Philosophical transactions. Series A, Mathematical, physical, and engineering sciences最新文献_第8页

Correction to 'Learning earth system models from observations: machine learning or data assimilation?' 更正“从观测中学习地球系统模型:机器学习还是数据同化?”

IF 5

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-04-04 Epub Date: 2022-02-14 DOI: 10.1098/rsta.2022.0004

A J Geer

引用次数: 0

Quality control of image sensors using gaseous tritium light sources. 气态氚光源图像传感器的质量控制。

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-04-04 Epub Date: 2022-02-14 DOI: 10.1098/rsta.2021.0130

David McFadden, Brad Amos, Rainer Heintzmann

引用次数: 0

Structured illumination ophthalmoscope: super-resolution microscopy on the living human eye. 结构照明检眼镜:活体人眼的超分辨率显微镜。

IF 5

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-04-04 Epub Date: 2022-02-14 DOI: 10.1098/rsta.2021.0151

Florian Schock, Gerrit Best, Nil Celik, Rainer Heintzmann, Stefan Dithmar, Christoph Cremer

{"title":"Structured illumination ophthalmoscope: super-resolution microscopy on the living human eye.","authors":"Florian Schock, Gerrit Best, Nil Celik, Rainer Heintzmann, Stefan Dithmar, Christoph Cremer","doi":"10.1098/rsta.2021.0151","DOIUrl":"https://doi.org/10.1098/rsta.2021.0151","url":null,"abstract":"In this paper, we present the prototype of an ophthalmoscope that uses structured illumination microscopy (SIM) to enable super-resolved imaging of the human retina, and give first insights into clinical application possibilities. The SIM technique was applied to build a prototype that uses the lens of the human eye as an objective to 'super-resolve' the retina of a living human. In our multidisciplinary collaboration, we have adapted this well-established technique in ophthalmology and successfully imaged a human retina using significantly lower light intensity than a state-of-the-art ophthalmoscope. Here, we focus on the technical implementation and highlight future perspectives of this method. A more application-oriented note for physicians on the diagnostic and disease-preventive value of this method, as well as the medical results of the clinical study carried out, will be published in a report addressed to an appropriate specialist audience. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.","PeriodicalId":286094,"journal":{"name":"Philosophical transactions. Series A, Mathematical, physical, and engineering sciences","volume":" ","pages":"20210151"},"PeriodicalIF":5.0,"publicationDate":"2022-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39789764","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}

引用次数: 3

Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis. 空间调制照明显微镜:在核纳米结构分析中的应用前景。

IF 5

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-04-04 Epub Date: 2022-02-14 DOI: 10.1098/rsta.2021.0152

Christoph Cremer, Udo Birk

{"title":"Spatially modulated illumination microscopy: application perspectives in nuclear nanostructure analysis.","authors":"Christoph Cremer, Udo Birk","doi":"10.1098/rsta.2021.0152","DOIUrl":"https://doi.org/10.1098/rsta.2021.0152","url":null,"abstract":"Thousands of genes and the complex biochemical networks for their transcription are packed in the micrometer sized cell nucleus. To control biochemical processes, spatial organization plays a key role. Hence the structure of the cell nucleus of higher organisms has emerged as a main topic of advanced light microscopy. So far, a variety of methods have been applied for this, including confocal laser scanning fluorescence microscopy, 4Pi-, STED- and localization microscopy approaches, as well as (laterally) structured illumination microscopy (SIM). Here, we summarize the state of the art and discuss application perspectives for nuclear nanostructure analysis of spatially modulated illumination (SMI). SMI is a widefield-based approach to using axially structured illumination patterns to determine the axial extension (size) of small, optically isolated fluorescent objects between less than or equal to 200 nm and greater than or equal to 40 nm diameter with a precision down to the few nm range; in addition, it allows the axial positioning of such structures down to the 1 nm scale. Combined with SIM, a three-dimensional localization precision of less than or equal to 1 nm is expected to become feasible using fluorescence yields typical for single molecule localization microscopy applications. Together with its nanosizing capability, this may eventually be used to analyse macromolecular complexes and other nanostructures with a topological resolution, further narrowing the gap to Cryoelectron microscopy. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.","PeriodicalId":286094,"journal":{"name":"Philosophical transactions. Series A, Mathematical, physical, and engineering sciences","volume":" ","pages":"20210152"},"PeriodicalIF":5.0,"publicationDate":"2022-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39789765","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}

引用次数: 3

Time-modulated excitation for enhanced single-molecule localization microscopy. 增强单分子定位显微镜的时间调制激发。

