jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Marko Babić | Goran Mauša | Ivan R. Sasselli | Daniela Kalafatović
Source: ACS Applied Materials & Interfaces (article, 2026-02-19)
Field: Materials Science — Biomaterials

Secondary Structure Bead-Encoded Amphiphilicity Biases Peptide Self-Assembly Prediction in MARTINI Coarse-Grained Simulations Sequence-dependent self-assembly of peptides yields ordered supramolecular structures with diverse nanotechnological applications. In the absence of simple design rules linking sequence to supramolecular morphology, coarse-grained molecular dynamics (CG-MD) simulations have become valuable tools for guiding the design of self-assembling peptides. The MARTINI model, despite the lack of explicit hydrogen bonding, can predict self-assembling sequences and structural features by introducing secondary structure-specific beads that adjust backbone polarity. Extended β-sheet encoding is typically used as input for short peptides, based on experimental observations. However, this assumption becomes increasingly unreliable beyond six to ten residues, where folded conformations begin to emerge. In this study, we investigated the effect of different secondary structure encodings on self-assembly simulations of hexapeptides and decapeptides using MARTINI 2.2p. The results confirmed that changes in the secondary structure encoding significantly impact the predicted self-assembly behavior, with AP scores for the same peptide varying by up to one unit─shifting from fully dissolved (AP ≈ 1) to well-aggregated states (AP > 2) in specific cases. This effect arises from alterations in overall peptide amphiphilicity caused by shifts in backbone polarity. However, the magnitude and direction of this influence depend on side-chain polarity and peptide length, making the resulting bias highly sequence-specific and difficult to anticipate or correct systematically. These findings emphasize the need to reevaluate the conventional use of extended β-sheet encoding (E-flag) and advocate for more native-like backbone representations in peptide self-assembly simulations. Peptide ; Protein secondary structure ; Sequence (biology) ; Supramolecular chemistry ; Molecular dynamics ; Polarity (international relations) ; Encoding (memory) Supramolecular Self-Assembly in Materials ; Supramolecular Chemistry and Complexes ; Diatoms and Algae Research
Authors: Angeliki Doukaki | Aikaterini Frantzi | Stamatina Xenou | Fotoula Schoina | Georgia Katsimperi | Nychas George-John | Nikos Chorianopoulos
Source: Pathogens (article, 2026-01-08)
Field: Materials Science — Biomaterials

Antimicrobial Effect of Oregano Essential Oil in Na-Alginate Edible Films for Shelf-Life Extension and Safety of Feta Cheese The use of natural antimicrobials and advanced sensor technologies is increasingly explored to improve the safety and quality of dairy products like cheese. The current work evaluated the effect of sodium alginate edible films enriched with oregano essential oil (EO) on the microbial spoilage of Feta cheese and the fate of <i>Escherichia coli</i> O157:H7 and <i>Listeria monocytogenes</i> during storage. Samples were inoculated with approximately a 4 log CFU/g of pathogens and subsequently wrapped with edible films containing EO or left without, serving as controls. Samples were stored under aerobic and vacuum conditions at 4 and 12 °C. Microbiological analyses, pH, and sensory attributes were monitored during storage, while multispectral imaging (MSI) devices were used for rapid, non-invasive quality assessment. EO films moderately suppressed spoilage and pathogen survival, particularly under aerobic conditions. The MSI spectral data coupled with machine learning models provided reasonable results for the estimation of yeast and mould populations, with the best models coming from aerobic conditions, from benchtop-MSI data, with R<sup>2</sup> = 0.726 and RMSE = 0.426 from the Neural Networks model, and R<sup>2</sup> = 0.661 and RMSE = 0.696 from the LARS model. The results highlight the combined potential of natural antimicrobial films and MSI-based sensors for extending Feta cheese shelf life and enabling rapid, non-destructive monitoring, respectively. Food spoilage ; Antimicrobial ; Essential oil ; Aerobic bacteria ; Biocide ; Microorganism Nanocomposite Films for Food Packaging ; Advanced Chemical Sensor Technologies ; Listeria monocytogenes in Food Safety
Authors: Sung-Kwang Shin | Niti Sharma | Seong Soo A. An | Meyoung-Kon Kim
Source: Nanomaterials (article, 2026-01-19)
Field: Materials Science — Materials Chemistry

