Setting up the experiment

Before running a simulation, you need to set up the experiment that you wish to study. Several components of the experiment need to be chosen, including the proteins being separated, the buffer, the salt concentrations and the resin.

To define an experiment, use the controls that are located on the right side of the simulation window to the following:

1. Select the initial salt concentration and the final salt concentration. The values of the concentrations must be between 0M and 1M NaCl. The application is designed to start with a low salt concentration in solvent A and a higher salt concentration in solvent B.
2. Select the buffer using the Buffer radio buttons. All buffers have a concentration of 20 mM and are designed with pH = pK_A for the buffer.
3. Select the resin using the Resin radio buttons. CM Sephadex is a cation exchanger and DEAE Sephadex is an anion exchanger.
4. Select up to five proteins using the Add Protein and Remove Protein buttons. All of the proteins that are available for this experiment are listed in the scrolling listbox. Select a protein from this list, enter the amount of protein in the edit box next to the Add Protein button and click the Add Protein button. The amount entered must be between 1 and 400 mg. The proteins that have been selected for the experiment appear in the larger list box. To remove a selected protein, highlight the protein in the larger listbox and click the Remove Protein button.

Click the Load Experiment button to load the selected settings. Now the simulation may be run.

You may change the settings in the controls at any time, but new settings will not be used until the Load Experiment button is clicked. You may restore the settings that are currently being used by the simulation by clicking the Reset Settings button.