jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Bas Kreupeling | Daan Hoogers | Simon Chen | Pien A. Meulenhoff | Wouter A. Remmerswaal | Jeroen D. C. Codée | Francesco Buda
Source: The Journal of Chemical Physics (article, 2025-10-13)
Field: Chemistry — Organic Chemistry

Semi-empirical metadynamics simulations for chemical glycosylation reactions Glycosylation, the formation of glycosidic bonds, is a central yet challenging step in the chemical synthesis of complex carbohydrates due to its intricate regio- and stereochemical control. This study explores explicitly solvated, semi-empirical molecular dynamics (MD) simulations combined with multiple walker well-tempered metadynamics to investigate the mechanistic landscape of glycosylation involving a constrained glucose donor and a series of simple alcohol nucleophiles varying in nucleophilicity: ethanol, 2-monofluoroethanol, 2,2-difluoroethanol, and 2,2,2-trifluoroethanol. Our simulations reveal several mechanistic pathways depending on the nucleophile and substitution site. Stronger nucleophiles favor concerted SN2 displacement, while weaker nucleophiles increasingly promote dissociative SN1-like mechanisms and frontside attack pathways. This study demonstrates how semi-empirical MD simulations, combined with explicit solvation, can provide insights to understand the glycosylation reaction pathways. Metadynamics ; Nucleophile ; SN2 reaction ; Glycosylation ; Glycosidic bond ; Molecular dynamics ; Reaction mechanism ; Chemical Dynamics Carbohydrate Chemistry and Synthesis ; Glycosylation and Glycoproteins Research ; Genomics and Phylogenetic Studies
Authors: Md Abdur Rahim Badsha | Michael E. Kjelland | Chad A. Ulven | Khwaja Hossain
Source: Polymers (article, 2025-09-15)
Field: Materials Science — Biomaterials

Arabinoxylan-Based Bioplastic from Wheat Bran: A Promising Replacement for Synthetic Plastics The milling process of wheat annually generates over 150 million tons of wheat bran (WB), which has significant potential for bioplastic production. However, the production of bioplastics from these resources has never been explored until now. Wheat bran (WB) polymer was evaluated for its potential as an environmentally friendly biodegradable plastic, exhibiting a tensile strength of 2.3 MPa, elongation exceeding 100%, and resistance to diluted mineral acids, thereby highlighting its suitability for food packaging and related applications. The biodegradable plastic films were prepared through a molding process that involved three steps: (1) extraction of arabinoxylan from wheat bran, (2) hydrolysis and plasticization with glycerol, and (3) blending with polyvinyl alcohol (PVA) in varying proportions. The resulting bioplastic exhibits competitive mechanical properties and biodegradability. Furthermore, the biodegradable plastic developed in this research contributes to agricultural waste management, the development of value-added products, and the reduction of carbon emissions incurred from plastic industries. Additionally, it can replace and reduce reliance on synthetic plastics, which are non-degradable and a source of severe environmental pollution. Bioplastic ; Bran ; Biodegradable plastic ; Plasticizer ; Biodegradation ; Molding (decorative) ; Environmentally friendly ; Ultimate tensile strength biodegradable polymer synthesis and properties ; Nanocomposite Films for Food Packaging ; Advanced Cellulose Research Studies
Authors: Danilo Silva Ferreira | Luiz Carlos Lobato dos Santos | SANDY SOUZA SANTANA | George Simonelli | Kleberson Ricardo de Oliveira Pereira
Source: Revista de Gestão e Secretariado (Management and Administrative Professional Review) (article, 2025-05-06)
Field: Chemistry — Analytical Chemistry

