jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Sajjad Ansari | Mohammad-Reza Mohammadi | Hamid Bahmaninia | Abdolhossein Hemmati‐Sarapardeh | Mahin Schaffie | Saeid Norouzi-Apourvari | Mohammad Ranjbar
Source: Scientific Reports (article, 2023-01-04)
Field: Chemistry — Analytical Chemistry

Experimental measurement and modeling of asphaltene adsorption onto iron oxide and lime nanoparticles in the presence and absence of water Asphaltene precipitation and its adsorption on different surfaces are challenging topics in the upstream and downstream of the oil industries and the environment. In this research, the phenomenon of asphaltenes adsorption in the presence and absence of water on the surface of magnetite, hematite, calcite, and dolomite nanoparticles (NPs) was investigated. Five asphaltenes of different origins, four NPs as adsorbents and Persian Gulf water were used for three-phase (asphaltene/toluene solution + NPs + water) experiments. Characterization of asphaltenes and NPs was performed using Fourier transform infrared spectroscopic (FTIR), dynamic light scattering (DLS), elemental analysis, and field emission scanning electron microscopy (FESEM). Adsorption experiments were performed in two- (asphaltene/toluene solution + NPs) and three-phase systems. The results showed that the most effective parameters for asphaltene adsorption onto these NPs are the asphaltene composition, namely nitrogen content, and the aromaticity of asphaltenes. The significant effects of these parameters were also confirmed by the relevancy factor function as a sensitivity analysis. In the competition of asphaltene adsorption capacity by NPs, iron oxide NPs had the highest adsorption (Magnetite NPs > Hematite NPs > Calcite NPs > Dolomite NPs). From the results of the experiments in the presence of water phase, it could be pointed out that the asphaltenes adsorption onto the NPs was accompanied by a decrease compared to the experiments in the absence of water. The modeling also showed that physical adsorption has a significant contribution to the asphaltenes adsorption on the surface of iron oxides and lime NPs. The results of this research can assist in a better understanding of the asphaltene adsorption phenomenon and the role of iron oxide and lime NPs in solving this problem. Asphaltene ; Adsorption ; Chemical engineering ; Fourier transform infrared spectroscopy ; Dynamic light scattering ; Magnetite ; Iron oxide ; Nanoparticle ; Toluene ; Hematite ; Chemistry ; Inorganic chemistry ; Materials science ; Organic chemistry ; Mineralogy ; Metallurgy Petroleum Processing and Analysis ; Enhanced Oil Recovery Techniques ; Hydrocarbon exploration and reservoir analysis
Authors: Ravipat Lapcharoensuk | Chawisa Fhaykamta | Watcharaporn Anurak | Wasita Chadwut | Agustami Sitorus
Source: Foods (article, 2023-02-23)
Field: Chemistry — Analytical Chemistry

Nondestructive Detection of Pesticide Residue (Chlorpyrifos) on Bok Choi (Brassica rapa subsp. Chinensis) Using a Portable NIR Spectrometer Coupled with a Machine Learning Approach The contamination of agricultural products, such as vegetables, by pesticide residues has received considerable attention worldwide. Pesticide residue on vegetables constitutes a potential risk to human health. In this study, we combined near infrared (NIR) spectroscopy with machine learning algorithms, including partial least-squares discrimination analysis (PLS-DA), support vector machine (SVM), artificial neural network (ANN), and principal component artificial neural network (PC-ANN), to identify pesticide residue (chlorpyrifos) on bok choi. The experimental set comprised 120 bok choi samples obtained from two small greenhouses that were cultivated separately. We performed pesticide and pesticide-free treatments with 60 samples in each group. The vegetables for pesticide treatment were fortified with 2 mL/L of chlorpyrifos 40% EC residue. We connected a commercial portable NIR spectrometer with a wavelength range of 908-1676 nm to a small single-board computer. We analyzed the pesticide residue on bok choi using UV spectrophotometry. The most accurate model correctly classified 100% of the samples used in the calibration set in terms of the content of chlorpyrifos residue on samples using SVM and PC-ANN with raw data spectra. Thus, we tested the model using an unknown dataset of 40 samples to verify the robustness of the model, which produced a satisfactory F1-score (100%). We concluded that the proposed portable NIR spectrometer coupled with machine learning approaches (PLS-DA, SVM, and PC-ANN) is appropriate for the detection of chlorpyrifos residue on bok choi. Chlorpyrifos ; Pesticide residue ; Pesticide ; Residue (chemistry) ; Support vector machine ; Brassica rapa ; Partial least squares regression ; Artificial intelligence ; Pattern recognition (psychology) ; Chemistry ; Mathematics ; Computer science ; Machine learning ; Horticulture ; Biology ; Brassica ; Agronomy Spectroscopy and Chemometric Analyses ; Pesticide Residue Analysis and Safety ; Water Quality Monitoring and Analysis
Authors: Paul L. Houston | Chen Qu | Qi Yu | Riccardo Conte | Apurba Nandi | Jeffrey K. Li | Joel M. Bowman
Source: The Journal of Chemical Physics (article, 2023-01-04)
Field: Materials Science — Materials Chemistry

