Deduction

Phenotype

Having completed parameters simulation（插入链接到拟合），we can now use our model to make assessments about GFP and ErbB3 with the confidence that we have maximized our potential to obtain insights that will be directly relevant to the use of our trim21-antibody system. To investigate the relation between antibody phenotype and time as well as the concentration of plasmid dosage, we respectively introduced equations between the phenotype and the corresponding protein concentration into our model.

For gfp, the relationship between the general fluorescence intensity and the concentration of the fluorescent substance is . In the wetlab,as the concentration of gfp is counted in nanomole and the content is very low,it can be considered that the relationship at this time is in accordance with .At this time, the fluorescence intensity is proportional to the concentration of the fluorescent substance.Simultaneously, we obtained a large number of images of gfp fluorescence intensity at different time points through wetlab. These images were expressed by imagej to quantify their fluorescence intensity. Then, we use Excel to process the acquired data. For example, the shooting parameters (background brightness, contrast) of images obtained under different conditions is adjusted to reduce noise. Finally, we used the previous construction to obtain the relationship between plasmid concentration and fluorescence intensity decay. The relationship between plasmid concentration and fluorescence intensity decay was constructed using the previous method to analyze.

Sensitivity analysis

Sensitivity analysis is one of the commonly used methods for analyzing uncertainty in models，which identifies the sensitive factors that have great influences on the calculation results of the concentration of reactant in the mechanism from the multiple uncertain factors. By analyzing and measuring the degree of influence and sensitivity of the calculation results, we can offer some advice to wetlab.. If a small change in variable can cause a large change in the calculation result, the variable is called a sensitivity factor, otherwise it is called a non-sensitive factor. For our system, we used MATLAB for sensitivity analysis to get the influence of different factors on the calculation results. Then combined with our design, we draw some conclusions for our experiment:

1、The effect of each step on the whole is determined by the parameters. For example，a number of reaction rate is described by the law of mass action（ ,the reaction rate is proportional to the reactant concentration ）, the size of the parameter determines the effect of the reactant on the speed of the step, thereby ascertaining the effect of the reaction on the whole)（放一张敏感性分析的图）

2、The concentration of a certain reactant（such as enzyme or ub ）will affect the overall reaction rate. According to the model, when the concentration of the reactant is very low, the reaction rate increases as the concentration of the reactant increases.（这里放浓度增加反应速度增加的图） However, when the initial concentration of reactant exceeds a certain level, their overall impact will be reduced （结合模型）Our analysis believes that there is a constraint relationship between each step of the reaction. It is limited to increase the concentration of a certain reactant alone to accelerate the overall response , and other restrictive factors need to be considered.（这里放设定浓度模拟的图）（参数扫描的图？？）

3、Factors affecting the sensitivity of various reactants.The reactions that the reactants actually participate also play a role,which determine the proportion of the effect of the reactants in the whole process.For instance,Ub is involved in the whole process of ubiquitination of antigen-antibody complexes from activation to connecting to the compound, while E1,E2 enzyme only participates in a certain step（E1 only acts on the activation of ub molecules and E2 only transfers the ub）（这里放相关方程的图）Therefore, the reaction rate is more sensitive to ub than to E1,E2.

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