You can reference Mathematica, SystemModeler, and other Wolfram products in your published work just as you would reference a book or any other publication. The standard citation elements are:

SystemModeler 4.2

Author: Wolfram Research, Inc.
Title: SystemModeler
Edition: Version 4.2
Publisher: Wolfram Research, Inc.
Place of publication: Champaign, Illinois
Date of publication: 2015

A sample citation of this form would be:

Wolfram Research, Inc., SystemModeler, Version 4.2, Champaign, IL (2015).