jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: E. I. Vasilenko | Dmitry N. Ivankov
Source: bioRxiv (Cold Spring Harbor Laboratory) (preprint, 2025-09-24)
Field: Chemistry — Spectroscopy

Insights into structures of peptide aggregation nuclei from concentration dependence of lag time Abstract Many peptides and proteins self-assemble into large fibrillar aggregates, reaching sizes of several micrometers. This process typically involves nucleation, formation of transient oligomeric species ranging from dimers to assemblies comprising hundreds of monomers. The roles of these heterogeneous oligomers in initiating fibril growth vary significantly, as only a subset converts into primary nuclei, the smallest assemblies capable of spontaneous elongation. Consequently, the initial stages of peptide aggregation remain a critical challenge in elucidating amyloid fibril formation. Here, we analyze the aggregation lag time as a function of initial peptide concentration, employing linear regression on a double logarithmic scale to derive the critical nucleus size from the slope. We compare potential shifts in kinetic regimes with critical concentrations associated with the assembly of larger oligomers. Although peptide length has no clear correlation with nucleus size, extended helical regions may promote the formation of larger nuclei, stabilizing preliminary oligomers and prolonging the lag phase. We quantified the contributions of higher-order oligomers as on- and off-pathway species across multiple peptides, identifying a common critical micelle concentration range. We prove that linear growth models can not capture the weak concentration dependence of lag times for several peptides. We demonstrate that the inclusion of capping and fragmentation mechanisms substantially improves the plausibility of the model. Knowledge of nucleus size facilitates molecular dynamics simulations to capture transitions to fibril-prone conformations. The insights advance our understanding of amyloid nucleation, identifying toxic aggregates in human neuroglial cells, and research on drug safety and biotechnological applications. Peptide ; Protein aggregation ; Nucleus ; Fibril ; Lag time ; Molecular dynamics ; Amyloid (mycology) ; Amyloid fibril Advanced Proteomics Techniques and Applications
Authors: Hyeon Cheol Kim | Woo Seok Lim | Si Young Ha | Jae–Kyung Yang
Source: BioResources (article, 2025-08-27)
Field: Chemistry — Analytical Chemistry

Extreme gradient boosting model to predict antioxidant activity of extract from Ainsliaea acerifolia A machine learning (ML)-based framework was developed for predicting and optimizing the antioxidant activity of Ainsliaea acerifolia water extracts. while the response surface methodology (RSM) is deficient in modeling nonlinear interactions. In this study, three machine learning (ML) algorithms, Extreme Gradient Boosting (XGB), Random Forest (RF), and Support Vector Machine (SVM), were evaluated using extraction variables (temperature, time, and solvent-to-solid ratio) along with flavonoid and polyphenol content as input features. Among the models evaluated, the XGB model showed the most advanced antioxidant prediction capabilities, as evidenced by its R² of 0.9835 and RMSE of 2.52 on the test data set. The biological significance of the features was explored using SHAP analysis, revealing flavonoid content and extraction temperature as key contributors. A graphical user interface (GUI) was developed to facilitate real-time prediction, enhancing accessibility for researchers and industrial users. This approach improves operational efficiency by optimizing extraction conditions, predicting antioxidant activity from data including flavonoids and polyphenols, and reducing reagent usage. This study highlights the potential of ML as a sustainable alternative for natural product optimization and lays the groundwork for future research that integrates bioactivity prediction with formulation design. Boosting (machine learning) ; Antioxidant ; Gradient boosting ; Materials science ; Biological system ; Artificial intelligence ; Traditional medicine ; Computer science ; Chemistry ; Medicine ; Biology ; Biochemistry ; Random forest Spectroscopy and Chemometric Analyses
Authors: I Szabo | Florin Mariașiu | Thomas Imre Cyrille Buidin
Source: Fire (article, 2025-02-04)
Field: Materials Science — General Materials Science

