Output & Publications

Output & Publications

Below you will find all publications and other interesting output from the SuperCol project.

Publications

2020

  • Frank Scheffold: Pathways and challenges towards a complete characterization of microgels Nature Commun 11, 4315 (2020) DOI: 10.1038/s41467-020-17774-5

2021

  • Indra Van Zundert, Maria Bravo, Olivier Deschaume, Pierre Cybulski, Carmen Bartic, Johan Hofkens, Hiroshi Uji-i, Beatrice Fortuni and Susana Rocha: Versatile and robust method for antibody conjugation to nanoparticles with high targeting efficiency Pharmaceutics 2021, 13, 2153. DOI: 10.3390/pharmaceutics13122153
  • Yuyang Wang, Heiner Friedrich, Ilja Voets, Peter Zijlstra, Lorenzo Albertazzi: Correlative imaging for polymer science Polymer Science 59, 1232 (2021). DOI: 10.1002/pol.20210013

2022

  • Rodrigo Rivas-Barbosa, Jose Ruiz-Franco, Mayra A. Lara-Peña, Jacopo Cardellini, Angel Licea-Claverie, Fabrizio Camerin, Emanuela Zaccarelli, Marco Laurati: Link between morphology, structure and interactions of composite microgels Macromolecules 2022, 55, 5, 1834–1843 DOI: 10.1021/acs.macromol.1c02171
  • Aleksandra K. Adamczyk, Teun A. P. M. Huijben, Miguel Sison, Andrea Di Luca, Germán Chiarelli, Stefano Vanni, Sophie Brasselet, Kim I. Mortensen, Fernando D. Stefani, Mauricio Pilo-Pais, and Guillermo P. Acuna: DNA Self-Assembly of Single Molecules with Deterministic Position and Orientation ACSNano first published September 6, 2022. DOI: 10.1021/acsnano.2c06936
  • Wenxin Wei, Francesca Mazzotta, Ingo Lieberwirth, Katharina Landfester, Calum T. J. Ferguson, and Kai A. I. Zhang: Aerobic Photobiocatalysis Enabled by Combining Core–Shell Nanophotoreactors and Native Enzymes  J. Am. Chem. Soc. 144, 7320–7326 (2022) DOI: 10.1021/jacs.2c00576
  • Marina de Souza Melchiors, Tsvetomir Ivanov, Iain Harley, Claudia Sayer, Pedro HH Araújo, Lucas Caire da Silva, Calum TJ Ferguson, Katharina Landfester Membrane Manipulation of Giant Unilamellar Polymer Vesicles with a Temperature‐Responsive Polymer Angewandte Chemie 2022 DOI: 10.1002/anie.202207998
  • Yong Ren ,Zhixuan Zhou ,Konrad Maxeiner ,Anke Kaltbeitzel ,Iain Harley ,Jiaqi Xing ,Yingke Wu ,Manfred Wagner ,Katharina Landfester ,Ingo Lieberwirth ,Tanja Weil,David Y.W. Ng : Phasor-Fluorescence Lifetime Imaging Correlates Dynamics of in-situ Amyloid Nanostructures to Respiratory Dysfunction ChemRxiv preprint DOI: 10.26434/chemrxiv-2022-rk7pv-v2

