Getting started is not always easy. If you are an absolute beginner with chromatography simulation, we recommend you a hands-on start. On this page, you can find an assortment of tutorials. These have been successfully used in an educational environment and introduced many students into chromatography modeling. For more showcases, we refer to the scientific references.
This first tutorial starts by stating the weak formulation of the convection-diffusion problem and shows how to discretize the partial differential equations in space with finite elements. The remaining ordinary differential equations are solved with MATLAB’s built-in time stepping scheme and, of course, ChromX. The files containing DBC use Danckwerts Boundary conditions.
The second tutorial adds pore diffusion models to the convection diffusion equation. We consider a Lumped and a General Rate Model. The first assumes immediate concentration exchange in the pores of a particle, while the General Rate Model models radially dependent pore concentrations.
In the third tutorial, we add the final third phase: A stationary phase concentration. The adsorption and desorption is modeled by multi-component isotherm equations, here a Langmuir model and a Steric Mass Action model used for ion-exchange chromatography of proteins.
We now consider an artificial two component mixture that is going to be separated in bind-elute mode. We use the Steric Mass Action model to simulate elution by a salt step. The optimal step concentration is found with deterministic and heuristic methods.
We use the framework developed for optimization to estimate unknown isotherm parameters by curve fitting. In ChromX, we demonstrate how to estimate parameters for a single component from different experiments, e.g. different salt gradient heights or lengths.
Mechanistic modeling of protein chromatography has long been part of the curriculum at Karlsruhe Institute of Technology (KIT), since 2012 supported by exercises with ChromX. To allow students to gain hands-on experience in model-based optimization, an undergraduate lab course practices mAb purification with ChromX. This tutorial recapitulates the results from the winter semester 2013/2014 and serves as template for generic single-step chromatography optimization with ChromX.
ChromX writes chromatograms and intra-column time series in the VTK DataFile Version 2.0 format, defined by the open-source Visualization Toolkit (VTK) available from www.vtk.org. This tutorial demonstrates visualization with ParaView, available from www.paraview.org, a VTK-based open-source plotting and rendering software.
The simplest way to use ChromX with MATLAB is to write a cmx parameter file for ChromX, start the simulation and read the results back into MATLAB. As an example we will use the isocratic elution with SMA isotherm from the third numerics tutorial.
Originally designed for the Downstream Days Summer School 2013, this file shows that even a spreadsheet can be sufficient to simulate and optimize a separation. We implemented an equilibrium dispersive model with SMA isotherm for three proteins in gradient elution.