Comparative Analysis of BTM Systems Made of a Fireproof Composite Material with Nano Boron Nitride The paper presents a numerical analysis of the possibilities of replacing the aluminum serpentines in the current construction of battery thermal management systems (BTMS) with cooling serpentines made of fireproof composite materials with high heat transfer parameters (fireproof epoxy resin + nano boron nitride). This approach was given by the need to replace aluminum (which, in case of fire, maintains and accelerates the combustion process) with fireproof materials that reduce/eliminate the fire risk due to improper battery operation. Numerical analysis methods were used through simulation to identify the most efficient design among the single-channel, multichannel, multiflow and multiple coolant inlet–outlet solutions for cooling serpentine. In addition to these geometric constructive parameters, the variation of the coolant flow rate (9, 12, 15 and 18 L/min) and coolant inlet temperature (17, 20 and 25 °C) was also considered. The obtained results showed that the single-inlet nanocomposite resin cooling serpentine four-channel configuration presents the highest cooling efficiency of the cells that form the battery module while ensuring very good thermal uniformity as well. These findings are supported by the lowest average heat absorption by the batteries, of 34.44 kJ, as well as the lowest average internal resistance difference (caused by thermal gradients), of 5.23%. Future research is needed to identify the degree of structural resistance of serpentines made of fireproof composite material to external stresses (vibrations characteristic of the operation of electric vehicles). Boron nitride ; Composite number ; Nano- ; Materials science ; Boron ; Composite material ; Chemistry Material Properties and Applications ; Tribology and Wear Analysis ; Boron and Carbon Nanomaterials Research
Authors: Brenda de Souza Ferrari | Ronaldo Giro | M. Steiner
Source: Journal of Cheminformatics (article, 2025-10-28)
Field: Materials Science — Materials Chemistry

HTA - An open-source software for assigning head and tail positions to monomer SMILES in polymerization reactions Artificial Intelligence (AI) techniques are transforming the computational discovery and design of polymers. The key enablers for polymer informatics are machine-readable molecular string representations of the building blocks of a polymer, i.e., the monomers. In monomer strings, such as SMILES, symbols at the head and tail atoms indicate the locations of bond formation during polymerization. Since the linking of monomers determines a polymer's properties, the performance of AI prediction models will, ultimately, be limited by the accuracy of the head and tail assignments in the monomer SMILES. Considering the large number of polymer precursors available in chemical data bases, reliable methods for the automated assignment of head and tail atoms are needed. Here, we report a method for assigning head and tail atoms in monomer SMILES by analyzing the reactivity of their functional groups based on the atomic index of nucleophilicity. In a reference data set containing 206 polymer precursors, the HeadTailAssign (HTA) algorithm correctly predicted the polymer class of 204 monomer SMILES, achieving an accuracy of 99%. The head and tail atoms were correctly assigned to 187 monomer SMILES, representing an accuracy of 91%. The HTA code is available for validation and reuse at https://github.com/IBM/HeadTailAssign . SCIENTIFIC CONTRIBUTION: The algorithm was successfully applied to data pre-processing by tagging the linkage bonds in monomers for defining the repeat units in polymerization reactions. Monomer ; Polymerization ; Polymer ; String (physics) ; Software ; Set (abstract data type) ; Head (geology) Machine Learning in Materials Science ; Advanced Polymer Synthesis and Characterization ; Computational Drug Discovery Methods
Authors: Ty Hanna | T - Chandni
Source: International Journal on Science and Technology (article, 2025-04-08)
Field: Chemistry — Analytical Chemistry

A Comparative Study of Fluorescent Dyes for TLC Detection of Arson Accelerants: Identifying a safer alternative to Rhodamine B Thin Layer Chromatography (TLC) is a most widely used technique in arson investigations and Rhodamine B is the commonly used fluorescent dye in this technique due to its strong fluorescence but it have chemical hazard concerns. This study explores Eosin Yellow, Rose Bengal, Fluorescein Sodium, and Coumarin as potential substitutes, assessing their fluorescence, stability, and detection efficiency. The objective is to find a safer yet equally effective alternative for forensic applications. Arson ; Chromatography ; Rhodamine ; Fluorescence ; Chemistry ; Geography ; Archaeology ; Optics ; Physics Dye analysis and toxicity ; bioluminescence and chemiluminescence research ; Analytical Chemistry and Sensors
Authors: Takao Fujita
Source: ChemRxiv (article, 2025-08-27)
Field: Chemistry — Physical and Theoretical Chemistry