2023

  • Xhorxhina Shaulli, Rodrigo Rivas-Barbosa, Maxime J. Bergman, Chi Zhang, Nicoletta Gnan, Frank Scheffold, and Emanuela Zaccarelli: Probing Temperature Responsivity of Microgels and Its Interplay with a Solid Surface by Super-Resolution Microscopy and Numerical Simulations. ACS Nano 2023, Published online January 19, 2023. DOI: 10.1021/acsnano.2c07569
  • Teun A. P. M. Huijben, Sarojini Mahajan, Peter Zijlstra, Rodolphe Marie, Kim I. Mortensen: Exact particle-enhanced point-spread function unlocks 3D super-resolution localization microscopy on nanoparticles arXiv:2306.08148 DOI: 10.48550/arXiv.2306.08148
  • Tetsuhiro Kudo, Boris Louis, Hikaru Sotome, Jui-Kai Chen, Syoji Ito, Hiroshi Miyasaka, Hiroshi Masuhara, Johan Hofkens and Roger Bresolí-Obach : Gaining control on optical force by the stimulated-emission resonance effect Chem. Sci., 14, 10087-10095 (2023) DOI: 10.1039/D3SC01927F
  • Jiyao Yu ,Tommaso Marchesi D’Alvise ,Iain Harley ,Adam Krysztofik ,Ingo Lieberwirth ,Przemyslaw Pula ,Pawel W. Majewski ,Bartlomiej Graczykowski ,Johannes Hunger ,Katharina Landfester ,Christopher V. Synatschke ,Tanja Weil : Ion and Molecular Sieving with Ultrathin Polydopamine Nanomembranes ChemRxiv preprint DOI: 10.26434/chemrxiv-2023-3btbw
  • Arjaree Jobdeedamrong, Shoupeng Cao, Iain Harley, Daniel Crespy, Katharina Landfester and Lucas Caire da Silva: Assembly of biomimetic microreactors using caged-coacervate droplets Nanoscale 15, 2561-2566 (2023) DOI: 10.1039/D2NR05101J
  • Patrick Roth, Raphael Meyer, Iain Harley, Katharina Landfester, Ingo Lieberwirth, Manfred Wagner, David YW Ng, Tanja Weil Supramolecular assembly guided by photolytic redox cycling Nature Synthesis 2, 980–988 2023 DOI: 10.1038/s44160-023-00343-1
  • Maria Antonieta Ramirez-Morales, Elisa De Luca, Chiara Coricciati, Alberto Rainer, Giuseppe Gigli, Giuseppe Mele, Pier Paolo Pompa, and Maria Ada Malvindi. Dual-color core–shell silica nanosystems for advanced super-resolution biomedical imaging. Nanoscale Adv. (2023), doi: 10.1039/d3na00310h
  • Andrea Belluati, Iain Harley, Ingo Lieberwirth, Nico Bruns An Outer Membrane‐Inspired Polymer Coating Protects and Endows Escherichia coli with Novel Functionalities Small 2023 DOI:10.1002/smll.202303384
  • José Ruiz-Franco, Rodrigo Rivas-Barbosa, Mayra A. Lara-Peña,de José R. Villanueva-Valencia, Angel Licea-Claverie, Emanuela Zaccarelli and Marco Laurati. Concentration and temperature dependent interactions and state diagram of dispersions of copolymer microgels. Soft Matter 19, 3614-3628 (2023) DOI: 10.1039/D3SM00120B

2024

  • Vincenzo Lamberti, Mathias Dolci, and Peter Zijlstra: Continuous Monitoring Biosensing Mediated by Single-Molecule Plasmon-Enhanced Fluorescence in Complex Matrices ACS Nano 18, 5805–5813 (2024) DOI: 10.1021/acsnano.3c12428
  • Aleksandra K. Adamczyk, Teun A.P.M. Huijben, Karol Kolataj, Fangjia Zhu, Rodolphe Marie, Fernando D. Stefani, Guillermo P. Acuna: Towards full control of molecular exciton energy transfer via FRET in DNA origami assemblies arXiv:2402.06292 DOI: 10.48550/arXiv.2402.06292
  • Kasper R. Okholm, Sjoerd W. Nooteboom, Vincenzo Lamberti, Swayandipta Dey, Peter Zijlstra, Duncan S. Sutherland: Kinetics and dynamics of single-molecule multivalent interactions revealed by plasmon-enhanced fluorescence bioRxiv preprint DOI: 10.1101/2023.12.08.570798
  • Jeena M. Thekkeyil ,Julian Link ,Jian Zhang ,Luis Andre Baptista ,Hendrik R. A. Jonker ,Iain Harley ,Petri Turunen ,Liyang Cui ,Ingo Lieberwirth ,Katharina Landfester ,Robert Graf ,Manfred Wagner ,Jianghong Rao ,David Ng ,Tanja Weil : Chaperone-derived Cu(I)-binding peptide nanofibers disrupt copper homeostasis in cancer cells Angew. Chem. 63, e202412477 (2024) DOI: 10.1002/anie.202412477
  • Sjoerd W. Nooteboom,Kasper R. Okholm ,Vincenzo Lamberti ,Bas Oomen ,Duncan S.Sutherland ,Peter Zijlstra: Real-time microsecond dynamics of single biomolecules probed by plasmon-enhanced fluorescence Nano Lett. 24, 11641–11647 (2024) DOI: 10.1021/acs.nanolett.4c03220
  • Diego Herrera-Ochoa ,Iván Llano ,Consuelo Ripoll ,Pierre Cybulski ,Martin Kreuzer,Susana Rocha ,Eva M. García-Frutos ,Iván Bravo ,Andrés Garzón Ruiz: A Fluorescent Probe for Protein Misfolding and Aggregation Due to Oxidative Stress Based on a 7-Azaindole-BODIPY Derivative ChemRxiv preprint DOI: 10.26434/chemrxiv-2024-94b66
  • Swayandipta Dey,Rodrigo Rivas-Barbosa,Francesco Sciortino, Emanuela Zaccarelli and Peter Zijlstra: Biomolecular interactions on densely coated nanoparticles: a single-molecule perspective Nanoscale 16, 4872-4879 (2024) DOI: 10.1039/D3NR06140J
  • Teun A.P.M. Huijben, Rodolphe Marie, Kim I. Mortensen: Quantitative Analysis for Single-Molecule Localization Microscopy:“From PSF to Information” SRM for Material Science, 111-132 (2024) Taylor Francis 10.1201/9781003220688-6
  • Kasper R Okholm, Sjoerd W Nooteboom, Johan Nygaard Vinther, Vincenzo Lamberti, Swayandipta Dey, Ebbe Sloth Andersen, Peter Zijlstra, Duncan S Sutherland: Single-Molecule Multivalent Interactions Revealed by Plasmon-Enhanced Fluorescence ACS Nano 18, 35429–35442 (2024) DOI: 10.1021/acsnano.4c12600
  • Teun APM Huijben, Sarojini Mahajan, Masih Fahim, Peter Zijlstra, Rodolphe Marie, Kim I Mortensen: Point-Spread Function Deformations Unlock 3D Localization Microscopy on Spherical Nanoparticles ACS Nano 18, 29832–29845 (2024) DOI: 10.1021/acsnano.4c09719
  • Diego Herrera-Ochoa, Iván Llano, Consuelo Ripoll, Pierre Cybulski, Martin Kreuzer, Susana Rocha, Eva M. García-Frutos, Iván Bravo, and Adrés Garzón-Ruiz: Protein aggregation monitoring in cells under oxidative stress: a novel fluorescent probe based on a 7-azaindole-BODIPY derivative J. Mater. Chem. B 12, 7577-7590 (2024) DOI: 10.1039/D4TB00567H
  • Aleksandra K. Adamczyk, Fangjia Zhu, Daniel Schäfer, Yuya Kanehira, Sergio Kogikoski Jr., Ilko Bald, Sebastian Schlücker, Karol Kołątaj, Fernando D. Stefani, Guillermo P. Acuna: Coupling Single Molecules to DNA-Based Optical Antennas with Position and Orientation Control ACS Photon. 11, 5267–5272 (2024) DOI: 10.1021/acsphotonics.4c01506

