samples were stored at 4 °C for 12 days, and evaluations were conducted by measuring film structural characteristics and quality indicators of shrimp surimi. Results showed that the ASC groups (where <i>Alpinia oxyphylla</i> polysaccharide was added at 20%, 30%, and 40% of the sodium alginate mass, designated as ASC 20%, ASC 30%, and ASC 40%) significantly outperformed the control group across all quality indicators. The ASC 30% group demonstrated the best overall preservation performance, effectively delaying oxidative browning, protein degradation, lipid oxidation, and microbial growth in shrimp surimi. The ASC 40% group exhibited particularly strong antibacterial effects, while the ASC 20% group also showed stable preservation performance. The composite film combines the antioxidant and antibacterial activities of <i>Alpinia oxyphylla</i> polysaccharide with the barrier and moisture-retention properties of sodium alginate, forming a stable three-dimensional network structure through calcium chloride cross-linking. It is superior to single/individual chemical preservatives in terms of film-forming ability, functionality, and safety, providing a natural, effective, and environmentally friendly preservation approach for shrimp surimi and other aquatic products. It also offers a theoretical foundation and practical reference for the development of natural preservation technologies in the food industry. Shrimp ; Preservative ; Ascorbic acid ; Antioxidant ; Sodium ; Distilled water ; Polysaccharide ; Vitamin C Nanocomposite Films for Food Packaging ; Meat and Animal Product Quality ; Aquaculture disease management and microbiota
Authors: Erik Kirstein | Pyeongjae Park | Woonghee Cho | Cristian D. Batista | Je-Geun Park | S. A. Crooker
Source: Nature Communications (article, 2026-01-31)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Tunable chiral and nematic states in the triple-Q antiferromagnet Co1/3TaS2 Complex spin configurations in magnetic materials, ranging from collinear single-Q to non-coplanar multi-Q states, exhibit rich symmetry and chiral properties. However, their detailed characterization is often hindered by the limited spatial resolution of neutron diffraction techniques. Here we employ magnetic circular dichroism and magnetic linear dichroism to investigate the triangular lattice antiferromagnet Co<sub>1/3</sub>TaS<sub>2</sub>, revealing three-state (Z<sub>3</sub>) nematicity and also spin chirality across its multi-Q magnetic phases. At intermediate temperatures, the presence of linear dichroism identifies nematicity arising from a single-Q stripe phase, while at high magnetic fields and low temperatures, a phase characterized solely by circular dichroism emerges, signifying a purely chiral non-coplanar triple-Q state. Notably, at low temperatures and small fields, we discover a unique phase where both chirality and nematicity coexist. A theoretical analysis based on a continuous multi-Q manifold captures the emergence of these distinct magnetic phases, as a result of the interplay between four-spin interactions and weak magnetic anisotropy. Additionally, both circular and linear dichroism microscopy spatially resolves the chiral and nematic domains. Our findings establish Co<sub>1/3</sub>TaS<sub>2</sub> as a rare platform hosting diverse multi-Q states with distinct combinations of spin chirality and nematicity while demonstrating the effectiveness of polarized optical techniques in characterizing complex magnetic textures. Chirality (physics) ; Circular dichroism ; Linear dichroism ; Antiferromagnetism ; Liquid crystal ; Dichroism ; Spin (aerodynamics) ; Magnetic circular dichroism Iron-based superconductors research ; Advanced Condensed Matter Physics ; Topological Materials and Phenomena
Authors: A. Martinelli
Source: Zeitschrift für Kristallographie - Crystalline Materials (article, 2026-01-14)
Field: Materials Science — Materials Chemistry

Extending the Williamson-Hall method: a qualitative approach for microstructural analysis under non-ideal conditions Abstract As a first approximation, the Williamson Hall plot method can be applied for obtaining a quantitative assessment of particle size and strain by analysing the integral breadth of the diffraction lines as a function of the reciprocal interplanar spacing. For this purpose, it is necessary to use a reference sample with negligible structural imperfections. Not infrequently, the relative variation of one of these parameters as a function of some experimental variable is of greater interest than the estimate of their absolute value. The proposed differential Williamson-Hall method qualitatively evaluates the strain/size difference between a sample and a non-standard reference material (in which a sizeable size and/or strain contribution to the diffraction broadening is not negligible) as they are subjected to an intensive parameter (temperature, pressure, composition, defectivity). The method can be applied to compare the microstructural properties of related specimens or in the case the use of a standard sample is prevented by the experimental set-up; it thus provides a convenient visualization of microstructural trends among related samples. The results obtained using this differential method are shown to be in excellent qualitative agreement with those derived from an ideal standard sample. Diffraction ; Function (biology) ; Plot (graphics) ; Differential (mechanical device) ; Sample (material) ; Reciprocal ; Sample size determination ; Variable (mathematics) Microstructure and mechanical properties ; Advanced Electron Microscopy Techniques and Applications ; High-pressure geophysics and materials
Authors: Kylie Yang | Caleb Marsh | Lisa J. White | Fergus W Molyneux | Thomas Laurie Allam | Precious I. A. Popoola | Olivia Keers | Matthew Rice | Kira L. F. Hilton | Hiral A. Kotak | J. Mark Sutton | Jose Luis L. Ortega-Roldan | Charlotte K. Hind | Jennifer R. Hiscock | Cally J. E. Haynes
Source: Chemical Science (article, 2026-01-01)
Field: Chemistry — Spectroscopy