Some Meta-Graph Structures: Mixed Graph, DiHyperGraph, Knowledge Graph, Intersection Graph, and Chemical Graph Graph theory studies mathematical structures composed of vertices and edges in order to model relationships and connectivity [1, 2]. A MetaGraph is a higher-level construct in which the vertices are themselves graphs, and the edges represent specified relations among those graphs. An Iterated MetaGraph extends this concept recursively: its vertices are MetaGraphs, producing a hierarchy of graph-of-graphs structures across multiple levels. In this work, we explore the possibility of extending Mixed Graphs, DiHyperGraphs, Knowledge Graphs, Intersection Graphs, and Chemical Graphs within the framework of MetaGraphs and Iterated MetaGraphs. Line graph ; Null graph ; Butterfly graph ; Voltage graph ; Simplex graph ; Combinatorics ; Intersection graph ; Graph ; Complement graph ; Cubic graph ; Mathematics ; Discrete mathematics ; Computer science History and advancements in chemistry
Authors: M. Suganthi | R. Sambasivam | S. Ramalingam | V. Vetrivelan | P.B. Nagabalasubramanian
Source: Discover Chemistry. (article, 2025-12-14)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Molecular spectroscopic and computational pharmacokinetic investigation of linsidomine for cardiovascular applications In this study, a detailed spectroscopic and computational analysis was carried out on 5-azanidyl-3-(morpholin-4-yl)-1,2,3λ⁵-oxadiazol-3-ylium (Linsidomine), a well-established nitric oxide donor with significant therapeutic relevance in cardiovascular pharmacology. The compound was characterized experimentally using FT-IR, FT-Raman, UV–Visible, and NMR spectroscopy, supported by quantum chemical simulations at the HF and B3LYP/6-311 + + G(d, p) levels. The observed vibrational frequencies were systematically assigned and validated through theoretical data, including the identification of key functional group vibrations such as N = O, C–N, and N = N. Frontier molecular orbital analysis revealed a moderate HOMO–LUMO gap of 3.836 eV, indicating a balance between stability and reactivity. Electrostatic potential mapping and Mulliken charge distributions highlighted electrophilic and nucleophilic zones responsible for biological interaction and NO release mechanisms. The drug-likeness, pharmacokinetic parameters, and medicinal chemistry filters confirm the compound’s oral bioavailability, metabolic safety, and synthetic accessibility. Moreover, the simulated Vibrational Circular Dichroism (VCD) spectrum and NMR chemical shifts reinforced its conformational and stereoelectronic consistency. Together, these results demonstrate Linsidomine’s strong potential as a bioactive molecule, offering insights into its structure-activity relationships and supporting its continued development in NO-based cardiovascular therapeutics. Electrophile ; Molecular orbital ; Mulliken population analysis ; Circular dichroism ; Density functional theory ; Molecule ; Nucleophile ; Metabolic stability ; Quantum chemical ; Nuclear magnetic resonance spectroscopy Nonlinear Optical Materials Research ; Magnetism in coordination complexes ; Molecular spectroscopy and chirality
Authors: Aditya Srivastava | Gaurav Sharma
Source: ChemRxiv (preprint, 2025-01-24)
Field: Materials Science — Biomaterials

Aptamer-Driven Nanovehicles for Targeted Therapy of HER2 Overexpressing Breast Cancer Cells Aptamers are single-stranded small nucleotide segments capable of interacting with numerous biomolecules with solid affinity and have gained significant attention in cancer biomarkers and targeted therapy. Recently, a drug delivery nanovehicle incorporating an anticancer compound targeting the HER2 receptor in breast cancer has been developed. This demonstrates how useful aptamer-based nanovehicles are for creating indicators unique to cancer, reducing side effects, and enhancing treatment effectiveness. The interior of the nanovehicle contains a protamine-aptamer complex that binds to epigallocatechin gallate (EGCG: an anticancer medication), while the surface comprises a HER2 affinity aptamer. The nanovehicle is a carrier bound to cancer cells and transports the anticancer medication into them. Our hypothesis is that the HB5 aptamer on the nanovehicle surface interacts with the particular HER2 receptor area to identify HER2+ cancer cells. AlphaFold web server was used for the HER2 receptor 3D structure. We conducted in silico investigations to estimate aptamers' three-dimensional structure and interactions with HER2 and protamine. We discovered that the surface aptamer creates a particular linear shape necessary for HER2 receptor interactions. The inner aptamer is small and forms a patterned structure with the protamine, releasing EGCG into the cytoplasm in the presence of abundant cytoplasmic ATP. These findings would benefit in understanding aptamer-receptor binding, cancer medicine release mechanism, and creating a possible accurate and safe drug-delivery vehicle. Aptamer ; Breast cancer ; Targeted therapy ; Cancer research ; Cancer therapy ; Cancer ; Medicine ; Chemistry ; Oncology ; Internal medicine ; Molecular biology ; Biology Nanoparticle-Based Drug Delivery ; Dendrimers and Hyperbranched Polymers ; Supramolecular Self-Assembly in Materials
Authors: Affan Malik | Robert Termuhlen | Andreas Brandl | Dirk Colbry | Hui-Chia Yu
Source: MRS Communications (article, 2025-09-22)
Field: Materials Science — Materials Chemistry

