jablonkagroup/rise_ai_scientists huggingface dataset:
Source: Biointerface Research in Applied Chemistry (article, 2023-10-15)
Field: Chemistry — Physical and Theoretical Chemistry

Density Functional Theory Analyses of Nanostructures for the Delivery of 1-Aminoadamantane Antidyskinetic Drug This work was performed to analyze the nanostructures for delivering a 1-aminoadamantane (ADM) antidyskinetic drug. ADM has been mainly used for the medication of dyskinesia of Parkinson's disease, besides treating some types of influenza. To this point, the drug delivery of ADM was assessed in this work with the assistance of two representative models of nanostructures, including graphene (G) and fullerene (F). In both G and F nanostructures, an iron (Fe) atom was doped to provide an active site of interactions between the ADM substance and the nanostructure. Density functional theory (DFT) calculations were performed to achieve the required results of singular and complex models. Stabilized structures and related electronic features were evaluated for the investigated model systems. Possibilities of formations for both ADM@G and ADM@F complex models were found, and the involved interactions of complexes were analyzed based on the features of the quantum theory of atoms in the molecule (QTAIM). The results indicated a higher benefit of the formation of the ADM@F complex in comparison with the formation of the ADM@G complex. Variations of levels of frontier molecular orbitals also indicated a possibility for the recognition of complex formations. Consequently, the obtained results indicated the suitability of the investigated complex models of ADM@G and ADM@F for conducting the desired drug delivery processes using appropriate nano-based surfaces as carriers. Drug ; Drug delivery ; Materials science ; Density functional theory ; Nanotechnology ; Medicine ; Pharmacology ; Chemistry ; Computational chemistry thermodynamics and calorimetric analyses ; Nonlinear Optical Materials Research ; Computational Drug Discovery Methods
Authors: Banafshe Abadi | Fatemeh Askarian | Neda Mohammadi | Behzad Behnam
Source: Research Square (preprint, 2023-12-13)
Field: Materials Science — Materials Chemistry

Fluorescent carbon dots from cumin seeds: preparation, characterization and in vitro biocompatibility test for cell imaging application <title>Abstract</title> Carbon dots (CDs) are a new type of nanomaterial with great potential in bioimaging, biosensing, and drug delivery. In this study, novel CDs were prepared from cumin seeds (<italic>Cuminum cyminum</italic> L) by pyrolysis. The pyrolysis method and several extraction steps were optimized to fabricate CDs from cumin seeds. The size, structure, chemical composition, and photoluminescence properties of the CDs were characterized using a size analyzer, TEM, SEM, EDX, UV-Vis, fluorescence spectroscopy, and FTIR. The influences of the CDs on cell viability were investigated in A549, 3T3, and MCF-7 cell lines via MTT assay. The cancer cell imaging potential of the CDs was assessed using fluorescence microscopy. The results showed that the CDs with a mean diameter of 13.42 nm could be obtained through the pyrolysis of cumin seeds. The obtained CDs exhibited strong and unique fluorescence properties once they were excited at different wavelengths, particularly at 350 nm. The CDs were highly stable over time, and their fluorescence properties remained unchanged after three months. Apart from the physicochemical properties of the CD, cell viability assays showed that these CDs were non-toxic to A549, MCF-7, and 3T3 cells, over 90% of the cells were viable after 24 h, even at the highest concentration (1000 µg/ml). The CDs successfully penetrated the MCF-7 cells as revealed by fluorescent images. Taken together, the fluorescent CDs derived from cumin seeds indicated excellent and stable fluorescence properties. In addition, these CDs were highly biocompatible and could be a potential option for theragnostic applications. Fluorescence ; Biocompatibility ; Nanomaterials ; Nuclear chemistry ; Viability assay ; Photoluminescence ; Fluorescence microscope ; Materials science ; MTT assay ; Fourier transform infrared spectroscopy ; Chemistry ; Nanotechnology ; Chemical engineering ; In vitro ; Organic chemistry ; Biochemistry Carbon and Quantum Dots Applications ; Nanocluster Synthesis and Applications ; Selenium in Biological Systems
Authors: Katja‐Sophia Csizi | Markus Reiher
Source: arXiv (Cornell University) (preprint, 2023-07-30)
Field: Materials Science — Materials Chemistry

