jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Levente M. Mihalovits | György G. Ferenczy | György M. Keserű
Source: International Journal of Quantum Chemistry (article, 2021-07-15)
Field: Materials Science — Materials Chemistry

The role of quantum chemistry in covalent inhibitor design Abstract The recent ascent of targeted covalent inhibitors (TCI) in drug discovery brings new opportunities and challenges to quantum chemical reactivity calculations supporting discovery efforts. TCIs typically form a covalent bond with the targeted nucleophilic amino acid side chain. Their reactivity that can be both computed and experimentally measured is therefore one of the key factors in determining inhibitory potency. Calculation of relevant quantum chemical descriptors and corresponding reaction barriers of model reactions represent efficient ways to predict intrinsic reactivities of covalent ligands. A more comprehensive description of covalent ligand binding is offered by mixed quantum mechanical/molecular mechanical (QM/MM) potentials. Reaction mechanisms can be investigated by the exploration of the potential energy surface as a function of suitable reaction coordinates, and free energy surfaces can also be calculated with molecular dynamics based simulations. Here we review the methodological aspects and discuss applications with primary focus on high‐end QM/MM simulations to illustrate the current status of quantum chemical support to covalent inhibitor design. Available QM approaches are suitable to identify likely reaction mechanisms and rate determining steps in the binding of covalent inhibitors. The efficient QM/MM prediction of ligand reactivities complemented with the computational description of the recognition step makes these computations highly useful in covalent drug discovery. Covalent bond ; Chemistry ; QM/MM ; Computational chemistry ; Reactivity (psychology) ; Quantum chemistry ; Drug discovery ; Potential energy surface ; Ligand (biochemistry) ; Reaction coordinate ; Quantum ; Nucleophile ; Dynamic covalent chemistry ; Molecular dynamics ; Combinatorial chemistry ; Nanotechnology ; Chemical physics ; Molecule ; Materials science ; Physics ; Quantum mechanics ; Organic chemistry ; Supramolecular chemistry Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Click Chemistry and Applications
Authors: Lorenzo Cotrozzi
Source: Journal of Forestry Research (review, 2021-08-14)
Field: Chemistry — Analytical Chemistry

Spectroscopic detection of forest diseases: a review (1970–2020) Abstract Sustainable forest management is essential to confront the detrimental impacts of diseases on forest ecosystems. This review highlights the potential of vegetation spectroscopy in improving the feasibility of assessing forest disturbances induced by diseases in a timely and cost-effective manner. The basic concepts of vegetation spectroscopy and its application in phytopathology are first outlined then the literature on the topic is discussed. Using several optical sensors from leaf to landscape-level, a number of forest diseases characterized by variable pathogenic processes have been detected, identified and quantified in many country sites worldwide. Overall, these reviewed studies have pointed out the green and red regions of the visible spectrum, the red-edge and the early near-infrared as the spectral regions most sensitive to the disease development as they are mostly related to chlorophyll changes and symptom development. Late disease conditions particularly affect the shortwave-infrared region, mostly related to water content. This review also highlights some major issues to be addressed such as the need to explore other major forest diseases and geographic areas, to further develop hyperspectral sensors for early detection and discrimination of forest disturbances, to improve devices for remote sensing, to implement long-term monitoring, and to advance algorithms for exploitation of spectral data. Achieving of these goals will enhance the capability of vegetation spectroscopy in early detection of forest stress and in managing forest diseases. Hyperspectral imaging ; Vegetation (pathology) ; Remote sensing ; Environmental science ; Forest ecology ; Red edge ; Environmental resource management ; Sustainable forest management ; Agroforestry ; Forest management ; Ecosystem ; Geography ; Ecology ; Biology ; Medicine Spectroscopy and Chemometric Analyses ; Remote Sensing in Agriculture ; Essential Oils and Antimicrobial Activity
Authors: V. L. Okulov | I. K. Kabardin | D. G. Mukhin | К. И. Степанов | Nastasia Okulova
Source: Energies (article, 2021-10-16)
Field: Materials Science — Surfaces, Coatings and Films

