NanoDynamicsLab

We like things that move – at the nanoscale.

Welcome!

At the Nano Dynamics Lab, we are fascinated by the molecular dynamics found in biomolecules, and we strive to investigate them experimentally at the single-molecule level using cutting-edge nanopore & smFRET techniques.

Proteins are the molecular makers in our body. They perform all vital cellular functions to maintain life as we know it: cell growth & division, genome replication & repair, energy harvesting & conversion, self-defence & attack, environmental sensing & reaction to it, etc. etc. To do this all, proteins adopt different 3D conformations and change their interaction partners dynamically. However, these essential molecular dynamics are challenging to observe and dissect experimentally, because they usually happen unsynchronized in a large molecular ensemble.

To tackle this, in the NanoDynamicsLab, we use & develop innovative single-molecule techniques to gain quantitative insight into biomolecular dynamics, in order to understand the molecular basis of protein function and also malfunction leading to disease. In particular, we are fascinated by how functional dynamics arise from specific structural elements (protein domains, or even single atoms) in the context of diverse energy sources, including thermal and chemical energy, light, ion gradients etc. And we aim to understand and alter such nanoscale processes in a controlled way.

Visit also our RESEARCH section, and JOIN US if you share our enthusiasm for biomolecular dynamics, one molecule at a time.

Lab News

15/03/2022. [Team] We’re happy to welcome two new members: Floor and Ben join us for a BSc thesis on zero-mode waveguides and an internship on pattern recognition, respectively. Welcome!

03/03/2022. [Talk] Sonja speaks at the Single-Molecule Biophysics Meeting at Les Houches (F). Yey, first in-person conference in 2 years! Thanks David, Nynke, Willem & all for organizing!

11/02/2022. [Talk] Sonja speaks at the ‘Online-Symposium BioPhysikalische Chemie’ at LMU Munich. Thank you for the invitation, Philip!

10/02/2022. [Talk] Sonja speaks at Uni Ottawa’s Physics Department Colloquium. Thanks, Vincent, for the invite!

08/02/2022. [Paper] Benjamin’s first preprint is out: Can DyeCycling break the photobleaching limit in single-molecule FRET? We think yes, and describe how and why.

02/02/2022. Exciting: the first thesis defense at the NanoDynamicsLab. David did a great job in this collaboration with Raymond Staals’ Microbio group. More to come...

08/12/2021. [Talk] Sonja gives a seminar at EPFL’s Institute of Chemical Sciences and Engineering. Thank you Christian Heinis for the invitation.

24/11/2021. [Paper] New preprint: Inferring kinetic rate constants from single-molecule FRET trajectories – a blind benchmark of kinetic analysis tools. A great collaborative multi-lab effort that we initiated 3 years ago.

10/11/2021. [Talk] Sonja speaks at the Biochemical Society webinar series organized by the Biochemical Society (UK). Thanks for the invitation.

16/10/2021. What a nice surprise: the NEOtrap was selected to illustrate the November issue of Nature Nanotechnology.

15/10/2021. [Team] Chenyu Wen joins the lab for a joint postdoc between Cees Dekker’s and our lab. Welcome Chenyu!

11/10/2021. [Talk] Sonja gives a plenary talk at the Dutch Biophysics annual conference – online this time: PROTEIN DYNAMICS ACROSS SCALES – investigating the vibrant nature of proteins. Grateful for this opportunity to present our work to the creative Dutch Biophysics community!

11/10/2021. WUR’s press team explains the many applications of the NEOtrap to the general public: The NEOtrap's great potential.

25/09/2021. [Paper] New perspective article in iScience: The NEOtrap – en route with a new single-molecule technique

17/09/2021. A. Aksimentiev wrote a News&Views about our NEOtrap in Nature Nanotechnology – spot on!

06/09/2021. [Team] Raluca Vintan joins us for her MSc thesis. Welcome Raluca!

05/09/2021 Read here Sonja’s behind-the-paper blogpost for Nature Portfolio: My personal road to the NEOtrap – a long-term dream of better time-resolved protein nanodynamics.

30/08/2021. [Paper] The NEOtrap – Sonja’s postdoc work – is now published in Nature Nanotechnology: Nanopore electro-osmotic trap for the label-free study of single proteins and their conformations.

02/08/2021. [Team] David Fuentenebro-Navas joins the lab as a first MSc student. Welcome, David!

30/07/2021. [Team] Time flies: we have to say bye to Mattia. All the best with your future plans, Mattia!

07/06/2021. [Paper] New collaborative perspective in Nature Methods to which we could contribute: The emerging landscape of single-molecule protein sequencing technologies.

17/05/2021. [Talk] Sonja speaks at Munich’s ‘Physik Kolloquium’ by LMU&TUM. Thanks, Jan, for the invite!

16/04/2021. [Talk] Sonja gives her introductory seminar at Wageningen University. Thanks for the nice discussions!

16/04/2021. [Paper] New review article out in Essays in Biochemistry: Nanopores – a versatile tool to study protein dynamics.

01/04/2021. [Team] Benjamin Vermeer joins the lab as the first PhD student. Welcome, Benjamin!

26/03/2021. [Talk] Sonja speaks at the Uni Iowa’s Dept. of Biochemistry Virtual Seminar: Protein Dynamics Across Timescales – using optical & electrical detection. Thank you for the invitation, Maria Spiess.

22/03/2021. [Talk] Sonja presents the NEOtrap at the international ‘Nanopore Weekly Meeting’ online: Put a Lid on It: Hold & Sense Single Proteins Using the Nanopore Electro-Osmotic Trap (NEOtrap). Thank you for the invitation, Profs Winterhalter, Wanunu, Long.

02/01/2021. Here we go: the NanoDynamicsLab is officially open! Happy & grateful to start up the lab together with postdoc Mattia Fontana, and as part of the Laboratory of Biophysics at WUR.