One of the commonly used simulations in chemistry is the silulation of Rutherford's Gold Foil Experiment. Here is an example from YouTube.
Simulations improve student understanding by showing the student an image of what may be too small to actually see. In this simulations atoms and alpha particles are visible when in fact, they are way too small to see.
"Scientific discovery learning is a highly self-directed and constructivistic form of learning. A computer simulation is a type of computer-based environment that is well suited for discovery learning, the main task of the learner being to infer, through experimentation, characteristics of the model underlying the simulation." (De Jong). I use simulations all the time in my teaching. I have found the best ones are those that are available as textbook resources. Simulations can also be found on the internet or on YouTube. They do not tend to be quite as good as the textbook resources but they are sometimes more fun. The textbook simulations are usually very serious in nature but sometimes the ones found on the internet are created by students and have fun music or fun images. I would highly recommend the use of simulations for those who teach either the physical sciences or the life sciences.
De Jong, Ton and Van Jooligan, Wouter R., REVIEW OF EDUCATIONAL RESEARCH June 1998 vol. 68 no. 2 179-201
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