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)

January 19th, 2023

MomaLab is part of the Orbital Cinema project!

September 8th, 2022

Warmest congratulations to Taner Esat for winning the Gerhard Ertl Young Investigator Award for his outstanding work in surface science, particularly metastable standing molecules.

April 7th, 2022

Want to make your own standing molecule? "Design Principles for Metastable Standing Molecules" Read at J. Phys. Chem. C

October 10th, 2021

We finally knocked it down: "The stabilization potential of a standing molecule" Read at Science Advances Press release

October 22nd, 2020

Introducing machine learning to the nanoscale: "Autonomous robotic nanofabrication with reinforcement learning" Read at Science Advances Press release

July 2020

Our Helmholtz-AI project MomoNano (together with HZB and TU-Berlin) successfully competed for a three year funding by the Helmholtz Association.

September 2nd, 2020

"The theory of scanning quantum dot microscopy" Read at J Phys. Cond. Mat.
Meet us at
▶   "...home"