jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Franziska Walterspiel | Begoña Ugarte‐Uribe | Alex Cabrera | Asad U. Khan | Stefan Terjung | Claire Deo
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-11-13)
Field: Materials Science — Materials Chemistry

Photoclickable HaloTag Ligands for Spatiotemporal Multiplexed Protein Labeling on Living Cells ABSTRACT Precise spatiotemporal control over fluorescence labeling is a powerful approach for selective marking and tracking of proteins of interest within living systems. Here, we report a photoclickable labeling platform based on the 2,3-diaryl-indanone epoxide (DIO) photoswitch scaffold and the self-labeling protein HaloTag. Upon illumination, the protein-bound DIO undergoes reversible photoisomerization to form a metastable oxidopyrylium ylide (PY) that reacts with ring-strained dipolarophiles via [5+2] cycloaddition, enabling covalent spatiotemporal labeling. We synthesize and characterize a library of DIO-HaloTag and DIO-SNAP- tag ligands, systematically examining the effects of linker architecture and scaffold substitution on the photoswitching and photoclick reactivity in vitro and on living cells. We identify a naphthyl-substituted DIO ligand exhibiting superior photoswitching and photoclick efficiency, allowing robust and selective labeling of HaloTag on the surface of living cells using visible light activation. Using this system, we achieve two- and three-color labeling of defined cell surface regions with excellent spatial and temporal precision, additionally allowing combinatorial labeling. Together, this work establishes a versatile framework for multiplexed, light- directed protein labeling compatible with living systems, with promising future applications in long-term tracking and cellular barcoding. Photoswitch ; Linker ; Photoisomerization ; Fluorescence ; Scaffold ; Fluorescent labelling ; Ligand (biochemistry) ; Covalent bond ; Depsipeptide Photochromic and Fluorescence Chemistry ; Click Chemistry and Applications ; Biotin and Related Studies
Authors: Kendell M. Pawelec | Erik M. Shapiro
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-10-25)
Field: Materials Science — Biomaterials

Distinct Roles of Surface Nanostructure and Polymer Degradation in Fibroblast Response to Device Design Fibrotic encapsulation of implanted biomedical devices represents the highest cause of device failure across numerous fields, including orthopedics, breast implants and neural electrodes. While most research has focused on the immune system for driving the foreign body response to devices, fibroblasts are emerging as another key regulator of tissue response. In the present study, we evaluated the effects of porous device design on the activation of primary human dermal fibroblasts into myofibroblasts, a contractile cell that is a hallmark of fibrosis, over four weeks in culture. In particular two factors were studied 1) the introduction of nanoparticles, as they are increasingly being used for device functionalization, and 2) the polymer matrix, which dictates chemistry, mechanics and degradation. The addition of tantalum oxide (TaOx) nanoparticles (0-20wt%) had a minimal effect on fibroblasts, significantly down-regulating expression of alpha smooth muscle actin (αSMA) (0.31 ± 0.1), likely driven by the increase in nanoscale surface roughness. The polymer matrix of the device caused significant changes to myofibroblast activation, with the fast degrading polymer, poly(lactide co-glycolide) (PLGA) 50:50, significantly up-regulating multiple myofibroblast markers, including αSMA (5.16 ± 2.5), vinculin, integrin β<sub>1</sub>, and integrin β<sub>5</sub>, compared to non-degrading polycaprolactone (PCL). The effect was due to the release of degradation products, namely lactic acid, which affects cellular metabolism. Together this highlights that device design affects biological response immediately post-implantation in ways that impact the ultimate success or failure of biomedical devices. Myofibroblast ; Polycaprolactone ; Integrin ; Fibroblast ; Immune system ; Extracellular matrix ; Nanostructure ; Polymer ; Crosstalk Electrospun Nanofibers in Biomedical Applications
Authors: Williams García-Argote | Erika Medel | Diego Inostroza | Alejandro Vásquez‐Espinal | José Solar‐Encinas | Luis Leyva‐Parra | Lina Ruíz | Osvaldo Yáñez | William Tiznado
Source: Molecules (article, 2025-05-14)
Field: Materials Science — Materials Chemistry