PESPIP: Software to fit complex molecular and many-body potential energy surfaces with permutationally invariant polynomials We wish to describe a potential energy surface by using a basis of permutationally invariant polynomials whose coefficients will be determined by numerical regression so as to smoothly fit a dataset of electronic energies as well as, perhaps, gradients. The polynomials will be powers of transformed internuclear distances, usually either Morse variables, exp(-r<sub>i,j</sub>/λ), where λ is a constant range hyperparameter, or reciprocals of the distances, 1/r<sub>i,j</sub>. The question we address is how to create the most efficient basis, including (a) which polynomials to keep or discard, (b) how many polynomials will be needed, (c) how to make sure the polynomials correctly reproduce the zero interaction at a large distance, (d) how to ensure special symmetries, and (e) how to calculate gradients efficiently. This article discusses how these questions can be answered by using a set of programs to choose and manipulate the polynomials as well as to write efficient Fortran programs for the calculation of energies and gradients. A user-friendly interface for access to monomial symmetrization approach results is also described. The software for these programs is now publicly available. Invariant (physics) ; Fortran ; Monomial ; Computer science ; Orthogonal polynomials ; Range (aeronautics) ; Mathematics ; Pure mathematics ; Physics ; Quantum mechanics ; Programming language Machine Learning in Materials Science ; Advanced Chemical Physics Studies ; Computational Drug Discovery Methods
Authors: Thomas A. R. Purcell | Matthias Scheffler | Luca M. Ghiringhelli
Source: The Journal of Chemical Physics (article, 2023-09-18)
Field: Materials Science — Materials Chemistry

Recent advances in the SISSO method and their implementation in the SISSO++ code Accurate and explainable artificial-intelligence (AI) models are promising tools for accelerating the discovery of new materials. Recently, symbolic regression has become an increasingly popular tool for explainable AI because it yields models that are relatively simple analytical descriptions of target properties. Due to its deterministic nature, the sure-independence screening and sparsifying operator (SISSO) method is a particularly promising approach for this application. Here, we describe the new advancements of the SISSO algorithm, as implemented into SISSO++, a C++ code with Python bindings. We introduce a new representation of the mathematical expressions found by SISSO. This is a first step toward introducing "grammar" rules into the feature creation step. Importantly, by introducing a controlled nonlinear optimization to the feature creation step, we expand the range of possible descriptors found by the methodology. Finally, we introduce refinements to the solver algorithms for both regression and classification, which drastically increase the reliability and efficiency of SISSO. For all these improvements to the basic SISSO algorithm, we not only illustrate their potential impact but also fully detail how they operate both mathematically and computationally. Computer science ; Symbolic regression ; Python (programming language) ; Solver ; Artificial intelligence ; Feature (linguistics) ; Code (set theory) ; Simple (philosophy) ; Theoretical computer science ; Range (aeronautics) ; Machine learning ; Operator (biology) ; Programming language ; Genetic programming Machine Learning in Materials Science ; Ferroelectric and Negative Capacitance Devices ; Electron and X-Ray Spectroscopy Techniques
Authors: Karsten Heinz | Sven M. J. Rogge | Andreas Kalytta‐Mewes | Dirk Volkmer | Hana Bunzen
Source: Inorganic Chemistry Frontiers (article, 2023-01-01)
Field: Chemistry — Inorganic Chemistry

