Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov model
Diffusion of nanoparticles in the cytoplasm of live cells has frequently been reported to exhibit an anomalous and even heterogeneous character, i.e. particles seem to switch gears during their journey. Here we show by means of a hidden Markov model that individual trajectories of quantum dots in th...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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IOP Publishing
2021-01-01
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| Series: | New Journal of Physics |
| Subjects: | |
| Online Access: | https://doi.org/10.1088/1367-2630/abf204 |
| _version_ | 1797750226017058816 |
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| author | Joanna Janczura Michał Balcerek Krzysztof Burnecki Adal Sabri Matthias Weiss Diego Krapf |
| author_facet | Joanna Janczura Michał Balcerek Krzysztof Burnecki Adal Sabri Matthias Weiss Diego Krapf |
| author_sort | Joanna Janczura |
| collection | DOAJ |
| description | Diffusion of nanoparticles in the cytoplasm of live cells has frequently been reported to exhibit an anomalous and even heterogeneous character, i.e. particles seem to switch gears during their journey. Here we show by means of a hidden Markov model that individual trajectories of quantum dots in the cytoplasm of living cultured cells feature a dichotomous switching between two distinct mobility states with an overall subdiffusive mode of motion of the fractional Brownian motion (FBM) type. Using the extracted features of experimental trajectories as input for simulations of different variants of a two-state FBM model, we show that the trajectory-intrinsic and the ensemble-wise heterogeneity in the experimental data is mostly due to variations in the (local) transport coefficients, with only minor contributions due to locally varying anomaly exponents. Altogether, our approach shows that diffusion heterogeneities can be faithfully extracted and quantified from fairly short trajectories obtained by single-particle tracking in highly complex media. |
| first_indexed | 2024-03-12T16:29:32Z |
| format | Article |
| id | doaj.art-837859fbb76f4f3cb19919937a1d2e09 |
| institution | Directory Open Access Journal |
| issn | 1367-2630 |
| language | English |
| last_indexed | 2024-03-12T16:29:32Z |
| publishDate | 2021-01-01 |
| publisher | IOP Publishing |
| record_format | Article |
| series | New Journal of Physics |
| spelling | doaj.art-837859fbb76f4f3cb19919937a1d2e092023-08-08T15:34:07ZengIOP PublishingNew Journal of Physics1367-26302021-01-0123505301810.1088/1367-2630/abf204Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov modelJoanna Janczura0https://orcid.org/0000-0001-6110-3394Michał Balcerek1https://orcid.org/0000-0003-3637-5501Krzysztof Burnecki2https://orcid.org/0000-0002-1754-4472Adal Sabri3Matthias Weiss4https://orcid.org/0000-0001-8814-9915Diego Krapf5https://orcid.org/0000-0002-2833-5553Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology , Wyspiańskiego 27, 50-370 Wrocław, PolandFaculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology , Wyspiańskiego 27, 50-370 Wrocław, PolandFaculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wrocław University of Science and Technology , Wyspiańskiego 27, 50-370 Wrocław, PolandExperimental Physics I, University of Bayreuth , D-95440 Bayreuth, GermanyExperimental Physics I, University of Bayreuth , D-95440 Bayreuth, GermanyDepartment of Electrical and Computer Engineering, and School of Biomedical Engineering, Colorado State University , Fort Collins, CO 80523, United States of AmericaDiffusion of nanoparticles in the cytoplasm of live cells has frequently been reported to exhibit an anomalous and even heterogeneous character, i.e. particles seem to switch gears during their journey. Here we show by means of a hidden Markov model that individual trajectories of quantum dots in the cytoplasm of living cultured cells feature a dichotomous switching between two distinct mobility states with an overall subdiffusive mode of motion of the fractional Brownian motion (FBM) type. Using the extracted features of experimental trajectories as input for simulations of different variants of a two-state FBM model, we show that the trajectory-intrinsic and the ensemble-wise heterogeneity in the experimental data is mostly due to variations in the (local) transport coefficients, with only minor contributions due to locally varying anomaly exponents. Altogether, our approach shows that diffusion heterogeneities can be faithfully extracted and quantified from fairly short trajectories obtained by single-particle tracking in highly complex media.https://doi.org/10.1088/1367-2630/abf204hidden Markov modelheterogeneous diffusionfractional Brownian motionswitchinganomalous diffusion |
| spellingShingle | Joanna Janczura Michał Balcerek Krzysztof Burnecki Adal Sabri Matthias Weiss Diego Krapf Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov model New Journal of Physics hidden Markov model heterogeneous diffusion fractional Brownian motion switching anomalous diffusion |
| title | Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov model |
| title_full | Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov model |
| title_fullStr | Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov model |
| title_full_unstemmed | Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov model |
| title_short | Identifying heterogeneous diffusion states in the cytoplasm by a hidden Markov model |
| title_sort | identifying heterogeneous diffusion states in the cytoplasm by a hidden markov model |
| topic | hidden Markov model heterogeneous diffusion fractional Brownian motion switching anomalous diffusion |
| url | https://doi.org/10.1088/1367-2630/abf204 |
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