The Evolution of Nanoparticle Regulation: A Meta-Analysis of Research Trends and Historical Parallels (2015–2025) <b>Objective</b>: We analyzed nanoparticle regulation research to examine the evolution of regulatory frameworks, identify major thematic structures, and evaluate current challenges in the governance of rapidly advancing nanotechnologies. By drawing parallels with the historical development of radiation regulation, the study aimed to contextualize emerging regulatory strategies and derive lessons for future governance. <b>Methods</b>: A total of 9095 PubMed-indexed articles published between January 2015 and October 2025 were analyzed using text mining, keyword frequency analysis, and topic modeling. Preprocessed titles and abstracts were transformed into a TF-IDF (Term Frequency-Inverse Document Frequency) document-term matrix, and NMF (Non-negative Matrix Factorization) was applied to extract semantically coherent topics. Candidate topic numbers (K = 1-12) were evaluated using UMass coherence scores and qualitative interpretability criteria to determine the optimal topic structure. <b>Results</b>: Six major research topics were identified, spanning energy and sensor applications, metal oxide toxicity, antibacterial silver nanoparticles, cancer nano-therapy, and nanoparticle-enabled drug and mRNA delivery. Publication output increased markedly after 2019 with interdisciplinary journals driving much of the growth. Regulatory considerations were increasingly embedded within experimental and biomedical research, particularly in safety assessment and environmental impact analyses. <b>Conclusions:</b> Nanoparticle regulation matured into a dynamic multidisciplinary field. Regulatory efforts should prioritize adaptive, data-informed, and internationally harmonized frameworks that support innovation while ensuring human and environmental safety. These findings provide a data-driven overview of how regulatory thinking was evolved alongside scientific development and highlight areas where future governance efforts were most urgently needed. Parallels ; Interpretability ; Multidisciplinary approach ; Corporate governance ; Thematic analysis ; Topic model ; Coherence (philosophical gambling strategy) ; Terminology ; Multimethodology Nanoparticles: synthesis and applications ; Radiation Therapy and Dosimetry ; Meta-analysis and systematic reviews
Authors: Demet Sariyer | Elif Yıldırım
Source: International Journal of Computational and Experimental Science and Engineering (article, 2026-01-29)
Field: Materials Science — Materials Chemistry

A Hybrid Monte Carlo–Machine Learning Framework for High-Energy Neutron Shielding Using Boron-Enhanced Concrete Secondary neutrons produced by proton-target interactions in high-energy proton accelerator facilities present a major shielding challenge due to their high penetrability and broad energy spectra. In this study, neutron dose attenuation in B₄C- and FeB-enhanced concretes containing 5%, 10%, and 15% additives was investigated at a proton energy of 1000 MeV using FLUKA-based Monte Carlo (MC) simulations coupled with Machine-learning (ML) surrogate models.MC-generated dose data were used to train log-linear Linear Regression (log-linear LR), K-Nearest Neighbors (KNN), Random Forest (RF), and Gradient Boosting Regressor (GBR) models to enable rapid dose prediction. The results show that RF and GBR achieve the highest predictive accuracy under all configurations, with test-set R² values of approximately 0.98-0.99 in tunnel air and 0.99-0.996 in concrete shielding. In contrast, the LR model performs poorly in shielding regions due to strong nonlinearity, while KNN also provides high predictive accuracy exceeding 90%, albeit with lower performance compared to RF and GBR. A comparative analysis reveals that FeB-enhanced concrete exhibits more complex attenuation behavior due to the combined effects of iron-induced scattering and boron absorption. Overall, the validated hybrid MC-ML framework demonstrates that RF- and GBR-based surrogate models provide a fast, reliable, and computationally efficient approach for neutron dose estimation and shielding optimization in high-energy proton accelerator facilities. Electromagnetic shielding ; Attenuation ; Monte Carlo method ; Neutron ; Proton ; Neutron capture ; Scattering ; Neutron transport Radiation Shielding Materials Analysis ; Radiation Therapy and Dosimetry ; Graphite, nuclear technology, radiation studies
Authors: Qian Chen | Yun Huang | Chuanbin Wu | Xin Pan | Changjiang Yu | Jinhua Wang | Wei Wang | Zhengwei Huang
Source: Pharmaceutics (article, 2026-01-07)
Field: Materials Science — Biomaterials

