jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Alexey V. Solomonov | Anna Kozell | Ulyana Shimanovich
Source: Angewandte Chemie (article, 2024-01-09)
Field: Materials Science — Biomaterials

Designing Multifunctional Biomaterials via Protein Self‐Assembly Abstract Protein self‐assembly is a fundamental biological process where proteins spontaneously organize into complex and functional structures without external direction. This process is crucial for the formation of various biological functionalities. However, when protein self‐assembly fails, it can trigger the development of multiple disorders, thus making understanding this phenomenon extremely important. Up until recently, protein self‐assembly has been solely linked either to biological function or malfunction; however, in the past decade or two it has also been found to hold promising potential as an alternative route for fabricating materials for biomedical applications. It is therefore necessary and timely to summarize the key aspects of protein self‐assembly: how the protein structure and self‐assembly conditions (chemical environments, kinetics, and the physicochemical characteristics of protein complexes) can be utilized to design biomaterials. This minireview focuses on the basic concepts of forming supramolecular structures, and the existing routes for modifications. We then compare the applicability of different approaches, including compartmentalization and self‐assembly monitoring. Finally, based on the cutting‐edge progress made during the last years, we summarize the current knowledge about tailoring a final function by introducing changes in self‐assembly and link it to biomaterials’ performance. Compartmentalization (fire protection) ; Nanotechnology ; Self-assembly ; Function (biology) ; Computer science ; Process (computing) ; Biochemical engineering ; Materials science ; Chemistry ; Engineering ; Biology Silk-based biomaterials and applications ; Polymer Surface Interaction Studies ; Bacteriophages and microbial interactions
Authors: Tao Yan | Fan Weng | Ming Yang | Shijie Zhu | Miao Zhu | Chunsheng Wang | Changfa Guo | Kai Zhu
Source: Biosensors (review, 2024-07-08)
Field: Chemistry — Spectroscopy

Luminescence Probes in Bio-Applications: From Principle to Practice Bioanalysis based on optical imaging has gained significant progress in the last few decades. Luminescence probes are capable of detecting, monitoring, and tracing particular biomolecules in complex biological systems to figure out the roles of these molecules in organisms. Considering the rapid development of luminescence probes for bio-applications and their promising future, we have attempted to explore the working principles and recent advances in bio-applications of luminescence probes, in the hope of helping readers gain a detailed understanding of luminescence probes developed in recent years. In this review, we first focus on the current widely used luminescence probes, including fluorescence probes, bioluminescence probes, chemiluminescence probes, afterglow probes, photoacoustic probes, and Cerenkov luminescence probes. The working principles for each type of luminescence probe are concisely described and the bio-application of the luminescence probes is summarized by category, including metal ions detection, secretion detection, imaging, and therapy. Luminescence ; Afterglow ; Nanotechnology ; Luminescent Measurements ; Biomolecule ; Bioanalysis ; Chemiluminescence ; Bioluminescence ; Chemistry ; Materials science ; Optoelectronics ; Physics Molecular Sensors and Ion Detection ; bioluminescence and chemiluminescence research ; Analytical Chemistry and Sensors
Authors: Austin H. Cheng | Alston Lo | Santiago Miret | Brooks H. Pate | Alán Aspuru‐Guzik
Source: The Journal of Chemical Physics (article, 2024-03-28)
Field: Chemistry — Spectroscopy