MOFs for long-term gas storage: exploiting kinetic trapping in ZIF-8 for on-demand and stimuli-controlled gas release Pores as high-pressure containers: MOFs with a flexible pore opening for long-term gas storage under ambient conditions in air. Trapping ; On demand ; Term (time) ; Materials science ; Chemical engineering ; Nanotechnology ; Process engineering ; Environmental science ; Computer science ; Engineering ; Physics Metal-Organic Frameworks: Synthesis and Applications ; Nanoplatforms for cancer theranostics ; Enhanced Oil Recovery Techniques
Authors: Mohammad A. Altamimi | Saeed Ali Syed | Burak Tüzün | Mohammad Rashid Alhazani | Osamah Abdulrahman Alnemer | Ahmed Bari
Source: Journal of Enzyme Inhibition and Medicinal Chemistry (article, 2023-12-11)
Field: Chemistry — Organic Chemistry

Synthesis biological evaluation and molecular docking of isatin hybrids as anti-cancer and anti-microbial agents Isatin, known as 1<i>H</i>-indole-2,3-dione, was originally recognised as a synthetic molecule until its discovery in the fruits of the cannonball tree, <i>Couroupita guianensis</i>. It is naturally occurring in plants of the genus <i>Isatis</i> and serves as a metabolic derivative of adrenaline in humans. Isatin possesses significant pharmacological importance, and its synthetic versatility has prompted extensive interest in its derivative compounds due to their diverse biological and pharmacological properties. These derivatives represent a valuable class of heterocyclic compounds with potential applications as precursors for synthesizing numerous valuable drugs. In the pursuit of advancing our research on isatin hybrids, we investigate the utilisation of readily available hydrazonoindolin-2-one and isatin as starting materials for the synthesis of a wide range of analogues. Characterisation of the synthesized compounds was carried out through various analytical techniques. Furthermore, the obtained compounds were subjected to extensive testing to evaluate their anticancer and antimicrobial activities. Specifically, their efficacy against key proteins, namely <i>Staphylococcus aureus</i> protein (PDB ID: 1JIJ), <i>Escherichia coli</i> protein (PDB ID: 1T9U), <i>Pseudomonas aeruginosa</i> protein (PDB ID: 2UV0), and <i>Acinetobacter baumannii</i> protein (PDB ID: 4HKG), was examined through molecular docking calculations. Several molecules, such as 3, 4, 6, 16, and 19, displayed remarkable activity against the renal cancer cell line UO-31. Additionally, the results of antimicrobial activity testing revealed that compound <b>16</b> exhibited significant cytotoxicity against <i>Candida albicans</i> and <i>Cryptococcus neoformans</i>. Subsequently, ADME/T calculations were performed to gain insights into the potential effects and reactions of these molecules within human metabolism. This comprehensive study provides valuable insights into the potential pharmacological applications of isatin derivatives and underscores their significance in drug development. Isatin ; Protein Data Bank (RCSB PDB) ; Docking (animal) ; ADME ; Candida albicans ; Chemistry ; Antimicrobial ; Biochemistry ; Acinetobacter baumannii ; Cytotoxicity ; Cryptococcus neoformans ; Stereochemistry ; Combinatorial chemistry ; Biology ; Computational biology ; Pseudomonas aeruginosa ; Microbiology ; Bacteria ; Organic chemistry ; In vitro Synthesis and biological activity ; Cancer therapeutics and mechanisms ; Bioactive Compounds and Antitumor Agents
Authors: Jesse A. Jones | Robert Benisch | Tobias W. Giessen
Source: Journal of Materials Chemistry B (review, 2023-01-01)
Field: Materials Science — Biomaterials

Encapsulin cargo loading: progress and potential Encapsulins are a recently discovered class of prokaryotic self-assembling icosahedral protein nanocompartments measuring between 24 and 42 nm in diameter, capable of selectively encapsulating dedicated cargo proteins <i>in vivo</i>. They have been classified into four families based on sequence identity and operon structure, and thousands of encapsulin systems have recently been computationally identified across a wide range of bacterial and archaeal phyla. Cargo encapsulation is mediated by the presence of specific targeting motifs found in all native cargo proteins that interact with the interior surface of the encapsulin shell during self-assembly. Short C-terminal targeting peptides (TPs) are well documented in Family 1 encapsulins, while more recently, larger N-terminal targeting domains (TDs) have been discovered in Family 2. The modular nature of TPs and their facile genetic fusion to non-native cargo proteins of interest has made cargo encapsulation, both <i>in vivo</i> and <i>in vitro</i>, readily exploitable and has therefore resulted in a range of rationally engineered nano-compartmentalization systems. This review summarizes current knowledge on cargo protein encapsulation within encapsulins and highlights select studies that utilize TP fusions to non-native cargo in creative and useful ways. Forensic engineering ; Materials science ; Environmental science ; Business ; Engineering Electrospun Nanofibers in Biomedical Applications ; Nanoparticle-Based Drug Delivery ; Electrohydrodynamics and Fluid Dynamics
Authors: Yulei Wang | Rong Zhao | Lutz Ackermann
Source: Advanced Materials (review, 2023-03-25)
Field: Materials Science — Polymers and Plastics

