Molecular self-assembly is the process by which molecules adopt a defined arrangement without guidance or management from an outside source. This is one of the ways Mother Nature makes biomolecules that support life. For example, the amino acids of a protein self-assembles themselves and fold into a conformation determined primarily by its primary structure (the sequence of amino acids). It has inspired scientists to invent nanotechnology that is based on self-assembly.

Ab initio simulations of self-assembly involve many atoms and take a long time to run. For intermolecular self-assembly, most of the time the molecules’ internal chemical structures do not change much. The Molecular Workbench has a coarse-grained model that simulates the soft, sticky character of the molecular surfaces, which is the most important factor during self-assembly. With this model, we have created a sequence of simulations for teaching the concept of self-assembly (see the images for an example). These simulations have been well-received and used in many classrooms as an introduction to nanotechnology.

You can explore these simulations with this applet.

Several of these simulations were used by a research scientist, Dr. Frank Balzer at NanoSYD of the University of Southern Denmark, in his presentation to illustrate the principles for nanofabrication laboratory experiments.