An increased throughput workflow to identify ion transport and membrane lysis agents for antimicrobial discovery Small molecule ion transporters have shown promise as potential therapeutics for microbial infections, cancer and channelopathies. However, there are still gaps in our understanding of how ion transport function in model vesicle membranes translates to cell membranes of interest. The lipid composition of the membranes of bacterial and cancer cells differs markedly from normal human cells, yet the influence of the lipid composition on membrane function is rarely investigated - in part because of the low throughput and high cost of ion transport experiments. Here, we report an increased throughput Workflow to identify biologically relevant, pH-driven ion transport and membrane lysis pathways in vesicle membranes. We developed a set of four assays designed to report on different transport and lysis processes. We validated our assays against a panel of known transporters and produced a stepwise Workflow for the evaluation of libraries of compounds. We applied our Workflow to screen a library (Library 1) of 31 supramolecular, self-associating amphiphiles (SSAs) for transport and lysis activity in a range of vesicles with different lipid compositions, designed to mimic different types of cells, and consequently identified seven promising transporters. Antimicrobial experiments found that six of these promising transporters showed good antimicrobial activity against clinically relevant <i>Staphylococcus aureus</i> strains, highlighting the promise of our Workflow in identifying potential antimicrobial agents. We then applied our Workflow to investigate the ion transport and lysis properties of a second library (Library 2) of SSAs with established antimicrobial and anticancer properties, aiming to provide insight into the biological modes of action. Lysis ; Throughput ; Workflow ; Ion transporter ; Function (biology) ; Membrane transport ; Membrane ; Transporter Molecular Sensors and Ion Detection ; Antimicrobial agents and applications ; ATP Synthase and ATPases Research
Authors: Sushant Kumar | Joseph Zambreno | Ashfaq Khokhar | Shoaib Akram | Fahad Saeed
Source: bioRxiv (Cold Spring Harbor Laboratory) (article, 2026-02-17)
Field: Chemistry — Spectroscopy

FiCOPS: Hardware/Software Co-Design of FPGA Computational Framework for Mass Spectrometry-Based Peptide Database Search Improving the speed and efficiency of database search algorithms that deduce peptides from mass spectrometry (MS) data has been an active area of research for more than three decades. The significance of the need for faster database search methods has rapidly increased due to the growing interest in studying non-model organisms, meta-proteomics, and proteogenomic data, which are notorious for their enormous search space. Poor scalability of serial algorithms with the growing size of the database and increasing parameters of post-translational modifications is a widely recognized problem. While high-performance computing techniques can be used on supercomputing machines, the need for real-time, on-the-instrument solutions necessitates the development of an efficient system-on-chip that optimizes design constraints such as cost, performance, and power of the system. To show case that such a system can work, we present an FPGA-based computational framework called FiCOPS to accelerate database search using a hardware/software co-design methodology. First, we theoretically analyze the database-search algorithm (closed-search) to reveal opportunities for parallelism and uncover computational bottlenecks. We then design an FPGA-based architectural template to exploit parallelism inherent in the search workload. We also formulate an analytical performance model for the architecture template to perform rapid design space exploration and find a near-optimal accelerator configuration. Finally, we implement our design on the Intel Stratix 10 FPGA platform and evaluate it using real-world datasets. Our experiments demonstrate that FiCOPS achieves 3.5 times speed-up over existing CPU solutions and 3 times and 5 times reduction in power consumption compared to existing CPU and GPU solutions. Scalability ; Stratix ; Field-programmable gate array ; Reduction (mathematics) ; Supercomputer ; Parallelism (grammar) ; Exploit ; Design space exploration ; Big data Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Machine Learning in Bioinformatics
Authors: Bhawana Singh | Oleg A. Karpov | Manuel Mayr
Source: Atherosclerosis (article, 2026-01-08)
Field: Chemistry — Spectroscopy

Clinical proteomics in cardiovascular medicine: Current capabilities, limitations, and future directions Beyond risk prediction, proteomics offers opportunities to elucidate disease mechanisms and enable drug repurposing. To realize the clinical potential of plasma proteomics, absolute or reliably recalibratable relative quantification will be required to guide patient care. Ultimately, the clinical value of proteomics will be determined by the quality rather than the quantity of protein measurements. Proteomics ; Disease ; Current (fluid) ; Quantitative proteomics ; MEDLINE ; Value (mathematics) Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Annika Topitsch | Niko Pinter | Tilman Werner | Katja Nelson | Tobias Fretwurst | Oliver Schilling
Source: Clinical Proteomics (article, 2026-01-24)
Field: Chemistry — Spectroscopy

