jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: A. Krishna | Tran Doan Huan | Chaofan Huang | Rampi Ramprasad | V. Roshan Joseph
Source: INFORMS Journal on Data Science (article, 2023-04-10)
Field: Materials Science — Materials Chemistry

Adaptive Exploration and Optimization of Materials Crystal Structures A central problem of materials science is to determine whether a hypothetical material is stable without being synthesized, which is mathematically equivalent to a global optimization problem on a highly nonlinear and multimodal potential energy surface (PES). This optimization problem poses multiple outstanding challenges, including the exceedingly high dimensionality of the PES, and that PES must be constructed from a reliable, sophisticated, parameters-free, and thus very expensive computational method, for which density functional theory (DFT) is an example. DFT is a quantum mechanics-based method that can predict, among other things, the total potential energy of a given configuration of atoms. DFT, although accurate, is computationally expensive. In this work, we propose a novel expansion-exploration-exploitation framework to find the global minimum of the PES. Starting from a few atomic configurations, this “known” space is expanded to construct a big candidate set. The expansion begins in a nonadaptive manner, where new configurations are added without their potential energy being considered. A novel feature of this step is that it tends to generate a space-filling design without the knowledge of the boundaries of the domain space. If needed, the nonadaptive expansion of the space of configurations is followed by adaptive expansion, where “promising regions” of the domain space (those with low-energy configurations) are further expanded. Once a candidate set of configurations is obtained, it is simultaneously explored and exploited using Bayesian optimization to find the global minimum. The methodology is demonstrated using a problem of finding the most stable crystal structure of aluminum. History: Kwok Tsui served as the senior editor for this article. Funding: The authors acknowledge a U.S. National Science Foundation Grant DMREF-1921873 and XSEDE through Grant DMR170031. Data Ethics &amp; Reproducibility Note: The code capsule is available on Code Ocean at https://doi.org/10.24433/CO.3366149.v1 and in the e-Companion to this article (available at https://doi.org/10.1287/ijds.2023.0028 ). Materials science ; Geology ; Computer science ; Nanotechnology Machine Learning in Materials Science ; X-ray Diffraction in Crystallography ; Crystallization and Solubility Studies
Authors: Qinshu Li | Fang Liu | Yizhe Liu | Tao Wang | Xinqiang Wang | Bo Sun
Source: Journal of Applied Physics (article, 2023-12-18)
Field: Materials Science — Materials Chemistry

Effect of the alloyed interlayer on the thermal conductance of Al/GaN interface Understanding the interfacial phonon transport is essential for optimizing the thermal management of microelectronics, especially for high energy density devices. Some calculations have suggested that introducing interfacial defects or disorders will increase the interfacial thermal conductance, which helps heat dissipation, while some studies suggested otherwise. In this work, we introduced substitutional impurities in GaN by growing a ∼2-nm-thick AlxGa1−xN or InxGa1−xN alloyed interlayer at the Al/GaN interface and measured the interface thermal conductance by time-domain thermoreflectance at room temperature. Our results show that substituting Ga atoms near the interface with either lighter Al atoms or heavier In atoms at a nominal concentration of 20% or less will not necessarily change the thermal conductance of the Al/alloy interface but is detrimental to the thermal transport across the total Al/GaN interface, which provides an experimental guideline for the thermal design of GaN-based devices. Microelectronics ; Materials science ; Thermal conductivity ; Phonon ; Conductance ; Impurity ; Thermal ; Condensed matter physics ; Work (physics) ; Wide-bandgap semiconductor ; Alloy ; Optoelectronics ; Thermodynamics ; Composite material ; Chemistry Thermal properties of materials ; GaN-based semiconductor devices and materials ; Silicon Carbide Semiconductor Technologies
Authors: Anthi Petrou | Athina Geronikaki | В. Г. Карцев | Antonios Kousaxidis | Aliki Papadimitriou‐Tsantarliotou | Marina Kostić | Marija Ivanov | Marina Sokóvić | Ioannis Nicolaou | Ioannis S. Vizirianakis
Source: Pharmaceuticals (article, 2023-01-16)
Field: Chemistry — Organic Chemistry

