jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Chenglong Lin | Yanyan Li | Yusi Peng | Shuai Zhao | Meimei Xu | Lingxia Zhang | Zhengren Huang | Jianlin Shi | Yong Yang
Source: Journal of Nanobiotechnology (review, 2023-05-06)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Recent development of surface-enhanced Raman scattering for biosensing Surface-Enhanced Raman Scattering (SERS) technology, as a powerful tool to identify molecular species by collecting molecular spectral signals at the single-molecule level, has achieved substantial progresses in the fields of environmental science, medical diagnosis, food safety, and biological analysis. As deepening research is delved into SERS sensing, more and more high-performance or multifunctional SERS substrate materials emerge, which are expected to push Raman sensing into more application fields. Especially in the field of biological analysis, intrinsic and extrinsic SERS sensing schemes have been widely used and explored due to their fast, sensitive and reliable advantages. Herein, recent developments of SERS substrates and their applications in biomolecular detection (SARS-CoV-2 virus, tumor etc.), biological imaging and pesticide detection are summarized. The SERS concepts (including its basic theory and sensing mechanism) and the important strategies (extending from nanomaterials with tunable shapes and nanostructures to surface bio-functionalization by modifying affinity groups or specific biomolecules) for improving SERS biosensing performance are comprehensively discussed. For data analysis and identification, the applications of machine learning methods and software acquisition sources in SERS biosensing and diagnosing are discussed in detail. In conclusion, the challenges and perspectives of SERS biosensing in the future are presented. Biosensor ; Nanotechnology ; Biomolecule ; Raman scattering ; Materials science ; Computer science ; Raman spectroscopy ; Physics Gold and Silver Nanoparticles Synthesis and Applications ; Advanced biosensing and bioanalysis techniques ; Biosensors and Analytical Detection
Authors: Judit Knisz | Richard B. Eckert | Lisa M. Gieg | Andrea Koerdt | Jaydie Lee | Elisabete R. Silva | Torben Lund Skovhus | B A An Stepec | Scott A. Wade
Source: FEMS Microbiology Reviews (review, 2023-07-11)
Field: Materials Science — Materials Chemistry

Microbiologically influenced corrosion—more than just microorganisms Microbiologically influenced corrosion (MIC) is a phenomenon of increasing concern that affects various materials and sectors of society. MIC describes the effects, often negative, that a material can experience due to the presence of microorganisms. Unfortunately, although several research groups and industrial actors worldwide have already addressed MIC, discussions are fragmented, while information sharing and willingness to reach out to other disciplines are limited. A truly interdisciplinary approach, which would be logical for this material/biology/chemistry-related challenge, is rarely taken. In this review, we highlight critical non-biological aspects of MIC that can sometimes be overlooked by microbiologists working on MIC but are highly relevant for an overall understanding of this phenomenon. Here, we identify gaps, methods, and approaches to help solve MIC-related challenges, with an emphasis on the MIC of metals. We also discuss the application of existing tools and approaches for managing MIC and propose ideas to promote an improved understanding of MIC. Furthermore, we highlight areas where the insights and expertise of microbiologists are needed to help progress this field. Microorganism ; Biology ; Corrosion ; Microbiology ; Bacteria ; Metallurgy ; Materials science ; Genetics Corrosion Behavior and Inhibition ; Marine Biology and Environmental Chemistry ; Bacterial biofilms and quorum sensing
Authors: Zhongwei Yang | Jiawei Guo | Longwei Wang | Jian Zhang | Longhua Ding | Hong Liu | Xin Yu
Source: Small (review, 2023-11-20)
Field: Materials Science — Materials Chemistry