Determining 3D structure from molecular formula and isotopologue rotational spectra in natural abundance with reflection-equivariant diffusion Structure determination is necessary to identify unknown organic molecules, such as those in natural products, forensic samples, the interstellar medium, and laboratory syntheses. Rotational spectroscopy enables structure determination by providing accurate 3D information about small organic molecules via their moments of inertia. Using these moments, Kraitchman analysis determines isotopic substitution coordinates, which are the unsigned |x|, |y|, |z| coordinates of all atoms with natural isotopic abundance, including carbon, nitrogen, and oxygen. While unsigned substitution coordinates can verify guesses of structures, the missing +/- signs make it challenging to determine the actual structure from the substitution coordinates alone. To tackle this inverse problem, we develop Kreed (Kraitchman REflection-Equivariant Diffusion), a generative diffusion model that infers a molecule's complete 3D structure from only its molecular formula, moments of inertia, and unsigned substitution coordinates of heavy atoms. Kreed's top-1 predictions identify the correct 3D structure with near-perfect accuracy on large simulated datasets when provided with substitution coordinates of all heavy atoms with natural isotopic abundance. Accuracy decreases as fewer substitution coordinates are provided, but is retained for smaller molecules. On a test set of experimentally measured substitution coordinates gathered from the literature, Kreed predicts the correct all-atom 3D structure in 25 of 33 cases, demonstrating experimental potential for de novo 3D structure determination with rotational spectroscopy. Isotopologue ; Abundance (ecology) ; Reflection (computer programming) ; Diffusion ; Spectral line ; Rotational diffusion ; Equivariant map ; Physics ; Chemistry ; Mathematics ; Optics ; Biology ; Astronomy ; Thermodynamics ; Ecology ; Computer science ; Pure mathematics Molecular Spectroscopy and Structure ; Spectroscopy and Laser Applications ; Advanced Chemical Physics Studies
Authors: Gang Li | Shuangcheng Deng
Source: Processes (article, 2024-01-26)
Field: Chemistry — Analytical Chemistry

Quantitative Analysis of Near-Infrared Spectroscopy Using the BEST-1DConvNet Model In the quest for enhanced precision in near-infrared spectroscopy (NIRS), in this study, the application of a novel BEST-1DConvNet model for quantitative analysis is investigated against conventional support vector machine (SVM) approaches with preprocessing such as multiplicative scatter correction (MSC) and standard normal variate (SNV). We assessed the performance of these methods on NIRS datasets of diesel, gasoline, and milk using a Fourier Transform Near-Infrared (FT-NIR) spectrometer having a wavelength range of 900–1700 nm for diesel and gasoline and 4000–10,000 nm for milk, ensuring comprehensive spectral capture. The BEST-1DConvNet’s effectiveness in chemometric predictions was quantitatively gauged by improvements in the coefficient of determination (R2) and reductions in the root mean square error (RMSE). The BEST-1DConvNet model achieved significant performance enhancements compared to the MSC + SNV + 1D + SVM model. Notably, the R2 value for diesel increased by approximately 48.85% despite a marginal RMSE decrease of 0.92%. R2 increased by 11.30% with a 3.32% RMSE reduction for gasoline, and it increased by 8.71%, accompanied by a 3.51% RMSE decrease for milk. In conclusion, the BEST-1DConvNet model demonstrates superior predictive accuracy and reliability in NIRS data analysis, marking a substantial leap forward in spectral analysis technology. This advancement could potentially streamline their integration into various industrial applications and highlight the role of convolutional neural networks in future chemometric methodologies. Spectroscopy ; Infrared spectroscopy ; Infrared ; Materials science ; Chemistry ; Optics ; Physics ; Astronomy Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Water Quality Monitoring and Analysis
Authors: Giulia Lo Dico | Lorenzo Lisuzzo | V. Carcelén | Giuseppe Cavallaro | Maciej Harańczyk
Source: Materials (article, 2024-05-09)
Field: Materials Science — Biomaterials