N-Derivatives of (Z)-Methyl 3-(4-Oxo-2-thioxothiazolidin-5-ylidene)methyl)-1H-indole-2-carboxylates as Antimicrobial Agents—In Silico and In Vitro Evaluation Herein, we report the experimental evaluation of the antimicrobial activity of seventeen new (<i>Z</i>)-methyl 3-(4-oxo-2-thioxothiazolidin-5-ylidene)methyl)-1<i>H</i>-indole-2-carboxylate derivatives. All tested compounds exhibited antibacterial activity against eight Gram-positive and Gram-negative bacteria. Their activity exceeded those of ampicillin as well as streptomycin by 10-50 fold. The most sensitive bacterium was <i>En. Cloacae</i>, while <i>E. coli</i> was the most resistant one, followed by <i>M. flavus.</i> The most active compound appeared to be compound <b>8</b> with MIC at 0.004-0.03 mg/mL and MBC at 0.008-0.06 mg/mL. The antifungal activity of tested compounds was good to excellent with MIC in the range of 0.004-0.06 mg/mL, with compound <b>15</b> being the most potent. <i>T. viride</i> was the most sensitive fungal, while <i>A. fumigatus</i> was the most resistant one. Docking studies revealed that the inhibition of <i>E. coli</i> MurB is probably responsible for their antibacterial activity, while 14a-lanosterol demethylase of CYP51Ca is involved in the mechanism of antifungal activity. Furthermore, drug-likeness and ADMET profile prediction were performed. Finally, the cytotoxicity studies were performed for the most active compounds using MTT assay against normal MRC5 cells. Antimicrobial ; Chemistry ; Antibacterial activity ; Cytotoxicity ; Lanosterol ; Stereochemistry ; Microbiology ; In vitro ; Bacteria ; Biochemistry ; Organic chemistry ; Biology ; Sterol Synthesis and biological activity ; Multicomponent Synthesis of Heterocycles ; Quinazolinone synthesis and applications
Authors: Saeed Reza Hormozi Jangi
Source: Petroleum and Chemical Industry International (review, 2023-11-28)
Field: Materials Science — Materials Chemistry

Detection Mechanism and Principles of the Multinanozyme Systems as the New Generation of Nanozyme-Mediated Sensing Assays: A Critical Review Nanozymes are defined as nanoscale materials with enzyme-like properties. Due to their higher stability and lower cost than native enzymes, nanozymatic systems have been utilized for several practical applications, especially for sensing and detection. Most of the common nanozymatic sensors are single-nanozyme-based systems, however, recently a new generation of nanozyme-based systems called “multinanozyme system’ was introduced by Hormozi Jangi et al. (2020). Since the first report of multinanozyme systems, several multinanozyme systems have been developed and utilized for highly sensitive and selective sensing aims. The main advantages of multinanozyme systems compared of common singlenanozymatic sensors are their impact on simultaneous enhancing selectivity and sensitivity of detection systems along with improving the kinetics performances of system via applying two nanozymes with identical enzyme mimic activity (e.g., two peroxidase mimics) in a well-designed detection process. Since, the principles of design and detection mechanism of this new generation is not well-described in the literature, the aim of this article is the fast review of the principles of design of this new generation of nanozyme-based sensing and detection. Besides, the mechanism of the multinanozyme detection system was also described and reviewed. Computer science ; Nanotechnology ; Mechanism (biology) ; Biochemical engineering ; Process (computing) ; Materials science ; Engineering ; Physics Advanced Nanomaterials in Catalysis ; Advanced biosensing and bioanalysis techniques ; Biosensors and Analytical Detection
Authors: Yuri A. Vorotnikov | Natalya A. Vorotnikova | Michael A. Shestopalov
Source: Materials (review, 2023-08-27)
Field: Materials Science — Materials Chemistry

Silica-Based Materials Containing Inorganic Red/NIR Emitters and Their Application in Biomedicine The low absorption of biological substances and living tissues in the red/near-infrared region (therapeutic window) makes luminophores emitting in the range of ~650-1350 nm favorable for in vitro and in vivo imaging. In contrast to commonly used organic dyes, inorganic red/NIR emitters, including ruthenium complexes, quantum dots, lanthanide compounds, and octahedral cluster complexes of molybdenum and tungsten, not only exhibit excellent emission in the desired region but also possess additional functional properties, such as photosensitization of the singlet oxygen generation process, upconversion luminescence, photoactivated effects, and so on. However, despite their outstanding functional applicability, they share the same drawback-instability in aqueous media under physiological conditions, especially without additional modifications. One of the most effective and thus widely used types of modification is incorporation into silica, which is (1) easy to obtain, (2) biocompatible, and (3) non-toxic. In addition, the variety of morphological characteristics, along with simple surface modification, provides room for creativity in the development of various multifunctional diagnostic/therapeutic platforms. In this review, we have highlighted biomedical applications of silica-based materials containing red/NIR-emitting compounds. Materials science ; Photon upconversion ; Nanotechnology ; Biological imaging ; Luminescence ; Biocompatibility ; Singlet oxygen ; Biocompatible material ; Surface modification ; Ruthenium ; Lanthanide ; Chemical engineering ; Chemistry ; Fluorescence ; Optoelectronics ; Oxygen ; Catalysis ; Organic chemistry Lanthanide and Transition Metal Complexes ; Nanocluster Synthesis and Applications ; Nanoplatforms for cancer theranostics
Authors: Janeth Arias Guadalupe | Dorin Copaci | Paloma Mansilla Navarro | Luís Moreno | Dolores Blanco
Source: Mechatronics (article, 2023-02-06)
Field: Materials Science — Materials Chemistry

