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

Vreumingen, Dyon van; Tewari, Sumit; Verbeek, Fons J.; Ruitenbeek, J. M. van

doi:10.3390/mi9060270

Cited by 4 publications

(4 citation statements)

References 35 publications

(38 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, one has to think about the correct description of the interaction between the metallic system and the molecules. Typically MD is used for molecules in solution or for solid-state bulk materials [57], rarely for metal surfaces in contact with molecules [58]. The right way to go would be fitting a force field to experimental observations at UHV and low temperatures as in [59–60].…”

Section: Resultsmentioning

confidence: 99%

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

Tewari¹,

Bakermans²,

Wagner³

et al. 2019

Beilstein J. Nanotechnol.

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

confidence: 99%

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

Tewari¹,

Bakermans²,

Wagner³

et al. 2019

Beilstein J. Nanotechnol.

Self Cite

View full text Add to dashboard Cite

show abstract

“…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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

View full text Add to dashboard Cite

Low-temperature scanning tunneling microscopy is used here to study the dynamic bonding of gold atoms on surfaces under low coordination conditions. In the experiments, using an atomically sharp gold tip, a gold adatom is deposited onto a gold surface with atomic precision either on the first hollow site near a step edge or far away from it. Classical molecular dynamics simulations at 4.2 K and density-functional theory calculations serve to elucidate the difference in the bonding behavior between these two different placements, while also providing information on the crystalline classification of the STM tips based on their experimental performance.

show abstract

“…Analysis using a molecular simulation is one way to elucidate such nanoscale phenomena [32,33]. In previous studies, wettability and the contact angle of droplets with nanoscale surfaces were analyzed using molecular dynamics simulations [6,34,35].…”

Section: Introductionmentioning

confidence: 99%

Molecular Dynamics Simulation of the Influence of Nanoscale Structure on Water Wetting and Condensation

et al. 2019

View full text Add to dashboard Cite

Recent advances in the microfabrication technology have made it possible to control surface properties at micro- and nanoscale levels. Functional surfaces drastically change wettability and condensation processes that are essential for controlling of heat transfer. However, the direct observation of condensation on micro- and nanostructure surfaces is difficult, and further understanding of the effects of the microstructure on the phase change is required. In this research, the contact angle of droplets with a wall surface and the initial condensation process were analyzed using a molecular dynamics simulation to investigate the impact of nanoscale structures and their adhesion force on condensation. The results demonstrated the dependence of the contact angle of the droplets and condensation dynamics on the wall structure and attractive force of the wall surface. Condensed water droplets were adsorbed into the nanostructures and formed a water film in case of a hydrophilic surface.

show abstract

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

Cited by 4 publications

References 35 publications

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

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

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

Molecular Dynamics Simulation of the Influence of Nanoscale Structure on Water Wetting and Condensation

Contact Info

Product

Resources

About