Deep Learning and Single-Molecule Localization Microscopy Reveal Nanoscopic Dynamics of DNA Entanglement Loci Article Swipe
Maged F. Serag
,
Maram Abadi
,
Hajar Al‐Zarah
,
Omar Adel Ibrahim
,
Satoshi Habuchi
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1021/acsnano.4c15364
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1021/acsnano.4c15364
Understanding molecular dynamics at the nanoscale remains challenging due to limitations in the temporal resolution of current imaging techniques. Deep learning integrated with Single-Molecule Localization Microscopy (SMLM) offers opportunities to probe these dynamics. Here, we leverage this integration to reveal entangled polymer dynamics at a fast time scale, which is relatively poorly understood at the single-molecule level. We used Lambda DNA as a model system and modeled their entanglement using the self-avoiding wormlike chain model, generated simulated localizations along the contours, and trained the deep learning algorithm on these simulated images to predict chain contours from sparse localization data. We found that the localizations are heterogeneously distributed along the contours. Our assessments indicated that chain entanglement creates local diffusion barriers for switching buffer molecules, affecting the photoswitching kinetics of fluorescent dyes conjugated to the DNA molecules at discrete DNA segments. Tracking these segments demonstrated stochastic and subdiffusive migration of the entanglement loci. Our approach provides direct visualization of nanoscale polymer dynamics and local molecular environments previously inaccessible to conventional imaging techniques. In addition, our results suggest that the switching kinetics of the fluorophores in SMLM can be used to characterize nanoscopic local environments.
Related Topics
Concepts
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/acsnano.4c15364
- OA Status
- hybrid
- Cited By
- 5
- References
- 38
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4407127253
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4407127253Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1021/acsnano.4c15364Digital Object Identifier
- Title
-
Deep Learning and Single-Molecule Localization Microscopy Reveal Nanoscopic Dynamics of DNA Entanglement LociWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-02-04Full publication date if available
- Authors
-
Maged F. Serag, Maram Abadi, Hajar Al‐Zarah, Omar Adel Ibrahim, Satoshi HabuchiList of authors in order
- Landing page
-
https://doi.org/10.1021/acsnano.4c15364Publisher landing page
- Open access
-
YesWhether a free full text is available
- OA status
-
hybridOpen access status per OpenAlex
- OA URL
-
https://doi.org/10.1021/acsnano.4c15364Direct OA link when available
- Concepts
-
Nanoscopic scale, Quantum entanglement, Nanotechnology, Materials science, Microscopy, DNA, Dynamics (music), Chemical physics, Molecule, Atomic force microscopy, Biophysics, Chemistry, Biology, Physics, Optics, Genetics, Quantum, Organic chemistry, Acoustics, Quantum mechanicsTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
5Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 5Per-year citation counts (last 5 years)
- References (count)
-
38Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
Full payload
| id | https://openalex.org/W4407127253 |
|---|---|
| doi | https://doi.org/10.1021/acsnano.4c15364 |
| ids.doi | https://doi.org/10.1021/acsnano.4c15364 |
| ids.pmid | https://pubmed.ncbi.nlm.nih.gov/39903818 |
| ids.openalex | https://openalex.org/W4407127253 |
| fwci | 40.72916612 |
| mesh[0].qualifier_ui | |
| mesh[0].descriptor_ui | D000077321 |
| mesh[0].is_major_topic | True |
| mesh[0].qualifier_name | |
| mesh[0].descriptor_name | Deep Learning |
| mesh[1].qualifier_ui | Q000737 |
| mesh[1].descriptor_ui | D004247 |
| mesh[1].is_major_topic | True |
| mesh[1].qualifier_name | chemistry |
| mesh[1].descriptor_name | DNA |
| mesh[2].qualifier_ui | Q000379 |
| mesh[2].descriptor_ui | D000072760 |
| mesh[2].is_major_topic | True |
| mesh[2].qualifier_name | methods |
| mesh[2].descriptor_name | Single Molecule Imaging |
| mesh[3].qualifier_ui | Q000737 |
| mesh[3].descriptor_ui | D005456 |
| mesh[3].is_major_topic | False |
| mesh[3].qualifier_name | chemistry |
| mesh[3].descriptor_name | Fluorescent Dyes |
| mesh[4].qualifier_ui | |
| mesh[4].descriptor_ui | D007700 |
| mesh[4].is_major_topic | False |
| mesh[4].qualifier_name | |
| mesh[4].descriptor_name | Kinetics |
| mesh[5].qualifier_ui | |
| mesh[5].descriptor_ui | D000077321 |
| mesh[5].is_major_topic | True |
| mesh[5].qualifier_name | |
| mesh[5].descriptor_name | Deep Learning |
| mesh[6].qualifier_ui | Q000379 |
| mesh[6].descriptor_ui | D000072760 |
| mesh[6].is_major_topic | True |
| mesh[6].qualifier_name | methods |
| mesh[6].descriptor_name | Single Molecule Imaging |
| mesh[7].qualifier_ui | Q000737 |
| mesh[7].descriptor_ui | D004247 |
| mesh[7].is_major_topic | True |
| mesh[7].qualifier_name | chemistry |
| mesh[7].descriptor_name | DNA |