IF 5

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-04-04 Epub Date: 2022-02-14 DOI: 10.1098/rsta.2020.0299

Pierre Jouchet, Christian Poüs, Emmanuel Fort, Sandrine Lévêque-Fort

{"title":"Time-modulated excitation for enhanced single-molecule localization microscopy.","authors":"Pierre Jouchet, Christian Poüs, Emmanuel Fort, Sandrine Lévêque-Fort","doi":"10.1098/rsta.2020.0299","DOIUrl":"https://doi.org/10.1098/rsta.2020.0299","url":null,"abstract":"Structured illumination in single-molecule localization microscopy provides new information on the position of molecules and thus improves the localization precision compared to standard localization methods. Here, we used a time-shifted sinusoidal excitation pattern to modulate the fluorescence signal of the molecules whose position information is carried by the phase and recovered by synchronous demodulation. We designed two flexible fast demodulation systems located upstream of the camera, allowing us to overcome the limiting camera acquisition frequency and thus to maximize the collection of photons in the demodulation process. The temporally modulated fluorescence signal was then sampled synchronously on the same image, repeatedly during acquisition. This microscopy, called ModLoc, allows us to experimentally improve the localization precision by a factor of 2.4 in one direction, compared to classical Gaussian fitting methods. A temporal study and an experimental demonstration both show that the short lifetimes of the molecules in blinking regimes impose a modulation frequency in the kilohertz range, which is beyond the reach of current cameras. A demodulation system operating at these frequencies would thus be necessary to take full advantage of this new localization approach. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.","PeriodicalId":286094,"journal":{"name":"Philosophical transactions. Series A, Mathematical, physical, and engineering sciences","volume":" ","pages":"20200299"},"PeriodicalIF":5.0,"publicationDate":"2022-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39789761","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}

引用次数: 2

UCsim2: two-dimensionally structured illumination microscopy using UC2. UCsim2:使用UC2的二维结构照明显微镜。

IF 5

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-04-04 Epub Date: 2022-02-14 DOI: 10.1098/rsta.2020.0148

Haoran Wang, René Lachmann, Barbora Marsikova, Rainer Heintzmann, Benedict Diederich

{"title":"UCsim2: two-dimensionally structured illumination microscopy using UC2.","authors":"Haoran Wang, René Lachmann, Barbora Marsikova, Rainer Heintzmann, Benedict Diederich","doi":"10.1098/rsta.2020.0148","DOIUrl":"https://doi.org/10.1098/rsta.2020.0148","url":null,"abstract":"State-of-the-art microscopy techniques enable the imaging of sub-diffraction barrier biological structures at the price of high costs or a lack of transparency. We try to reduce some of these barriers by presenting a super-resolution upgrade to our recently presented open-source optical toolbox UC2. Our new injection moulded parts allow larger builds with higher precision. The 4× lower manufacturing tolerance compared to three-dimensional printing makes assemblies more reproducible. By adding consumer-grade available open-source hardware such as digital mirror devices and laser projectors, we demonstrate a compact three-dimensional multimodal setup that combines image scanning microscopy and structured illumination microscopy. We demonstrate a gain in resolution and optical sectioning using the two different modes compared to the widefield limit by imaging Alexa Fluor ® 647- and Silicon Rhodamine-stained HeLa cells. We compare different objective lenses and by sharing the designs and manuals of our setup, we make super-resolution imaging available to everyone. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.","PeriodicalId":286094,"journal":{"name":"Philosophical transactions. Series A, Mathematical, physical, and engineering sciences","volume":" ","pages":"20200148"},"PeriodicalIF":5.0,"publicationDate":"2022-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39789767","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}

引用次数: 0

Simulations of molecular photodynamics in long timescales 长时间尺度下分子光动力学的模拟

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-03-28 DOI: 10.1098/rsta.2020.0382