2025

  • Francesca Mazzotta, Sharafudheen Pottanam Chali, Ingo Lieberwirth, Calum T. J. Ferguson, and Katharina Landfester: Tailoring reactive handles on the surface of nanoparticles for covalent conjugation of biomolecules Polym. Chem. 16, 433-440 (2025) DOI: 10.1039/d4py01119h
  • Xhorxhina Shaulli, Aura Maria Moreno-Echeverri, Mariza Andoni, Eileen Waeber, Shivaprakash N. Ramakrishna, Cornelia Fritsch, Dimitri Vanhecke, Barbara Rothen-Rutishauser, Frank Scheffold: Polymer Nano-Carrier-Mediated Gene Delivery: Visualizing and Quantifying DNA Encapsulation Using dSTORM Small 21, 2405929 (2025) DOI: 10.1002/smll.202405929
  • Rodrigo Rivas-Barbosa, Fabrizio Camerin, Jacopo Vialetto, Shivaprakash N. Ramakrishna, Lucio Isa, Emanuela Zaccarelli: Comparing the Structure of Microgels at Liquid–Liquid and Solid–Liquid Interfaces Langmuir 41, 16674–16684 (2025) DOI: 10.1021/acs.langmuir.5c02599
  • Pierre Cybulski, Maria Bravo, Jim Jui-Kai Chen, Indra Van Zundert, Sandra Krzyzowska, Farsai Taemaitree, Hiroshi Uji-i, Johan Hofkens, Susana Rocha, Beatrice Fortuni: Nanoparticle Accumulation and Penetration in 3D Tumor Models: the Effect of Size, Shape, and Surface Charge Front. Cell Dev. Biol. 12, 1520078 (2025) DOI: 10.3389/fcell.2024.1520078
  • Tiziano Di Giulio, Maria Antonieta Ramírez-Morales, Valentina Mastronardi, Giuseppe Mele, Rosaria Brescia, Pier Paolo Pompa, Cosimino Malitesta, Giuseppe Egidio De Benedetto, Mauro Moglianetti, Maria Ada Malvindi, Elisabetta Mazzotta: Electrochemical Determination of Gallic Acid in Tea Samples Using Pyramidal Pt Nanoparticles Adv. Elec. Mater. 11, 2400792 (2025) DOI: 10.1002/aelm.202400792
  • Iain Harley, Anke Kaltbeitzel, Francesca Mazzotta, Kaloian Koynov, Sarah S. Lembke, Thao P. Doan-Nguyen, Katharina Landfester, and Ingo Lieberwirth: Nanoparticle characterisation via 2D classification using single particle averaging Nanoscale Horiz. 10, 1642-1652 (2025) DOI: 10.1039/D5NH00094G
  • Sarojini Mahajan, Yuyang Wang, Teun APM Huijben, Rodolphe Marie, Peter Zijlstra: Single-shot Stokes polarimetry of plasmon-coupled single-molecule fluorescence Nanophotonics, accepted (2025) DOI: 10.1515/nanoph-2025-0352
  • Iain Harley, Francesca Mazzotta, Xhorxhina Shaulli, Frank Scheffold, Katharina Landfester, Ingo Lieberwirth: Practical considerations for plunge freezing samples over 40 °C for Cryo-EM Micron 188, 103745 (2025) DOI: 10.1016/j.micron.2024.103745

