Model1: L-Asp diffusion

iGEM UT-Tokyo

Aim

We needed to know the behavior of L-Asp diffusion to perform our entire simulation (model3). We experimentaly researched Asp diffusion using TLC method but the results were insufficient for the entire simulation. So we decided to investigate the Asp diffusion by numerical simulation.

Method

We first estimated the value of diffusion coefficient by interpolating molecular mass of L-Asp (133) from the relationship between molecular weight and diffusion constant^[1] as shown in figure 1.

Figure 1. Molecular Weight v.s. Diffusion Constant

The estimated value was D = 0.001 [mm²/sec].

Then we tried to verify the value was correct by showing we could predict the experimental result theoretically using this value as a diffusion constant.

Experimental data of L-Asp diffusion are shown in figure 2. This is the result of TLC experiment. We dropped 2×10^-7 mol L-Asp on the center of agar gel at the beginning. Horizontal rows indicates elapssed time and vertical columns indicates the distance from the center.

Figure 2.The Result of TLC Experiment

We simulated the time development of the L-Asp concentration distribution. We solved the diffusion equation using 1st order finite difference method.

A indicates the L-Asp concentration and D means the diffusion coefficient. The shape of system was a circle with radius 5cm. We dropped 2×10^-7 mol Asp at the center of the circle as the initial state.

Result

Figure 3. Change in L-Asp Concentration Over Time (2, 6, 8 mm from the center)

The time change of logarithmic values of L-Asp concentration at 2, 6, 8 mm from the center is shown in figure 3.

Discussion

The result of the simulation shown in fig. 3 were similar to the result of experiment shown in fig. 2. So we judged that the diffusion coefficient D=0.001 was adequate value.

References