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Computer Program Detail Page

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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.

Please note that this resource requires at least version 1,6 of Java (JRE).
2 supplemental documents are available
1 source code document is available
Subjects Levels Resource Types
Modern Physics
- Biophysics
Thermo & Stat Mech
- Probability
= Random Walks
- Statistical Physics
- Upper Undergraduate
- Graduate/Professional
- Informal Education
- Instructional Material
= Interactive Simulation
Intended Users Formats Ratings
- Learners
- Educators
- application/java
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Access Rights:
Free access
Program released under GNU-GPL. Narrative is copyrighted.
License:
This material is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.
Rights Holder:
Ryan Kozlowski
Record Cloner:
Metadata instance created June 1, 2014 by Wolfgang Christian
Record Updated:
June 5, 2014 by Wolfgang Christian
ComPADRE is beta testing Citation Styles!

Record Link
AIP Format
R. Kozlowski, Computer Program SIMPLE HYDROPHOBIC/HYDROPHILIC PROTEIN FOLDING MODEL, Version 1.0 (2014), WWW Document, (https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13257&DocID=3782).
AJP/PRST-PER
R. Kozlowski, Computer Program SIMPLE HYDROPHOBIC/HYDROPHILIC PROTEIN FOLDING MODEL, Version 1.0 (2014), <https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13257&DocID=3782>.
APA Format
Kozlowski, R. (2014). Simple Hydrophobic/Hydrophilic Protein Folding Model (Version 1.0) [Computer software]. Retrieved December 13, 2017, from https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13257&DocID=3782
Chicago Format
Kozlowski, Ryan. "Simple Hydrophobic/Hydrophilic Protein Folding Model." Version 1.0. https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13257&DocID=3782 (accessed 13 December 2017).
MLA Format
Kozlowski, Ryan. Simple Hydrophobic/Hydrophilic Protein Folding Model. Vers. 1.0. Computer software. 2014. Java (JRE) 1,6. 13 Dec. 2017 <https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13257&DocID=3782>.
BibTeX Export Format
@misc{ Author = "Ryan Kozlowski", Title = {Simple Hydrophobic/Hydrophilic Protein Folding Model}, Year = {2014} }
Refer Export Format

%A Ryan Kozlowski
%T Simple Hydrophobic/Hydrophilic Protein Folding Model
%D 2014
%U https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13257&DocID=3782
%O 1.0
%O application/java

EndNote Export Format

%0 Computer Program
%A Kozlowski, Ryan
%D 2014
%T Simple Hydrophobic/Hydrophilic Protein Folding Model
%7 1.0
%U https://www.compadre.org/Repository/document/ServeFile.cfm?ID=13257&DocID=3782


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Citation Source Information

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The APA Style presented is based on information from APA Style.org: Electronic References.

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Simple Hydrophobic/Hydrophilic Protein Folding Model:

Is Based On Easy Java Simulations Modeling and Authoring Tool

The Easy Java Simulations Modeling and Authoring Tool is needed to explore the computational model used in the Simple Hydrophobic/Hydrophilic Protein Folding Model.

relation by Wolfgang Christian

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