Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add SMA-like binding model with pseudo pH dependence #14

Closed
sleweke opened this issue Mar 4, 2020 · 0 comments
Closed

Add SMA-like binding model with pseudo pH dependence #14

sleweke opened this issue Mar 4, 2020 · 0 comments
Labels

Comments

@sleweke
Copy link
Member

sleweke commented Mar 4, 2020

Add a new binding model based on Huuk et al. 2017.
The binding model is an extension of the SMA model and adds a pseudo molecule that provides the local pH.

The equations are given by

\frac{\partial q_i}{\partial t} = k_{a,i}(c_p, q, pH) * (Lambda - \sum_j \frac{nu_j(pH) + sigma_j}{f_j} * q_j )^(nu_i(pH)) * c_{p,i} - k_{d,i}(c_p, q, pH) * c_{p,0}^(nu_i(pH)) * q_i
nu_i(pH) = nu_{i,0} + pH * nu_{i,1} + pH^2 * nu_{i,2}
k_{a,i}(c_p, q, pH) = k_{a,i,0} * exp(k_{a,i,1} * pH + k_{a,i,2} * pH^2) * exp(k_{a,i,salt} * c_{p,0} + k_{a,i,prot} * c_{p,i})
k_{d,i}(c_p, q, pH) = k_{d,i,0} * exp(k_{d,i,1} * pH + k_{d,i,2} * pH^2) * exp(k_{d,i,sdlt} * c_{p,0} + k_{d,i,prot} * c_{p,i})

The pH pseudo component will have index 1, since by convention salt already has index 0.
The pH component is non-binding.

@sleweke sleweke added the feature Feature request label Mar 4, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant