(161b) How to Design a Fast Nanocar

How can we design the world’s smallest machines—machines that operate at an extraordinarily small scale with molecular moving parts? Just as experimental research on electric motors and combustion engines by nineteenth-century scientists led to revolutionary technologies, exploration of molecular motors, actuators, logic gates, and other molecular machines could lead to similarly transformative discoveries and innovations in the future. However, at present, the focus of computational chemistry software is on exploring various molecular phenomena, not on designing new molecular machines. Whereas computer-aided design (CAD) software has become mainstream in the design of new cars, airplanes, and other “macro” machines, CAD tools that can design molecular machines have yet to be developed. Developing comprehensive software for this purpose might seem daunting, even impossible, but a promising starting point is to focus on the design of molecular components that can eventually be incorporated into molecular machines.

In this work we developed a nanocar builder tool that can be used with a user interface and/or as a Python library for automated building of nanocars. Nanocars are single molecule vehicles that resemble macroscopic automobiles and they are important for understanding how to control molecular diffusion on surfaces. This process is commonly utilized in cells to transport molecular cargo: enzyme molecules are moved along protein filament tracks converting chemical energy into mechanical work. The nanocar builder tool was developed as a plug-in for Avogadro 2 molecular visualizer and a complementary Python package was developed to perform the geometric operations for building the nanocar. The current release allows users to build a nanocar molecule from components of chassis and wheel molecules. Additionally, users can build a metal surface to place the molecular car and assign force field parameters for the system which provides an initial configuration to study diffusion behavior of these molecules. Using the nanocar builder Python library we generated hypothetical nanocars and studied their diffusion using Molecular Dynamics simulations. We investigated how the molecular interactions effect the diffusion of nanocars and outlined guidelines on how to design faster nanocars.

Currently, the plug-in is available on GitHub (https://github.com/kbsezginel/nanocar-avogadro) including a webpage where users can find detailed written instructions on installation and usage, as well as video tutorials (https://kbsezginel.github.io/nanocar-avogadro). With the upcoming 2^nd International Nanocar Race our nanocar builder can be used to improve nanocar designs by understanding how the molecular components of the nanocar affect the diffusion behavior. Additionally, we believe this plug-in serves as a proof-of-concept for a unique platform to build complex molecular machine systems.