Modeling

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mRNA Class

Figure 3.1 - Process of Transcription. The red polymerase signifies translation. The red rod being created is the mRNA with the yellow sphere mRBS attached on the top

The mRNA class performs all of the functions that mRNA do in living cells and is directly related to the process of transcription and translation. Once an RNA polymerase, which is represented visually as a large violet sphere, binds onto the DNA, the process of transcription occurs and a mRNA is created, as seen in Figure 3.1. As transcription progresses, which is the process of turning DNA nucleotide sequence information into RNA sequence information, the mRNA gets gradually larger. When transcription finishes, the mRNA is released, where it moves randomly within the space of the model. Because of how the simulation software was created, mRNA could not be represented as a thin ribbon-like shape that is seen in textbooks or other conventional models. Instead, the mRNA is represented visually as a long, thin, red rod. Contained within each mRNA is information required for the sequencing of proteins.

Ribosome Class

Figure 3.2 - Process of Translation. The blue box signifies the process of translation where protein will be created.

Once the mRNA is created, the ribosomes are able to bind to mRNA and perform the process of translation, shown in Figure 3.2. Ribosomes in this simulation are represented as a large yellow cube. In reality, ribosomes are actually two different parts that attach to a mRNA on different sides upon translation. However, for the purposes of this simulation, the ribosome is represented as a single part. As a result, this prevents unnecessary complications and simplifies the computation. Since ribosomes are quite dense and heavy in cells, they are modeled with a relatively heavy mass in the simulation; their velocities and accelerations, as a result, are very small. When a ribosome attaches to an mRNA, the cubic ribosome turns into a teal colour to signify the occurrence of translation - the process of protein synthesis. After attaching, the ribosome continues with translation by moving along the mRNA. Upon completion, protein molecules are released into the cell, and the ribosome detaches itself, regaining its yellow colour.

mRBS Class

Transcription and Translation

Half Life

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 == Ribosome Class ==
+[[Image:Evogem_translation.PNG‎|thumb|250px|left|Figure 3.2 - Process of Translation. The blue box signifies the process of translation where protein will be created.]]
+Once the mRNA is created, the ribosomes are able to bind to mRNA and perform the process of translation, shown in Figure 3.2. Ribosomes in this simulation are represented as a large yellow cube. In reality, ribosomes are actually two different parts that attach to a mRNA on different sides upon translation. However, for the purposes of this simulation, the ribosome is represented as a single part. As a result, this prevents unnecessary complications and simplifies the computation. Since ribosomes are quite dense and heavy in cells, they are modeled with a relatively heavy mass in the simulation; their velocities and accelerations, as a result, are very small. When a ribosome
+attaches to an mRNA, the cubic ribosome turns into a teal colour to signify the occurrence of translation - the process of protein synthesis. After attaching, the ribosome continues with translation by moving along the mRNA. Upon completion, protein molecules are released into the cell, and the ribosome detaches itself, regaining its yellow colour.
 == mRBS Class ==