Predictive modeling of Demulsification Efficiency in Brazilian Crude Oil During oil processing, chemical demulsification plays a crucial role in promoting the separation of produced water. However, the laboratory evaluation of demulsifier efficiency under different operational conditions is predominantly conducted through trial and error, leading to high consumption of time and resources for drawing conclusive insights on the process. Aiming to overcome this issue and introduce a systematic approach to demulsification studies, this work employed Design of Experiments (DOE) as a methodological tool to evaluate the efficiency of a commercial demulsifier formulation, composed of 67% alkoxylated resin, 17% ethylene oxide/propylene oxide (EO/PO) block copolymer, and 17% xylene as solvent. The process temperature and demulsifier concentration were the independent variables studied, while demulsification efficiency (%DE) was defined as the response variable. Demulsification efficiency was assessed using the Bottle Test, conducted over a 60-minute period with a heavy oil sample from the Sergipe Basin – Brazil. The laboratory results allowed the development of a predictive and statistically significant mathematical model of the response variable. In the experimental domain investigated, temperature was the statistically significant variable, and the best operational condition was identified at 75 ºC and 300 ppm formulation concentration, achieving 90.34% efficiency. Crude oil ; Petroleum engineering ; Pulp and paper industry ; Environmental science ; Chromatography ; Chemistry ; Engineering Petroleum Processing and Analysis ; Enhanced Oil Recovery Techniques ; Hydrocarbon exploration and reservoir analysis
Authors: Divya Nori | Anisha Parsan | Caroline Uhler | Wengong Jin
Source: ArXiv.org (preprint, 2025-05-27)
Field: Materials Science — Materials Chemistry

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design Protein binder design has been transformed by hallucination-based methods that optimize structure prediction confidence metrics, such as the interface predicted TM-score (ipTM), via backpropagation. However, these metrics do not reflect the statistical likelihood of a binder-target complex under the learned distribution and yield sparse gradients for optimization. In this work, we propose a method to extract such likelihoods from structure predictors by reinterpreting their confidence outputs as an energy-based model (EBM). By leveraging the Joint Energy-based Modeling (JEM) framework, we introduce pTMEnergy, a statistical energy function derived from predicted inter-residue error distributions. We incorporate pTMEnergy into BindEnergyCraft (BECraft), a design pipeline that maintains the same optimization framework as BindCraft but replaces ipTM with our energy-based objective. BECraft outperforms BindCraft, RFDiffusion, and ESM3 across multiple challenging targets, achieving higher in silico binder success rates while reducing structural clashes. Furthermore, pTMEnergy establishes a new state-of-the-art in structure-based virtual screening tasks for miniprotein and RNA aptamer binders. Pipeline (software) ; Statistical model ; Function (biology) ; Interface (matter) ; Protein structure prediction ; Energy (signal processing) ; Maximum likelihood ; Design of experiments Machine Learning in Materials Science ; Additive Manufacturing and 3D Printing Technologies
Authors: Xiaoqian Fu | Xiaojia Fang | Lin Yang | Yawen Liu | Fengnan Jia | Gang Ye | Lian Yuan | Xiao‐Bin Zhang | Yansong Liu | Chuanwei Li | Xiangdong Du
Source: Scientific Reports (article, 2025-11-27)
Field: Chemistry — Spectroscopy

Alpha-actinin-1, profilin-1, filamin-A, integrin alpha-M and glutathione synthase were identified to be associated with cognitive and social functions of schizophrenia Mass spectrometry-based proteomics is a powerful analytical technique for identifying and quantifying proteins in the human plasma, which may be related to the onset, course or the prognosis of schizophrenia. Our study enrolled 46 patients with schizophrenia and 43 healthy controls, who were collected morning fasting venous blood and completed scale assessment. Then mass spectrometry analysis was performed to identify differential proteins and correlation analysis and multiple regression were conducted to explore the relationship between protein biomarkers and psychiatric symptoms, cognitive function and social function in patients with schizophrenia. Compared with the control group, the patient group showed lower immediate and delayed accuracy rates in pattern recognition memory. Alpha-actinin-1 and profilin-1 were positively associated with immediate pattern recognition accuracy. Both were also negatively associated with total number of errors of spatial working memory. Meanwhile, filamin-A was positively associated with immediate accuracy rate and delay accuracy rate of pattern recognition memory. In addition, integrin alpha-M was negatively correlated with factor I of the scale of social function and glutathione synthetase was positively correlated with the total score, factor I, factor II and factor III of the scale of social function in psychosis inpatients. Our study indicated that alpha-actinin-1, profilin-1 and filamin-A may be related to cognitive functions, integrin alpha-M and glutathione synthase may be related to social function outcome of patients with schizophrenia. Schizophrenia (object-oriented programming) ; Psychosis ; Cognition ; Glutathione ; Social cognition ; Proteomics ; Venous blood ; Correlation Advanced Proteomics Techniques and Applications ; Tryptophan and brain disorders ; Biotin and Related Studies
Authors: Anna N. Morozovska | S. Cherifi | Eugene А. Eliseev | Victoria V. Khist | Riccardo Hertel | Dean R. Evans
Source: Journal of Applied Physics (article, 2025-07-16)
Field: Materials Science — Materials Chemistry