Thermogravimetric Analysis of Moisture in Natural and Thermally Treated Clay Materials Clays are a class of porous materials; their surfaces are naturally covered by moisture. Weak thermal treatment may be considered practical to remove the water molecules, changing the surface properties and making the micro- and/or mesoporosities accessible to interact with other molecules. Herein, a modulated thermogravimetric analysis (MTGA) study of the moisture behavior on the structures of five, both fibrous and laminar, clay minerals is reported. The effect of the thermal treatment at 150 °C, which provokes the release of weakly adsorbed water molecules, was also investigated. The activation energies for the removal of the adsorbed water (Ea) were calculated, and they were found to be higher, namely, from 160 to 190 kJ mol<sup>-1</sup>, for fibrous clay minerals compared to lamellar structures, ranging in this latter case from 80 to 100 kJ mol<sup>-1</sup>. The thermal treatment enhances the rehydration in Na-montmorillonite, stevensite, and sepiolite structures with a decrease in the energy required to remove it, while Ea increases significantly in palygorskite (from 164 to 273 kJ mol<sup>-1</sup>). As a proof of concept, the MTGA results are statistically correlated, together with a full characterization of the physico-chemical properties of the five clay minerals, with the adsorption of two molecules, i.e., aflatoxin B1 (AFB1) and β-carotene. Herein, the amount of adsorbed molecules ranges from 12 to 97% for the former and from 22 to 35% for the latter, depending on the particular clay. The Ea was correlated with AFB1 adsorption with a Spearman score of -0.9. When the adsorbed water is forcibly removed, e.g., under vacuum conditions and high temperatures, the structure becomes the most important, decreasing the Spearman score between β-carotene and Ea to -0.6. Thermogravimetric analysis ; Moisture ; Materials science ; Natural (archaeology) ; Composite material ; Chemistry ; Geology ; Organic chemistry Clay minerals and soil interactions ; Recycling and utilization of industrial and municipal waste in materials production ; Soil and Unsaturated Flow
Authors: Devin McGlamery | Charles McDaniel | Dylan M. Ladd | Yang Ha | Martín A. Mosquera | Michael T. Mock | Nicholas P. Stadie
Source: Chemical Science (article, 2024-01-01)
Field: Materials Science — Materials Chemistry

Halide-free synthesis of metastable graphitic BC <sub>3</sub> Layered BC<sub>3</sub>, a metastable phase within the binary boron-carbon system that is composed of graphite-like sheets with hexagonally symmetric C<sub>6</sub>B<sub>6</sub> units, has never been successfully crystallized. Instead, poorly-crystalline BC<sub>3</sub>-like materials with significant stacking disorder have been isolated, based on the co-pyrolysis of a boron trihalide precursor with benzene at around 800 °C. The halide leaving group (-X) is a significant driving force of these reactions, but the subsequent evolution of gaseous HX species at such high temperatures hampers their scaling up and also prohibits their further use in the presence of hard-casting templates such as ordered silicates. Herein, we report a novel halide-free synthesis route to turbostratic BC<sub>3</sub> with long-range in-plane ordering, as evidenced by multi-wavelength Raman spectroscopy. Judicious pairing of the two molecular precursors is crucial to achieving B-C bond formation and preventing phase-segregation into the thermodynamically favored products. A simple computational method used herein to evaluate the compatibility of bottom-up molecular precursors can be generalized to guide the future synthesis of other metastable materials beyond the boron-carbon system. Halide ; Metastability ; Chemistry ; Materials science ; Inorganic chemistry ; Organic chemistry Graphene research and applications ; Boron and Carbon Nanomaterials Research ; Advancements in Battery Materials
Authors: Shun Tian | Ke Zhou | Wan‐Jian Yin | Yilun Liu
Source: Nature Communications (article, 2024-08-14)
Field: Materials Science — Materials Chemistry

Machine learning enables the discovery of 2D Invar and anti-Invar monolayers Materials demonstrating positive thermal expansion (PTE) or negative thermal expansion (NTE) are quite common, whereas those exhibiting zero thermal expansion (ZTE) are notably scarce. In this work, we identify the mechanical descriptors, namely in-plane tensile stiffness and out-of-plane bending stiffness, that can effectively classify PTE and NTE 2D crystals. By utilizing high throughput calculations and the state-of-the-art symbolic regression method, these descriptors aid in the discovery of ZTE or 2D Invar monolayers with the linear thermal expansion coefficient (LTEC) within ±2 × 10<sup>-6</sup> K<sup>-1</sup> in the middle range of temperatures. Additionally, the descriptors assist the discovery of large PTE and NTE 2D monolayers with the LTEC larger than ±15 × 10<sup>-6</sup> K<sup>-1</sup>, which are so-called 2D anti-Invar monolayers. Advancing our understanding of materials with exceptionally low or high thermal expansion is of substantial scientific and technological interest, particularly in the development of next-generation electronics at the nanometer or even Ångstrom scale. Invar ; Computer science ; Materials science ; Thermal expansion ; Metallurgy 2D Materials and Applications ; Graphene research and applications ; Ferroelectric and Negative Capacitance Devices
Authors: Shahira H. EL‐Moslamy | Ahmed H. Rezk | Marwa Elkady | Hassan Shokry
Source: Arabian Journal for Science and Engineering (article, 2024-01-29)
Field: Materials Science — Materials Chemistry