| mesh[8].qualifier_ui | Q000737 |
| mesh[8].descriptor_ui | D005456 |
| mesh[8].is_major_topic | False |
| mesh[8].qualifier_name | chemistry |
| mesh[8].descriptor_name | Fluorescent Dyes |
| mesh[9].qualifier_ui | |
| mesh[9].descriptor_ui | D036103 |
| mesh[9].is_major_topic | False |
| mesh[9].qualifier_name | |
| mesh[9].descriptor_name | Nanotechnology |
| mesh[10].qualifier_ui | |
| mesh[10].descriptor_ui | D008856 |
| mesh[10].is_major_topic | False |
| mesh[10].qualifier_name | |
| mesh[10].descriptor_name | Microscopy, Fluorescence |
| mesh[11].qualifier_ui | |
| mesh[11].descriptor_ui | D007700 |
| mesh[11].is_major_topic | False |
| mesh[11].qualifier_name | |
| mesh[11].descriptor_name | Kinetics |
| mesh[12].qualifier_ui | |
| mesh[12].descriptor_ui | D000077321 |
| mesh[12].is_major_topic | True |
| mesh[12].qualifier_name | |
| mesh[12].descriptor_name | Deep Learning |
| mesh[13].qualifier_ui | Q000379 |
| mesh[13].descriptor_ui | D000072760 |
| mesh[13].is_major_topic | True |
| mesh[13].qualifier_name | methods |
| mesh[13].descriptor_name | Single Molecule Imaging |
| mesh[14].qualifier_ui | Q000737 |
| mesh[14].descriptor_ui | D004247 |
| mesh[14].is_major_topic | True |
| mesh[14].qualifier_name | chemistry |
| mesh[14].descriptor_name | DNA |
| mesh[15].qualifier_ui | Q000737 |
| mesh[15].descriptor_ui | D005456 |
| mesh[15].is_major_topic | False |
| mesh[15].qualifier_name | chemistry |
| mesh[15].descriptor_name | Fluorescent Dyes |
| mesh[16].qualifier_ui | |
| mesh[16].descriptor_ui | D036103 |
| mesh[16].is_major_topic | False |
| mesh[16].qualifier_name | |
| mesh[16].descriptor_name | Nanotechnology |
| mesh[17].qualifier_ui | |
| mesh[17].descriptor_ui | D008856 |
| mesh[17].is_major_topic | False |
| mesh[17].qualifier_name | |
| mesh[17].descriptor_name | Microscopy, Fluorescence |
| mesh[18].qualifier_ui | |
| mesh[18].descriptor_ui | D007700 |
| mesh[18].is_major_topic | False |
| mesh[18].qualifier_name | |
| mesh[18].descriptor_name | Kinetics |
| mesh[19].qualifier_ui | |
| mesh[19].descriptor_ui | D000077321 |
| mesh[19].is_major_topic | True |
| mesh[19].qualifier_name | |
| mesh[19].descriptor_name | Deep Learning |
| mesh[20].qualifier_ui | Q000737 |
| mesh[20].descriptor_ui | D004247 |
| mesh[20].is_major_topic | True |
| mesh[20].qualifier_name | chemistry |
| mesh[20].descriptor_name | DNA |
| mesh[21].qualifier_ui | Q000379 |
| mesh[21].descriptor_ui | D000072760 |
| mesh[21].is_major_topic | True |
| mesh[21].qualifier_name | methods |
| mesh[21].descriptor_name | Single Molecule Imaging |
| mesh[22].qualifier_ui | Q000737 |
| mesh[22].descriptor_ui | D005456 |
| mesh[22].is_major_topic | False |
| mesh[22].qualifier_name | chemistry |
| mesh[22].descriptor_name | Fluorescent Dyes |
| mesh[23].qualifier_ui | |
| mesh[23].descriptor_ui | D007700 |
| mesh[23].is_major_topic | False |
| mesh[23].qualifier_name | |
| mesh[23].descriptor_name | Kinetics |
| mesh[24].qualifier_ui | |
| mesh[24].descriptor_ui | D000077321 |
| mesh[24].is_major_topic | True |
| mesh[24].qualifier_name | |
| mesh[24].descriptor_name | Deep Learning |
| mesh[25].qualifier_ui | Q000737 |
| mesh[25].descriptor_ui | D004247 |
| mesh[25].is_major_topic | True |
| mesh[25].qualifier_name | chemistry |
| mesh[25].descriptor_name | DNA |
| mesh[26].qualifier_ui | Q000379 |
| mesh[26].descriptor_ui | D000072760 |
| mesh[26].is_major_topic | True |
| mesh[26].qualifier_name | methods |
| mesh[26].descriptor_name | Single Molecule Imaging |
| mesh[27].qualifier_ui | Q000737 |
| mesh[27].descriptor_ui | D005456 |
| mesh[27].is_major_topic | False |
| mesh[27].qualifier_name | chemistry |
| mesh[27].descriptor_name | Fluorescent Dyes |
| mesh[28].qualifier_ui | |
| mesh[28].descriptor_ui | D007700 |
| mesh[28].is_major_topic | False |
| mesh[28].qualifier_name | |
| mesh[28].descriptor_name | Kinetics |
| mesh[29].qualifier_ui | |
| mesh[29].descriptor_ui | D000077321 |
| mesh[29].is_major_topic | True |
| mesh[29].qualifier_name | |
| mesh[29].descriptor_name | Deep Learning |
| mesh[30].qualifier_ui | Q000379 |
| mesh[30].descriptor_ui | D000072760 |
| mesh[30].is_major_topic | True |
| mesh[30].qualifier_name | methods |
| mesh[30].descriptor_name | Single Molecule Imaging |
| mesh[31].qualifier_ui | Q000737 |
| mesh[31].descriptor_ui | D004247 |
| mesh[31].is_major_topic | True |
| mesh[31].qualifier_name | chemistry |
| mesh[31].descriptor_name | DNA |
| mesh[32].qualifier_ui | Q000737 |
| mesh[32].descriptor_ui | D005456 |
| mesh[32].is_major_topic | False |
| mesh[32].qualifier_name | chemistry |
| mesh[32].descriptor_name | Fluorescent Dyes |
| mesh[33].qualifier_ui | |
| mesh[33].descriptor_ui | D036103 |
| mesh[33].is_major_topic | False |
| mesh[33].qualifier_name | |
| mesh[33].descriptor_name | Nanotechnology |
| mesh[34].qualifier_ui | |
| mesh[34].descriptor_ui | D008856 |
| mesh[34].is_major_topic | False |
| mesh[34].qualifier_name | |
| mesh[34].descriptor_name | Microscopy, Fluorescence |
| mesh[35].qualifier_ui | |
| mesh[35].descriptor_ui | D007700 |