Charge Effects: Influence of Surface Charge on Protein Corona Adsorption Behavior on Liposomal Formulations <b>Background</b>: Liposomes have been successfully used in clinics as an excellent drug delivery system. However, once they enter the body, they adsorb surrounding proteins and form a protein corona, which affects how liposomes behave in vivo. Therefore, controlling the formation of the protein corona is crucial for achieving effective treatment outcomes. Among the many variables affecting liposome protein corona formation, the composition of the liposomes themselves and the surrounding ionic environment are two particularly critical factors. <b>Methods</b>: In this context, this study selected bovine serum albumin as a model protein to investigate the influence and mechanism of physiologically relevant inorganic ions (magnesium chloride) and varying proportions of cationic lipid components (1,2-dioleoyl-3-trimethylammonium-propane (DOTAP)) on protein adsorption behavior of liposomes. We evaluated characterization parameters, including particle size and zeta potential, and employed various spectroscopic techniques to elucidate the changes during the interaction between bovine serum albumin and liposomes. <b>Results</b>: The zeta potential results showed that liposomes without DOTAP exhibited a significantly negative potential (-45.20 ± 0.24 mV), while the zeta potential became increasingly positive with higher DOTAP proportions (+19.64 ± 0.39 mV and +51.03 ± 1.74 mV). Correspondingly, the amount of protein adsorption also increased with the rising DOTAP content. Furthermore, fluorescence spectroscopy indicated that the addition of either DOTAP or magnesium ions led to a decrease in both the <i>K</i><sub>sv</sub> and <i>K</i><sub>a</sub> parameters. <b>Conclusions</b>: Specific hypothetical models were advanced subsequently; per the varying proportion of DOTAP, we proposed an insertion or surface adsorption model, and further examined the influence of magnesium chloride on the interactions between the liposomes and proteins. We believe this study will provide a new research paradigm for the design and application of liposomes, laying a foundation for further in vivo investigations. Zeta potential ; Liposome ; Adsorption ; Bovine serum albumin ; Protein adsorption ; Cationic liposome ; Surface charge ; Cationic polymerization ; Ionic strength Nanoparticle-Based Drug Delivery ; Advanced Drug Delivery Systems ; Lipid Membrane Structure and Behavior
Authors: Nicola Berner | Florian Bayer | Amy L. George | Nicole Kabella | F. Luna Bergamasco | Bernhard Küster
Source: Targetome (article, 2026-01-01)
Field: Chemistry — Spectroscopy

Proteome-wide dose-response measurements for the characterization of drug mechanism of action Almost all drugs exert their effects in a dose-dependent fashion, but a central challenge in drug discovery and pharmacology is to bridge the gap between observed phenotypic and the often complex underlying molecular mechanisms. Important questions to answer are: which proteins are physically bound by the compound, which pathways are engaged in the cell and how is the cell molecularly and physiologically reprogrammed <italic>en route</italic> to its eventual, drug-determined fate? In light of the advances in quantitative mass spectrometry speed and sensitivity over the past decade, it has become feasible to perform systematic full dose-response experiments at the level of: (1) target deconvolution; (2) pathway engagement; (3) proteome reprogramming; and (4) cellular consequences. Each enables the extraction of potency and effect size information for thousands of proteins and post-translational modification sites in parallel. In this mini-review, the conceptual framework of system-level dose-response measurements is outlined and key published studies are used to illustrate how such data inform successive layers of drug mechanisms of action. Proteome ; Drug discovery ; Mechanism of action ; Drug ; Systems pharmacology ; Drug action ; Action (physics) ; Mechanism (biology) ; Key (lock) Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Click Chemistry and Applications
Authors: Bart Roland Van Puyvelde | Robbe Devreese | Cristina Chiva | Eduard Sabido | Sibylle Pfammatter | Christian Panse | Jeewan Babu Rijal | Charline Keller | Ihor Batruch | Patrick Pribil | Jean-Baptiste Vincendet | F.-G. Fontaine | L. J. LeFever | Pedro Magalhães | Dieter Deforce | Paolo Nanni | Bart Ghesquière | Yasset Pérez‐Riverol | Lennart Martens | Christine Carapito | Robbin Bouwmeester | Maarten Dhaenens
Source: bioRxiv (Cold Spring Harbor Laboratory) (article, 2026-02-02)
Field: Chemistry — Spectroscopy

LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients Abstract Recent advances in liquid chromatography–mass spectrometry (LC-MS) have accelerated the adoption of high-throughput workflows that deliver deep proteome coverage using minimal sample amounts. This trend is largely driven by clinical and single-cell proteomics, where sensitivity and reproducibility are essential. Here, we extend our previous benchmark dataset (PXD028735) using next-generation LC-MS platforms optimized for rapid proteome analysis. We generated an extensive DDA/DIA dataset using a human-yeast- E. coli hybrid proteome. The proteome sample was distributed across multiple laboratories together with standardized analytical protocols specifying two short LC gradients (5 and 15 min) and low sample input amounts. This dataset includes data acquired on four different platforms, and features new scanning quadrupole-based implementations, extending coverage across different instruments and acquisition strategies. Our comprehensive evaluation highlights how technological advances and reduced LC gradients may affect proteome depth, quantitative precision, and cross-instrument consistency. The release of this benchmark dataset via ProteomeXchange (PXD070049 and PXD071205), allows for the acceleration of cross-platform algorithm development, enhance data mining strategies, and supports standardization of short-gradient, high-throughput LC-MS-based proteomics. Workflow ; Benchmark (surveying) ; Proteome ; Standardization ; Sample (material) ; Data acquisition ; Proteomics ; Quantitative proteomics Advanced Proteomics Techniques and Applications ; Mass Spectrometry Techniques and Applications ; Single-cell and spatial transcriptomics
Authors: Rachael A. Otunla | Adekunle Akanni Adeleke | Adebayo Isaac Olosho | Temitayo S. Ogedengbe | Peter P. Ikubanni | Hauwa A. Rasheed | Adebisi A. Bamgbade
Source: Journal of Engineering and Applied Science (article, 2026-02-14)
Field: Materials Science — Polymers and Plastics

Gypsum in the 21st century: multifaceted applications and emerging opportunities Gypsum has evolved into a material of critical significance across a diverse array of modern industries. This review explores the expanding landscape of gypsum applications in the twenty-first century, beginning with an overview of its physicochemical properties, such as fire resistance, acoustic insulation, and compatibility with additives that underpin its versatile utility. In the construction sector, the material has undergone considerable innovation through the integration of Phase Change Materials (PCMs) into gypsum plasterboards for thermal regulation and sustainability, as well as increased efforts in recycling and closed-loop systems supported by Life Cycle Assessment (LCA) frameworks. Beyond traditional domains, novel research has focused on reinforcing gypsum composites with agricultural fibers (e.g., straw, hemp, and sisal) and polymers to improve mechanical strength, thermal conductivity, and ecological footprint. Additionally, the review highlights emerging biomedical applications, including gypsum-based surgical splints and scaffolds, underscoring its potential in healthcare. Drawing from recent advances and sustainability trends, this paper provides a comprehensive outlook on the transformative role of gypsum and identifies promising directions for future research and industrial practice. Gypsum ; Sustainability ; Transformative learning ; Life-cycle assessment ; Construction industry ; Emerging technologies Natural Fiber Reinforced Composites ; Hygrothermal properties of building materials ; Concrete and Cement Materials Research
Authors: W. Czapiewski | Stanisław Pałubicki | J. Plichta | Krzysztof Nadolny
Source: Applied Sciences (article, 2026-01-13)
Field: Materials Science — Materials Chemistry

