U model (analysis)

 

Binding of one ligand molecules to one receptor monomer

 

 

R + L = RL

 

Evgenii L. Kovrigin

01-15-2014

 

 

 

 

 

Contents

 

Goals

 

1. Load equations

 

2. Simulation

 

3. Summary of test results

 

 

Conclusions

 

 

 

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Goals

 

Here I am analyzing the U model solution

 

 

 

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1. Load equations

 

clean up workspace

reset()

 

STEP 1: Set path to saved derivation results

NOTE: make sure the path ends with slash character "/".

ProjectName:="U_model_derivation";
CurrentPath:="/Volumes/Leopard_Partition/Users/kovrigin/Documents/Workspace/Global Analysis/IDAP/Mathematical_models/Equilibrium_thermodynamic_models/U/";

"U_model_derivation"
"/Volumes/Leopard_Partition/Users/kovrigin/Documents/Workspace/Global Analysis/IDAP/Mathematical_models/Equilibrium_thermodynamic_models/U/"

 

 

 

Read results of derivations

filename:=CurrentPath.ProjectName.".mb";
fread(filename,Quiet):
anames(User);

"/Volumes/Leopard_Partition/Users/kovrigin/Documents/Workspace/Global Analysis/IDAP/Mathematical_models/Equilibrium_thermodynamic_models/U/U_model_derivation.mb"
{CurrentPath, ProjectName, eqLeq, eqReq, eqRLeq, fLeq_U, filename, pnReq_U, pnRLeq_U}

 

STEP 2: Assume values and test procedures:

Rtot_value:=1e-3:
K_A_value:= 1e7:
LR_ratio_value:= 0.8:

 

Test calculations:

fLeq_U(Rtot_value, LR_ratio_value, K_A_value);
pnReq_U(Rtot_value, LR_ratio_value, K_A_value);
pnRLeq_U(Rtot_value, LR_ratio_value, K_A_value);

0.0000003990044749
0.0002003990045
0.0007996009955

 

=> all operational

 

 

 

STEP 3: Make wrapper functions for plotting dependent only on one parameter x=L/R:

fnLeq_U:=x -> fLeq_U(Rtot_value, x, K_A_value):
fnReq_U:=x -> pnReq_U(Rtot_value, x, K_A_value):
fnRLeq_U:=x -> pnRLeq_U(Rtot_value, x, K_A_value):

 

 

 

 

 

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2. Simulation

 

 

2.1 Macroscopic B model

 

ModelName:="U":
// Thermodynamic parameters
Rtot_value:=1e-3:
K_A_value:= 1e5:
LR_ratio_max:= 1.5:

// Plotting parameters
LW:=1: x_min:=1e-6:


// Compute dependent constants
// None in this model

p_Leq:=  plot::Function2d(Function=(fnLeq_U), LegendText="[L]", Color = RGB::Green, XMin=(x_min),XMax=(LR_ratio_max),XName=(x),TitlePositionX=(0) ,LineWidth=LW):
p_Req:=  plot::Function2d(Function=(fnReq_U), LegendText="[R]", Color = RGB::Black, XMin=(x_min),XMax=(LR_ratio_max),XName=(x),TitlePositionX=(0) ,LineWidth=LW):
p_RLeq:=  plot::Function2d(Function=(fnRLeq_U), LegendText="[RL]", Color = RGB::Blue, XMin=(x_min),XMax=(LR_ratio_max),XName=(x),TitlePositionX=(0) ,LineWidth=LW):


// Report constants
print(Unquoted,"Model: ".ModelName);
print(Unquoted,"R(total):=".Rtot_value.":");
print(Unquoted,"K_A:=".K_A_value.":");

// Plot all
// plot all together
plot(p_Leq,p_Req, p_RLeq,   YAxisTitle="M", Header=("Model: ".ProjectName), Height=160, Width=100,TicksLabelFont=["Helvetica",12,[0,0,0],Left], AxesTitleFont=["Helvetica",14,[0,0,0],Left], XGridVisible=TRUE, YGridVisible=TRUE,LegendVisible=TRUE, LegendFont=["Helvetica",14,[0,0,0],Left]);

Model: U
R(total):=0.001:
K_A:=100000.0:
MuPAD graphics

 

 

 

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Conclusions

 

U model is ready for use in IDAP.

 

 

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