Optimizing Unknown Parameters in Algebraic Systems for Thermodynamic Bindings
This repository contains tools for optimizing unknown parameters in algebraic systems that describe thermodynamic bindings of dyes and guests to a host.
The package includes a script interface and a Shiny app for convenient usage.
Documentation
Documentation
Features
- Identification of specific parameters (kHD or kGuest, I0, IHD, and ID) of different algebraic systems using the R package tsf.
- Preliminary work involves defining systems in Maxima, and subsequent elimination of specific variables, yielding two polynomials.
More details can be found in documentation and maxima code.
- Each polynomial includes known variables (e.g., concentration of the host), variables to be optimized (e.g., kGuest), and an unknown variable (either d or hd).
- For each algebraic system, a loss function is defined in R, taking the four parameters to be optimized as arguments and returning an error for the received parameter set.
- The parameterset consists of kHD or kGuest, I0, IHD, and ID, along with constant parameters such as the concentration of the host and a data.frame
containing the independent variable (dye or guest) and the corresponding signal.
- Roots are calculated for each polynomial at each concentration of the independent variable, defining the concentration of either d or hd to the independent variable.
- In silico signal calculation based on the formula: SignalInSilico = I0 + IHD[hd] + ID[d].
- Comparison of the in silico signal to the measured signal, with the error returned by the loss function indicating the match quality.
Installation
remotes::install_github("ComPlat/Thermosimfit", subdir = "tsf")