State of Knowledge in the Field of Regenerative Hardfacing Methods in the Context of the Circular Economy Regenerative hardfacing of steel substrates is an important technology for restoring the surface layer of components operating under wear conditions, supporting the goals of the circular economy (CE) by extending the service life of components, reducing material and energy consumption throughout their life cycle, and shortening downtime during machine repairs. The article provides a synthetic analysis of the literature on the production of functional layers exclusively on steels and systematizes process → structure → properties (PSP) relationships in the context of technological quality and the prediction of the functional properties of welds. The review covers methods used and developed in steel hardfacing (including arc processes and variants with increased energy concentration), analyzed on the basis of measurable process indicators: energy parameters (arc energy/heat input/volume energy), dilution, bead geometry, heat-affected zone characteristics, and the risk of welding defects. It has been shown that these factors determine the structural effects in the weld and the area at the fusion boundary (including phase composition and morphology, hardness gradient, and susceptibility to cracking), which translates into functional properties (hardness, wear resistance, adhesion, and fatigue life) and durability after regeneration. The main result of the work is the development of a PSP table dedicated to hardfacing on steel substrates, mapping the key “levers” of the process to structural consequences and trends in functional properties. This facilitates the identification of optimization directions (minimization of energy input and dilution while ensuring fusion continuity), which translates into longer durability after regeneration and a lower risk of defects—key, measurable effects of CE. Research gaps have also been identified regarding the comparability of results (standardization of energy metrics) and the need to determine and verify “technology windows” within the WPS/WPQR (welding procedure specification/welding procedure qualification record) for layers deposited on steels. Hardfacing ; Context (archaeology) ; Durability ; Welding ; Process (computing) ; Service life ; Fusion welding ; Work (physics) Metal Alloys Wear and Properties ; High Entropy Alloys Studies ; Surface Treatment and Coatings
Authors: Zixian Hu | Kingfai Li | Chi Li | Yushu Chen | Qichang Ma | Stefan A. Maier | Changxu Liu | Haoran Ren | Guixin Li
Source: Advanced Materials (article, 2026-01-02)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Spin–Orbit Interaction Enabled Nonlinear Metasurface Holography Nonlinear optical metasurfaces have emerged as a powerful platform for efficient and multi-dimensional manipulation of harmonic waves, offering distinct advantages such as high-integration capability and phase-matching-free operation. Spin and orbital angular momentum (SAM and OAM) provide rich degrees of freedom for advanced light field control. While SAM- and OAM-multiplexing metasurface holograms have been realized in the linear optical regime, their performance is hindered by a low signal-to-noise ratio stemming from residual light mode conversion. Nonlinear OAM holography has recently been demonstrated; however, its practicality remains limited by reliance on bulky nonlinear optical crystals that exhibit only intrinsic spin-orbit interaction (SOI). Here, we introduce nonlinear SOI holography via second harmonic generation on optical metasurfaces composed of gold plasmonic meta-atoms. By controlling the local rotational symmetry and topological charges, these metasurface holograms can fully harness optical SOI through both intrinsic and extrinsic angular momentum mode conversions. Information hidden in second harmonic holographic images can only be reconstructed from the spin-orbit tomography of the fundamental waves, ensuring high-security nonlinear optical encryption. The proposed approach offers promising applications in optical communications, optical information processing, high-dimensional optical storage, and so on. Holography ; Angular momentum ; Plasmon ; Nonlinear system ; Nonlinear optics ; Second-harmonic generation ; Harmonic ; Field (mathematics) Metamaterials and Metasurfaces Applications ; Orbital Angular Momentum in Optics ; Plasmonic and Surface Plasmon Research
Authors: Harald F. Krug
Source: BIOspektrum (article, 2026-02-01)
Field: Materials Science — Materials Chemistry

20 Jahre einer „neuen“ Toxikologie-Disziplin: Nanotoxikologie Abstract For several decades, we have been able to control and “observe” matter at the atomic level. However, manipulation at this level also entails risks that can originate from particles measuring just a few nanometres in size. The discussion began with criticism of the nanotechnology itself but ultimately ended with the definition of a new discipline within toxicology: nanotoxicology. For 30 years, scientists around the world have been grappling with questions surrounding the toxicology of nanomaterials. Criticism ; Control (management) ; Subject matter ; Human genetics Nanoparticles: synthesis and applications ; Heavy Metal Exposure and Toxicity ; Thallium and Germanium Studies