Physical De-Icing Techniques for Wind Turbine Blades The review reflects physical solutions for de-icing, one of the main problems that impedes the efficient use of wind turbines for autonomous energy resources in cold regions. This topic is currently very relevant for ensuring the dynamic development of wind energy in the Arctic. The review discusses an effective anti-icing strategy for wind turbine blades, including various passive and active physical de-icing techniques using superhydrophobic coatings, thermal heaters, ultrasonic and vibration devices, operating control to determine the optimal methods and their combinations. After a brief description of the active methods, the energy consumption required for their realization is estimated. Passive methods do not involve extra costs, so the review focuses on the most promising solutions with superhydrophobic coatings. Among them, special attention is paid to plastic coatings with a lithographic method of applying micro and nanostructures. This review is of interest to researchers who develop new effective solutions for protection against icing, in particular, when choosing systems for protecting wind turbines. Icing ; Wind power ; Turbine ; Energy consumption ; Marine engineering ; Engineering ; Computer science ; Automotive engineering ; Mechanical engineering ; Environmental science ; Meteorology ; Electrical engineering Surface Modification and Superhydrophobicity ; Icing and De-icing Technologies ; Fluid Dynamics and Heat Transfer
Authors: Xihu Yang | Xiaowei Song | Xiaoxin Zhang | Vishnu Shankar | Shuai Wang | Yan Yang | Sheng Chen | Lei Zhang | Yanhong Ni | Richard N. Zare | Qingang Hu
Source: EBioMedicine (article, 2021-08-01)
Field: Chemistry — Spectroscopy

In situ DESI-MSI lipidomic profiles of mucosal margin of oral squamous cell carcinoma This study was supported by Nanjing Municipal Key Medical Laboratory Constructional Project Funding (since 2016) and the Centre of Nanjing Clinical Medicine Tumour (since 2014). Lasso (programming language) ; Surgical margin ; H&E stain ; Medicine ; Margin (machine learning) ; Pathology ; Staining ; Resection ; Surgery ; Computer science ; Machine learning Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Jiashuai Xu | Wenwen Liu | Zhengyong Song
Source: IEEE photonics journal (article, 2021-07-26)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Terahertz Dynamic Beam Steering Based on Graphene Coding Metasurfaces Coding metasurfaces incorporated with reconfigurable elements can dynamically control electromagnetic waves to realize reconfigurable multiple functionalities. The mostly existing active devices usually work in microwave band and have little ability to dynamically control terahertz waves. Here, a graphene-based coding metasurface (GBCM) is presented to realize dynamic beam steering for terahertz waves. The coding state “1” of the proposed GBCM can be continuously tuned to “0” by Fermi level of an integral graphene film. In order to verify the working principle, two examples are designed to demonstrate the dynamic tunability of the proposed GBCM for terahertz waves. One is dynamic multi-beam switching and another is dynamic diffusion switching. Under the normal illumination of terahertz waves, a 1D periodic-sequence GBCM produces dual-, tri- and single-beam by setting Fermi level as 0.05 eV, 0.15 eV and 0.70 eV, respectively. Similarly, a 2D periodic-sequence GBCM produces quad-, penta- and single-beam by setting Fermi level as 0.05 eV, 0.11 eV and 0.70 eV, respectively. In the case of aperiodic coding sequence, reflected waves can be dynamically switched from diffusion to mirror reflection by increasing Fermi level from 0.05 eV to 0.70 eV. The above functionalities are well verified by theoretical calculations and numerical simulations. Terahertz radiation ; Graphene ; Fermi Gamma-ray Space Telescope ; Physics ; Optics ; Beam steering ; Coding (social sciences) ; Fermi level ; Optoelectronics ; Beam (structure) ; Condensed matter physics Metamaterials and Metasurfaces Applications ; Antenna Design and Analysis ; Advanced Antenna and Metasurface Technologies
Authors: Hui Li | Xingyu Yang | Yue Zhang | Zhiyan Gao | Yuting Liang | Jinming Chen | Tao Shi
Source: Scientific Data (article, 2021-01-29)
Field: Chemistry — Analytical Chemistry

Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera Sacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net ). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus. Lotus ; Germplasm ; Biology ; Genome ; Genomics ; Lotus japonicus ; Database ; Gene ; Genetics ; Botany Chromatography in Natural Products ; Phytochemical Studies and Bioactivities ; Genetic diversity and population structure
Authors: Syazwan Afif Mohd Zobir | Asgar Ali | Fariz Adzmi | Mohd Roslan Sulaiman | Khairulmazmi Ahmad
Source: Biology (review, 2021-10-21)
Field: Materials Science — Materials Chemistry

A Review on Nanopesticides for Plant Protection Synthesized Using the Supramolecular Chemistry of Layered Hydroxide Hosts The rapid growth in the human population has triggered increased demand for food supply, and in turn has prompted a higher amount of agrochemical usage to meet the gaps between food production and consumption. The problem with conventional agro-nanochemicals is the reduced effectiveness of the active ingredient in reaching the target, along with leaching, evaporation, etc., which ultimately affect the environment and life, including humans. Fortunately, nanotechnology platforms offer a new life for conventional pesticides, which improves bioavailability through different kinetics, mechanisms and pathways on their target organisms, thus enabling them to suitably bypass biological and other unwanted resistances and therefore increase their efficacy. This review is intended to serve the scientific community for research, development and innovation (RDI) purposes, by providing an overview on the current status of the host-guest supramolecular chemistry of nanopesticides, focusing on only the two-dimensional (2D), brucite-like inorganic layered hydroxides, layered hydroxide salts and layered double hydroxides as the functional nanocarriers or as the hosts in smart nanodelivery systems of pesticides for plant protection. Zinc layered hydroxides and zinc/aluminum-layered double hydroxides were found to be the most popular choices of hosts, presumably due to their relative ease to prepare and cheap cost. Other hosts including Mg/Al-, Co/Cr-, Mg/Fe-, Mg/Al/Fe-, Zn/Cr- and Zn/Cu-LDHs were also used. This review also covers various pesticides which were used as the guest active agents using supramolecular host-guest chemistry to combat various pests for plant protection. This looks towards a new generation of agrochemicals, "agro-nanochemicals", which are more effective, and friendly to life, humans and the environment. Layered double hydroxides ; Hydroxide ; Brucite ; Nanotechnology ; Supramolecular chemistry ; Population ; Nanocarriers ; Green chemistry ; Pesticide ; Materials science ; Biology ; Chemical engineering ; Drug delivery ; Chemistry ; Organic chemistry ; Ecology ; Metallurgy ; Magnesium Layered Double Hydroxides Synthesis and Applications ; Magnesium Oxide Properties and Applications ; Mesoporous Materials and Catalysis
Authors: Yinjuan Chen | Hongying Zhuo | Yuan Pan | Jinxia Liang | Chenguang Liu | Jun Li
Source: Science China Materials (article, 2021-05-18)
Field: Materials Science — Materials Chemistry

Triazine COF-supported single-atom catalyst (Pd1/trzn-COF) for CO oxidation Catalysis ; Heteroatom ; Materials science ; Triazine ; Imine ; Covalent organic framework ; Density functional theory ; Conjugated system ; Covalent bond ; Atom (system on chip) ; Nucleophile ; Ring (chemistry) ; Combinatorial chemistry ; Photochemistry ; Computational chemistry ; Polymer chemistry ; Organic chemistry ; Chemistry ; Polymer Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Catalytic Processes in Materials Science
Authors: Sabiha Sultana | Sriram Mansingh | Kulamani Parida
Source: Materials Advances (article, 2021-01-01)
Field: Materials Science — Materials Chemistry

Crystal facet and surface defect engineered low dimensional CeO<sub>2</sub>(0D, 1D, 2D) based photocatalytic materials towards energy generation and pollution abatement Low dimensional CeO 2 based photocatalytic systems for energy and environmental application. Photocatalysis ; Facet (psychology) ; Materials science ; Crystal (programming language) ; Pollution ; Environmental pollution ; Low energy ; Nanotechnology ; Chemical engineering ; Crystal growth ; Engineering physics ; Optoelectronics ; Environmental science ; Crystallography ; Chemistry ; Engineering ; Computer science ; Environmental protection ; Physics ; Catalysis Catalytic Processes in Materials Science ; Advanced Photocatalysis Techniques ; Copper-based nanomaterials and applications
Authors: Yifei Ding | Mohamed H. Hassan | Otto Jan Bakker | S. Hinduja | Paulo Bártolo
Source: Materials (review, 2021-07-28)
Field: Materials Science — Polymers and Plastics