Automated Preparation of Nanoscopic Structures: Graph-Based Sequence Analysis, Mismatch Detection, and pH-Consistent Protonation with Uncertainty Estimates Structure and function in nanoscale atomistic assemblies are tightly coupled, and every atom with its specific position and even every electron will have a decisive effect on the electronic structure, and hence, on the molecular properties. Molecular simulations of nanoscopic atomistic structures therefore require accurately resolved three-dimensional input structures. If extracted from experiment, these structures often suffer from severe uncertainties, of which the lack of information on hydrogen atoms is a prominent example. Hence, experimental structures require careful review and curation, which is a time-consuming and error-prone process. Here, we present a fast and robust protocol for the automated structure analysis, and pH-consistent protonation, in short, ASAP. For biomolecules as a target, the ASAP protocol integrates sequence analysis and error assessment of a given input structure. ASAP allows for pKa prediction from reference data through Gaussian process regression including uncertainty estimation and connects to system-focused atomistic modeling described in (J. Chem. Theory Comput. 16, 2020, 1646). Although focused on biomolecules, ASAP can be extended to other nanoscopic objects, because most of its design elements rely on a general graph-based foundation guaranteeing transferability. The modular character of the underlying pipeline supports different degrees of automation, which allows for (i) efficient feedback loops for human-machine interaction with a low entrance barrier and for (ii) integration into autonomous procedures such as automated force field parametrizations. This facilitates fast switching of the pH-state through on-the-fly system-focused reparametrization during a molecular simulation at virtually no extra computational cost. Computer science ; Modular design ; Molecular dynamics ; Nanoscopic scale ; Algorithm ; Theoretical computer science ; Chemistry ; Nanotechnology ; Computational chemistry ; Materials science Machine Learning in Materials Science ; Protein Structure and Dynamics ; Computational Drug Discovery Methods
Authors: Franco Pellegrini | Ruggero Lot | Yusuf Shaidu | Emine Küçükbenli
Source: arXiv (Cornell University) (preprint, 2023-05-19)
Field: Materials Science — Materials Chemistry

PANNA 2.0: Efficient neural network interatomic potentials and new architectures We present the latest release of PANNA 2.0 (Properties from Artificial Neural Network Architectures), a code for the generation of neural network interatomic potentials based on local atomic descriptors and multilayer perceptrons. Built on a new back end, this new release of PANNA features improved tools for customizing and monitoring network training, better GPU support including a fast descriptor calculator, new plugins for external codes and a new architecture for the inclusion of long-range electrostatic interactions through a variational charge equilibration scheme. We present an overview of the main features of the new code, and several benchmarks comparing the accuracy of PANNA models to the state of the art, on commonly used benchmarks as well as richer datasets. Computer science ; Artificial neural network ; Perceptron ; Code (set theory) ; Plug-in ; Range (aeronautics) ; Computational science ; Computer architecture ; Artificial intelligence ; Materials science ; Operating system ; Programming language ; Set (abstract data type) Machine Learning in Materials Science ; X-ray Diffraction in Crystallography ; Electron and X-Ray Spectroscopy Techniques
Authors: Yuki Nagai | Yutaka Iwasaki | Koichi Kitahara | Yoshiki Takagiwa | Kaoru Kimura | Motoyuki Shiga
Source: arXiv (Cornell University) (preprint, 2023-02-28)
Field: Materials Science — Materials Chemistry