High-throughput style screening for desired material microstructures Abstract This work presents a high-throughput microstructure simulation framework for use in the discipline of computational materials science to screen out desirable structures. As motivation, we present a brief study of battery microstructural architecture optimization. Realistic 3D microstructures are reconstructed from voxel data. The voxel data can be easily modified, enabling rapid manipulation and making high-throughput investigation possible. The microstructure-level simulations are made computationally feasible by using the Smoothed Boundary Method to embed complicated microstructures in the computational domain. Additionally, our efforts toward an open-source microscale battery simulation software, titled BESFEM, are previewed. Graphical Abstract Microscale chemistry ; Microstructure ; Voxel ; Work (physics) ; Boundary (topology) ; Battery (electricity) Machine Learning in Materials Science ; Advanced Materials Characterization Techniques ; Solidification and crystal growth phenomena
Authors: M. Ayaz Ahmad | Omar Youssef | Khaled Ali Tareq
Source: Fusion of Multidisciplinary Research An International Journal (article, 2025-10-17)
Field: Materials Science — Biomaterials

Advancing Precision Medicine through Nanotechnology-Enabled Drug Delivery Systems Nanotechnology has emerged as a transformative force in modern medicine, revolutionizing how therapeutic agents are designed, delivered, and monitored within the human body. By engineering nanoparticles at the molecular scale, researchers have developed smart drug delivery systems capable of crossing complex biological barriers and achieving targeted, controlled release of therapeutics. Lipid-based nanocarriers, such as liposomes, solid lipid nanoparticles, and lipid nanoparticles (LNPs), have redefined treatment efficiency—most notably demonstrated through the success of mRNA vaccine technologies. Similarly, polymeric, dendrimer, and albumin-based nanosystems provide biocompatible platforms for sustained and site-specific delivery of complex drugs. Inorganic nanomaterials, including gold, magnetic, and silica nanoparticles, add new dimensions through stimuli-responsive and multifunctional capabilities. Recent breakthroughs in crossing the blood–brain barrier, integrating theranostic platforms, and applying artificial intelligence for nanocarrier design further expand the scope of precision medicine. Despite challenges in large-scale production, biocompatibility, and regulatory standardization, nanotechnology continues to reshape therapeutic strategies, offering unprecedented opportunities for personalized, efficient, and minimally invasive healthcare solutions. Precision medicine ; Biocompatible material ; Nanocarriers ; Drug delivery ; Scope (computer science) ; Transformative learning ; Healthcare delivery ; Targeted drug delivery ; Nanomedicine Nanoparticle-Based Drug Delivery ; 3D Printing in Biomedical Research ; Innovative Microfluidic and Catalytic Techniques Innovation
Authors: Bingyan Wu | Luyang Zhang | Lin Chen | Jiankun Wang | Z. Gao | Jing Feng
Source: Coatings (article, 2025-10-13)
Field: Materials Science — Ceramics and Composites

