Intuitive human interface to a scanning tunnelling microscope: observation of parity oscillations for a single atomic chain

Abstract

A new way to control individual molecules and monoatomic chains is devised by preparing a human–machine augmented system in which the operator and the machine are connected by a real-time simulation. Here, a 3D motion control system is integrated with an ultra-high vacuum (UHV) low-temperature scanning tunnelling microscope (STM). Moreover, we coupled a real-time molecular dynamics (MD) simulation to the motion control system that provides a continuous visual feedback to the operator during atomic manipulation. This allows the operator to become a part of the experiment and to make any adaptable tip trajectory that could be useful for atomic manipulation in three dimensions. The strength of this system is demonstrated by preparing and lifting a monoatomic chain of gold atoms from a Au(111) surface in a well-controlled manner. We have demonstrated the existence of Fabry–Pérot-type electronic oscillations in such a monoatomic chain of gold atoms and determined its phase, which was difficult to ascertain previously. We also show here a new geometric procedure to infer the adatom positions and therefore information about the substrate atoms, which are not easily visible on clean metallic surfaces such as gold. This method enables a new controlled atom manipulation technique, which we will refer to as point contact pushing (PCP) technique.

Towards Controlled Single-Molecule Manipulation Using “Real-Time” Molecular Dynamics Simulation: A GPU Implementation

“…Here, the positions of the gold atoms in contact with the molecule were calculated taking into account both the external input and the relaxation of the molecule. The interaction between the substrate gold atoms was calculated using an embedded atom-potential [ 24 , 25 ], while the tip gold atoms were treated using a harmonic potential (the parameters used in the simulation are given in Appendix Table A1 ). The lifting of a molecule in experiments was helped by the higher reactivity of the tip apex atoms (as a consequence of the lower coordination number) as compared to the substrate gold atoms.…”

“…The molecule that we studied to test our simulation is 1,4-bis(4-pyridyl)benzene, shown in Figure 1 . The gold-gold interaction is modeled as before [ 24 , 25 ] using a semi-empirical potential. The atoms making up the molecule are joined together by covalent bonds for the chosen molecule and are thus modeled as spring-mass systems using harmonic potentials.…”

“…However, it will lead to two problems in our situation. Firstly, this time-scale has to be larger than the one associated time-scale of the external impulse used to steer the STM tip [ 24 , 25 ]. Otherwise, the Au atoms in the tip being heavier will not follow the external steering input coming from the 3D motion control system.…”

“…Although this cannot replace experimental observations, it can serve as a tool for guiding the experiments. For this, we developed a system [ 24 , 25 ] where we attach a real-time molecular dynamics simulation to a low-temperature UHV STM. This simulation first takes the STM image as an input to create a 3D simulation stage similar to the experiment.…”

Dynamic bonding influenced by the proximity of adatoms to one atom high step edges

“…motion and manipulate the position of a single adatom on a surface and measure the electronic transport. To improve the control of the STM tip and the adatom, a real-time molecular dynamics simulator and a 3D motion control system have been incorporated in this experimental setup [27][28][29]. To emulate the experiment and permit synchronization with the 3D motion system, there are only a few atoms interacting via low computational cost potentials in the real-time molecular dynamics simulator.…”