| mesh[35].is_major_topic | False |
| mesh[35].qualifier_name | |
| mesh[35].descriptor_name | Kinetics |
| type | article |
| title | Deep Learning and Single-Molecule Localization Microscopy Reveal Nanoscopic Dynamics of DNA Entanglement Loci |
| biblio.issue | 6 |
| biblio.volume | 19 |
| biblio.last_page | 6249 |
| biblio.first_page | 6236 |
| topics[0].id | https://openalex.org/T10857 |
| topics[0].field.id | https://openalex.org/fields/13 |
| topics[0].field.display_name | Biochemistry, Genetics and Molecular Biology |
| topics[0].score | 0.9994999766349792 |
| topics[0].domain.id | https://openalex.org/domains/1 |
| topics[0].domain.display_name | Life Sciences |
| topics[0].subfield.id | https://openalex.org/subfields/1315 |
| topics[0].subfield.display_name | Structural Biology |
| topics[0].display_name | Advanced Electron Microscopy Techniques and Applications |
| topics[1].id | https://openalex.org/T10923 |
| topics[1].field.id | https://openalex.org/fields/31 |
| topics[1].field.display_name | Physics and Astronomy |
| topics[1].score | 0.9993000030517578 |
| topics[1].domain.id | https://openalex.org/domains/3 |
| topics[1].domain.display_name | Physical Sciences |
| topics[1].subfield.id | https://openalex.org/subfields/3107 |
| topics[1].subfield.display_name | Atomic and Molecular Physics, and Optics |
| topics[1].display_name | Force Microscopy Techniques and Applications |
| topics[2].id | https://openalex.org/T11582 |
| topics[2].field.id | https://openalex.org/fields/22 |
| topics[2].field.display_name | Engineering |
| topics[2].score | 0.9980000257492065 |
| topics[2].domain.id | https://openalex.org/domains/3 |
| topics[2].domain.display_name | Physical Sciences |
| topics[2].subfield.id | https://openalex.org/subfields/2204 |
| topics[2].subfield.display_name | Biomedical Engineering |
| topics[2].display_name | Nanopore and Nanochannel Transport Studies |
| funders[0].id | https://openalex.org/F4320322320 |
| funders[0].ror | https://ror.org/01q3tbs38 |
| funders[0].display_name | King Abdullah University of Science and Technology |
| is_xpac | False |
| apc_list | |
| apc_paid | |
| concepts[0].id | https://openalex.org/C45206210 |
| concepts[0].level | 2 |
| concepts[0].score | 0.8615248203277588 |
| concepts[0].wikidata | https://www.wikidata.org/wiki/Q2415817 |
| concepts[0].display_name | Nanoscopic scale |
| concepts[1].id | https://openalex.org/C121040770 |
| concepts[1].level | 3 |
| concepts[1].score | 0.6842541098594666 |
| concepts[1].wikidata | https://www.wikidata.org/wiki/Q215675 |
| concepts[1].display_name | Quantum entanglement |
| concepts[2].id | https://openalex.org/C171250308 |
| concepts[2].level | 1 |
| concepts[2].score | 0.591877818107605 |
| concepts[2].wikidata | https://www.wikidata.org/wiki/Q11468 |
| concepts[2].display_name | Nanotechnology |
| concepts[3].id | https://openalex.org/C192562407 |
| concepts[3].level | 0 |
| concepts[3].score | 0.5585938692092896 |
| concepts[3].wikidata | https://www.wikidata.org/wiki/Q228736 |
| concepts[3].display_name | Materials science |
| concepts[4].id | https://openalex.org/C147080431 |
| concepts[4].level | 2 |
| concepts[4].score | 0.5290388464927673 |
| concepts[4].wikidata | https://www.wikidata.org/wiki/Q1074953 |
| concepts[4].display_name | Microscopy |
| concepts[5].id | https://openalex.org/C552990157 |
| concepts[5].level | 2 |
| concepts[5].score | 0.5279454588890076 |
| concepts[5].wikidata | https://www.wikidata.org/wiki/Q7430 |
| concepts[5].display_name | DNA |
| concepts[6].id | https://openalex.org/C145912823 |
| concepts[6].level | 2 |
| concepts[6].score | 0.5272471308708191 |
| concepts[6].wikidata | https://www.wikidata.org/wiki/Q113558 |
| concepts[6].display_name | Dynamics (music) |
| concepts[7].id | https://openalex.org/C159467904 |
| concepts[7].level | 1 |
| concepts[7].score | 0.49813294410705566 |
| concepts[7].wikidata | https://www.wikidata.org/wiki/Q2001702 |
| concepts[7].display_name | Chemical physics |
| concepts[8].id | https://openalex.org/C32909587 |
| concepts[8].level | 2 |
| concepts[8].score | 0.47753655910491943 |
| concepts[8].wikidata | https://www.wikidata.org/wiki/Q11369 |
| concepts[8].display_name | Molecule |
| concepts[9].id | https://openalex.org/C102951782 |
| concepts[9].level | 2 |
| concepts[9].score | 0.4477611780166626 |
| concepts[9].wikidata | https://www.wikidata.org/wiki/Q49295 |
| concepts[9].display_name | Atomic force microscopy |
| concepts[10].id | https://openalex.org/C12554922 |
| concepts[10].level | 1 |
| concepts[10].score | 0.38709577918052673 |
| concepts[10].wikidata | https://www.wikidata.org/wiki/Q7100 |
| concepts[10].display_name | Biophysics |
| concepts[11].id | https://openalex.org/C185592680 |
| concepts[11].level | 0 |
| concepts[11].score | 0.23489168286323547 |
| concepts[11].wikidata | https://www.wikidata.org/wiki/Q2329 |
| concepts[11].display_name | Chemistry |
| concepts[12].id | https://openalex.org/C86803240 |
| concepts[12].level | 0 |
| concepts[12].score | 0.17984655499458313 |
