the Simple Hydrophobic/Hydrophilic Protein Folding Model implements a 2-Dimensional hydrophobic/hydrophilic (HP) folding protein  to test the energetics of protein folding, the change in size of a protein relative to energy, and the computation time for complex protein problems. A Metropolis Monte-Carlo algorithm is used to determine if randomly guided movements are carried out by monomers (non-specific amino acids) within the polymer (protein tertiary structure). The Monte-Carlo steps are run in a worker task (separate to EJS) while size and energy are periodically updated according to the Frames Per Second (FPS). A worker task isolates a single thread from the operating computer and uses that to cycle through a block of code as quickly as possible. In this case, one cycle constitutes one Monte-Carlo time step, the time unit. To accurately update data from a thread that runs outside of the EJS module, atomic variables are used. Every time the program updates the evolution page, the atomic variables for size and energy are recorded and added to the view (i.e. plots) for the polymer structure that occurred in the nearest worker task cycle to that evolution update.

The Simple Hydrophobic/Hydrophilic Protein Folding Model was created using the Easy Java/JavaScript Simulations (EjsS) version 5 modeling tool.  It is distributed as a ready-to-run (compiled) Java archive.

Please note that this resource requires at least version 1,6 of Java (JRE).