ProteoBoostR: an interactive framework for supervised machine learning in clinical proteomics ProteoBoostR is an open-source application that empowers proteomics researchers to perform advanced ML classification. It can be readily applied to other proteomic datasets and disease contexts, promoting reproducible ML analyses in proteomics and accelerating the translation of omics-based classifiers into clinical research. Proteomics ; Translation (biology) ; Clinical diagnosis ; Training set ; Supervised learning Advanced Proteomics Techniques and Applications ; Machine Learning in Bioinformatics ; Clusterin in disease pathology
Authors: Luca Placidi | Anil Misra | Gabriele La Valle | Casey Rodriguez
Source: ZAMM ‐ Journal of Applied Mathematics and Mechanics / Zeitschrift für Angewandte Mathematik und Mechanik (article, 2026-02-01)
Field: Materials Science — Materials Chemistry

Revised identification of strain gradient elastic parameters Abstract The work reported in “Granular micromechanics‐based identification of isotropic strain gradient parameters for elastic geometrically nonlinear deformations” misidentified key terms in the grain‐pair objective relative displacement when accounting for the second gradient of placement. In this paper, we correct that oversight by deriving a revised expression for the grain‐pair objective relative displacement within the granular micromechanics framework. The amended terms, which resemble Christoffel symbols expressed in terms of strain gradients, modify the contributions of both the normal and tangential components to the strain energy and, consequently, alter the identified strain‐gradient elastic parameters. Importantly, the identification of the standard (first gradient) elastic tensor remains unchanged. This brief paper presents the corrected derivation, the resulting stiffness tensors for anisotropic strain‐gradient elasticity, and updated analytical expressions for the material parameters in both 2D and 3D isotropic settings. Isotropy ; Infinitesimal strain theory ; Stiffness ; Micromechanics ; Displacement (psychology) ; Hyperelastic material ; Anisotropy ; Tensor (intrinsic definition) ; Work (physics) ; Strain energy density function Nonlocal and gradient elasticity in micro/nano structures ; Composite Material Mechanics ; Thermoelastic and Magnetoelastic Phenomena
Authors: William J. Hughes | Péter Horák
Source: Physical review. A/Physical review, A (article, 2026-01-14)
Field: Materials Science — Surfaces, Coatings and Films

Retroreflective surface optimization for optical cavities with custom mirror profiles Coupling an emitter to a Fabry-Pérot optical cavity can provide a coherent and strong light-matter interface whose performance in a variety of applications depends critically on the emitter-photon coupling strength. Altering the typically spherical profiles of the cavity mirrors can improve this coupling strength, but directly optimizing the mirror shape is numerically challenging as the multidimensional parameter space features many local optima. Here we develop a two-step method to optimize mirror surface profiles while avoiding these issues. First, we optimize the target cavity eigenmode for the chosen application directly, and, second, we construct the mirror surfaces to retroreflect this optimized target mode at both ends of the cavity. We apply our procedure to different emitter-cavity coupling scenarios. We show that mirror shaping can increase the cooperativity of coupling to a central emitter by a factor of approximately 3 across a wide range of geometries and that, for coupling two or more emitters to a single cavity mode, the improvement factors can far exceed an order of magnitude. Coupling (piping) ; Common emitter ; Surface (topology) ; Curved mirror ; Range (aeronautics) ; Mode (computer interface) ; Space (punctuation) ; Q factor Optical Coatings and Gratings ; Adaptive optics and wavefront sensing ; Photonic and Optical Devices
Authors: Maira Khafagy | AbdelRahman M. Ghanim | Mohamed A. Swillam
Source: Scientific Reports (article, 2026-02-11)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Tunable multi-band terahertz sensor based on graphene plasmonic metasurfaces This study introduces a highly sensitive and tunable plasmonic refractive index sensor based on a novel metal-dielectric-dielectric-metal (MDDM) metasurface architecture operating in the Terahertz (THz) region. The proposed structure consists of a graphene-based fractal pattern integrated with a dielectric layer, a silicon substrate, and a bottom aluminum layer, leveraging commercially available and easy-to-fabricate materials. This multilayer configuration supports strong plasmonic resonances and enhanced absorption, enabling triple-band refractive index sensing with high sensitivities of 10 μm/RIU, 3 μm/RIU, and 2.75 μm/RIU across three distinct modes, surpassing previously reported single- and dual-band plasmonic sensors. Unlike conventional metal-dielectric-metal (MDM) absorbers, the dual-dielectric configuration enhances field localization and supports three distinct resonance modes: a dipolar mode at approximately 7.69 THz, a quadrupolar mode near 25.4 THz, and a hybridized higher-order mode around 30.2 THz. These hybridized resonances arise from the coupled interactions between the central hexagonal graphene core and the concentric double nanorings, producing intense localized electromagnetic "hot spots" that significantly amplify the sensor's spectral response. The multiple resonances offer improved flexibility for detecting various analytes or extending the sensing range. The proposed MDDM sensor maintains stable and tunable performance under environmental variations, demonstrating significant potential for practical applications in biomedical diagnostics, gas sensing, and glucose monitoring. Plasmon ; Terahertz radiation ; Refractive index ; Graphene ; Dielectric ; Resonance (particle physics) ; Silicon ; Dipole Metamaterials and Metasurfaces Applications ; Plasmonic and Surface Plasmon Research ; Terahertz technology and applications