Nanozyme‐Enhanced Electrochemical Biosensors: Mechanisms and Applications Nanozymes, as innovative materials, have demonstrated remarkable potential in the field of electrochemical biosensors. This article provides an overview of the mechanisms and extensive practical applications of nanozymes in electrochemical biosensors. First, the definition and characteristics of nanozymes are introduced, emphasizing their significant role in constructing efficient sensors. Subsequently, several common categories of nanozyme materials are delved into, including metal-based, carbon-based, metal-organic framework, and layered double hydroxide nanostructures, discussing their applications in electrochemical biosensors. Regarding their mechanisms, two key roles of nanozymes are particularly focused in electrochemical biosensors: selective enhancement and signal amplification, which crucially support the enhancement of sensor performance. In terms of practical applications, the widespread use of nanozyme-based electrochemical biosensors are showcased in various domains. From detecting biomolecules, pollutants, nucleic acids, proteins, to cells, providing robust means for high-sensitivity detection. Furthermore, insights into the future development of nanozyme-based electrochemical biosensors is provided, encompassing improvements and optimizations of nanozyme materials, innovative sensor design and integration, and the expansion of application fields through interdisciplinary collaboration. In conclusion, this article systematically presents the mechanisms and applications of nanozymes in electrochemical biosensors, offering valuable references and prospects for research and development in this field. Biosensor ; Nanotechnology ; Computer science ; Biomolecule ; Biochemical engineering ; Materials science ; Engineering Advanced Nanomaterials in Catalysis ; Nanocluster Synthesis and Applications ; Advanced biosensing and bioanalysis techniques
Authors: Kolja Stahl | Andrea Graziadei | Therese Dau | Oliver Brock | Juri Rappsilber
Source: Nature Biotechnology (article, 2023-03-20)
Field: Chemistry — Spectroscopy

Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning While AlphaFold2 can predict accurate protein structures from the primary sequence, challenges remain for proteins that undergo conformational changes or for which few homologous sequences are known. Here we introduce AlphaLink, a modified version of the AlphaFold2 algorithm that incorporates experimental distance restraint information into its network architecture. By employing sparse experimental contacts as anchor points, AlphaLink improves on the performance of AlphaFold2 in predicting challenging targets. We confirm this experimentally by using the noncanonical amino acid photo-leucine to obtain information on residue-residue contacts inside cells by crosslinking mass spectrometry. The program can predict distinct conformations of proteins on the basis of the distance restraints provided, demonstrating the value of experimental data in driving protein structure prediction. The noise-tolerant framework for integrating data in protein structure prediction presented here opens a path to accurate characterization of protein structures from in-cell data. Mass spectrometry ; Chemistry ; Chromatography Mass Spectrometry Techniques and Applications ; Advanced Proteomics Techniques and Applications ; Metabolomics and Mass Spectrometry Studies
Authors: Fei Pan | Kun Ni | Tao Xu | Huaican Chen | Yusong Wang | Ke Gong | Cai Liu | Xin Li | Miao‐Ling Lin | Shengyuan Li | Xia Wang | Wensheng Yan | Wen Yin | Ping‐Heng Tan | Litao Sun | Dapeng Yu | Rodney S. Ruoff | Yanwu Zhu
Source: Nature (article, 2023-01-11)
Field: Chemistry — Organic Chemistry

Long-range ordered porous carbons produced from C60 Materials science ; Fullerene ; Raman spectroscopy ; Graphene ; Carbon fibers ; Magic angle spinning ; Chemical physics ; Analytical Chemistry (journal) ; Chemistry ; Nuclear magnetic resonance spectroscopy ; Nanotechnology ; Organic chemistry ; Composite material Fullerene Chemistry and Applications ; Graphene research and applications ; Advanced Battery Materials and Technologies
Authors: Suzhi Cai | Xiaokang Yao | Huili Ma | Huifang Shi | Zhongfu An
Source: Aggregate (article, 2023-02-02)
Field: Materials Science — Materials Chemistry

Manipulating intermolecular interactions for ultralong organic phosphorescence Abstract Ultralong organic phosphorescence (UOP) materials have received considerable attention in the field of organic optoelectronics due to their long lifetime, high exciton utilization, large Stokes shift, and so on. Great advancements have been achieved through manipulating intermolecular interactions for high‐performance UOP materials in recent years. This review will discuss the influence of various intermolecular interactions, including π‐π interactions, n‐π interactions, halogen bonding, hydrogen bonding, coordinative bonding, and ionic bonding on phosphorescent properties at room temperature, respectively. We summarize the rule of manipulating intermolecular interactions for UOP materials with superior phosphorescent properties. This review will provide a guideline for developing new UOP materials with superior phosphorescent properties for potential applications in organic electronics and bioelectronics. Phosphorescence ; Intermolecular force ; Materials science ; Hydrogen bond ; Halogen bond ; Nanotechnology ; Exciton ; Molecule ; Chemistry ; Organic chemistry ; Physics ; Fluorescence Luminescence and Fluorescent Materials ; Organic Light-Emitting Diodes Research ; Molecular Sensors and Ion Detection
Authors: Lei Tang | Yuanjiu Xiao | Feng Wu | Jin‐Lan Zhou | Tongtong Xu | Jian‐Jun Feng
Source: Angewandte Chemie International Edition (article, 2023-10-12)
Field: Chemistry — Organic Chemistry