A novel multi-wire SMA-based actuator with high-frequency displacement Shape Memory Alloys (SMA) are a group of metallic alloys that can return to their original shape when subjected to a temperature transformation between two phases. SMAs have been used as an alternative solution to conventional actuators in different applications of the robotics, biomedical, aerospace and automation domains because of their characteristics; being one of the leading solutions in different fields such as soft robotics and bio-inspired mechanisms. However, these actuators are still limited due to their operating frequency, their electrical efficiency, and their control performance due to their non-linearities. This paper presents a new multi-wire actuator structure based on SMA, with two different activation strategies. By combining the use of a multi-wire SMA in an alternative way, the overall recovery time is reduced. Thus, higher frequencies can be achieved in the reference signal. In this study, the effect of the diameter, geometry and activation temperature of the wires is evaluated in two different configurations. Firstly, when the actuator produces a linear displacement and, secondly, in an antagonistic configuration where the final displacement is a rotating movement. The results prove that the operating frequency of the multi-wire actuator increases considerably, when compared to the configuration where only one SMA wire is used. Moreover, it can be stated that the performance of the actuator improves when using wires with a thinner diameter and a higher activation temperature, with weights closer to the maximum force supported and a geometrical disposition of the wires that brings them as close as possible. Actuator ; SMA* ; Shape-memory alloy ; Displacement (psychology) ; Robotics ; Soft robotics ; Mechanical engineering ; Control theory (sociology) ; Materials science ; Transformation (genetics) ; Acoustics ; Computer science ; Engineering ; Robot ; Artificial intelligence ; Physics ; Algorithm Shape Memory Alloy Transformations
Authors: Graciela Granados-Guzmán | Mónica Díaz-Hernández | Rocío Álvarez-Román | Norma Cavazos-Rocha | Omar J. Portillo-Castillo
Source: Reviews in Analytical Chemistry (review, 2023-01-01)
Field: Chemistry — Analytical Chemistry

A brief review of the application of microextraction by packed sorbent for antibiotics analysis from biological, food, and environmental samples Abstract Currently, sample preparation is the most laborious part of the analytical process, requiring the most time and being susceptible to the most errors. In this context, numerous investigations have focused on the miniaturization of these techniques to reduce work time, costs, and errors. In this regard, microextraction by packed sorbent (MEPS) is a simple, fast, and robust sample preparation technique suitable for easy automation in several analytical systems and is applied to a wide variety of samples. Antibiotics are among the most commonly used drugs; however, their extensive and inappropriate use has garnered significant attention in the environment, human health, and food safety. This brief review is intended to provide an overview of recently reported antibiotic extraction methods based on MEPS, with a special interest in those applied to the analysis of biological, environmental, and food samples. In addition, the sample pretreatment step before extraction by the MEPS device was highlighted, as was the description of the sample-related steps within the MEPS procedure, such as extraction, washing, and elution. Sample preparation ; Context (archaeology) ; Extraction (chemistry) ; Sorbent ; Chromatography ; Computer science ; Process engineering ; Sample (material) ; Biochemical engineering ; Chemistry ; Adsorption ; Engineering Analytical chemistry methods development ; Pharmaceutical and Antibiotic Environmental Impacts ; Biosensors and Analytical Detection
Authors: Gwenyth Newman | Audrey Leclerc | William Arditi | Silvia Tea Calzuola | Thomas Feaugas | Emmanuel Roy | Cécile M. Perrault | Constance Porrini | Mikhaël Bechelany
Source: Frontiers in Bioengineering and Biotechnology (review, 2023-08-17)
Field: Materials Science — Surfaces, Coatings and Films

