{"title":"Fluorescence resonance energy transfer at the single-molecule level","authors":"","doi":"10.1038/s43586-024-00306-6","DOIUrl":"10.1038/s43586-024-00306-6","url":null,"abstract":"This PrimeView highlights the fluorophores used in smFRET experiments and how they affect measurement of energy transfer at the single-molecule level.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00306-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140310409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Taekjip Ha, Jingyi Fei, Sonja Schmid, Nam Ki Lee, Ruben L. Gonzalez Jr, Sneha Paul, Sanghun Yeou
{"title":"Fluorescence resonance energy transfer at the single-molecule level","authors":"Taekjip Ha, Jingyi Fei, Sonja Schmid, Nam Ki Lee, Ruben L. Gonzalez Jr, Sneha Paul, Sanghun Yeou","doi":"10.1038/s43586-024-00298-3","DOIUrl":"10.1038/s43586-024-00298-3","url":null,"abstract":"Fluorescence resonance energy transfer (FRET) is a powerful spectroscopic method for measuring distances in the 2–8 nm range. Often, conformational changes and molecular interactions are difficult or impossible to synchronize, or too rare or transient to detect using ensemble FRET. Single-molecule FRET (smFRET) opens new opportunities to probe biomolecular conformational changes or interactions that are missing in static snapshots provided by traditional structural biology tools, as well as to measure the kinetics of these dynamics on various timescales and under physiological conditions, including inside cells. Advances in labelling technologies, combining smFRET with optical and magnetic tweezers and Bayesian inference-based and information theory-based analysis tools are revealing rich biomolecular dynamics. We also discuss the challenges and opportunities in integrating dynamics into traditionally static structural biology approaches, extending smFRET into cells and tissues, advancing technical innovations and democratizing the practice of smFRET. Analysing single-molecule fluorescence resonance energy transfer (smFRET) enables an unprecedented view of the dynamics and kinetics of biomolecular conformational changes and interactions. In this Primer, Ha et al. discuss technological advances that have led to smFRET and how the method can be adapted to address various research questions in structural and molecular biology.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-18"},"PeriodicalIF":0.0,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140310419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biocarbon materials","authors":"","doi":"10.1038/s43586-024-00305-7","DOIUrl":"10.1038/s43586-024-00305-7","url":null,"abstract":"This PrimeView highlights the range of applications of biocarbon materials including composite materials, energy storage and conversion, and environmental remediation.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00305-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140123812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Amar K. Mohanty, Singaravelu Vivekanandhan, Oisik Das, Lina M. Romero Millán, Naomi B. Klinghoffer, Ange Nzihou, Manjusri Misra
{"title":"Biocarbon materials","authors":"Amar K. Mohanty, Singaravelu Vivekanandhan, Oisik Das, Lina M. Romero Millán, Naomi B. Klinghoffer, Ange Nzihou, Manjusri Misra","doi":"10.1038/s43586-024-00297-4","DOIUrl":"10.1038/s43586-024-00297-4","url":null,"abstract":"Biocarbons are carbonaceous solids derived from renewable and sustainable feedstocks and their combinations through thermochemical conversion at high temperatures (>350 °C) in the absence of oxygen or in limited oxygen. Expanding their applications from soil and fuel into advanced arenas of polymer composites, energy and environment is the key strategy to substitute for a wide range of conventional fossil-based carbon materials with the added benefits of sustainability and circularity. This Primer discusses biocarbon research, including feedstock selection, characterization, pyrolysis techniques, post-modification strategies, diversified applications and challenges. A critical assessment of carbon sequestration, waste reduction, economic impact, material sustainability and circularity and future perspectives is presented. This Primer mainly focuses on materials (polymer composites), energy (storage and conversion) and environmental remediation (wastewater treatment and CO2 capture). The hurdles that biocarbon-based materials must overcome are effective market propagation, industry-standard adherence and maintenance of a steady flow of feedstocks to guarantee continuous production. Maintenance of reproducibility of biocarbon materials with similar physicochemical and functional properties is another challenging task, which needs more investigation with the support of theoretical modelling and database generation. The Primer also delves into techno-economic analysis, which integrates biomass logistics and their industrial processing, which will enable a new manufacturing platform in biocarbon production for large-scale technological applications. Biocarbons are carbonaceous solids derived from renewable and sustainable feedstocks through thermochemical conversion at high temperatures. In this Primer, Mohanty et al. discuss feedstock selection, pyrolysis techniques and post-modification strategies, as well as waste reduction and the economic impact of biocarbons.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-21"},"PeriodicalIF":0.0,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140123825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gabriele Corso, Hannes Stark, Stefanie Jegelka, Tommi Jaakkola, Regina Barzilay