| concepts[12].wikidata | https://www.wikidata.org/wiki/Q420 |
| concepts[12].display_name | Biology |
| concepts[13].id | https://openalex.org/C121332964 |
| concepts[13].level | 0 |
| concepts[13].score | 0.17335951328277588 |
| concepts[13].wikidata | https://www.wikidata.org/wiki/Q413 |
| concepts[13].display_name | Physics |
| concepts[14].id | https://openalex.org/C120665830 |
| concepts[14].level | 1 |
| concepts[14].score | 0.12071722745895386 |
| concepts[14].wikidata | https://www.wikidata.org/wiki/Q14620 |
| concepts[14].display_name | Optics |
| concepts[15].id | https://openalex.org/C54355233 |
| concepts[15].level | 1 |
| concepts[15].score | 0.11100679636001587 |
| concepts[15].wikidata | https://www.wikidata.org/wiki/Q7162 |
| concepts[15].display_name | Genetics |
| concepts[16].id | https://openalex.org/C84114770 |
| concepts[16].level | 2 |
| concepts[16].score | 0.09684982895851135 |
| concepts[16].wikidata | https://www.wikidata.org/wiki/Q46344 |
| concepts[16].display_name | Quantum |
| concepts[17].id | https://openalex.org/C178790620 |
| concepts[17].level | 1 |
| concepts[17].score | 0.0 |
| concepts[17].wikidata | https://www.wikidata.org/wiki/Q11351 |
| concepts[17].display_name | Organic chemistry |
| concepts[18].id | https://openalex.org/C24890656 |
| concepts[18].level | 1 |
| concepts[18].score | 0.0 |
| concepts[18].wikidata | https://www.wikidata.org/wiki/Q82811 |
| concepts[18].display_name | Acoustics |
| concepts[19].id | https://openalex.org/C62520636 |
| concepts[19].level | 1 |
| concepts[19].score | 0.0 |
| concepts[19].wikidata | https://www.wikidata.org/wiki/Q944 |
| concepts[19].display_name | Quantum mechanics |
| keywords[0].id | https://openalex.org/keywords/nanoscopic-scale |
| keywords[0].score | 0.8615248203277588 |
| keywords[0].display_name | Nanoscopic scale |
| keywords[1].id | https://openalex.org/keywords/quantum-entanglement |
| keywords[1].score | 0.6842541098594666 |
| keywords[1].display_name | Quantum entanglement |
| keywords[2].id | https://openalex.org/keywords/nanotechnology |
| keywords[2].score | 0.591877818107605 |
| keywords[2].display_name | Nanotechnology |
| keywords[3].id | https://openalex.org/keywords/materials-science |
| keywords[3].score | 0.5585938692092896 |
| keywords[3].display_name | Materials science |
| keywords[4].id | https://openalex.org/keywords/microscopy |
| keywords[4].score | 0.5290388464927673 |
| keywords[4].display_name | Microscopy |
| keywords[5].id | https://openalex.org/keywords/dna |
| keywords[5].score | 0.5279454588890076 |
| keywords[5].display_name | DNA |
| keywords[6].id | https://openalex.org/keywords/dynamics |
| keywords[6].score | 0.5272471308708191 |
| keywords[6].display_name | Dynamics (music) |
| keywords[7].id | https://openalex.org/keywords/chemical-physics |
| keywords[7].score | 0.49813294410705566 |
| keywords[7].display_name | Chemical physics |
| keywords[8].id | https://openalex.org/keywords/molecule |
| keywords[8].score | 0.47753655910491943 |
| keywords[8].display_name | Molecule |
| keywords[9].id | https://openalex.org/keywords/atomic-force-microscopy |
| keywords[9].score | 0.4477611780166626 |
| keywords[9].display_name | Atomic force microscopy |
| keywords[10].id | https://openalex.org/keywords/biophysics |
| keywords[10].score | 0.38709577918052673 |
| keywords[10].display_name | Biophysics |
| keywords[11].id | https://openalex.org/keywords/chemistry |
| keywords[11].score | 0.23489168286323547 |
| keywords[11].display_name | Chemistry |
| keywords[12].id | https://openalex.org/keywords/biology |
| keywords[12].score | 0.17984655499458313 |
| keywords[12].display_name | Biology |
| keywords[13].id | https://openalex.org/keywords/physics |
| keywords[13].score | 0.17335951328277588 |
| keywords[13].display_name | Physics |
| keywords[14].id | https://openalex.org/keywords/optics |
| keywords[14].score | 0.12071722745895386 |
| keywords[14].display_name | Optics |
| keywords[15].id | https://openalex.org/keywords/genetics |
| keywords[15].score | 0.11100679636001587 |
| keywords[15].display_name | Genetics |
| keywords[16].id | https://openalex.org/keywords/quantum |
| keywords[16].score | 0.09684982895851135 |
| keywords[16].display_name | Quantum |
| language | en |
| locations[0].id | doi:10.1021/acsnano.4c15364 |
| locations[0].is_oa | True |
| locations[0].source.id | https://openalex.org/S145476921 |
| locations[0].source.issn | 1936-0851, 1936-086X |
| locations[0].source.type | journal |
| locations[0].source.is_oa | False |
| locations[0].source.issn_l | 1936-0851 |
| locations[0].source.is_core | True |
| locations[0].source.is_in_doaj | False |
| locations[0].source.display_name | ACS Nano |
| locations[0].source.host_organization | https://openalex.org/P4310320006 |
| locations[0].source.host_organization_name | American Chemical Society |
| locations[0].source.host_organization_lineage | https://openalex.org/P4310320006 |
| locations[0].source.host_organization_lineage_names | American Chemical Society |