Silver‐Catalyzed Dearomative [2π+2σ] Cycloadditions of Indoles with Bicyclobutanes: Access to Indoline Fused Bicyclo[2.1.1]hexanes** Bicyclo[2.1.1]hexanes (BCHs) are becoming ever more important in drug design and development as bridged scaffolds that provide underexplored chemical space, but are difficult to access. Here a silver-catalyzed dearomative [2π+2σ] cycloaddition strategy for the synthesis of indoline fused BCHs from N-unprotected indoles and bicyclobutane precursors is described. The strain-release dearomative cycloaddition operates under mild conditions, tolerating a wide range of functional groups. It is capable of forming BCHs with up to four contiguous quaternary carbon centers, achieving yields of up to 99 %. In addition, a scale-up experiment and the synthetic transformations of the cycloadducts further highlighted the synthetic utility. Indoline ; Cycloaddition ; Bicyclic molecule ; Catalysis ; Chemistry ; Combinatorial chemistry ; Chemical space ; Organic chemistry ; Drug discovery Catalytic C–H Functionalization Methods ; Cyclopropane Reaction Mechanisms ; Oxidative Organic Chemistry Reactions
Authors: Wei‐Chun Chou | Qiran Chen | Long Yuan | Yi‐Hsien Cheng | Chunla He | Nancy A. Monteiro‐Riviere | Jim E. Riviere | Zhoumeng Lin
Source: Journal of Controlled Release (article, 2023-07-31)
Field: Materials Science — Biomaterials

An artificial intelligence-assisted physiologically-based pharmacokinetic model to predict nanoparticle delivery to tumors in mice The critical barrier for clinical translation of cancer nanomedicine stems from the inefficient delivery of nanoparticles (NPs) to target solid tumors. Rapid growth of computational power, new machine learning and artificial intelligence (AI) approaches provide new tools to address this challenge. In this study, we established an AI-assisted physiologically based pharmacokinetic (PBPK) model by integrating an AI-based quantitative structure-activity relationship (QSAR) model with a PBPK model to simulate tumor-targeted delivery efficiency (DE) and biodistribution of various NPs. The AI-based QSAR model was developed using machine learning and deep neural network algorithms that were trained with datasets from a published "Nano-Tumor Database" to predict critical input parameters of the PBPK model. The PBPK model with optimized NP cellular uptake kinetic parameters was used to predict the maximum delivery efficiency (DEmax) and DE at 24 (DE24) and 168 h (DE168) of different NPs in the tumor after intravenous injection and achieved a determination coefficient of R<sup>2</sup> = 0.83 [root mean squared error (RMSE) = 3.01] for DE24, R<sup>2</sup> = 0.56 (RMSE = 2.27) for DE168, and R<sup>2</sup> = 0.82 (RMSE = 3.51) for DEmax. The AI-PBPK model predictions correlated well with available experimentally-measured pharmacokinetic profiles of different NPs in tumors after intravenous injection (R<sup>2</sup> ≥ 0.70 for 133 out of 288 datasets). This AI-based PBPK model provides an efficient screening tool to rapidly predict delivery efficiency of a NP based on its physicochemical properties without relying on an animal training dataset. Pharmacokinetics ; Nanoparticle ; Pharmacology ; Chemistry ; Medicine ; Nanotechnology ; Materials science Nanoparticle-Based Drug Delivery ; Field-Flow Fractionation Techniques ; Gold and Silver Nanoparticles Synthesis and Applications
Authors: Irena Senkovska | Volodymyr Bon | Leila Abylgazina | Matthias Mendt | Jan Berger | Gregor Kieslich | Petko St. Petkov | Jhonatan Luiz Fiorio | Jan‐Ole Joswig | Thomas Heine | Larissa Schaper | Christopher Bachetzky | Rochus Schmid | Roland A. Fischer | Andreas Pöppl | Eike Brunner | Stefan Kaskel
Source: Angewandte Chemie International Edition (review, 2023-04-13)
Field: Chemistry — Inorganic Chemistry