A Review on Microcellular Injection Moulding Microcellular injection moulding (MuCell<sup>®</sup>) is a polymer processing technology that uses a supercritical fluid inert gas, CO<sub>2</sub> or N<sub>2</sub>, to produce light-weight products. Due to environmental pressures and the requirement of light-weight parts with good mechanical properties, this technology recently gained significant attention. However, poor surface appearance and limited mechanical properties still prevent the wide applications of this technique. This paper reviews the microcellular injection moulding process, main characteristics of the process, bubble nucleation and growth, and major recent developments in the field. Strategies to improve both the surface quality and mechanical properties are discussed in detail as well as the relationships between processing parameters, morphology, and surface and mechanical properties. Modelling approaches to simulate microcellular injection moulding and the mathematical models behind Moldex 3D and Moldflow, the two most commonly used software tools by industry and academia, are reviewed, and the main limitations are highlighted. Finally, future research perspectives to further develop this technology are also discussed. Injection moulding ; Materials science ; Supercritical fluid ; Mechanical engineering ; Process engineering ; Blowing agent ; Process (computing) ; Composite material ; Computer science ; Engineering ; Polyurethane Polymer Foaming and Composites ; Injection Molding Process and Properties ; Phase Equilibria and Thermodynamics
Authors: Mojtaba Barzegari | Di Mei | Sviatlana V. Lamaka | Liesbet Geris
Source: Corrosion Science (article, 2021-07-08)
Field: Materials Science — Biomaterials

Computational modeling of degradation process of biodegradable magnesium biomaterials Despite the advantages of using biodegradable metals in implant design, their uncontrolled degradation and release remain a challenge in practical applications. A validated computational model of the degradation process can facilitate tuning implant biodegradation properties. In this study, a mathematical model of the chemistry of magnesium biodegradation was developed and implemented in a 3D computational model. The parameters were calibrated by Bayesian optimization using dedicated experimental data. The model was validated by comparing the predicted and experimentally obtained pH change in saline and buffered solutions, showing maximum 5% of difference, demonstrating the model's validity to be used for practical cases. Biodegradation ; Degradation (telecommunications) ; Corrosion ; Magnesium ; Materials science ; Process (computing) ; Computational model ; Biological system ; Computer science ; Process engineering ; Chemistry ; Metallurgy ; Engineering ; Algorithm ; Organic chemistry Magnesium Alloys: Properties and Applications ; Corrosion Behavior and Inhibition ; Hydrogen Storage and Materials
Authors: Hsing-Ying Tsai | T. Fujita | Siqian Wang | Masanobu Naito
Source: Science and Technology of Advanced Materials (article, 2021-03-17)
Field: Materials Science — Polymers and Plastics

Environmentally friendly recycling system for epoxy resin with dynamic covalent bonding Recycling of epoxy resin and its composites is extremely difficult due to its thermoset nature. In this study, we proposed the environmentally-friendly recycling system of epoxy resin with dynamic covalent bonding in the assistance of cysteine-containing tripeptide, so-called glutathione. The glutathione attached on the epoxy resin and resulted in the cleavage of dynamic disulfide bonds of epoxy resin through thiol-disulfide exchange reaction between the thiol group of glutathione and disulfide bonding of epoxy resin, followed by the scission of epoxy networks. Therefore, the degraded epoxy residue was dissolved into chloroform. Finally, this resulting product could be reused as reagent for preparation the new epoxy materials with approximately 90% of initial mechanical strength via regeneration of disulfide bonding through heating. This work demonstrated the different aspect to understand the decomposition and recycling of thermosetting networks and the wide application under more environmentally friendly condition. Epoxy ; Thermosetting polymer ; Environmentally friendly ; Covalent bond ; Curing (chemistry) ; Materials science ; Reagent ; Gelcoat ; Polymer chemistry ; Organic chemistry ; Composite material ; Chemical engineering ; Chemistry Polymer composites and self-healing ; Photopolymerization techniques and applications ; Advanced Polymer Synthesis and Characterization
Authors: Alexandru B. Georgescu | Peiwen Ren | Aubrey R. Toland | Shengtong Zhang | Kyle D. Miller | Daniel W. Apley | Elsa Olivetti | Nicholas Wagner | James M. Rondinelli
Source: Chemistry of Materials (article, 2021-07-06)
Field: Materials Science — Materials Chemistry