Challenge of material haemocompatibility for microfluidic blood-contacting applications Biological applications of microfluidics technology is beginning to expand beyond the original focus of diagnostics, analytics and organ-on-chip devices. There is a growing interest in the development of microfluidic devices for therapeutic treatments, such as extra-corporeal haemodialysis and oxygenation. However, the great potential in this area comes with great challenges. Haemocompatibility of materials has long been a concern for blood-contacting medical devices, and microfluidic devices are no exception. The small channel size, high surface area to volume ratio and dynamic conditions integral to microchannels contribute to the blood-material interactions. This review will begin by describing features of microfluidic technology with a focus on blood-contacting applications. Material haemocompatibility will be discussed in the context of interactions with blood components, from the initial absorption of plasma proteins to the activation of cells and factors, and the contribution of these interactions to the coagulation cascade and thrombogenesis. Reference will be made to the testing requirements for medical devices in contact with blood, set out by International Standards in ISO 10993-4. Finally, we will review the techniques for improving microfluidic channel haemocompatibility through material surface modifications—including bioactive and biopassive coatings—and future directions. Microfluidics ; Nanotechnology ; Context (archaeology) ; Computer science ; Materials science Polymer Surface Interaction Studies ; Electrospun Nanofibers in Biomedical Applications ; 3D Printing in Biomedical Research
Authors: Zaida Ortega | Paula Douglas | Paul R. Hanna | Jake Kelly-Walley | Mark McCourt
Source: Composites Communications (article, 2023-12-20)
Field: Materials Science — Polymers and Plastics

Influence of mold pressurization on cycle time in rotational molding composites with welded ignimbrite as loading In the context of rising energy costs and climate emergencies, there is a need to incorporate novel procedures or materials to meet sustainability requirements and increase the efficiency of processes and use of resources. Although rotational molding might seem disadvantageous due to the long cycle times and high energy consumption, its inherent advantages, including the production of hollow parts of any size without wasting materials, with good surface reproducibility and no internal stresses, using cost-effective tooling remain noteworthy. To address energy consumption concerns, increase productivity, and enhance the environmental footprint of rotomolded products, this work proposes the incorporation of residual welded ignimbrite from quarries, a dusty material with over 60 % of SiO2, combined with the mold pressurization, finding a 4 % reduction of total cycle time with ignimbrite, which is further shortened to 12 % when pressure is applied. Particularly notable is the reduction 27 % reduction in oven time when using ignimbrite at 10 % under pressure. The thermomechanical and rheological characterizations revealno adverse effects either by the use of pressure or the mineral dust, thus establishing a viable alternative for energy (and cost) reduction. Besides, the obtained parts show good aesthetics, a stone-like aspect, which might provide additional features for applications such as outdoor furniture or storage tanks. Cabin pressurization ; Energy consumption ; Materials science ; Molding (decorative) ; Context (archaeology) ; Sustainability ; Welding ; Reduction (mathematics) ; Cost reduction ; Charring ; Composite material ; Raw material ; Carbon footprint ; Environmental science ; Mold ; Life-cycle assessment ; Work (physics) ; Waste management ; Mechanical engineering ; Production (economics) ; Engineering ; Greenhouse gas ; Geology Polymer Foaming and Composites ; biodegradable polymer synthesis and properties ; Advanced Materials and Mechanics
Authors: Jake Kline | Rafael D. Melani | Luca Fornelli
Source: International Journal of Mass Spectrometry (article, 2023-08-17)
Field: Chemistry — Spectroscopy

Mass spectrometry characterization of antibodies at the intact and subunit levels: From targeted to large-scale analysis Antibody ; Chemistry ; Monoclonal antibody ; Computational biology ; Epitope ; Mass spectrometry ; Characterization (materials science) ; Antigen ; Nanotechnology ; Immunology ; Chromatography ; Biology Mass Spectrometry Techniques and Applications ; Monoclonal and Polyclonal Antibodies Research ; Protein purification and stability
Authors: Leena R. Pade | Camille Lombard‐Banek | Jie Li | Péter Nemes
Source: Journal of Proteome Research (article, 2023-11-23)
Field: Chemistry — Spectroscopy

