Extended model for water formation

[Arda Keleş]

Hello everyone, 

I've tried to write the extended version of the water formation system (OH included). I wonder if anyone else has tried it so we can compare our codes. Here is the function:

complex_water_formation <- function(N, r1_rate, r2_rate, r3_rate, r4_rate, H_ini, O_ini, OH_ini, W_ini) {

  

  W <- d_W <- rep(NA, N)

  OH <- d_OH <- rep(NA, N)

  O <- d_O <- rep(NA, N)

  H <- d_H <- rep(NA, N)

  

  W[1] <- W_ini

  OH[1] <- OH_ini

  O[1] <- O_ini

  H[1] <- H_ini

  

  d_W[1] <- d_OH[1] <- d_O[1] <- d_H[1] <- 0

  

  for(i in 2:N) {

    

    d_W[i] <- r4_rate * d_OH[i-1] * d_H[i-1] - r3_rate * d_W[i-1]

    d_OH[i] <- -r4_rate * d_H[i-1] * d_OH[i-1] - r2_rate * d_OH[i-1] + r1_rate * d_O[i-1] * d_H[i-1] + r3_rate * d_W[i-1]

    d_O[i] <- -r1_rate * d_H[i-1] * d_O[i-1] + r2_rate * d_OH[i-1]

    d_H[i] <- r2_rate * d_OH[i-1] + r3_rate * d_W[i-1] - r1_rate * d[H-1] * d_O[i-1] - r4_rate * d_H[i-1] * d_OH[i-1]

    

    W[i] <- W[i-1] + d_W[i]

    OH[i] <- OH[i-1] + d_OH[i]

    O[i] <- O[i-1] + d_O[i]

    H[i] <- H[i-1] + d_H[i]

      

  }

  

 return(data.frame(W, H, O, OH))

   

}

Take care,
Arda

[Dr. Andrés Aravena]

Hi

sorry for the late reply. I reorganized your code to understand it better. I think it is better to write first the formulas for each reaction. The key part of your code is

r1 <- r1_rate * d_H[i-1] * d_O[i-1]

r2 <- r2_rate * d_OH[i-1]

r3 <- r3_rate * d_W[i-1]

r4 <- r4_rate * d_OH[i-1] * d_H[i-1]

d_W[i] <- r4 - r3

d_OH[i] <- -r4 - r2 + r1 + r3

d_O[i] <- -r1 + r2

d_H[i] <- r2 + r3 - r1 - r4

I think this corresponds to the diagram on the blog.

Good work. Well done

[Arda Keleş]

Yes sir, 
What I did at first, it looks 'ugly'. Writing the formulas for each reaction at first is so much better. I think it was a rookie mistake :)
Take care,
Arda Keleş

Dr. Andrés Aravena <andres....@istanbul.edu.tr>, 9 May 2021 Paz, 12:56 tarihinde şunu yazdı:

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Nazım Arda KELEŞ

İstanbul Üniversitesi - Moleküler Biyoloji ve Genetik

[Andres Aravena]

On Wed, 12 May 2021 at 20:18, Arda Keleş <ardak...@gmail.com> wrote:

Yes sir, 
What I did at first, it looks 'ugly'. Writing the formulas for each reaction at first is so much better. I think it was a rookie mistake :)

In fact it is not. It is my fault. I teach it the wrong way. Even this semester I sent a text with the confusing text. I really need to change it. I'm sorry for the confusion.

take care