| locations[0].license | cc-by |
| locations[0].pdf_url | |
| locations[0].version | publishedVersion |
| locations[0].raw_type | journal-article |
| locations[0].license_id | https://openalex.org/licenses/cc-by |
| locations[0].is_accepted | True |
| locations[0].is_published | True |
| locations[0].raw_source_name | ACS Nano |
| locations[0].landing_page_url | https://doi.org/10.1021/acsnano.4c15364 |
| locations[1].id | pmid:39903818 |
| locations[1].is_oa | False |
| locations[1].source.id | https://openalex.org/S4306525036 |
| locations[1].source.issn | |
| locations[1].source.type | repository |
| locations[1].source.is_oa | False |
| locations[1].source.issn_l | |
| locations[1].source.is_core | False |
| locations[1].source.is_in_doaj | False |
| locations[1].source.display_name | PubMed |
| locations[1].source.host_organization | https://openalex.org/I1299303238 |
| locations[1].source.host_organization_name | National Institutes of Health |
| locations[1].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[1].license | |
| locations[1].pdf_url | |
| locations[1].version | publishedVersion |
| locations[1].raw_type | |
| locations[1].license_id | |
| locations[1].is_accepted | True |
| locations[1].is_published | True |
| locations[1].raw_source_name | ACS nano |
| locations[1].landing_page_url | https://pubmed.ncbi.nlm.nih.gov/39903818 |
| locations[2].id | pmh:oai:pubmedcentral.nih.gov:11841032 |
| locations[2].is_oa | True |
| locations[2].source.id | https://openalex.org/S2764455111 |
| locations[2].source.issn | |
| locations[2].source.type | repository |
| locations[2].source.is_oa | False |
| locations[2].source.issn_l | |
| locations[2].source.is_core | False |
| locations[2].source.is_in_doaj | False |
| locations[2].source.display_name | PubMed Central |
| locations[2].source.host_organization | https://openalex.org/I1299303238 |
| locations[2].source.host_organization_name | National Institutes of Health |
| locations[2].source.host_organization_lineage | https://openalex.org/I1299303238 |
| locations[2].license | cc-by |
| locations[2].pdf_url | |
| locations[2].version | submittedVersion |
| locations[2].raw_type | Text |
| locations[2].license_id | https://openalex.org/licenses/cc-by |
| locations[2].is_accepted | False |
| locations[2].is_published | False |
| locations[2].raw_source_name | ACS Nano |
| locations[2].landing_page_url | https://www.ncbi.nlm.nih.gov/pmc/articles/11841032 |
| indexed_in | crossref, pubmed |
| authorships[0].author.id | https://openalex.org/A5067447903 |
| authorships[0].author.orcid | https://orcid.org/0000-0002-6153-1089 |
| authorships[0].author.display_name | Maged F. Serag |
| authorships[0].countries | SA |
| authorships[0].affiliations[0].raw_affiliation_string | Biological and Environmental Science and Engineering Division |
| authorships[0].affiliations[1].institution_ids | https://openalex.org/I71920554 |
| authorships[0].affiliations[1].raw_affiliation_string | King Abdullah University of Science and Technology |
| authorships[0].institutions[0].id | https://openalex.org/I71920554 |
| authorships[0].institutions[0].ror | https://ror.org/01q3tbs38 |
| authorships[0].institutions[0].type | education |
| authorships[0].institutions[0].lineage | https://openalex.org/I71920554 |
| authorships[0].institutions[0].country_code | SA |
| authorships[0].institutions[0].display_name | King Abdullah University of Science and Technology |
| authorships[0].author_position | first |
| authorships[0].raw_author_name | Maged F. Serag |
| authorships[0].is_corresponding | False |
| authorships[0].raw_affiliation_strings | Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology |
| authorships[1].author.id | https://openalex.org/A5017035265 |
| authorships[1].author.orcid | https://orcid.org/0000-0003-3802-8669 |
| authorships[1].author.display_name | Maram Abadi |
| authorships[1].countries | SA |
| authorships[1].affiliations[0].raw_affiliation_string | Biological and Environmental Science and Engineering Division |
| authorships[1].affiliations[1].institution_ids | https://openalex.org/I71920554 |
| authorships[1].affiliations[1].raw_affiliation_string | King Abdullah University of Science and Technology |
| authorships[1].institutions[0].id | https://openalex.org/I71920554 |
| authorships[1].institutions[0].ror | https://ror.org/01q3tbs38 |
| authorships[1].institutions[0].type | education |
| authorships[1].institutions[0].lineage | https://openalex.org/I71920554 |
| authorships[1].institutions[0].country_code | SA |
| authorships[1].institutions[0].display_name | King Abdullah University of Science and Technology |
| authorships[1].author_position | middle |
| authorships[1].raw_author_name | Maram Abadi |
| authorships[1].is_corresponding | False |
| authorships[1].raw_affiliation_strings | Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology |
| authorships[2].author.id | https://openalex.org/A5007263246 |
| authorships[2].author.orcid | https://orcid.org/0000-0002-5755-4210 |
| authorships[2].author.display_name | Hajar Al‐Zarah |