The role of flexoelectric coupling and chemical strains in the emergence of polar chiral nano-structures This theoretical review examines the conditions that give rise to the formation of flexo-sensitive chiral polar structures in thin films and core–shell ferroelectric nanoparticles. It also analyzes possible mechanisms by which the flexoelectric effect impacts the polarization structure in core–shell ferroelectric nanoparticles. Special attention is given to the role of the anisotropic flexoelectric effect in forming a unique type of polarization states with distinct chiral properties, referred to as “flexons.” In the first half of the review, we study the influence of the flexoelectric coupling on the polarity, chirality, and branching of metastable labyrinthine domain structures in uniaxial ferroelectric core–shell nanoparticles. We reveal that the transition from sinuous branched domain stripes to spiral-like domains occurs gradually as the flexoelectric coupling strength is increased. Our findings indicate that the joint action of the flexoelectric effect and chemical strains, termed as “flexo-chemical” coupling, can significantly influence the effective Curie temperature, polarization distribution, domain morphology, and chirality in multiaxial ferroelectric core–shell nanoparticles. Furthermore, we demonstrate that the combination of flexo-chemical coupling and screening effects leads to the appearance and stabilization of a chiral polarization morphology in nanoflakes of van der Waals ferrielectrics covered by a shell of ionic-electronic screening charge. In the second half of the review, we discuss several advanced applications of flexo-sensitive chiral polar structures in core–shell ferroelectric nanoparticles for nanoelectronics elements and cryptography. We underline the possibilities of the flexoelectric control of multiple-degenerated labyrinthine states, which may correspond to a differential negative capacitance (NC) state stabilized in the uniaxial ferroelectric core by the presence of a screening shell. We show that the paraelectric-like state of van der Waals ferrielectric nanoflakes covered by a shell of ionic-electronic screening charge exhibits a pronounced NC effect over a relatively wide range of nanoflake thicknesses, flexo-chemical strains, and surface charge densities. Polar ; Flexoelectricity ; Nano- ; Coupling (piping) ; Materials science ; Chemical physics ; Condensed matter physics ; Nanotechnology ; Chemistry ; Physics ; Dielectric ; Optoelectronics ; Composite material ; Quantum mechanics Ferroelectric and Piezoelectric Materials ; Multiferroics and related materials ; Nonlocal and gradient elasticity in micro/nano structures
Authors: Jie Zhang | You-Quan Dou | Peiyi Zhang | Xi Shu | Meng Lei
Source: Processes (article, 2025-11-08)
Field: Chemistry — Analytical Chemistry

Radial Basis Function Kolmogorov–Arnold Network for Coal Calorific Value Prediction Using Portable Near-Infrared Spectroscopy The calorific value of coal is a key parameter for pricing, trade, and combustion management. Conventional bomb calorimetry provides accurate results but is time-consuming, labor-intensive, and destructive. Near-infrared (NIR) spectroscopy offers a rapid and non-destructive alternative, yet its application is limited by strong band correlations, nonlinear spectral responses, and the lack of interpretability in many predictive models. In this study, the Kolmogorov–Arnold Network (KAN) is applied to the prediction of coal calorific value, demonstrating its capability to describe nonlinear spectral relationships within an interpretable mathematical structure. Based on this framework, a Radial Basis Function KAN (RBF-KAN) is further developed by replacing the B-spline bases in the KAN with radial basis functions, allowing improved representation of localized and irregular spectral variations while maintaining model transparency. Using 671 coal-powder samples measured by a portable MicroNIR spectrometer, the RBF-KAN achieved an RMSE of 1.35 MJ/kg and an MAE of 0.92 MJ/kg under five-fold cross-validation, outperforming conventional regression models, deep neural networks, and other KAN variants. Analysis of RBF activations and spectral attribution maps indicates that the model consistently responds to characteristic O-H and C-H overtone regions, which correspond to known absorption features in coal. These results suggest that the RBF-KAN provides a practical and interpretable framework for on-site estimation of coal calorific value, complementing traditional calorimetric analysis. Heat of combustion ; Radial basis function ; Coal ; Combustion ; Artificial neural network ; Basis (linear algebra) ; Nonlinear system ; Interpretability ; Basis function Spectroscopy and Chemometric Analyses ; Thermochemical Biomass Conversion Processes ; Coal Properties and Utilization
Authors: Yusuke Asakuma | Ryohei Yakata | Anita Hyde | Chi M. Phan | Anh Son Hoang
Source: Microwave (article, 2025-10-18)
Field: Chemistry — Organic Chemistry