Semi-industrial Bio-fabrication of ZnO/MnO2 Nanocomposite Using Endophytic Streptomyces coelicolor: Characterization, Statistical Design, Exponential Pulse Fed-Batch Fermentation, and Its Antimicrobial Application Abstract In our study, we examined how well six Streptomyces strains bio-fabricated ZnONPs, MnONPs, and/or ZnO/MnO 2 nanocomposite. The most potent strain that generated efficient antimicrobial nanoparticles was then picked to increase the production of those particles in a semi-industrial pilot plant unit. Consequently, the intracellular extract of endophytic Streptomyces coelicolor strain E72 was used to achieve the bio-fabrication reaction of the spherical ZnO/MnO 2 nanocomposite (6–18 nm). The bio-fabricated ZnO/MnO 2 nanocomposite was validated and characterized using FTIR, XRD, SEM, TEM, TGA, and EDS analyses. Additionally, the production of this ZnO/MnO 2 nanocomponent was scaled up to a pilot plant unit with a semi-industrial size. The Plackett–Burman experimental method was used to maximize the production of ZnO/MnO 2 nanocomposites, which had increased 2.7-fold from their initial state. The bio-fabricated ZnO/MnO 2 nanocomposite was subsequently scaled up 31.25 times using an exponential pulse-feeding fermentation technique in a 70-L bioreactor. This ZnO/MnO 2 nanocomposite exhibited effective antimicrobial efficacy against all tested antibiotic-resistant human pathogens. The antimicrobial effects against Salmonella paratyphi (53.17 ± 2.8 mm) and Candida albicans (50.2 ± 1.01 mm) were the most potent at 90 and 130 µg/ml of ZnO/MnO 2 nanocomposite, respectively. This is the first full explanation of the ZnO/MnO 2 nanocomposite bio-fabrication at a semi-industrial scale employing endophytic strain E72 extract as a reducing/capping agent that reacted with MnCl 2 ·4H 2 O and Zn (CH 3 COO) 2 ·2H 2 O as precursors. This bio-fabricated ZnO/MnO 2 nanocomposite has the potential to be utilized in the development of pharmaceuticals, cosmetics, wound dressings, and burn therapy due to its powerful antimicrobial capabilities. Streptomyces coelicolor ; Nanocomposite ; Fabrication ; Characterization (materials science) ; Materials science ; Antimicrobial ; Fermentation ; Streptomyces ; Nanotechnology ; Chemistry ; Food science ; Bacteria ; Biology ; Organic chemistry Nanoparticles: synthesis and applications ; Bone Tissue Engineering Materials ; Graphene and Nanomaterials Applications
Authors: Ming-Yen Tsai | Li‐Chiang Lin
Source: The Journal of Physical Chemistry B (article, 2024-08-26)
Field: Chemistry — Inorganic Chemistry

Pervaporation Separation of Isopropanol/Water Using Zeolite Nanosheets: A Molecular Simulation Study Reducing greenhouse gas emissions plays a crucial role in slowing down the rise of the global temperature. One of the viable options is to employ renewable energy sources such as alcohols that can be produced from biomass. Specifically, one of the most common alcohols is isopropanol (IPA). Energy-intensive distillation processes are however involved in its production because of the rather low product concentration from fermentation. Membrane technologies, specifically pervaporation (PV), represent a promising alternative to the IPA/water separation. Particularly, employing zeolite nanosheets as PV membranes may provide great opportunities to extract IPA owing to their ultrathin and hydrophobic nature. By employing molecular dynamics simulations, this study conducts a systematic study on a diverse set of nanosheet candidates with the aim of exploring their potential and identifying top-performing structures. The best candidate among structures studied herein is predicted to offer an exceptional IPA/water selectivity of more than 400 with an unprecedentedly large flux. Structure-property-performance relationships have also been established to offer insights into the rational design of PV membranes with improved performance. Pervaporation ; Zeolite ; Separation (statistics) ; Chemical engineering ; Materials science ; Membrane ; Chromatography ; Chemistry ; Organic chemistry ; Computer science ; Catalysis ; Engineering Zeolite Catalysis and Synthesis ; Membrane Separation and Gas Transport ; Ammonia Synthesis and Nitrogen Reduction
Authors: Hong Liu | Honggao Liu | Jieqing Li | Yuanzhong Wang
Source: Journal of Chemometrics (article, 2024-07-03)
Field: Chemistry — Analytical Chemistry