| authorships[2].countries | SA |
| authorships[2].affiliations[0].institution_ids | https://openalex.org/I71920554 |
| authorships[2].affiliations[0].raw_affiliation_string | King Abdullah University of Science and Technology |
| authorships[2].affiliations[1].raw_affiliation_string | Biological and Environmental Science and Engineering Division |
| authorships[2].institutions[0].id | https://openalex.org/I71920554 |
| authorships[2].institutions[0].ror | https://ror.org/01q3tbs38 |
| authorships[2].institutions[0].type | education |
| authorships[2].institutions[0].lineage | https://openalex.org/I71920554 |
| authorships[2].institutions[0].country_code | SA |
| authorships[2].institutions[0].display_name | King Abdullah University of Science and Technology |
| authorships[2].author_position | middle |
| authorships[2].raw_author_name | Hajar Al-Zarah |
| authorships[2].is_corresponding | False |
| authorships[2].raw_affiliation_strings | Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology |
| authorships[3].author.id | https://openalex.org/A5034712757 |
| authorships[3].author.orcid | https://orcid.org/0000-0002-0171-8757 |
| authorships[3].author.display_name | Omar Adel Ibrahim |
| authorships[3].countries | SA |
| authorships[3].affiliations[0].raw_affiliation_string | Biological and Environmental Science and Engineering Division |
| authorships[3].affiliations[1].institution_ids | https://openalex.org/I71920554 |
| authorships[3].affiliations[1].raw_affiliation_string | King Abdullah University of Science and Technology |
| authorships[3].institutions[0].id | https://openalex.org/I71920554 |
| authorships[3].institutions[0].ror | https://ror.org/01q3tbs38 |
| authorships[3].institutions[0].type | education |
| authorships[3].institutions[0].lineage | https://openalex.org/I71920554 |
| authorships[3].institutions[0].country_code | SA |
| authorships[3].institutions[0].display_name | King Abdullah University of Science and Technology |
| authorships[3].author_position | middle |
| authorships[3].raw_author_name | Omar Ibrahim |
| authorships[3].is_corresponding | False |
| authorships[3].raw_affiliation_strings | Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology |
| authorships[4].author.id | https://openalex.org/A5014133370 |
| authorships[4].author.orcid | https://orcid.org/0000-0002-6663-2807 |
| authorships[4].author.display_name | Satoshi Habuchi |
| authorships[4].countries | SA |
| authorships[4].affiliations[0].raw_affiliation_string | Biological and Environmental Science and Engineering Division |
| authorships[4].affiliations[1].institution_ids | https://openalex.org/I71920554 |
| authorships[4].affiliations[1].raw_affiliation_string | King Abdullah University of Science and Technology |
| authorships[4].institutions[0].id | https://openalex.org/I71920554 |
| authorships[4].institutions[0].ror | https://ror.org/01q3tbs38 |
| authorships[4].institutions[0].type | education |
| authorships[4].institutions[0].lineage | https://openalex.org/I71920554 |
| authorships[4].institutions[0].country_code | SA |
| authorships[4].institutions[0].display_name | King Abdullah University of Science and Technology |
| authorships[4].author_position | last |
| authorships[4].raw_author_name | Satoshi Habuchi |
| authorships[4].is_corresponding | False |
| authorships[4].raw_affiliation_strings | Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology |
| has_content.pdf | False |
| has_content.grobid_xml | False |
| is_paratext | False |
| open_access.is_oa | True |
| open_access.oa_url | https://doi.org/10.1021/acsnano.4c15364 |
| open_access.oa_status | hybrid |
| open_access.any_repository_has_fulltext | False |
| created_date | 2025-10-10T00:00:00 |
| display_name | Deep Learning and Single-Molecule Localization Microscopy Reveal Nanoscopic Dynamics of DNA Entanglement Loci |
| has_fulltext | False |
| is_retracted | False |
| updated_date | 2025-11-06T03:46:38.306776 |
| primary_topic.id | https://openalex.org/T10857 |
| primary_topic.field.id | https://openalex.org/fields/13 |
| primary_topic.field.display_name | Biochemistry, Genetics and Molecular Biology |
| primary_topic.score | 0.9994999766349792 |
| primary_topic.domain.id | https://openalex.org/domains/1 |
| primary_topic.domain.display_name | Life Sciences |
| primary_topic.subfield.id | https://openalex.org/subfields/1315 |
| primary_topic.subfield.display_name | Structural Biology |
| primary_topic.display_name | Advanced Electron Microscopy Techniques and Applications |
| related_works | https://openalex.org/W2258058860, https://openalex.org/W2065830994, https://openalex.org/W2092555887, https://openalex.org/W1964921276, https://openalex.org/W2741523612, https://openalex.org/W2102682197, https://openalex.org/W2101135880, https://openalex.org/W2071709897, https://openalex.org/W2345344602, https://openalex.org/W4394584065 |
| cited_by_count | 5 |
| counts_by_year[0].year | 2025 |
| counts_by_year[0].cited_by_count | 5 |
| locations_count | 3 |
| best_oa_location.id | doi:10.1021/acsnano.4c15364 |