S. Mukherjee, Max Pinheiro, Baptiste Demoulin, M. Barbatti

{"title":"Simulations of molecular photodynamics in long timescales","authors":"S. Mukherjee, Max Pinheiro, Baptiste Demoulin, M. Barbatti","doi":"10.1098/rsta.2020.0382","DOIUrl":"https://doi.org/10.1098/rsta.2020.0382","url":null,"abstract":"Nonadiabatic dynamics simulations in the long timescale (much longer than 10 ps) are the next challenge in computational photochemistry. This paper delimits the scope of what we expect from methods to run such simulations: they should work in full nuclear dimensionality, be general enough to tackle any type of molecule and not require unrealistic computational resources. We examine the main methodological challenges we should venture to advance the field, including the computational costs of the electronic structure calculations, stability of the integration methods, accuracy of the nonadiabatic dynamics algorithms and software optimization. Based on simulations designed to shed light on each of these issues, we show how machine learning may be a crucial element for long time-scale dynamics, either as a surrogate for electronic structure calculations or aiding the parameterization of model Hamiltonians. We show that conventional methods for integrating classical equations should be adequate to extended simulations up to 1 ns and that surface hopping agrees semiquantitatively with wave packet propagation in the weak-coupling regime. We also describe our optimization of the Newton-X program to reduce computational overheads in data processing and storage. This article is part of the theme issue ‘Chemistry without the Born–Oppenheimer approximation’.","PeriodicalId":286094,"journal":{"name":"Philosophical transactions. Series A, Mathematical, physical, and engineering sciences","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116650101","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}

引用次数: 11

Instanton theory for Fermi’s golden rule and beyond 费米黄金法则的瞬时子理论

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-03-28 DOI: 10.1098/rsta.2020.0378

Imaad M. Ansari, E. Heller, George Trenins, Jeremy O. Richardson

引用次数: 13

Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics 量子力学/分子力学轨迹表面跳变非绝热动力学中的采样效应

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-03-28 DOI: 10.1098/rsta.2020.0381

Davide Avagliano, Emilio Lorini, L. González

{"title":"Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics","authors":"Davide Avagliano, Emilio Lorini, L. González","doi":"10.1098/rsta.2020.0381","DOIUrl":"https://doi.org/10.1098/rsta.2020.0381","url":null,"abstract":"The impact of different initial conditions in non-adiabatic trajectory surface hopping dynamics within a hybrid quantum mechanical/molecular mechanics scheme is investigated. The influence of a quantum sampling, based on a Wigner distribution, a fully thermal sampling, based on classical molecular dynamics, and a quantum sampled system, but thermally equilibrated with the environment, is investigated on the relaxation dynamics of solvated fulvene after light irradiation. We find that the decay from the first singlet excited state to the ground state shows high dependency on the initial condition and simulation parameters. The three sampling methods lead to different distributions of initial geometries and momenta, which then affect the fate of the excited state dynamics. We evaluated both the effect of sampling geometries and momenta, analysing how the ultrafast decay of fulvene changes accordingly. The results are expected to be of interest to decide how to initialize non-adiabatic dynamics in the presence of the environment. This article is part of the theme issue ‘Chemistry without the Born–Oppenheimer approximation’.","PeriodicalId":286094,"journal":{"name":"Philosophical transactions. Series A, Mathematical, physical, and engineering sciences","volume":"65 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124750398","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}

引用次数: 10

Preface to ‘The future of mathematical cosmology' 《数学宇宙学的未来》序言

Philosophical transactions. Series A, Mathematical, physical, and engineering sciences Pub Date : 2022-03-14 DOI: 10.1098/rsta.2022.0002

S. Cotsakis, A. Yefremov

{"title":"Preface to ‘The future of mathematical cosmology'","authors":"S. Cotsakis, A. Yefremov","doi":"10.1098/rsta.2022.0002","DOIUrl":"https://doi.org/10.1098/rsta.2022.0002","url":null,"abstract":"This is the first part of the theme issue ‘The Future of Mathematical Cosmology’ which is published in two separate volumes by the Philosophical Transactions of the Royal Society A. Overall, the two volumes contain a number of research, review and opinion articles, covering multiform aspects of mathematical and theoretical cosmology. The subject of mathematical cosmology plays a fundamental role in theoretical physics today and has deep applications in contemporary astronomy and astrophysics. Motivating important new ties and connections with general relativity and correlating with diverse features of string theory and quantum gravity, theoretical cosmology is in fact the most obvious ‘testing agent’ for many of the most advanced, pioneering or speculative ideas in these fields. Mathematical cosmology has acquired a unique status, potential and independence as a scientific field. It reveals its own problems, methods and techniques, often with the stimulus of general relativity, quantum field theory and above all differential geometry, but it also serves as the inevitable tank of ideas and models for use of the more data-driven, ‘actual’ physical cosmology. In fact, mathematical theoretical cosmology provides the driving force behind modern attempts to explain the— now manifold—observational cosmology data. We believe that this theme issue will be useful as a lasting guide and reference for interested people entering the field, as well as for experienced researchers who seek to expand their field of vision in this most majestic of scientific enterprises.","PeriodicalId":286094,"journal":{"name":"Philosophical transactions. Series A, Mathematical, physical, and engineering sciences","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2022-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128960556","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}

引用次数: 3