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Simple Hydrophobic/Hydrophilic Protein Folding Model Documents

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Main Document

Simple Hydrophobic/Hydrophilic Protein Folding Model 

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.

Last Modified June 5, 2014

This file has previous versions.

Supplemental Documents (2)

Simple Hydrophobic/Hydrophilic Protein Folding Project Report 

Final report for Computational Physics (Phy 200).

Last Modified June 1, 2014

This file is included in the full-text index.

Simple Hydrophobic/Hydrophilic Protein Folding Model Poster 

Davidson College student Research Symposium poster presentation.

Last Modified June 1, 2014

This file is included in the full-text index.

Source Code Documents

Simple Hydrophobic/Hydrophilic Protein Folding Source Code 

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.

Last Modified June 5, 2014

This file has previous versions.

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