Molecular Manipulation Lab

Molecular simulations

Real time simulation of molecular manipulation

In the SPM-based manipulation of single organic molecules, the amount of information that can be gathered at any given point in time is limited to the output of a few (typically three) measurement channels. This is in great contrast to the amount of information needed to describe (and thus to determine) the complete conformation of the molecule at any such point during manipulation. Reconstructing the molecular conformation during manipulation thus constitutes an underdetermined, inverse problem. Molecular simulations provide a way to address the forward problem, if they can generate the SPM measurement output. In the MoMaLab we develop molecular mechanics simulations that are fast enough to simulate the SPM output, more specifically the force gradient measurement channel (Δf), alongside the actual manipulation experiment, i.e., in real time. At the same time we work hard to make the simulations as accurate as possible, such that a quantitative reproduction of experimental results is possible. Both aspects combined, speed and accuracy, are needed for the final task: To use our simulations to solve the inverse experimental problem described above by forward simulation of a multitude of alternative manipulation scenarios from which the best can be identified. The relevant framework for this observation task can be found in the field of control theory.
Read how control theory enables observation of molecular geometries...
We construct our molecular mechanics force fields for the specific molecules under investigation. Like this we ensure a maximum of accuracy. The parameters are determined by fitting to DFT simulations and experimental data.

Read the original publications:
[1] C. Wagner et al. Measurement of the Binding Energies of the PTCDA/Au(111) Bonds by Molecular Manipulation, PRL (2012) [2 ]C. Wagner et al. Non-additivity of molecule-surface van der Waals potentials from force measurements, Nat. Commun. (2014) [3] C. Wagner et al. The role of surface corrugation and tip oscillation in single-molecule manipulation with a NC-AFM, Beilstein J. Nanotechnol. (2014)

June 27th, 2019

"The theory of scanning quantum dot microscopy" Read at J Phys. Cond. Mat.

June 10th, 2019

New scanning quantum dot microscopy (SQDM) paper online. Quantitative measurements of surface potentials and dipoles. New window to the nanoscale world. Read at Nature Materials Read full-text w/o subscription Press release

February 15th, 2019

We welcome Joshua Scheidt, computer science student at Maastricht University, who joins the MoMaLab for his master thesis.

February 4th, 2019

Hand-controlled STM-based atomic manipulation with real-time visual feedback from an MD simulation Read at Beilstein..

October 25th, 2018

We have been granted 2 Mio core‑h on JURECA for our simulation work on molecular adsorption and manipulation.
Meet us at
The 22nd International Conference on NC-AFMRegensburg, Germany, July 29 - August 2, 2019
Hands-on DFT and beyondBarcelona, Spain, August 26 - September 6, 2019
▶   704. WE-Heraeus-Seminar "Exploring the Limits of Nanoscience with Scanning Probe Methods"Bad Honnef, Germany, 27-31 October 2019