SuperCol Training Sessions

  • Super-resolution microscopy (SRM) and data analysis (13 April, 2021).
  • Modeling of Particle interactions (May 2021).
  • CV Canvas Model session, by Ttopstart in Copenhagen (March 2022).
  • Workshop Outreach, by ElementC in Copenhagen (March 2022).
  • Statistical Analysis, by Dr. Raffaele Vitale (multiple sessions from July 5th 2022 onwards).
  • Writing CVs, cover letters and job applications, by Chiara Marti & Andrea Micoli in Lecce (13 October 2022).
  • Workshop Science Writing, by ElementC in Fribourg (March 2023).

Scientific presentations (oral)

At the Focus on Microscopy online conference (April 10-13, 2022)
Teun Huijben: How nanoparticles distort the PSF.

At the DNANanotechnology2022 conference (Jena, May 12-14, 2022)
Aleksandra Adamczyk: Orienting single molecules in DNA origami constructs.

At the 5th Functional Nanotechnology Workshop (Rome, May 25-27, 2022)
Aleksandra Adamczyk: Orienting single molecules in DNA origami constructs.

Swiss Physical Society Annual Meeting (Fribourg, June 27-30, 2022)
Aleksandra Adamczyk: Orienting single molecules in DNA origami constructs.

At the OPTICA Imaging and Applied Optics Congress (Vancouver, July 13, 2022)
Vincenzo Lamberti: Single Molecule DNA sensing via Plasmon Enhanced Fluorescence (online contribution).

At the congress of the Mexican Chemical Society (Mérida, Yucatán, August 29 – September 2, 2022)
Maria Antoinetta Ramirez: Tailored synthesis and functionalization of silica nanosystems for biomedical approaches (online contribution).

At the Single-Molecule Localization Microscopy Symposium 2022 (Paris, August 29-31, 2022)
Teun Huijben: Imaging single molecules on nanoparticles: exploiting PSF deformations for precise localization.

At the 36th European Colloid & Interface Society Conference (Chania, September 4-9, 2022)
Xhorxhina Shaulli: Probing temperature-responsitivity of microgels by super-resolution microscopy (Best Oral Presentation Award).

At the 27th International Workshop on Single Molecule Spectroscopy and Super-resolution Microscopy (Berlin, September 7-9, 2022)
Sarojini Mahajan: Localization microscopy on Plasmonic particles: using PSF distortion to our advantage.

At the 22nd Trends in Nanotechnology International Conference (TNT2022) (Tirana, 3-7 October 2022)
Xhorxhina Shaulli: Probing temperature-responsivity of pNIPAM microgels by super-resolution microscopy and numerical simulations.

At the III virtual meeting of condensed matter & nanotechnology (online, Mexican Society of Physics, October 24-27).
Rodrigo Rivas Barbosa: Simulation microgels in solid-liquids interfaces.
Maria Ramírez: Synthesis and functionalization of nanosystems for biomedical approaches.

At the Nanophotonics and Micro/Nano Optics International Conference 2022 (Paris, October 25-27, 2022)
Vincenzo Lamberti: Nanoantenna enhanced single molecule biosensing using transient DNA interactions.
Teun Huijben: Imaging single molecules on nanoparticles: exploiting PSF deformations for precise localization.