ATR‐FTIR Spectroscopy Preprocessing Technique Selection for Identification of Geographical Origins of <i>Gastrodia elata</i> Blume ABSTRACT Gastrodia elata Blume from different regions varies in growth conditions, soil types, and climate, which directly affects the content and quality of its medicinal components. Accurately identifying the origin can effectively ensure the medicinal value of G. elata Bl., prevent the circulation of counterfeit products, and thus protect the interests and health of consumers. Attenuated total reflectance Fourier transform infrared (ATR‐FTIR) spectroscopy is a rapid and effective method for verifying the authenticity of traditional Chinese medicines. However, the presence of scattering effects in the spectra poses challenges in establishing reliable discrimination models. Therefore, employing appropriate scattering correction techniques is crucial for improving the quality of spectral data and the accuracy of discrimination models. This study uses two ensemble preprocessing approaches; the first type is series fusion of scatter correction technologies (SCSF), and another method is sequential preprocessing through orthogonalization (SPORT). Four discriminant models were established using a single scattering correction technique and two ensemble preprocessing approaches. The results show that the data‐driven version of the soft independent modeling of class analogy (DD‐SIMCA) model built based on multiplicative scatter correction (MSC) preprocessing has a sensitivity of 0.98 and a specificity of 0.91, able to effectively distinguish whether a sample of G. elata Bl. originates from Zhaotong. In addition, three discriminant models including support vector machine (SVM), partial least squares discriminant analysis (PLS‐DA), and three gradient boosting machine (GBM) algorithms built using the ensemble preprocessing approach have good classification and generalization capabilities. Among them, the SCSF‐PLS‐DA model has the best performance with 99.68% and 98.08% accuracy for the training and test sets, respectively, and F1 of 0.97; the SPORT‐SVM model achieved the second‐best classification ability. The results show that the ensemble preprocessing approach used can improve the success rate of G. elata Bl. geographical origin classification. Artificial intelligence ; Linear discriminant analysis ; Preprocessor ; Pattern recognition (psychology) ; Data pre-processing ; Computer science ; Extreme learning machine ; Partial least squares regression ; Support vector machine ; Mathematics ; Biological system ; Machine learning ; Artificial neural network ; Biology Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research ; Metabolomics and Mass Spectrometry Studies
Authors: Yuchen Fu | Zhiyong Li | Sai Zhao | Honghao Hou | Yu Chai
Source: Science Advances (article, 2024-04-24)
Field: Materials Science — Materials Chemistry

Reconfigurable aqueous 3D printing with adaptive dual locks Using aqueous two-phase systems (ATPSs) for three-dimensional (3D) printed complex structures has attracted considerable attention in the field of biomedicine. In this study, we present an unusual approach to constructing reconfigurable 3D printed structures within an aqueous environment. Inspired by biological systems, we introduce both specific and nonspecific interactions to anchor functionalized nanoparticles to the water-water interface, thereby imparting adaptive dual locks of structural integrity and permeability to the 3D printed liquid structures. Using state-of-the-art in situ liquid-liquid interfacial atomic force microscopy imaging, we successfully demonstrate various morphologies of interfacial films formed at the ATPS interface. In addition, by incorporating d -glucose or sodium alginate into the systems, the dual locks can be easily manipulated. Our study paves a pathway for 3D printing multiresponsive all-aqueous systems with controllable structures and permeability, showing promising implications for the development of smart drug delivery systems and in vivo reactions. Aqueous solution ; Nanotechnology ; Materials science ; Aqueous two-phase system ; 3d printed ; Computer science ; 3D printing ; Nanoparticle ; Drug delivery ; Chemistry ; Biomedical engineering ; Organic chemistry Pickering emulsions and particle stabilization ; Electrostatics and Colloid Interactions ; Polymer Surface Interaction Studies