From Aromatic Motifs to Cluster-Assembled Materials: Silicon–Lithium Nanoclusters for Hydrogen Storage Applications Silicon-lithium clusters are promising candidates for hydrogen storage due to their lightweight composition, high gravimetric capacities, and favorable non-covalent binding characteristics. In this study, we employ density functional theory (DFT), global optimization (AUTOMATON and Kick-MEP), and Born-Oppenheimer molecular dynamics (BOMD) simulations to evaluate the structural stability and hydrogen storage performance of key Li-Si systems. The exploration of their potential energy surface (PES) reveals that the true global minima of Li<sub>6</sub>Si<sub>6</sub> and Li<sub>10</sub>Si<sub>10</sub> differ markedly from those of the earlier Si-Li structures proposed as structural analogs of aromatic hydrocarbons such as benzene and naphthalene. Instead, these clusters adopt compact geometries composed of one or two Si<sub>4</sub> (<i>T<sub>d</sub></i>) units and a Si<sub>2</sub> dimer, all stabilized by surrounding Li atoms. Motivated by the recurrence of the Si<sub>4</sub>-<i>T<sub>d</sub></i> motif, we explore oligomers of Li<sub>4</sub>Si<sub>4</sub>, which can be viewed as electronically transmuted analogues of P<sub>4</sub>, confirming the additive H<sub>2</sub> uptake across dimer, trimer, and tetramer assemblies. Within the series of Si-Li clusters evaluated, the Li<sub>12</sub>Si<sub>5</sub> sandwich complex, featuring a σ-aromatic Si<sub>5</sub><sup>10-</sup> ring encapsulated by two Li<sub>6</sub><sup>5+</sup> moieties, achieves the highest hydrogen capacity, adsorbing 34 H<sub>2</sub> molecules with a gravimetric density of 23.45 wt%. Its enhanced performance arises from the high density of accessible Li<sup>+</sup> adsorption sites and the electronic stabilization afforded by delocalized σ-bonding. BOMD simulations at 300 and 400 K confirm their dynamic stability and reversible storage behavior, while analysis of the interaction regions confirms that hydrogen adsorption proceeds via weak, dispersion-driven physisorption. These findings clarify the structure-property relationships in Si-Li clusters and provide a basis for designing modular, lightweight, and thermally stable hydrogen storage materials. Nanoclusters ; Hydrogen storage ; Cluster (spacecraft) ; Lithium (medication) ; Silicon ; Materials science ; Nanotechnology ; Hydrogen ; Chemistry ; Optoelectronics ; Organic chemistry ; Computer science Hydrogen Storage and Materials ; Boron and Carbon Nanomaterials Research ; Advancements in Battery Materials
Authors: Adyan Abdizadeh challoob | Najwa J. Jubier
Source: Journal of Physics Conference Series (article, 2025-03-01)
Field: Chemistry — Organic Chemistry