At the Physics PhD seminar (Sapienza Università di Roma, November 9, 2022)
Rodrigo Rivas Barbosa: DNA Origami

Scientific presentations (posters)

At the 5th Functional Nanotechnology Workshop (Rome, May 25-27, 2022)
Teun Huijben: Fast and exact reduction of mislocalizations near spherical nanoparticles by a fully analytical PSF.

At the 32nd Annual Conference of the European Society for Biomaterials (Bordeaux, September 4-8, 2022)
Maria Antonieta Ramirez: Taylored synthesis of dual-colored silica oxide nanosystems for biomedical approaches

At the 27th International Workshop on Single Molecule Spectroscopy and Super-resolution Microscopy (Berlin, September 7-9, 2022)
Aleksandra Adamczyk: DNA Self-Assembly of single molecules with deterministic position and orientation.

At the Dutch national chemistry conference CHAINS (CHemistry As INnovating Science) (Veldhoven, September 22-23, 2022)
Bárbara Malheiros and Bahar Rouhvand: What makes DNA coated colloids crystallize?

At the Nanophotonics and Micro/Nano Optics International Conference 2022 (Paris, October 25-27, 2022)
Masih Fahim: PSF distortion and mislocalization by dielectric nanoparticles in single-molecule microscopy.

At the 2023 MRS Spring Meeting & Exhibit (San Francisco, April 10-14, 2023)
As part of Symposium SB07 on Frontiers of Unconventional Polymer Networks
Xhorxhina Shaulli: Probing Temperature-Responsivity of Microgels by Superresolution Microscopy.

At the International Microscopy Conference (Busan, September 11-15, 2023)
Iain Harley: Studying the Self-Assembly of Temperature-Responsive Polymers with Cryo-EM.

At the International Microscopy Conference (Busan, September 11-15, 2023)
Iain Harley: Investigating Protein-Particle Interactions with Cryo-EM.

At the International Microscopy Conference (Busan, September 11-15, 2023)
Francesca Mazzotta: Unraveling Structural Characteristics of Self-Assembling Peptide Nanofibers.

At the International Microscopy Conference (Busan, September 11-15, 2023)
Francesca Mazzotta: Dual color imaging for the detection of polymeric NP composition.

Outreach

2021-06-01: Maria Ramirez: published an article in the science magazine iBIO (Mexico).
2021-10-28: Maria Ramirez contributed to a conference for high school students on Science and Technology (Celaya, Mexico).
2021-11-06: Maria Ramirez: explained SuperCol research in an online session for high-school students (Celaya, Mexico).
2021-12-14: Teun Huijben: presented a ‘DigDays Talk’ about AI algorithms to see particles at the nanometer scale (Copenhagen, Denmark).
2022-01-27: Rodrigo Rivas: online seminar on How to simulate the interaction of particles in microgels for the scientific blog ‘Suriciencia’ (Mexico).
2022-02-18: Maria Ramirez: online talk Trust me, I’m a female scientist for Suriencia (Mexico).
2022-03-10: Maria Ramirez: online talk for the conference of the Municipal Youth Institute (Leon, Mexico).
2022-05-06: Peter Zijlstra: presented SuperCol at an alumni event of Eindhoven University of Technology (Eindhoven, the Netherlands).
2022-10-22: SuperCol was part of the presentation of the Zijlstra group at the Dutch Design Week (Eindhoven, the Netherlands)
2022-09-30: María Ramirez: participated in The European Researchers’ Night (Lecce, Italy).
2022-10-15: Maria Ramirez: took part in the iGEM competition as a juror (online).
2022-12-20: Xhorxina Shaulli and Alexandra Adamczyk: presented SuperCol at the department outreach day (University of Fribourg).
2022-12-21: Ingo Lieberwirth: interviewed by idwNachrichten (Germany).
2022-12-22: Peter Zijlstra: interviewed by SPOT-ON Integrated Photonics magazine (the Netherlands).
2022-12-20: ICMS Highlights magazine features Supercol with quotes from Peter Zijstra and Bárbara Malheiros.
2023-03-16: Maria Ramirez and Rodrigo Rivas Barbosa: participated in Science is Wonderful! European outreach event in Brussels.
2023-04-22: Jui-Kai Chen participated in an Open Day at KU Leuven, presenting electron micrscopy.
2023-04-24: Bárbara Malheiros stars in a video for the platform ‘Eye Openers’ featuring talented young scientists.
2023-04-25: Teun Huijben presented a lecture for high school students in Slagelse, Denmark.
2023-05-08: Rodolphe Marie was interviewed on the website of DTU Health Tech.
2023-06-01: Peter Zijlstra was interviewed on the website of TU Eindhoven.

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