written by Ryan Kozlowski

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.

• Download ejs_life_science_ProteinFolding.jar - 2428kb Java Archive File

Last Modified June 5, 2014

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Final report for Computational Physics (Phy 200).

• Download Protein Folding Report.pdf - 691kb Adobe PDF Document

Last Modified June 1, 2014

This file is included in the full-text index.

Davidson College student Research Symposium poster presentation.

• Download Ryan Kozlowski Poster_Physics_Windows.pdf - 397kb Adobe PDF Document

Last Modified June 1, 2014

This file is included in the full-text index.

The source code zip archive contains an XML representation of the Simple Hydrophobic/Hydrophilic Protein Folding Model.   Unzip this archive in your EjsS workspace to compile and run this model using EjsS ver 5.

• Download ejs_life_science_ProteinFolding.zip - 751kb Compressed File

Last Modified June 5, 2014

This file has previous versions.