Green Synthesis of Ag-Cu NPs using Black Eggplant Extract as the Reducing and Stabilizing Agents: Characterization and Energy Band Gap Abstract The study successfully demonstrated an eco-friendly approach to synthesizing Ag, Cu nanoparticles, and Ag-Cu nanoparticle composites using Black eggplant extract as both a reducing and stabilizing agent, with calcination at 400°C. The research revealed distinct plasmonic properties through Surface Plasmon Resonance (SPR) bands observed at specific wavelengths: 400 nm for Ag, 524 nm for Cu, and dual bands at 406 nm (SPR1) and 600 nm (SPR2) for Ag-Cu nanoparticle composites. The energy gap values for Ag-Cu were identified at 1.8eV, 2.5eV, and 3.7eV. XRD analysis confirmed a polycrystalline structure with a face-centered cubic (FCC) phase pattern, while FE-SEM and EDX examinations revealed homogeneous morphology with Cu nanoparticles being larger than Ag nanoparticles. The Ag-Cu nanoparticle composite exhibited similar size and shape characteristics to Ag nanoparticles, with an average size of 46.5nm. These findings demonstrate the successful synthesis of discrete and stable nano-sized particles with superior plasmonic properties, suggesting potential applications in enhancing electron transfer efficiency in nano-sized metal surfaces and various sensing and detection applications. Characterization (materials science) ; Reducing agent ; Band gap ; Materials science ; Chemical engineering ; Nanotechnology ; Chemistry ; Optoelectronics ; Engineering Nanomaterials for catalytic reactions
Authors: Anthony N.A. Prempeh | Weiyue Xin | Maria M. Santore
Source: Biophysical Journal (article, 2025-02-01)
Field: Chemistry — Physical and Theoretical Chemistry

BPS2025 - Interactions of rigid objects in dynamic biomolecular membranes Membrane ; Biophysics ; Chemistry ; Computer science ; Nanotechnology ; Materials science ; Biology ; Biochemistry thermodynamics and calorimetric analyses
Authors: Hiroaki Onoda | Kanata Higuchi | Thitirat Charoonsuk | Phieraya Pulphol | Rangson Muanglhua | Naratip Vittayakorn
Source: Journal of Materials Science Materials in Engineering (article, 2025-12-23)
Field: Chemistry — Inorganic Chemistry

Unveiling unusual coloration in amorphous phosphate pigments: a study inspired by the mineral Brazilianite Brazilianite, with the formula NaAl3(PO4)2(OH)4, exhibits an intriguing pale yellow to green coloration, a phenomenon not readily explained by the absence of conventional d-block chromophoric metal ions. This study investigates the synthesis of amorphous phosphate-based pigments compositionally analogous to Brazilianite, aiming to replicate and understand the origin of its distinctive coloration through controlled precursor stoichiometry and thermal processing. Sodium, aluminum, and phosphate precursors were precisely mixed and thermally treated. X-ray diffraction (XRD) confirmed the predominantly amorphous nature of the synthesized materials, irrespective of achieving long-range crystalline order analogous to mineral Brazilianite. Despite this, samples processed at intermediate temperatures (e.g., 300–400 °C) exhibited a consistent yellowish hue. This non-conventional coloration, attributed to intrinsic electronic or structural features within the amorphous phosphate network rather than traditional chromophores, represents a significant scientific innovation. This coloration was found to be intrinsically linked to the phosphate network itself. Stability assessments in acidic (0.1 wt% H2SO4) and basic (0.1 wt% NaOH) environments revealed significant vulnerability, attributed to the facile dissolution of sodium and aluminum phosphate species. Notably, the yellowish coloration persisted across various Na/Al/P compositional ratios, even with systematic variations in aluminum or sodium content. This strongly suggests that the observed color is not critically dependent on a precise Na: Al stoichiometry but is fundamentally governed by the local electronic structure within the phosphate network, potentially involving defect centers or specific P-O-Al/Na linkages. These findings offer valuable insights into designing novel, non-toxic, color-stable pigments where coloration arises from mechanisms beyond traditional transition metal ion incorporation, highlighting the potential role of controlled disorder in phosphate-based materials for sustainable applications. Amorphous solid ; Dissolution ; Phosphate ; Stoichiometry ; Mineral ; Phosphate minerals ; Pigment Pigment Synthesis and Properties ; Cultural Heritage Materials Analysis ; Magnesium Oxide Properties and Applications
Authors: J.W. Miller | Charlotte H. Abrahamson | Marilyn F. Slininger Lee | Brett Palmero | Nolan W. Kennedy | Carolyn E. Mills | Danielle Tullman‐Ercek
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-07-25)
Field: Materials Science — Biomaterials

