Single-photon smFRET. I: Theory and conceptual basis
We present a unified conceptual framework and the associated software package for single-molecule Förster resonance energy transfer (smFRET) analysis from single-photon arrivals leveraging Bayesian nonparametrics, BNP-FRET. This unified framework addresses the following key physical complexities of...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-03-01
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| Series: | Biophysical Reports |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667074722000465 |
| _version_ | 1798004573582917632 |
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| author | Ayush Saurabh Mohamadreza Fazel Matthew Safar Ioannis Sgouralis Steve Pressé |
| author_facet | Ayush Saurabh Mohamadreza Fazel Matthew Safar Ioannis Sgouralis Steve Pressé |
| author_sort | Ayush Saurabh |
| collection | DOAJ |
| description | We present a unified conceptual framework and the associated software package for single-molecule Förster resonance energy transfer (smFRET) analysis from single-photon arrivals leveraging Bayesian nonparametrics, BNP-FRET. This unified framework addresses the following key physical complexities of a single-photon smFRET experiment, including: 1) fluorophore photophysics; 2) continuous time kinetics of the labeled system with large timescale separations between photophysical phenomena such as excited photophysical state lifetimes and events such as transition between system states; 3) unavoidable detector artefacts; 4) background emissions; 5) unknown number of system states; and 6) both continuous and pulsed illumination. These physical features necessarily demand a novel framework that extends beyond existing tools. In particular, the theory naturally brings us to a hidden Markov model with a second-order structure and Bayesian nonparametrics on account of items 1, 2, and 5 on the list. In the second and third companion articles, we discuss the direct effects of these key complexities on the inference of parameters for continuous and pulsed illumination, respectively. |
| first_indexed | 2024-04-11T12:25:43Z |
| format | Article |
| id | doaj.art-58648dbfdcfb4465a5bd5ff91d11b1e7 |
| institution | Directory Open Access Journal |
| issn | 2667-0747 |
| language | English |
| last_indexed | 2024-04-11T12:25:43Z |
| publishDate | 2023-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Biophysical Reports |
| spelling | doaj.art-58648dbfdcfb4465a5bd5ff91d11b1e72022-12-22T04:23:57ZengElsevierBiophysical Reports2667-07472023-03-0131100089Single-photon smFRET. I: Theory and conceptual basisAyush Saurabh0Mohamadreza Fazel1Matthew Safar2Ioannis Sgouralis3Steve Pressé4Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, ArizonaCenter for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, ArizonaCenter for Biological Physics, Arizona State University, Tempe, Arizona; Department of Mathematics and Statistical Science, Arizona State University, Tempe, ArizonaDepartment of Mathematics, University of Tennessee Knoxville, Knoxville, TennesseCenter for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona; School of Molecular Sciences, Arizona State University, Tempe, Arizona; Corresponding authorWe present a unified conceptual framework and the associated software package for single-molecule Förster resonance energy transfer (smFRET) analysis from single-photon arrivals leveraging Bayesian nonparametrics, BNP-FRET. This unified framework addresses the following key physical complexities of a single-photon smFRET experiment, including: 1) fluorophore photophysics; 2) continuous time kinetics of the labeled system with large timescale separations between photophysical phenomena such as excited photophysical state lifetimes and events such as transition between system states; 3) unavoidable detector artefacts; 4) background emissions; 5) unknown number of system states; and 6) both continuous and pulsed illumination. These physical features necessarily demand a novel framework that extends beyond existing tools. In particular, the theory naturally brings us to a hidden Markov model with a second-order structure and Bayesian nonparametrics on account of items 1, 2, and 5 on the list. In the second and third companion articles, we discuss the direct effects of these key complexities on the inference of parameters for continuous and pulsed illumination, respectively.http://www.sciencedirect.com/science/article/pii/S2667074722000465 |
| spellingShingle | Ayush Saurabh Mohamadreza Fazel Matthew Safar Ioannis Sgouralis Steve Pressé Single-photon smFRET. I: Theory and conceptual basis Biophysical Reports |
| title | Single-photon smFRET. I: Theory and conceptual basis |
| title_full | Single-photon smFRET. I: Theory and conceptual basis |
| title_fullStr | Single-photon smFRET. I: Theory and conceptual basis |
| title_full_unstemmed | Single-photon smFRET. I: Theory and conceptual basis |
| title_short | Single-photon smFRET. I: Theory and conceptual basis |
| title_sort | single photon smfret i theory and conceptual basis |
| url | http://www.sciencedirect.com/science/article/pii/S2667074722000465 |
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