| best_oa_location.is_oa | True |
| best_oa_location.source.id | https://openalex.org/S145476921 |
| best_oa_location.source.issn | 1936-0851, 1936-086X |
| best_oa_location.source.type | journal |
| best_oa_location.source.is_oa | False |
| best_oa_location.source.issn_l | 1936-0851 |
| best_oa_location.source.is_core | True |
| best_oa_location.source.is_in_doaj | False |
| best_oa_location.source.display_name | ACS Nano |
| best_oa_location.source.host_organization | https://openalex.org/P4310320006 |
| best_oa_location.source.host_organization_name | American Chemical Society |
| best_oa_location.source.host_organization_lineage | https://openalex.org/P4310320006 |
| best_oa_location.source.host_organization_lineage_names | American Chemical Society |
| best_oa_location.license | cc-by |
| best_oa_location.pdf_url | |
| best_oa_location.version | publishedVersion |
| best_oa_location.raw_type | journal-article |
| best_oa_location.license_id | https://openalex.org/licenses/cc-by |
| best_oa_location.is_accepted | True |
| best_oa_location.is_published | True |
| best_oa_location.raw_source_name | ACS Nano |
| best_oa_location.landing_page_url | https://doi.org/10.1021/acsnano.4c15364 |
| primary_location.id | doi:10.1021/acsnano.4c15364 |
| primary_location.is_oa | True |
| primary_location.source.id | https://openalex.org/S145476921 |
| primary_location.source.issn | 1936-0851, 1936-086X |
| primary_location.source.type | journal |
| primary_location.source.is_oa | False |
| primary_location.source.issn_l | 1936-0851 |
| primary_location.source.is_core | True |
| primary_location.source.is_in_doaj | False |
| primary_location.source.display_name | ACS Nano |
| primary_location.source.host_organization | https://openalex.org/P4310320006 |
| primary_location.source.host_organization_name | American Chemical Society |
| primary_location.source.host_organization_lineage | https://openalex.org/P4310320006 |
| primary_location.source.host_organization_lineage_names | American Chemical Society |
| primary_location.license | cc-by |
| primary_location.pdf_url | |
| primary_location.version | publishedVersion |
| primary_location.raw_type | journal-article |
| primary_location.license_id | https://openalex.org/licenses/cc-by |
| primary_location.is_accepted | True |
| primary_location.is_published | True |
| primary_location.raw_source_name | ACS Nano |
| primary_location.landing_page_url | https://doi.org/10.1021/acsnano.4c15364 |
| publication_date | 2025-02-04 |
| publication_year | 2025 |
| referenced_works | https://openalex.org/W4377046888, https://openalex.org/W4321611243, https://openalex.org/W4366819772, https://openalex.org/W4324329953, https://openalex.org/W2787020583, https://openalex.org/W2801396275, https://openalex.org/W4361207695, https://openalex.org/W3126069796, https://openalex.org/W4360619013, https://openalex.org/W403165401, https://openalex.org/W2902924420, https://openalex.org/W2008999895, https://openalex.org/W2332789681, https://openalex.org/W4388376074, https://openalex.org/W2742097753, https://openalex.org/W2248837496, https://openalex.org/W1509793409, https://openalex.org/W2019564971, https://openalex.org/W2468844020, https://openalex.org/W1997541110, https://openalex.org/W2124206695, https://openalex.org/W2772867596, https://openalex.org/W2730528681, https://openalex.org/W1973751550, https://openalex.org/W4376612519, https://openalex.org/W2901864024, https://openalex.org/W2050229457, https://openalex.org/W2115590079, https://openalex.org/W1978012472, https://openalex.org/W2103501660, https://openalex.org/W2002952493, https://openalex.org/W2020094987, https://openalex.org/W2624077781, https://openalex.org/W2087929985, https://openalex.org/W3098419284, https://openalex.org/W3104053397, https://openalex.org/W3100386331, https://openalex.org/W227143473 |
| referenced_works_count | 38 |
| abstract_inverted_index.a | 44, 62 |
| abstract_inverted_index.In | 171 |
| abstract_inverted_index.We | 57, 99 |
| abstract_inverted_index.as | 61 |
| abstract_inverted_index.at | 3, 43, 53, 136 |
| abstract_inverted_index.be | 186 |
| abstract_inverted_index.in | 11, 183 |
| abstract_inverted_index.is | 49 |
| abstract_inverted_index.of | 15, 128, 148, 157, 180 |
| abstract_inverted_index.on | 87 |
| abstract_inverted_index.to | 9, 29, 38, 91, 132, 167, 188 |
| abstract_inverted_index.we | 34 |
| abstract_inverted_index.DNA | 60, 134, 138 |
| abstract_inverted_index.Our | 110, 152 |
| abstract_inverted_index.and | 65, 81, 145, 161 |
| abstract_inverted_index.are | 104 |
| abstract_inverted_index.can | 185 |
| abstract_inverted_index.due | 8 |
| abstract_inverted_index.for | 120 |
| abstract_inverted_index.our | 173 |
| abstract_inverted_index.the | 4, 12, 54, 70, 79, 83, 102, 108, 125, 133, 149, 177, 181 |
| abstract_inverted_index.Deep | 19 |
| abstract_inverted_index.SMLM | 184 |
| abstract_inverted_index.deep | 84 |
| abstract_inverted_index.dyes | 130 |
| abstract_inverted_index.fast | 45 |
| abstract_inverted_index.from | 95 |