Atomic diffusion due to hyperatomic fluctuation for quasicrystals A quasicrystal is an ordered but non-periodic structure understood as a projection from a higher dimensional periodic structure. Some physical properties of quasicrystals are different from those of conventional solids. An anomalous increase in heat capacity at high temperatures has been discussed for over two decades as a manifestation of a hidden high dimensionality of quasicrystals. A plausible candidate for this origin has been phason, which has excitation modes originating from additional degrees of freedom in the higher-dimensional lattice. However, most theoretical studies on phasons have used toy models. A theoretical study of the heat capacity of realistic quasicrystals or their approximants has yet to be conducted because of the huge computational complexity. To bridge this gap between experiment and theory, we show experiments and molecular simulations on the same material, an Al--Pd--Ru quasicrystal, and its approximants. We show that at high temperatures, aluminum atoms diffuse with discontinuous-like jumps, and the diffusion paths of the aluminum can be understood in terms of jumps corresponding to hyperatomic fluctuations in six-dimensional space. It is concluded that the anomaly in the heat capacity of quasicrystals arises from extra degrees of freedom due to hyperatomic fluctuations that play a role in diffusive Nambu--Goldstone modes. Quasicrystal ; Phason ; Degrees of freedom (physics and chemistry) ; Condensed matter physics ; Curse of dimensionality ; Physics ; Lattice (music) ; Excitation ; Statistical physics ; Diffusion ; Materials science ; Thermodynamics ; Quantum mechanics ; Mathematics Quasicrystal Structures and Properties
Authors: Ángela Contreras | Mohamed Dahrouch | Nadia Katir | Daniela Andrade‐Acuña | Miguel Zárraga | Héctor Cobos-Aguilar
Source: Journal of the Chilean Chemical Society (article, 2023-12-01)
Field: Chemistry — Organic Chemistry

Silylated and germylated lineal polyesters obtained from a fatty alcohol, Undec-10-en-1-ol Polyester ; Alcohol ; Chemistry ; Fatty alcohol ; Chromatography ; Organic chemistry Chemical Synthesis and Reactions ; biodegradable polymer synthesis and properties ; Silicone and Siloxane Chemistry
Authors: Олена Скуйбіда
Source: Collection of Scientific Publications NUS (article, 2023-01-01)
Field: Materials Science — General Materials Science

OVERVIEW OF TECHNOLOGIES AND METHODS FOR SORTING AND CLASSIFYING END-OF-LIFE ALUMINUM Today the quality of castings obtained by aluminum recycling is determined by the technology and the culture of collecting, sorting and preparation of the secondary raw materials for the further processing.The aim of the work is to review modern technologies and methods for sorting and classifying aluminum scrap.As a rule, the collected aluminum scrap consists of a mixture of different materials and the alloys of different grades, which leads to a high content of unwanted impurities in the metal structure and, accordingly, low quality of the final material.Special attention was paid to the technological features of scrap sorting, which ensures the minimum content of iron in the final alloys obtained by processing aluminum.Practical cases of secondary aluminum metallurgy enterprises located in Ukraine, Austria, and Belgium were considered.The work was carried out using a system approach, methods of abstraction, system analysis, comparison and synthesis.Sorting of scrap and waste of aluminum by grade is carried out according to characteristic distinguishing features (color, nature of fracture, hardness, fragility), according to specific features of typical parts, spectral analysis, droplet sampling method, and others.If the current practice of collection of aluminum scrap is maintained, the amount of aluminum scrap collected will soon exceed the production capacity of cast aluminum alloys.Reducing the heterogeneity of scrap and waste can be achieved through the use of innovative technologies such as sorting sensors, spectrometric and X-ray studies, the use of infrared, ultraviolet, laser-induced breakdown spectroscopy, etc., which determine the directions for further research.The other challenge is to estimate economic and environmental advantages of implementing advanced sorting and scrap classification methods.The scientific task of theoretical and methodological substantiation of technologies and methods of sorting and classification of scrap aluminum and aluminum alloys was solved.Consolidated information on existing approaches that are effective, meet the requirements of the time and can be realistically implemented in secondary metallurgy enterprises in Europe.Also, scientific provisions, practical cases and work conclusions can be used in the process of teaching material science and aluminum technologies in higher education institutions and during research. Sorting ; End-to-end principle ; Computer science ; Card sorting ; Data science ; Artificial intelligence ; Engineering ; Algorithm ; Systems engineering Material Properties and Applications
Authors: Nur Farah Nadia Abd Karim | Faridah Lisa Supian | Yeong Yi Wong | Afiq Radzwan | Mazlina Musa | A. Shaari | Abdullah F. Al Naim
Source: Journal of Science and Mathematics Letters (article, 2023-11-09)
Field: Chemistry — Organic Chemistry

