Modeling is usually used to make sense of the experimental discovery in traditional biological studies. In this synthetic biology project, we believe that carefully carried out modeling will be critical for the experimental design and data analysis at different stages of the project. We hope to demonstrate that the modeling is especially helpful to finalize the microfluidics chip design, and determine the distribution of the C.elegans (Caenorhabditis elegans) in microfliudics, as well as the transfection of the MiniMos in our experiment.

Model for Chemical Diffusion

The diffusion process of chemicals in the PDMS chips is simulated in our model. 2 steps are included:

• The process to form a linear concentration gradient

• The chemical diffusion through the PDMS (Polydimethylsiloxane) layer

Total time consumption of the 2 processes is calculated, based on the Einstein and Brownian movement equation t=\frac{w^{2}}{2D} and Fick’s second law (\frac{\partial C}{\partial t}=D \frac{\partial^2 C}{\partial x^2}). The calculation results are used to guide our experiment design.

Fig.1 I. The Gaussian Plate. Ⅱ. The chemicals diffusion in PDMS. Ⅲ. The amorphous cell made by PDMS and diacetyl. Ⅳ. The diffusion coefficient of 2-nonanone and diacetyl in PDMS

See Details

Model for Worms Locomotion

This model describes how microfluidics Gaussian distribution plate works when we use this device to test C.elegans’ preference in the plate.

Fig.2

See Details

Model for Neuron Network

The purpose of this model is to select promoters used in downstream neurons of C.elegans’ which have greatest possibility to be lighted on when AWA and AWB (the main neurons in our project) are actived.

See Details

Model for Genetic Probability

This model describes the process in which we get 2 worm strains with stable genetic traits and the hybrid offspring. It was proposed at the beginning of our project to optimize our experimental design concerning how many worms we need to inject and how long it will take to make sure we get the expected result before iGEM Jamboree.

These 3 steps are considered in the model:

Inject plasmid (odr-10::CoCHR::GEM-GECO::mCherry and str-1::Chrimson::GEM-GECO::GFP) through miniMOS system.

Select the rescued worms using mCherry and GFP.

Mate the 2 strains to get the hybrid offspring of red fluorescence on AWA neuron and green fluorescence on AWB neuron.

Comparing the calculation and the experiment results, we demonstrate that the 2 strains that we finally get have the insertion gene on different chromosomes.

Fig.4 A) Stable inheritance probability. B)Chromosome crossing probability

See Details

References