Self-assembling protein materials with genetically programmable morphology and size Materials are challenging to synthetically program down to the atom level. Nature, however, excels at creating hierarchical materials from nanoscale building blocks, a feat that remains a major challenge in synthetic systems. A deeper understanding of the molecular rules governing self-assembly would unlock the potential for designing genetically programmable materials with atomic precision. Hexameric bacterial microcompartment (BMC-H) proteins offer a powerful model system for exploring this question. These sequence-defined proteins naturally assemble into complex architectures and can be expressed biologically, making them ideal candidates for studying how minor sequence variations influence supramolecular structure. In this work, we leverage cell-free protein synthesis (CFPS) alongside immunostaining and super-resolution microscopy to investigate the self-assembly behavior of two BMC-H proteins, PduA and PduJ. We find that both proteins form micro- to millimeter scale structures when expressed in vitro. Further, we demonstrate how single point mutation changes lead PduA and PduJ to form significantly different supramolecular structures when produced using CFPS. These studies support the future exploration of self-assembling proteins as programmable scaffolds in broad materials applications. Morphology (biology) ; Nanotechnology ; Computer science ; Materials science ; Biology ; Genetics Diatoms and Algae Research
Authors: Anggoro Dias Ainur Rasyid | Ervina Ahyudanari | Catur Arif Prastyanto | Susianto Susianto | Vicario Baroroh
Source: Journal of Advanced Research in Micro and Nano Engieering (article, 2025-05-31)
Field: Chemistry — Inorganic Chemistry

Enhancing Energy Efficiency: Exploring Natural Zeolite Addition to Pure Asbuton B 50/30 Mixture – Insights from SEM-EDX and FTIR Chemical Characterization This study introduces a novel approach to leverage Asbuton analytical properties by exploring its compatibility with a warm mixture of LTBA (thin layer asphalt concrete), supplemented with natural zeolite additives to lower the mixing temperature. The research focuses on assessing the characteristics of pure Asbuton B 50/30 and Marshall features, ensuring compliance with specifications. Various levels of natural zeolite additions to the warm mixture are tested at an optimum asphalt content of 5.95%. Results indicate that incorporating 1.5% natural zeolite yields properties meeting specification requirements: stability = 1179.564 kg; VIM = 4.252 %; VMA = 17.076 %; flow = 2,870 mm; VFA = 75.099%; and MQ = 410.998 kg/mm. Moreover, the mixing and compaction temperature with natural zeolite addition aligns with specifications at 145 ℃. SEM-EDX analysis reveals carbon compounds (C) as the primary component of Asbuton B 50/30, constituting 43.44% of its composition, while its porous nature renders it with fragile morphological characteristics. The incorporation of natural zeolite effectively reduces the mixing temperature of the Asbuton mixture, showcasing promising avenues for enhanced efficiency. Zeolite ; Fourier transform infrared spectroscopy ; Characterization (materials science) ; Natural (archaeology) ; Chemical engineering ; Chemistry ; Materials science ; Nanotechnology ; Catalysis ; Organic chemistry ; Geology ; Engineering Zeolite Catalysis and Synthesis
Authors: Madhuparna Chakraborty | Avanigadda Madhu Niharika | Zubair Khalid Baig | Manab Chakravarty
Source: Materials Advances (article, 2025-12-03)
Field: Materials Science — Materials Chemistry

Protonation-driven structural deformation in a conformationally twisted pyridyl-linked AIEgen: a platform to detect polyamines and nicotine Structural deformation is noticed upon protonation in a symmetrically substituted thiophene-anthracene linked π-conjugate bearing two terminal pyridyl units. Such a deformed molecule exhibits emission change and detect polyamines and nicotine. Deformation (meteorology) ; Molecule ; Protonation ; Nicotine ; Bearing (navigation) ; Molecular conformation Luminescence and Fluorescent Materials ; Molecular Sensors and Ion Detection ; Polyamine Metabolism and Applications
Authors: L. G. Nersisyan | Romik S. Harutyunyan | Armen I. Martiryan | H.R. Petrosyan
Source: Eurasian Chemico-Technological Journal (article, 2025-10-17)
Field: Materials Science — Materials Chemistry