Energy Band Gap Investigation using First Principle Simulation and Tauc Plot Method of Calixarene and Calixarene-Drug Inclusion Complexes Calixarene has attract attention especially in drug delivery and drug sensor systems due to its peculiar properties, such as functional diversity of the upper and lower rims, hydrophobic cavity, chemical stability, zero toxicity, and controlled release profile. These properties make this supramolecule an ideal candidate for drug encapsulation and sensors. P-aminobenzoic acid (PABA) is a drug in sunscreen which is widely used as a ultraviolet (UV) filter and sunburn protector to protect against solar rays. The calix[n]arene (n=4,6,8) and the host-guest interaction of calix[n]-PABA were characterized using UV–visible spectroscopy and the first-principles pseudopotential method, based on the density functional theory (DFT) and the plane-wave method as implemented into Quantum Espresso code. The DFT calculation is performed to find the estimated calix[n]arene and calix[n]arene-drug band gap. The band gap calculated using DFT has usually underestimated the insulating materials for about 30 – 50% of the experimental gap values, depending on the selected type of exchange-correlation chosen. The optical band gap value of calix[n]arene and calix[n]-PABA obtained from the UV-Visible absorption spectrum estimated using the Tauc plot are then compared with the band gap computed by DFT. The band gap narrowing shown by the complexes indicates that calix[n]arene and PABA reacted. Besides, calix[8]arene is the most promising host in this study since the calix[8]-PABA complex has the most significant binding energy. The band gaps and binding energy results will become a reference for future research in calixarene and calixarene-drug material. Calixarene ; Band gap ; Chemistry ; Density functional theory ; Pseudopotential ; Binding energy ; CASTEP ; Materials science ; Computational chemistry ; Physical chemistry ; Analytical Chemistry (journal) ; Crystallography ; Photochemistry ; Organic chemistry ; Optoelectronics ; Molecule ; Physics ; Atomic physics Polydiacetylene-based materials and applications ; Luminescence and Fluorescent Materials ; Conducting polymers and applications
Authors: Heba Allah Mandour | Ali Kahalfallah | Gharib Taha | Loai Nassart | Hamdy A. Zahran
Source: Egyptian Journal of Chemistry (article, 2023-10-02)
Field: Materials Science — Polymers and Plastics

Physico-Chemical and Electrical Properties of Epoxy Ethyl Esters of Various Vegetable Oils As Bio-Transformer Oils Chemically modified vegetable oils are biodegradable and eco-friendly particularly in comparison to petroleum transformer lubricant and insulating oils. These advantages motivate us to investigate the use of soybean, sunflower and cook waste. vegetable oils as suitable transformer oil alternatives. It is crucial to compare its physicochemical and electrical properties to those of transformer mineral oil to the American Standard Technical Methods (ASTM) specification to confirm its appropriateness. In This Study soybean, sunflower and cook waste oils undergo a two-step chemical modification by trans-esterification reaction with ethyl alcohol and potassium hydroxide as catalyst at 60 ᵒ C followed by epoxidation reaction with hydrogen peroxide and glacial acetic acid in amberlite IR – 120 resins. The physiochemical and electrical properties of synthesized bio-transformer oils were examined without the presence of tert butyl hydro quinone (TBHQ) as antioxidant and after applying oxidation conditions with the addition of TBHQ using approved methods. The chemical parameters that are measured include acid value, water content and oxidation stability. The physical characteristics that were tested were density, dynamic viscosity at 40 °C and flash point, breakdown voltage is the electrical property that was measured. Most of the data showed that the different characteristics properties of the ethyl ester of various vegetable oils meet the standard ASTM values after the addition of 2 grams of TBHQ antioxidant. Epoxidation of ethyl vegetable oil an improvement in the physico– chemical and electrical properties occurred with and without TBHQ antioxidant, Consequently, it can be used as a substitute for traditional transformer oil because it complies with most ASTM standard requirements. Epoxy ; Transformer oil ; Transformer ; Materials science ; Organic chemistry ; Chemistry ; Chemical engineering ; Pulp and paper industry ; Engineering ; Electrical engineering ; Voltage Synthesis and properties of polymers ; Lubricants and Their Additives
Authors: M. Mustafa Azeem | Qingyu Wang
Source: Journal of Composites Science (article, 2023-10-05)
Field: Materials Science — Materials Chemistry