Influence of the Shape Factor on the Heating of an Aqueous Solution by Microwave In this study, the microwave heating efficiency of a water body is investigated with different shape factors. In particular, the same water volume was deposited in cylindrical containers with different diameters. Here, “shape factor” refers to the ratio between the surface fluid layer, which strongly absorbs microwave energy, and the inner layer, which is heated largely via conduction. For a liquid in a cylindrical container, the shape factor is characterised as the ratio between the depth and diameter of the air/water surface area. The heating efficiency is characterised by relating the energy absorbed in the outer fluid layer with the energy gained in the bulk and monitoring the temperature in the fluid bulk at the point that the outer layer commences boiling. A correlation equation for the uniformity of the sample heating (with stirring) provided a simple link between the physical factors and microwave (MW) parameters. It was found that a depth/diameter ratio approaching 1:1 provided the most uniform heating. The correlations between the fitting parameters and physical conditions provide a simple yet effective method to characterise the thermal homogeneity of microwave heating that can assist with practical parameterisation of the design of microwave reactors. Microwave ; Shape factor ; Homogeneity (statistics) ; Microwave heating ; Thermal ; Aqueous solution ; Surface-area-to-volume ratio ; Volume (thermodynamics) ; Loss factor Microwave-Assisted Synthesis and Applications ; Freezing and Crystallization Processes
Authors: Jingjing Zeng | Miao Chen | Xinglong Wang | Huan Yu | Liang Zhang | Yong-xing Peng | Pingyu Wan | Zhongshi Huang | Fuqiang Ma | Jingtang Li
Source: Functional & Integrative Genomics (article, 2025-07-04)
Field: Materials Science — Biomaterials

Discovering novel type I collagen fragments from Cyprinus carpio supporting bone regeneration Fish collagen is gaining increasing attention in tissue engineering due to its exceptional bioactivity. This study aimed to isolate functional fish collagen fragments capable of microbial biosynthesis and supporting bone tissue regeneration. Collagen fragments of 150 amino acids were extracted from Cyprinus carpio collagen I (CcCOL1), and their bioactivity, net charge, and hydrophobicity were calculated and analyzed for correlations, these physicochemical and sequential features were using to train the machine learning model, which classified the fragments into three subgroups. Representative samples were selected from each cluster or directly from the original CcCOL1. Six out of eight variants were successfully secreted in Pichia pastoris, and all formed triple-helical structures, while only Var-2 and Var-3 retained self-assembly at 15 °C. Notably, Var-2 exhibited the highest capacity to induce osteoblast differentiation. To develop scaffolds with enhanced mechanical strength, Var-2 was combined with chitin and hydroxyapatite (HAP). The resulting composite demonstrated a compressive strength of 5.77 ± 0.32 MPa while maintaining high porosity at a chitin-HAP ratio of 2:1. Cytotoxicity assays confirmed biocompatibility, and fibroblast differentiation was comparable to Var-2 alone. In vivo rat tibia defect studies showed significant bone regeneration after 12 weeks, highlighting the potential of this fish collagen-chitin-HAP biomaterial for bone tissue engineering. Cyprinus ; Biology ; Regeneration (biology) ; Type (biology) ; Anatomy ; Computational biology ; Evolutionary biology ; Cell biology ; Fish <Actinopterygii> ; Fishery ; Ecology Collagen: Extraction and Characterization ; Silk-based biomaterials and applications ; Protein Hydrolysis and Bioactive Peptides
Authors: Baoxi Zhang | Zhanxiang Zhang | Shenglong Rui | Lifeng Wang
Source: Journal of the American Ceramic Society (article, 2025-04-12)
Field: Materials Science — Materials Chemistry