Luminescent Properties of a Solid-Phase Composite Based on Zirconium, Rare Earth Elements (Er, Nd) and Molybdenum As a result of the chemical synthesis, a heterogeneous compound with luminescent properties was obtained, containing rare-earth metal ions (Er3+, Nd3+), Mo6+, and Zr4+. The reaction was carried out using solutions of Na2MoO4, ZrOCl2, NdCl3, and ErCl3 at a temperature of 22 °C. After 30─35 days, the system reached equilibrium, and an insoluble greyish-blue precipitate was formed. ICP-AES analysis confirmed the presence of all the initial components and showed the heterogeneity of the material; the molar ratio nNa : nMo : nZr : nEr : nNd = 0.05 : 0.22 : 0.086 : 0.082 : 0.05 was confirmed in the system. X-ray microanalysis revealed a complex multiphase structure characterized by significant chemical diversity and the presence of nanoparticles. Partial emission of Nd3+ at a wavelength of around 885 nm (4F3/2 → 4I9/2 transition) was found by luminescence investigations; this can be utilised in medical near-infrared laser systems. Spectrometer constraints prevented the detection of Er3+ emission. The material's molybdenum-based structure and the presence of Zr4+ ions are responsible for the visible glow. Although more research is necessary to completely comprehend the Er3+ emission, the acquired findings suggest the possibility of developing complex heterogeneous luminous compounds containing rare earth ions for optical and medicinal applications. Luminescence ; Rare earth ; Ion ; Laser ; Molybdenum ; Analytical Chemistry (journal) ; Metal ; Metal ions in aqueous solution ; Composite number Luminescence Properties of Advanced Materials ; Lanthanide and Transition Metal Complexes ; Catalysis and Oxidation Reactions
Authors: Thomas Bugnand | M. Klüppel S. Aloui | Michel Bouquey | Delphine Chan‐Seng | Christophe A. Serra | Thibault Parpaite | Frédérick Lacemon | Isabelle Dulac
Source: Journal of Polymer Science (article, 2025-05-11)
Field: Materials Science — Polymers and Plastics

Modification of Thermo‐Mechanical Properties of Tailored Acrylic Elastomers With a Low Glass Transition Temperature ABSTRACT Copolymers based on mono and diacrylate monomers are synthesized to obtain elastomeric materials with a very low glass transition temperature (T g , below −60°C) and no phase transition on the rubbery plateau. These materials have been characterized by dynamic thermo‐mechanical analysis and differential scanning calorimetry. Nona(ethylene glycol) methyl ether acrylate (EG 9 MEA) is used as the main monomer. The corresponding homopolymer has a very low T g but exhibits a crystalline phase up to 0°C. This phenomenon is inhibited by copolymerizing EG 9 MEA with another monoacrylate (butyl acrylate or 4‐hydroxybutyl acrylate). The thermo‐mechanical stability initially sought is obtained by using 4‐hydroxybutyl acrylate at a rate above 30% by weight. The mechanical properties of EG 9 MEA‐based materials have been adjusted by the addition of a diacrylate monomer that increases the elastic modulus on the rubbery plateau, while being reduced by introducing a transfer agent. Finally, an experimental behavior law is proposed to predict the elastic modulus on the rubbery plateau as a function of the mass proportion of EG 9 MEA, diacrylate, and transfer agent initially introduced. Glass transition ; Elastomer ; Materials science ; Composite material ; Polymer science ; Polymer Polymer Nanocomposites and Properties ; Material Properties and Applications ; Silicone and Siloxane Chemistry
Authors: Benedikt Krause | Sebastian Müller | Thomas Puppe | Lars Liebermeister | Garrit Schwanke | Milan Deumer | Robert B. Kohlhaas | Rafał Wilk | Nico Vieweg | Sascha Preu
Source: Nature Communications (article, 2025-11-25)
Field: Chemistry — Spectroscopy