Understanding MOF Flexibility: An Analysis Focused on Pillared Layer MOFs as a Model System Flexible porous frameworks are at the forefront of materials research. A unique feature is their ability to open and close their pores in an adaptive manner induced by chemical and physical stimuli. Such enzyme-like selective recognition offers a wide range of functions ranging from gas storage and separation to sensing, actuation, mechanical energy storage and catalysis. However, the factors affecting switchability are poorly understood. In particular, the role of building blocks, as well as secondary factors (crystal size, defects, cooperativity) and the role of host-guest interactions, profit from systematic investigations of an idealized model by advanced analytical techniques and simulations. The review describes an integrated approach targeting the deliberate design of pillared layer metal-organic frameworks as idealized model materials for the analysis of critical factors affecting framework dynamics and summarizes the resulting progress in their understanding and application. Flexibility (engineering) ; Layer (electronics) ; Materials science ; Nanotechnology Metal-Organic Frameworks: Synthesis and Applications ; Magnetism in coordination complexes ; Lanthanide and Transition Metal Complexes
Authors: Johannes T. Margraf | Hyunwook Jung | Christoph Scheurer | Karsten Reuter
Source: Nature Catalysis (article, 2023-01-26)
Field: Materials Science — Materials Chemistry

Exploring catalytic reaction networks with machine learning Inference ; Computer science ; Context (archaeology) ; Perspective (graphical) ; Biochemical engineering ; Artificial intelligence ; Machine learning ; Engineering Machine Learning in Materials Science ; Computational Drug Discovery Methods ; Catalysis and Oxidation Reactions
Authors: He Li | Akhil Dilipkumar | Saifudin Abubakar | Dan Zhao
Source: Chemical Society Reviews (review, 2023-01-01)
Field: Materials Science — Materials Chemistry

Covalent organic frameworks for CO<sub>2</sub> capture: from laboratory curiosity to industry implementation CO<sub>2</sub> concentration in the atmosphere has increased by about 40% since the 1960s. Among various technologies available for carbon capture, adsorption and membrane processes have been receiving tremendous attention due to their potential to capture CO<sub>2</sub> at low costs. The kernel for such processes is the sorbent and membrane materials, and tremendous progress has been made in designing and fabricating novel porous materials for carbon capture. Covalent organic frameworks (COFs), a class of porous crystalline materials, are promising sorbents for CO<sub>2</sub> capture due to their high surface area, low density, controllable pore size and structure, and preferable stabilities. However, the absence of synergistic developments between materials and engineering processes hinders achieving the qualitative leap for net-zero emissions. Considering the lack of a timely review on the combination of state-of-the-art COFs and engineering processes, in this Tutorial Review, we emphasize the developments of COFs for meeting the challenges of carbon capture and disclose the strategies of fabricating COFs for realizing industrial implementation. Moreover, this review presents a detailed and basic description of the engineering processes and industrial status of carbon capture. It highlights the importance of machine learning in integrating simulations of molecular and engineering levels. We aim to stimulate both academia and industry communities for joined efforts in bringing COFs to practical carbon capture. Covalent bond ; Chemistry ; Covalent organic framework ; Nanotechnology ; Carbon fibers ; Computer science ; Process engineering ; Organic chemistry ; Materials science ; Engineering Covalent Organic Framework Applications ; Metal-Organic Frameworks: Synthesis and Applications ; Carbon Dioxide Capture Technologies
Authors: Weihan Li | Qian Ma | Che Liu | Yunfeng Zhang | Xianning Wu | Jiawei Wang | Shizhao Gao | Tianshuo Qiu | Tonghao Liu | Qiang Xiao | Jiaxuan Wei | Tingting Gu | Zhize Zhou | Fashuai Li | Qiang Cheng | Lianlin Li | Wenxuan Tang | Tie Jun Cui
Source: Nature Communications (article, 2023-02-22)
Field: Materials Science — Electronic, Optical and Magnetic Materials