Dilute to Enrich for Deeper Proteomics: A Yolk-Depleted Carrier for Limited Populations of Embryonic (Frog) Cells Abundant proteins challenge deep mass spectrometry (MS) analysis of the proteome. Yolk, the source of food in many developing vertebrate embryos, complicates chemical separation and interferes with detection. We report here a strategy that enhances bottom-up proteomics in yolk-laden specimens by diluting the interferences using a yolk-depleted carrier (YODEC) proteome via isobaric multiplexing quantification. This method was tested on embryos of the South African Clawed Frog (<i>Xenopus laevis</i>), where a >90% yolk proteome content challenges deep proteomics. As a proof of concept, we isolated neural and epidermal fated cell clones from the embryo by dissection or fluorescence-activated cell sorting. Compared with the standard multiplexing carrier approach, YODEC more than doubled the detectable <i>X. laevis</i> proteome, identifying 5,218 proteins from D11 cell clones dissected from the embryo. Ca. ∼80% of the proteins were quantified without dropouts in any of the analytical channels. YODEC with high-pH fractionation quantified 3,133 proteins from ∼8,000 V11 cells that were sorted from ca. 2 embryos (1.5 μg total, or 150 ng yolk-free proteome), marking a 15-fold improvement in proteome coverage vs the standard proteomics approach. About 60% of these proteins were only quantifiable by YODEC, including molecular adaptors, transporters, translation, and transcription factors. While this study was tailored to limited populations of <i>Xenopus</i> cells, we anticipate the approach of "dilute to enrich" using a depleted carrier proteome to be adaptable to other biological models in which abundant proteins challenge deep MS proteomics. Yolk ; Embryonic stem cell ; Yolk sac ; Biology ; Proteomics ; Cell biology ; Chemistry ; Embryo ; Ecology ; Biochemistry Advanced Proteomics Techniques and Applications ; Advanced Biosensing Techniques and Applications ; Cell Image Analysis Techniques
Authors: Haiping Zhong | Xingwei Li | Na Yu | Xi Zhang | Jingqing Mu | Tao Liu | Bo Yuan | Xiaoyong Yuan | Shutao Guo
Source: Chemical Science (article, 2023-01-01)
Field: Materials Science — Biomaterials

Fine-tuning the sequential drug release of nano-formulated mutual prodrugs dictates the combination effects The maintenance of robust ratiometric loading of dual therapeutic agents and fine-tuning release kinetics for consistent <i>in vitro</i> and <i>in vivo</i> optimization of combination effects is vital for discovering new anticancer drug combinations and remains challenging. Smart nanomedicine strategies have been investigated for this purpose, but most of the reported strategies focus either on ratiometric delivery or on unimodal sequential release of the two different agents, which hampers effective optimization of combination effects. Herein we report a sequential drug release system based on nanoformulated mutual prodrugs constructed by the formation of ketal linkages with different acid sensitivities, thus enabling the acid-triggered release of two anticancer drugs, paclitaxel and gemcitabine, in various sequences. We found that in several cell lines, the sequence of drug release substantially affected the combination effects; specifically, in A549 cells, time-staggered release profiles showed enhanced synergistic effects relative to those of a simultaneous release profile. Moreover, <i>in vivo</i> assessment of the antitumor efficacy of the nanoformulations in A549 xenograft models indicated that the best therapeutic effects were obtained with time-staggered release profiles, which was consistent with the <i>in vitro</i> results. Our strategy for precisely controlled sequential drug release can be expected to facilitate the screening of optimal drug combinations and maximize combination effects both <i>in vitro</i> and <i>in vivo</i>. Prodrug ; Nano- ; Drug ; Nanotechnology ; Chemistry ; Computer science ; Combinatorial chemistry ; Pharmacology ; Materials science ; Medicine ; Biochemistry Nanoparticle-Based Drug Delivery ; Advanced Drug Delivery Systems ; Drug Solubulity and Delivery Systems
Authors: Jaydeep Thik | Siwen Wang | Chuhong Wang | Hadi Mansourifar | Honghong Lin | Keiichi Okubo | Chen Ling
Source: Journal of Materials Chemistry A (article, 2023-01-01)
Field: Materials Science — Materials Chemistry

Realizing the cooking recipe of materials synthesis through large language models LLMs offer a promising and viable direction to convert materials synthesis descriptions into recipe-like outputs effectively preserving the order of synthesis steps. LLMs show true potential to guide experimental design using materials literature. Recipe ; Order (exchange) ; Computer science ; Biochemical engineering ; Engineering ; Business ; History Machine Learning in Materials Science ; Material Selection and Properties