Atomic Insights into the Structural Properties and Displacement Cascades in Ytterbium Titanate Pyrochlore (Yb2Ti2O7) and High-Entropy Pyrochlores Pyrochlore oxides (A2B2O7) are potential nuclear waste substrate materials due to their superior radiation resistance properties. We performed molecular dynamics simulations to study the structural properties and displacement cascades in ytterbium titanate pyrochlore (Yb2Ti2O7) and high-entropy alloys (HEPy), e.g., YbYTiZrO7, YbGdTiZrO7, and Yb0.5Y0.5Eu0.5Gd0.5TiZrO7. We computed lattice constants (LC) (ao) and threshold displacement energy (Ed). Furthermore, the calculation for ao and ionic radius (rionic) were performed by substituting a combination of cations at the A and B sites of the original pyrochlore structure. Our simulation results have demonstrated that the lattice constant is proportional to the ionic radius, i.e., ao α rionic. Moreover, the effect of displacement cascades of recoils of energies 1 keV, 2 keV, 5 keV, and 10 keV in different crystallographic directions ([100], [110], [111]) was studied. The number of defects is found to be proportional to the energy of incident primary knock-on atoms (PKA). Additionally, the Ed of pyrochlore exhibits anisotropy. We also observed that HEPy has a larger Ed as compared with Yb2Ti2O7. This establishes that Yb2Ti2O7 has characteristics of lower radiation damage resistance than HEPy. Our displacement cascade simulation result proposes that HEPy alloys have more tendency for trapping defects. This work will provide atomic insights into developing substrate materials for nuclear waste applications. Pyrochlore ; Ytterbium ; Ionic radius ; Materials science ; Ionic bonding ; Radiation damage ; Anisotropy ; Atomic radius ; Crystallography ; Ion ; Radiation ; Chemistry ; Physics ; Doping ; Optics ; Optoelectronics Nuclear materials and radiation effects ; Nuclear Materials and Properties ; High-pressure geophysics and materials
Authors: Yu Luo | Jason Meziere | German Samolyuk | Gus L. W. Hart | Mark R. Daymond | Laurent Karim Béland
Source: arXiv (Cornell University) (preprint, 2023-05-31)
Field: Materials Science — Materials Chemistry

A set of moment tensor potentials for zirconium with increasing complexity Machine learning force fields (MLFFs) are an increasingly popular choice for atomistic simulations due to their high fidelity and improvable nature. Here, we propose a hybrid small-cell approach that combines attributes of both offline and active learning to systematically expand a quantum mechanical (QM) database while constructing MLFFs with increasing model complexity. Our MLFFs employ the moment tensor potential formalism. During this process, we quantitatively assessed structural properties, elastic properties, dimer potential energies, melting temperatures, phase stability, point defect formation energies, point defect migration energies, free surface energies, and generalized stacking fault (GSF) energies of Zr as predicted by our MLFFs. Unsurprisingly, model complexity has a positive correlation with prediction accuracy. We also find that the MLFFs wee able to predict the properties of out-of-sample configurations without directly including these specific configurations in the training dataset. Additionally, we generated 100 MLFFs of high complexity (1513 parameters each) that reached different local optima during training. Their predictions cluster around the benchmark DFT values, but subtle physical features such as the location of local minima on the GSFE surface are washed out by statistical noise. Maxima and minima ; Statistical physics ; Computer science ; Quantum ; Moment (physics) ; Materials science ; Physics ; Algorithm ; Mathematics ; Quantum mechanics Machine Learning in Materials Science ; Nuclear Materials and Properties ; Ion-surface interactions and analysis