New Mexico Supercomputing Challenge

Pathogen RPS

Team: 144

School: School of Dreams Academy

Area of Science: Biology

Interim: Project definition

Everyone in the world is affected by pathogens of all kinds. Many people become infected by several pathogens at the same time, or by different mutations of the same pathogen. There is a need to be able to treat various strains of a disease or diseases.

The goal of the project is to figure out what the most effective treatment of someone infected by any RPS-style pathogens.

Problem Solution

This project will show how to treat a disease which has pathogens that can live in the same neighborhood and interact in a rock-paper-scissors (RPS) type of relationship. We will be using the RPS model that is used to show the interactions of different strains of E-Coli as our starting point. However, our model will have dynamic agents instead of stationary agents. Our RPS model will show how different agents could represent different pathogens interacting in a RPS manner while they travel in the bloodstream.

The model will be programmed using Netlogo and will show the blood stream going through the capillaries. There will be four agent types, three of them will be blood cells which are infect with a pathogen, and the fourth will be a blood cells which are not infected. The blood cells which are infected will be programmed to infect one of the blood cells which are not infected and one of the other types of infected blood cells.

Once the model is completed we will run it at least ten times, we will run it more if time constraints allow. While running it the end and beginning data for each test will be recorded, end and beginning data will include; the populations of each type of infected blood cell and the uninfected blood cell at the beginning of each test and the populations of each type of agent at the end of each test. Data may also include factors which may affect the populations and they may differ for each test.

Progress to Date

The progress to date includes doing more research on diseases which act in this behavior, and reading on the previous research project where scientists used e-coli to observe these behaviors. We have also been learning how to program in Netlogo due to our inexperience in Netlogo. After doing research we have thought about using one specific pathogen and several of its strains as agents instead of using a general agent that could represent any pathogen in the real world. We have also decided to include blood cells which are not infected also, we have also thought about starting the tests off with one infected blood cell for each of the three strains of the pathogen, and making the rest of the blood cells uninfected to observe infectivity. One other possibility we have also looked at is, making one of the pathogens beneficial to the “organism” that these tests are taking place in.

Expected Results

The results which we are expecting are for the virtual model to show us how the problem which was defined could be solved, or at least the best way to approach the problem.

Team Members:

  James Edington
  Denton Shaver

Sponsoring Teacher: Creighton Edington

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