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Micromachines (Basel). 2018 May 29;9(6). pii: E270. doi: 10.3390/mi9060270.

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

Author information

1
Huygens-Kamerlingh Onnes Laboratorium, Universiteit Leiden, 2333CA Leiden, The Netherlands. dyon@vanvreumingen.nl.
2
Leiden Insitute of Advanced Computer Science, Universiteit Leiden, 2333CA Leiden, The Netherlands. dyon@vanvreumingen.nl.
3
Huygens-Kamerlingh Onnes Laboratorium, Universiteit Leiden, 2333CA Leiden, The Netherlands. mecsumit@gmail.com.
4
Leiden Insitute of Advanced Computer Science, Universiteit Leiden, 2333CA Leiden, The Netherlands. f.j.verbeek@liacs.leidenuniv.nl.
5
Huygens-Kamerlingh Onnes Laboratorium, Universiteit Leiden, 2333CA Leiden, The Netherlands. Ruitenbeek@physics.leidenuniv.nl.

Abstract

Molecular electronics saw its birth with the idea to build electronic circuitry with single molecules as individual components. Even though commercial applications are still modest, it has served an important part in the study of fundamental physics at the scale of single atoms and molecules. It is now a routine procedure in many research groups around the world to connect a single molecule between two metallic leads. What is unknown is the nature of this coupling between the molecule and the leads. We have demonstrated recently (Tewari, 2018, Ph.D. Thesis) our new setup based on a scanning tunneling microscope, which can be used to controllably manipulate single molecules and atomic chains. In this article, we will present the extension of our molecular dynamic simulator attached to this system for the manipulation of single molecules in real time using a graphics processing unit (GPU). This will not only aid in controlled lift-off of single molecules, but will also provide details about changes in the molecular conformations during the manipulation. This information could serve as important input for theoretical models and for bridging the gap between the theory and experiments.

KEYWORDS:

controlled manipulation; graphics processing unit; molecular electronics; parallel computing; real-time simulation; scanning tunneling microscope; single-molecules

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