{"title":"Graph neural networks","authors":"Gabriele Corso, Hannes Stark, Stefanie Jegelka, Tommi Jaakkola, Regina Barzilay","doi":"10.1038/s43586-024-00294-7","DOIUrl":"10.1038/s43586-024-00294-7","url":null,"abstract":"iGraphs are flexible mathematical objects that can represent many entities and knowledge from different domains, including in the life sciences. Graph neural networks (GNNs) are mathematical models that can learn functions over graphs and are a leading approach for building predictive models on graph-structured data. This combination has enabled GNNs to advance the state of the art in many disciplines, from discovering new antibiotics and identifying drug-repurposing candidates to modelling physical systems and generating new molecules. This Primer provides a practical and accessible introduction to GNNs, describing their properties and applications to the life and physical sciences. Emphasis is placed on the practical implications of key theoretical limitations, new ideas to solve these challenges and important considerations when using GNNs on a new task. Graph neural networks are a class of deep learning methods that can model physical systems, generate new molecules and identify drug candidates. This Primer introduces graph neural networks and explores how they are applied across the life and physical sciences.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-13"},"PeriodicalIF":0.0,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140053266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Oliver Werzer, Stefan Kowarik, Fabian Gasser, Zhang Jiang, Joseph Strzalka, Christopher Nicklin, Roland Resel
{"title":"X-ray diffraction under grazing incidence conditions","authors":"Oliver Werzer, Stefan Kowarik, Fabian Gasser, Zhang Jiang, Joseph Strzalka, Christopher Nicklin, Roland Resel","doi":"10.1038/s43586-024-00293-8","DOIUrl":"10.1038/s43586-024-00293-8","url":null,"abstract":"Material properties frequently relate to structures at or near surfaces, particularly in thin films. As a result, it is essential to understand these structures at the molecular and atomistic levels. The most accurate and widely used techniques for characterizing crystallographic order are based on X-ray diffraction. When dealing with thin films or interfaces, standard approaches, such as single crystal or powder diffraction, are not suitable. However, X-ray diffraction under grazing incidence conditions can provide the required information. In this Primer, grazing incidence X-ray diffraction (GIXD) is comprehensively introduced, starting from basic considerations on X-ray diffraction at crystals with reduced dimensionality and the optical properties of X-rays, followed by a more in-depth description of an experimental performance, including X-ray sources, goniometers and detectors. Experimental errors, limitations and reproducibility are discussed. Various applications, from highly ordered inorganic single crystal surfaces to weakly ordered polymer thin films, are presented to illustrate the potential of GIXD. Data visualizations, representations and evaluation strategies are summarized, based on the example of anthracene thin films. The Primer compiles information relevant to perform high-quality GIXD experiments, evaluate data and interpret results, to extend knowledge about X-ray diffraction from surfaces, interfaces and thin films. Structures of surfaces and thin films can be investigated by performing X-ray diffraction under grazing incidence conditions. This Primer explores how grazing incidence X-ray diffraction is used to obtain crystallographic information, including in situ characterization, data collection, analysis and visualization, across a range of applications.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-20"},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139994016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Artificial molecular pumps","authors":"","doi":"10.1038/s43586-024-00300-y","DOIUrl":"10.1038/s43586-024-00300-y","url":null,"abstract":"This PrimeView highlights how artificial molecular pumps can be designed to harness an external energy source to accomplish a desired synthetic task.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-1"},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s43586-024-00300-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139916834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Long Zhang, Huang Wu, Xuesong Li, Hongliang Chen, R. Dean Astumian, J. Fraser Stoddart
{"title":"Artificial molecular pumps","authors":"Long Zhang, Huang Wu, Xuesong Li, Hongliang Chen, R. Dean Astumian, J. Fraser Stoddart","doi":"10.1038/s43586-024-00291-w","DOIUrl":"10.1038/s43586-024-00291-w","url":null,"abstract":"Reflecting on recent progress in bottom-up engineering focused on creating the smallest devices capable of controlling nanoscale motion, artificial molecular pumps (AMPs) are among some of the most highly studied wholly synthetic machines. In addition to exploring their applications in synthesizing mechanically bonded compounds, including polymers and materials, the design features and underlying fundamental physical principles of rotaxane-based AMPs are discussed in this Primer. Current limitations in AMP design are reviewed, and potential strategies to overcome these limitations are evaluated. Anticipated future developments in this rapidly evolving area of science are considered. Although still in their infancy, the design and synthesis of AMPs have already led to new insights into fundamental molecular principles, such as kinetic asymmetry, trajectory thermodynamics and the non-equilibrium pumping equality. With the ineluctable continuing development of AMPs, an increasing number of ground-breaking discoveries are anticipated in the physical and life sciences. Artificial molecular pumps are synthetic machines capable of performing complex tasks on a molecular scale. In this Primer, Zhang et al. discuss the design features and underlying fundamental physical principles of artificial molecular pumps.","PeriodicalId":74250,"journal":{"name":"Nature reviews. Methods primers","volume":" ","pages":"1-21"},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139916803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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