Database, Features, and Machine Learning Model to Identify Thermally Driven Metal–Insulator Transition Compounds Metal-insulator transition (MIT) compounds are materials that may exhibit insulating or metallic behavior, depending on the physical conditions, and are of immense fundamental interest owing to their potential applications in emerging microelectronics. There is a dearth of thermally-driven MIT materials, however, which makes delineating these compounds from those that are exclusively insulating or metallic challenging. Here we report a material database comprising temperature-controlled MITs (and metals and insulators with similar chemical composition and stoichiometries to the MIT compounds) from high quality experimental literature, built through a combination of materials-domain knowledge and natural language processing. We featurize the dataset using compositional, structural, and energetic descriptors, including two MIT relevant energy scales, an estimated Hubbard interaction and the charge transfer energy, as well as the structure-bond-stress metric referred to as the global-instability index (GII). We then perform supervised classification, constructing three electronic-state classifiers: metal vs non-metal (M), insulator vs non-insulator (I), and MIT vs non-MIT (T). We identify two important descriptors that separate metals, insulators, and MIT materials in a 2D feature space: the average deviation of the covalent radius and the range of the Mendeleev number. We further elaborate on other important features (GII and Ewald energy), and examine how they affect classification of binary vanadium and titanium oxides. We discuss the relationship of these atomic features to the physical interactions underlying MITs in the rare-earth nickelate family. Last, we implement an online version of the classifiers, enabling quick probabilistic class predictions by uploading a crystallographic structure file. Materials science ; Atomic radius ; Database ; Topological insulator ; Computer science ; Chemical physics ; Chemistry ; Physics ; Condensed matter physics ; Quantum mechanics Machine Learning in Materials Science ; Electronic and Structural Properties of Oxides ; Catalysis and Oxidation Reactions
Authors: Christophe Furger
Source: Antioxidants (review, 2021-06-11)
Field: Chemistry — Organic Chemistry

Live Cell Assays for the Assessment of Antioxidant Activities of Plant Extracts Plant extracts and pharmacopoeias represent an exceptional breeding ground for the discovery of new antioxidants. Until recently, the antioxidant activity was only measured by chemical hydrogen atom transfer (HAT) and single-electron transfer (SET) cell-free assays that do not inform about the actual effect of antioxidants in living systems. By providing information about the mode of action of antioxidants at the subcellular level, recently developed live cell assays are now changing the game. The idea of this review is to present the different cell-based approaches allowing a quantitative measurement of antioxidant effects of plant extracts. Up to date, only four different approaches have reached a certain degree of standardization: (1) the catalase-like assay using H<sub>2</sub>O<sub>2</sub> as a stressor, (2) the cell antioxidant assay (CAA) using AAPH as a stressor and DCFH-DA as a readout, (3) the AOP1 assay which uses photoinduction to monitor and control cell ROS production, and (4) the Nrf2/ARE gene reporter system. The molecular aspects of these assays are presented in detail along with their features, drawbacks, and benefits. The Nrf2/ARE gene reporter system dedicated to indirect antioxidant effect measurement currently represents the most standardized approach with high-throughput applications. AOP1, the first technology linking a fine-tuning of cell ROS production with a quantitative signal, appears to be the most promising tool for the assessment of direct cellular ROS-scavenging effects at an industrial scale. Antioxidant ; Computational biology ; Chemistry ; Catalase ; Cell ; Plant cell ; Biotechnology ; Biochemistry ; Reporter gene ; Cell biology ; Biology ; Gene ; Gene expression Free Radicals and Antioxidants ; Genomics, phytochemicals, and oxidative stress ; Vitamin C and Antioxidants Research