Intelligent metasurface system for automatic tracking of moving targets and wireless communications based on computer vision The fifth-generation (5G) wireless communication has an urgent need for target tracking. Digital programmable metasurface (DPM) may offer an intelligent and efficient solution owing to its powerful and flexible controls of electromagnetic waves and advantages of lower cost, less complexity and smaller size than the traditional antenna array. Here, we report an intelligent metasurface system to perform target tracking and wireless communications, in which computer vision integrated with a convolutional neural network (CNN) is used to automatically detect the locations of moving targets, and the dual-polarized DPM integrated with a pre-trained artificial neural network (ANN) serves to realize the smart beam tracking and wireless communications. Three groups of experiments are conducted for demonstrating the intelligent system: detection and identification of moving targets, detection of radio-frequency signals, and real-time wireless communications. The proposed method sets the stage for an integrated implementation of target identification, radio environment tracking, and wireless communications. This strategy opens up an avenue for intelligent wireless networks and self-adaptive systems. Computer science ; Wireless ; Convolutional neural network ; Tracking (education) ; Wireless network ; Communications system ; Real-time computing ; Artificial intelligence ; Telecommunications Metamaterials and Metasurfaces Applications ; Advanced Wireless Communication Technologies ; Antenna Design and Analysis
Authors: Chuang Hou | Guòan Tai | Yi Liu | Zitong Wu | Xinchao Liang | Xiang Liu
Source: Nano Research Energy (article, 2023-01-05)
Field: Materials Science — Materials Chemistry

Borophene-based materials for energy, sensors and information storage applications Borophene, as a rising-star monoelemental two-dimensional (2D) material, has motivated great interest because of its novel properties, such as anisotropic plasmonics, high carrier mobility, mechanical compliance, optical transparency, ultrahigh thermal conductance, and superconductivity. These properties make it an ideal candidate for use in the field of energy, sensors, and information storage. Stimulated by the realization of pioneering experimental works in 2015 and the follow-up synthesis experiments, a series of high-performance borophene-based devices in the fields, including supercapacitors, batteries, hydroelectric generators, humidity sensors, gas sensors, pressure sensors, and memories, have been experimentally reported in recent years, which are beneficial to the transition of borophene-based materials from experimental synthesis to practical application. Therefore, in addition to paying attention to the experimental preparation of borophene, significant efforts are needed to promote the advancement of related applications of borophene. In this review, after providing a brief overview of borophene evolution and synthesis, we mainly summarize the applications of borophene-based materials in energy storage, energy conversion, energy harvesting, sensors, and information storage. Finally, based on the current research status, some rational suggestions and discussions on the issues and challenges in the future research direction are proposed. Borophene ; Nanotechnology ; Energy storage ; Materials science ; Supercapacitor ; Computer science ; Engineering physics ; Capacitance ; Engineering ; Physics ; Power (physics) MXene and MAX Phase Materials ; Boron and Carbon Nanomaterials Research ; 2D Materials and Applications
Authors: Florian A. Rosenberger | Marvin Thielert | Maximilian T. Strauss | Lisa Schweizer | Constantin Ammar | Sophia C. Mädler | Andreas Metousis | Patricia Skowronek | Maria Wahle | Katherine Madden | Janine Gote-Schniering | Anna Semenova | Herbert B. Schiller | Edwin H. Rodriguez | Thierry M. Nordmann | Andreas Mund | Matthias Mann
Source: Nature Methods (article, 2023-10-01)
Field: Chemistry — Spectroscopy

Spatial single-cell mass spectrometry defines zonation of the hepatocyte proteome Single-cell proteomics by mass spectrometry is emerging as a powerful and unbiased method for the characterization of biological heterogeneity. So far, it has been limited to cultured cells, whereas an expansion of the method to complex tissues would greatly enhance biological insights. Here we describe single-cell Deep Visual Proteomics (scDVP), a technology that integrates high-content imaging, laser microdissection and multiplexed mass spectrometry. scDVP resolves the context-dependent, spatial proteome of murine hepatocytes at a current depth of 1,700 proteins from a cell slice. Half of the proteome was differentially regulated in a spatial manner, with protein levels changing dramatically in proximity to the central vein. We applied machine learning to proteome classes and images, which subsequently inferred the spatial proteome from imaging data alone. scDVP is applicable to healthy and diseased tissues and complements other spatial proteomics and spatial omics technologies. Proteome ; Proteomics ; Laser capture microdissection ; Computational biology ; Context (archaeology) ; Mass spectrometry imaging ; Mass spectrometry ; Biology ; Cell biology ; Chemistry ; Bioinformatics ; Biochemistry ; Gene expression ; Chromatography Advanced Proteomics Techniques and Applications ; Single-cell and spatial transcriptomics ; Cell Image Analysis Techniques