Boosting high‐temperature heat transfer of ceramic insulation tile with ordered‐conformation boron nitride Abstract Boosting heat transfer of ceramics has been an increasing challenge for spacecraft insulation tile. The concurrent superiorities of higher heat stability and comparative thermal conductivity on par with graphene make boron nitride (h‐BN) an ideal reinforcement. Yet, its characteristic of Kapitza thermal resistance inevitably aggravates heat transfer deterioration in aerodynamic in‐service environment. Here, we proposed a multiscale optimal approach to boost the heat transfer of Al 2 O 3 /h‐BN composites with nanoscale interfacial thermal conductance and mesoscale h‐BN ordered conformation. Interfacial thermal conductivity induced by a strong 5% Al‐N bonding configuration in the densification process is improved from 248 MW·m −2 ·K −1 at 300 K to 340 MW·m −2 ·K −1 at 1500 K, which depicts a priority of h‐BN than graphene in composites. Massive delocalized lower‐frequency phonons, an indicator of thermal flutter, are decomposed from localized high‐frequency phonon at high temperature. Mesoscale thermal conductivity of composites is increased from 15 W·m −1 ·K −1 of random distribution to 19 W·m −1 ·K −1 of ordered conformation at 1500 K. This optimal design of ordered conformation induced by external field in fabrication process constructs a rapid path of anisotropic thermal converge, and ameliorates heat transfer deterioration of random dispersion. This work provides an effective strategy for designing a novel ceramic insulation tile to extend the remaining life of next‐generation spacecraft. Boron nitride ; Ceramic ; Tile ; Materials science ; Boron ; Heat transfer ; Composite material ; Nitride ; Chemistry ; Thermodynamics Thermal properties of materials ; Advanced ceramic materials synthesis ; Thermal Expansion and Ionic Conductivity
Authors: Neani Tshilande | Лилиана Маммино
Source: Journal of Molecular Modeling (article, 2025-03-12)
Field: Chemistry — Organic Chemistry

Computable properties of selected monomeric acylphloroglucinols with anticancer and/or antimalarial activities and first-approximation docking study Computational studies of the selected ACPLs were performed using Gaussian-09, in vacuo and in-three-solvents with different polarities. Three different levels of theory were used - Hartree Fock (HF), Density Functional Theory (DFT) with the B3LYP functional, and second order Møller-Plesset Perturbation Theory (MP2). HF and MP2 used a 6-31G(d,p) basis set, while DFT used a 6-31G + (d,p), for consistency with previous studies on ACPLs. The investigated molecular properties include conformational preferences, intramolecular hydrogen bonding patterns, HOMO-LUMO energy gap, dipole moments, as well as the solvent effect for the three considered solvents. Virtual screening was conducted using the Schrödinger suite, including Maestro 9.3 with GLIDE for docking and GlideScore for evaluating binding affinities. In addition, the QikProp tool provided ADME-T predictions for pharmacokinetic properties. ADME ; Chemistry ; Antimalarial Agent ; Virtual screening ; Docking (animal) ; Combinatorial chemistry ; Context (archaeology) ; Moiety ; Drug ; Computational biology ; Computational chemistry ; Molecule ; Stereochemistry ; Pharmacology ; Plasmodium falciparum ; Molecular dynamics ; Organic chemistry ; Malaria ; Biochemistry ; Biology ; In vitro ; Medicine Free Radicals and Antioxidants ; Bioactive Compounds and Antitumor Agents ; Natural Compound Pharmacology Studies
Authors: Yang Yu | Siyuan Li | Ling Weng | Xiaorui Zhang | Laiweiqing Liu | Qing-Guo Chen
Source: Polymers (article, 2025-04-08)
Field: Materials Science — Materials Chemistry

Optimization of Insulation Structure Design for Enameled Wires Based on Molecular Structure Design The performance of enameled wires has an important impact on new energy vehicle motors. The mainstream practice of existing technology is to improve partial discharge inception voltage (PDIV) by doping powder to inhibit corona and increase varnish thickness, the limitations of which are also obvious. Powder doping has the problem of dispersion stability, and increasing the varnish thickness affects the size and power density of the motor. In this paper, a novel insulation structure design was given. The electronic field stress was controlled by using different dielectric constant materials, and the dielectric constants can be controlled by adjusting the free volume of the polymer. Finally, we specifically create a preparation scheme to increase the corona voltage and the PDIV, without a loss of the breakdown margin of the enameled wire, and the simulation results show that the outermost electric field strength of the enameled wire model decreases by 22.11% and the enameled wire breakdown margin increases by 26.85%. Materials science ; Dielectric ; Composite material ; Doping ; Dispersion (optics) ; Dielectric strength ; Thermosetting polymer ; Voltage ; Corona (planetary geology) ; Mechanical engineering ; Electrical engineering ; Optoelectronics ; Engineering ; Optics High voltage insulation and dielectric phenomena ; Advanced Sensor and Energy Harvesting Materials ; Electromagnetic wave absorption materials