Electrochemical Syntheses of Polycyclic Aromatic Hydrocarbons (PAHs) Polycyclic aromatic hydrocarbons (PAHs) have surfaced as increasingly viable components in optoelectronics and material sciences. The development of highly efficient and atom-economic tools to prepare PAHs under exceedingly mild conditions constitutes a long-term goal. Traditional syntheses of PAHs have largely relied on multistep approaches or the conventional Scholl reaction. However, Scholl reactions are largely inefficient with electron-deficient substrates, require stoichiometric chemical oxidants, and typically occur in the presence of strong acid. In sharp contrast, electrochemistry has gained considerable momentum during the past decade as an alternative for the facile and straightforward PAHs assembly, generally via electro-oxidative dehydrogenative annulation, releasing molecular hydrogen as the sole stoichiometric byproduct by the hydrogen evolution reaction. This review provides an overview on the recent and significant advances in the field of electrochemical syntheses of various PAHs until January 2023. Electrochemistry ; Stoichiometry ; Polycyclic aromatic hydrocarbon ; Materials science ; Nanotechnology ; Organic chemistry ; Chemistry ; Combinatorial chemistry ; Electrode ; Physical chemistry Conducting polymers and applications ; Organic Electronics and Photovoltaics ; Electrocatalysts for Energy Conversion
Authors: Yuan Zhang | Lei Zhang | Man Wang | Peifeng Li
Source: Theranostics (review, 2023-01-01)
Field: Materials Science — Materials Chemistry

The applications of nanozymes in neurological diseases: From mechanism to design Nanozymes are a class of nanomaterials with enzyme-like catalytic activities. Due to their multiple catalytic activities, as well as their good stability, modifiable activity and other advantages over natural enzymes, they have a wide range of application prospects in sterilization, the treatment of inflammation, cancer, and neurological diseases, and other fields. In recent years, it has been found that various nanozymes have antioxidant activity, allowing them to simulate the endogenous antioxidant system and play an important role in cell protection. Therefore, nanozymes can be applied in the treatment of reactive oxygen species (ROS)-related neurological diseases. Another advantage of nanozymes is that they can be customized and modified in a variety of ways to increase their catalytic activity beyond that of classical enzymes. In addition, some nanozymes have unique properties, such as the ability to effectively penetrate the blood‒brain barrier (BBB) or to depolymerize or otherwise eliminate misfolded proteins, making them potentially useful therapeutic tools for the treatment of neurological diseases. Here, we review the catalytic mechanisms of antioxidant-like nanozymes, as well as the latest research progress and strategies for designing therapeutic nanozymes, aiming to promote the development of more effective nanozymes for the treatment of neurological diseases in the future. Chemistry ; Nanotechnology ; Neuroscience ; Biology ; Materials science Advanced Nanomaterials in Catalysis ; Nanocluster Synthesis and Applications ; Carbon and Quantum Dots Applications
Authors: Tamara Lazarević‐Pašti | Tamara Tasić | Vedran Milanković | Nebojša Potkonjak
Source: Chemosensors (article, 2023-01-02)
Field: Chemistry — Analytical Chemistry