Influences of SiO2 Additions on the Structures and Thermal Properties of AlTaO4 Ceramics as EBC Materials Ceramic matrix composites (CMCs) are extensively utilized in aero engines due to their high-temperature stability; however, they are prone to environmental corrosion at high temperatures, and environmental barrier coatings (EBCs) are necessary to resist oxidation and corrosion. Among various EBC materials, AlTaO4 offers high cost-effectiveness and low thermal expansion coefficients (TECs), but its resistance to SiO2 erosion and high-temperature stability remain unclear. We investigated the influences of SiO2 additions on the structures and thermal properties of AlTaO4; and AlTaO4 mixtures containing 10 wt.% SiO2 were kept at 1400 °C for 30–120 h. AlTaO4 exhibited excellent high-temperature phase stability, and SiO2 dissolved into AlTaO4 to generate a solid solution. XRD Rietveld refinement was employed to confirm the position of Si in the lattices, while SEM and EDS characterizations demonstrated the homogeneous distribution of Si, Al, and Ta elements. At 1200 °C, the TECs of SiO2-AlTaO4 (4.65 × 10−6 K−1) were close to those of SiC (4.5–5.5 × 10−6 K−1). Additionally, the addition of SiO2 could reduce TECs of AlTaO4, a feature that helped alleviate the interface thermal stress between AlTaO4 and the Si bond coat in the EBC systems. At 900 °C, the thermal conductivity was reduced by 26.9% compared to that of AlTaO4, and the lowest value was 1.65 W·m−1·K−1. Accordingly, SiO2 will enter the lattices of AlTaO4 after heat treatments at 1400 °C, and SiO2 additions will reduce the thermal conductivity and TECs of AlTaO4, which is beneficial for its EBC applications. Thermal conductivity ; Ceramic ; Thermal expansion ; Thermal stability ; Phase (matter) ; Homogeneous ; Thermal ; Thermal barrier coating Advanced ceramic materials synthesis ; Microwave Dielectric Ceramics Synthesis ; Thermal Expansion and Ionic Conductivity
Authors: Jiayi Li
Source: Highlights in Science Engineering and Technology (article, 2025-02-18)
Field: Materials Science — Biomaterials

Research of Nanoparticle Drug Delivery System of Breast Cancer This passage talks about the formation of breast cancer and the traditional treatment of curing breast cancer. Breast cancer is one of the most common cancers all over the world. There are many people died because of this cancer. Now, doctors have several methods to cure this cancer, and the two most common methods are radiation therapy and surgery. Although these methods can cure breast cancer, they have several disadvantages and scientists try to find new ways to cure breast cancer. With the invention of technology, scientists invented the nanoparticle drug delivery system and tried to use nanoparticle drug delivery systems to treat breast cancer. Nanoparticle drug delivery systems also have different ways and limitations in curing breast cancer. The passage talks about three main ways: Liposomal nanoparticles system, Polymer-based nanoparticles system, and Superparamagnetic iron oxide nanoparticles system. Drug delivery ; Breast cancer ; Drug ; Nanoparticle ; Cancer ; Medicine ; Oncology ; Nanotechnology ; Pharmacology ; Materials science ; Internal medicine Nanoparticle-Based Drug Delivery ; HER2/EGFR in Cancer Research ; Cancer Cells and Metastasis
Authors: Mousa Hawan Naeem
Source: Iraqi Journal of Natural Sciences and Nanotechnology (article, 2025-12-28)
Field: Materials Science — Materials Chemistry

Enhancing Solar Cell Efficiency Through Advanced Nanomaterial Integration: A Comprehensive Review The results of the study “Improving the Efficiency of Solar Cells by Incorporating Advanced Nanomaterials” shows that incorporating nanomaterials into solar cells represents a major development towards increasing the efficiency of these cells. The main benefits of using nanomaterials include improving light absorption, reducing losses due to reflection, and increasing the overall efficiency of energy conversion. The study addresses several areas in which nanomaterials can contribute, such as the design of multi-layer solar cells (Tandem Solar Cells) that make better use of the solar spectrum, allowing them to exceed the traditional limit on solar cell efficiency. The study also addresses the importance of anti-reflection coatings and modifying the optical spectrum using these materials, which increases the quantity of light that is assimilated and transformed into electrical energy. The study considers that current challenges include the stability of nanomaterials and the possibility of large-scale manufacturing, but it remains optimistic about the future, with expectations of further improvements in efficiency as research and development in this field continue. This comprehensive overview of developments in the field of solar cells using nanomaterials reflects the future direction of making solar energy more effective and efficient. Nanomaterials ; Solar cell ; Efficient energy use ; Solar energy ; Photovoltaic system ; Renewable energy Chemical and Physical Properties of Materials ; TiO2 Photocatalysis and Solar Cells ; Laser-Ablation Synthesis of Nanoparticles