Scientific focus and article selection
Protocols, data, samples, comments, articles
Scientific focus and article selection. NanoBubbles’ replication initiative focuses on a scientific paradox: the publication of a large number of articles reporting the use of nanoparticles as probes for the detection of specific ions or molecules inside cells. It is a paradox because to detect their targets, probes need to be in contact with them and it has been known for many decades that nanoparticles enter cells by endocytosis, a phenomenon that results in their entrapment in compartments where they are isolated from the cell machinery. To shed light on this paradox, we attempt the replication of the most cited articles in this field. The approach we followed to select articles for replication is described in more details in Said et al, Selecting candidate articles for replication: the NanoBubbles replication initiative corpus creation.
Open science approach. We harness open science practices that have been pioneered in other fields but are either uncommon or non-existent yet in the field of bionanoscience: preprints (relatively common), post-publication peer review (uncommon), pre-registration of protocols (non-existent in this field), open peer review, full sharing of experimental data (uncommon). These practices have several advantages in general and specifically in a case of contested science: we are deliberately facilitating and encouraging the engagement of the authors of the articles we are replicating (and the community at large) from the drafting of protocols to the re-analysis of our work. We are even going further with a call for others to replicate our own work.
The team. The replication team was initially composed of Mustafa Gharib (post-doctoral researcher, chemistry), Maha Said (post-doctoral researcher, biology) and Raphaël Lévy (PI, physics, nanobio). Early 2026, Mustafa left us to take a new position in Istanbul (Turkey). In 2026, two other post-doctoral researchers in chemistry joined us: Valamarthi Mahendran and Omar El Dahshan. The team benefited from the essential support of NanoBubbles project managers, first Zoé Toure, who left early 2025 to take another position, and then Nikolina Domacinovic. For specific additional expertise or skills, we are reaching out to additional collaborators (e.g. for example, for the first replication, Samia Szrig, Thomas Pons, Nicole Hondlow).
Protocols, data, articles.
| Output type | Reference | Related to | DOI or other identifier |
|---|---|---|---|
| Preprint (not intended for publication in a journal) | Said, M.; Gharib, M.; Rost, N.C.V.; Lévy, R. Selecting candidate articles for replication: the NanoBubbles replication initiative corpus creation; Zenodo, 2025 | The replication initiative | doi:10.5281/zenodo.15432460 |
| Article (Perspective) | Said, M.; Gharib, M.; Lévy, R. Towards More Robust Nanobioscience: Launching the NanoBubbles Replication Initiative; Angewandte Chemie International Edition, 2026 | The replication initiative | doi:10.1002/anie.202511631 |
| Post-Publication peer review comment | Gharib, M.; Said, M.; Lévy, R.; Post-Publication Peer Review of ““Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions” by Zhu et al, 2012. PubPeer, 2023 | The first replication | https://pubpeer.com/publications/7C749EA281BD18BED4F3672FE6A126#2 |
| Preprint (Pre-registration) | Said, M.; Gharib, M.; Zrig, S.; Lévy, R. Replication of “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions.” Open Science Framework, 2023 | The first replication | doi:10.31219/osf.io/kf9qe |
| Post-Publication peer review comment | Gharib, M.; Response to concerns regarding the characterization of the AE-TPEA in our pre-registration. PubPeer, 2025 | The first replication | https://pubpeer.com/publications/C7A3BE191359B7442544072E569A34#5 |
| Preprint (Registered report) | Gharib, M.; Said, M.; Pons, T.; Hondow, N.; Zrig, S.; Lévy, R. Failed, Aborted Replication of “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions”. Open Science Framework, 2025 | The first replication | doi:10.31219/osf.io/2x3hv_v3 |
| Article (Correspondence) | Gharib, M.; Said, M.; Lévy, R. Correspondence on “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions”; Angewandte Chemie International Edition, 2026 | The first replication | doi:epdf/10.1002/anie.4904466 |
| Article (Registered report) | Gharib, M.; Said, M.; Pons, T.; Hondow, N.; Zrig, S.; Lévy, R. Failed, Aborted Replication of “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions”. R Soc Open Sci. 2026. | The first replication | doi:10.1098/rsos.252457 |
| Data set | Gharib, M.; Said, M.; Pons, T.; Hondow, N.; Zrig, S.; Lévy, R. FCS and TEM data of the replication of “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ion”. Zenodo. 2025 | The first replication | https://doi.org/10.5281/zenodo.15348672 |
| Chemical reaction and sample sharing at the Chemotion repository | Gharib, M.; Said, M.; Zrig, S.; Lévy, R.; Reaction ID CRR-53507 ; Product Name N’-[2-[bis(2-pyridylmethyl)amino]ethyl]-N’-(2-pyridylmethyl)ethane-1,2-diamine ; Sample vial available. Chemotion, 2025 | The first replication | doi:10.14272/reaction/SA-FUHFF-UHFFFADPSC-ICMHKEWHVR-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ |
| Post-Publication peer review comment | Gharib, M.; Said, M.; Lévy, R.; Response to Zhu et al’s response to our Post-Publication Peer Review and attempted Replication of their 2012 article entitled “Carbon-Dot-Based Dual-Emission Nanohybrid Produces a Ratiometric Fluorescent Sensor for In Vivo Imaging of Cellular Copper Ions”, PubPeer, 2026 | The first replication | https://pubpeer.com/publications/7C749EA281BD18BED4F3672FE6A126#5 |
| Preprint (Registered report) | Said, M.; Gharib, M.; Lévy, R. Replication of “Nano-Flares: Probes for Transfection and mRNA Detection in Living Cells” 2025. Open Science Framework | The second replication | doi:10.31219/osf.io/q8zsg_v3. |
Scientific advisory board. The team benefits from critical and supportive advice from an international multidisciplinary advisory board that has the following roles: 1) provide input, hints, tips and advice on the NanoBubbles replication project short- and long-term plans; 2) help to prioritize steps and redirect the project (should that be needed; 3) peer-review one or more of the registered reports. Membership of the board does not imply endorsement of any specific action of the replication team. We are grateful to Olavo Amaral (Brazil), Arwyn Jones (UK), Cécilia Ménard Moyon (France), Nicole C Nelson (USA), Wolfgang Parak (Germany) and Georgina Such (Australia) for their contributions to the board. Cécilia Ménard Moyon is chairing the board.
In the news:
- Nanoscience is latest discipline to embrace large-scale replication efforts, David Adam for Nature News, 17 February 2026
- La réplication est un sport de combat, Lucile Veissier for TheMetaNews, 27 February 2026
- De l’art difficile de reproduire des expériences scientifiques, David Larousserie pour Le Monde, 4 mars 2026