Molecularly Imprinted Plasmonic-Based Sensors for Environmental Contaminants—Current State and Future Perspectives The increase of production and consumption persistently introduce different pollutants into the environment. The constant development and improvement of analytical methods for tracking environmental contaminants are essential. The demand for high sample throughput analysis has hit the spotlight for developing selective sensors to avoid time-consuming sample preparation techniques. In addition, the sensor’s sensitivity should satisfy the rigorous demands of harmful compound tracking. Molecularly imprinted plasmonic-based sensors are excellent candidates to overcome selectivity and sensitivity issues. Molecularly imprinted polymers are robust, stable in aqueous and organic solvents, stable at extreme pHs and temperatures, and include a low-cost synthesis procedure. Combined with plasmonic-based techniques, they are the perspective choice for applications in the field of environmental protection. Plasmonic-based sensors offer a lower limit of detection, a broad linearity range, high sensitivity, and high selectivity compared to other detection techniques. This review outlines the optical plasmonic detection of different environmental contaminants with molecularly imprinted polymers as sensing elements. The main focus is on the environmental pollutants affecting human and animal health, such as pesticides, pharmaceuticals, hormones, microorganisms, polycyclic aromatic hydrocarbons, dyes, and metal particles. Although molecularly imprinted plasmonic-based sensors currently have their application mostly in the biomedical field, we are eager to point them out as a highly prospective solution for many environmental problems. Molecularly imprinted polymer ; Nanotechnology ; Pollutant ; Plasmon ; Contamination ; Molecular imprinting ; Materials science ; Biochemical engineering ; Environmental science ; Computer science ; Chemistry ; Selectivity ; Optoelectronics ; Engineering Analytical chemistry methods development ; Pharmaceutical and Antibiotic Environmental Impacts ; Biosensors and Analytical Detection
Authors: Rui Wang | Hang Lyu | Gerald Siu Hang Poon Ho | Huan-Huan Chen | Yufei Yuan | Ki‐Taek Bang | Yoonseob Kim
Source: Small (article, 2023-09-13)
Field: Materials Science — Materials Chemistry

Highly Conductive Covalent–Organic Framework Films Chemically inert organic networks exhibiting electrical conductivity comparable to metals can advance organic electronics, catalysis, and energy storage systems. Covalent-organic frameworks (COFs) have emerged as promising materials for those applications due to their high crystallinity, porosity, and tunable functionality. However, their low conductivity has limited their practical utilization. In this study, copper-coordinated-fluorinated-phthalocyanine and 2,3,6,7-tetrahydroxy-9,10-anthraquinone-based COF (CuPc-AQ-COF) films with ultrahigh conductivity are developed. The COF films exhibit an electrical conductivity of 1.53 × 10<sup>3</sup> S m<sup>-1</sup> and a Hall mobility of 6.02 × 10<sup>2</sup> cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup> at 298 K, reaching the level of metals. The films are constructed by linking phthalocyanines and anthraquinones through vapor-assisted synthesis. The high conductivity properties of the films are attributed to the molecular design of the CuPc-AQ-COFs and the generation of high-quality crystals via the vapor-assisted method. Density functional theory analysis reveals that an efficient donor-acceptor system between the copper-coordinated phthalocyanines and anthraquinones significantly promotes charge transfer. Overall, the CuPc-AQ-COF films set new records of COF conductivity and mobility and represent a significant step forward in the development of COFs for electronic, catalytic, and electrochemical applications. Materials science ; Conductivity ; Covalent organic framework ; Organic semiconductor ; Copper ; Phthalocyanine ; Chemical engineering ; Nanotechnology ; Crystallinity ; Porosity ; Chemistry ; Optoelectronics ; Composite material ; Physical chemistry Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Luminescence and Fluorescent Materials
Authors: Wen Zhang | Qiang Fu | Jiahui Li | B Lian | Yuze Xia | Liguo Zhou | Andrew T. S. Wee | Ping Kwan Johnny Wong
Source: Applied Physics Reviews (article, 2023-11-28)
Field: Materials Science — Materials Chemistry

Probing van der Waals magnetic surface and interface via circularly polarized X-rays Advances in research of magnetic two-dimensional van der Waals (2D vdW) materials have opened up new opportunities in miniaturization of spintronic devices at the atomically thin limit. One major research thrust, which is the subject of this review, is that the magnetism of 2D vdW materials and their derived hetero-interface may be significantly affected by the local atomic geometry and environment. As a result, there is a pressing need for powerful advanced technique to characterize magnetic vdW surface and interface. Circularly polarized X-rays from synchrotron radiation light sources are key to this endeavor, as they can probe the microscopic magnetism of a specific element, for their atomic sensitivity, element-specificity, core-level excitation as well as capability of separation for the spin and orbit moments. We review a series of representative experimental achievements, exploiting circularly polarized X-rays, in (1) 2D vdW magnet, (2) magnetic metal/vdW interface, (3) molecule/vdW interface as well as (4) vdW/2D interface. On the basis of the review, advantages of probing magnetic vdW surface and interface by circularly polarized X-rays are presented, and challenges and opportunities are also discussed. Magnetism ; van der Waals force ; Spintronics ; Synchrotron radiation ; Surface science ; Physics ; Condensed matter physics ; Optics ; Ferromagnetism ; Surface (topology) ; Geometry ; Quantum mechanics ; Molecule 2D Materials and Applications ; Graphene research and applications ; Topological Materials and Phenomena