| abstract_inverted_index.that | 101, 113, 176 |
| abstract_inverted_index.this | 36 |
| abstract_inverted_index.time | 46 |
| abstract_inverted_index.used | 58, 187 |
| abstract_inverted_index.with | 22 |
| abstract_inverted_index.Here, | 33 |
| abstract_inverted_index.along | 78, 107 |
| abstract_inverted_index.chain | 73, 93, 114 |
| abstract_inverted_index.data. | 98 |
| abstract_inverted_index.found | 100 |
| abstract_inverted_index.local | 117, 162, 191 |
| abstract_inverted_index.loci. | 151 |
| abstract_inverted_index.model | 63 |
| abstract_inverted_index.probe | 30 |
| abstract_inverted_index.their | 67 |
| abstract_inverted_index.these | 31, 88, 141 |
| abstract_inverted_index.using | 69 |
| abstract_inverted_index.which | 48 |
| abstract_inverted_index.(SMLM) | 26 |
| abstract_inverted_index.Lambda | 59 |
| abstract_inverted_index.buffer | 122 |
| abstract_inverted_index.direct | 155 |
| abstract_inverted_index.images | 90 |
| abstract_inverted_index.level. | 56 |
| abstract_inverted_index.model, | 74 |
| abstract_inverted_index.offers | 27 |
| abstract_inverted_index.poorly | 51 |
| abstract_inverted_index.reveal | 39 |
| abstract_inverted_index.scale, | 47 |
| abstract_inverted_index.sparse | 96 |
| abstract_inverted_index.system | 64 |
| abstract_inverted_index.creates | 116 |
| abstract_inverted_index.current | 16 |
| abstract_inverted_index.imaging | 17, 169 |
| abstract_inverted_index.modeled | 66 |
| abstract_inverted_index.polymer | 41, 159 |
| abstract_inverted_index.predict | 92 |
| abstract_inverted_index.remains | 6 |
| abstract_inverted_index.results | 174 |
| abstract_inverted_index.suggest | 175 |
| abstract_inverted_index.trained | 82 |
| abstract_inverted_index.Tracking | 140 |
| abstract_inverted_index.approach | 153 |
| abstract_inverted_index.barriers | 119 |
| abstract_inverted_index.contours | 94 |
| abstract_inverted_index.discrete | 137 |
| abstract_inverted_index.dynamics | 2, 42, 160 |
| abstract_inverted_index.kinetics | 127, 179 |
| abstract_inverted_index.learning | 20, 85 |
| abstract_inverted_index.leverage | 35 |
| abstract_inverted_index.provides | 154 |
| abstract_inverted_index.segments | 142 |
| abstract_inverted_index.temporal | 13 |
| abstract_inverted_index.wormlike | 72 |
| abstract_inverted_index.addition, | 172 |
| abstract_inverted_index.affecting | 124 |
| abstract_inverted_index.algorithm | 86 |
| abstract_inverted_index.contours, | 80 |
| abstract_inverted_index.contours. | 109 |
| abstract_inverted_index.diffusion | 118 |
| abstract_inverted_index.dynamics. | 32 |
| abstract_inverted_index.entangled | 40 |
| abstract_inverted_index.generated | 75 |
| abstract_inverted_index.indicated | 112 |
| abstract_inverted_index.migration | 147 |
| abstract_inverted_index.molecular | 1, 163 |
| abstract_inverted_index.molecules | 135 |
| abstract_inverted_index.nanoscale | 5, 158 |
| abstract_inverted_index.segments. | 139 |
| abstract_inverted_index.simulated | 76, 89 |
| abstract_inverted_index.switching | 121, 178 |
| abstract_inverted_index.Microscopy | 25 |
| abstract_inverted_index.conjugated | 131 |
| abstract_inverted_index.integrated | 21 |
| abstract_inverted_index.molecules, | 123 |
| abstract_inverted_index.nanoscopic | 190 |
| abstract_inverted_index.previously | 165 |
| abstract_inverted_index.relatively | 50 |
| abstract_inverted_index.resolution | 14 |
| abstract_inverted_index.stochastic | 144 |
| abstract_inverted_index.understood | 52 |
| abstract_inverted_index.assessments | 111 |
| abstract_inverted_index.challenging | 7 |
| abstract_inverted_index.distributed | 106 |
| abstract_inverted_index.fluorescent | 129 |
| abstract_inverted_index.integration | 37 |
| abstract_inverted_index.limitations | 10 |
| abstract_inverted_index.techniques. | 18, 170 |
| abstract_inverted_index.Localization | 24 |
| abstract_inverted_index.characterize | 189 |
| abstract_inverted_index.conventional | 168 |
| abstract_inverted_index.demonstrated | 143 |
| abstract_inverted_index.entanglement | 68, 115, 150 |
| abstract_inverted_index.environments | 164 |
| abstract_inverted_index.fluorophores | 182 |
| abstract_inverted_index.inaccessible | 166 |
| abstract_inverted_index.localization | 97 |
| abstract_inverted_index.subdiffusive | 146 |
| abstract_inverted_index.Understanding | 0 |
| abstract_inverted_index.environments. | 192 |
| abstract_inverted_index.localizations | 77, 103 |
| abstract_inverted_index.opportunities | 28 |
| abstract_inverted_index.self-avoiding | 71 |
| abstract_inverted_index.visualization | 156 |
| abstract_inverted_index.photoswitching | 126 |
| abstract_inverted_index.Single-Molecule | 23 |
| abstract_inverted_index.heterogeneously | 105 |
| abstract_inverted_index.single-molecule | 55 |
| cited_by_percentile_year.max | 98 |
| cited_by_percentile_year.min | 97 |
| countries_distinct_count | 1 |
| institutions_distinct_count | 5 |
| citation_normalized_percentile.value | 0.98896334 |
| citation_normalized_percentile.is_in_top_1_percent | True |
| citation_normalized_percentile.is_in_top_10_percent | True |