Terahertz photonic heterodyne spectral analysis with (sub-) kHz resolution and 6.5 THz frequency coverage Spectrum analyzers and spectrometers are essential for designing sources, analyzing material properties, layer structures and fingerprinting substances. We present an ultra-wideband, continuous-wave photonic receiver with kHz-level spectral resolution in the terahertz domain for both heterodyne and homodyne detection. Employed as a spectrum analyzer front end, it records the emitted spectrum of a source under test, assessing spectral purity, spectral shape and undesired frequency components. It outperforms state-of-the-art electronic systems in terms of frequency coverage and system cost with a competitive spectral resolution and noise floor on the few aW/Hz level at room temperature. It covers the important frequencies above 1.5 THz, yet commercially inaccessible, where sources like quantum cascade lasers operate. When combined with a comb-based photonic source, we demonstrate hetero- and homodyne spectroscopy over an unprecedented frequency range from below 100 GHz to 6.5 THz and a very low noise floor. Locking the photonic system to GPS enables tracing back the measured parameters to SI units, being of key importance for metrological applications. The presented setups offer the broadest continuous-wave frequency coverage to date, combined with a sharp spectral resolution, enabling diverse applications ranging from fast non-destructive testing, astronomic high-resolution spectroscopy, to frequency-modulated RADAR. Terahertz radiation ; Heterodyne (poetry) ; Photonics ; Spectrum analyzer ; Spectral resolution ; Spectrometer ; Direct-conversion receiver ; Superheterodyne receiver ; Homodyne detection ; Noise (video) Spectroscopy and Laser Applications ; Advanced Fiber Laser Technologies ; Terahertz technology and applications
Authors: Paul J. Besseling | Wojciech Szymczyk | Martin Teraa | Raechel J. Toorop | Paul A. A. Bartels | Boris Arts | Rob Driessen | A.M. Lichauco | Hidde C Bakker | Joost O. Fledderus | Gert J. de Borst | Patricia Y. W. Dankers | Carlijn V. C. Bouten | Marianne C. Verhaar
Source: Communications Materials (article, 2025-07-16)
Field: Materials Science — Biomaterials

Evaluation of in situ tissue-engineered arteriovenous grafts suitable for cannulation in a large animal model The sustainability of vascular access for hemodialysis is limited by frequent interventions and the inability of synthetic grafts to self-heal. Tissue engineering offers a solution through biodegradable grafts that remodel into autologous tissue. Here we assess electrospun polycarbonate-bis urea (PC-BU) vascular scaffolds (6mm-inner-Ø), reinforced with 3D-printed polycaprolactone coils, in a goat model, and compared them to expanded polytetrafluoroethylene (ePTFE) controls. The tissue-engineered grafts were repeatedly cannulated starting two weeks after implantation and were evaluated using computed tomography and histological analyses. By 12 weeks, the PC-BU grafts remodel into autologous tissue while maintaining structural integrity, maintaining integrity without dilations, ruptures, or aneurysms. Cannulation does not interfere with scaffold degradation or neo-tissue formation. Although the patency rate is lower for the PC-BU grafts (50%) compared to ePTFE (100%), the engineered grafts exhibit a self-healing response not seen in ePTFE. These findings demonstrate the potential of PC-BU tissue-engineered grafts as healing, functional vascular access solutions for hemodialysis, supporting cannulation during tissue transformation. Tissue engineering ; Decellularization ; Biomedical engineering ; Scaffold ; Medicine ; Polycaprolactone ; Surgery ; Soft tissue ; Materials science Electrospun Nanofibers in Biomedical Applications ; Central Venous Catheters and Hemodialysis ; Infectious Aortic and Vascular Conditions