The first step in simulating a sedimentation run is to define a model. This is accomplished by pressing the "Create New Model" button. This will display the Model Selection Dialogue. Select a model from the list. For the non-interacting model you can define the number of components to be modeled with the system. There is no limit to the number of components that can be modeled with this program. After selecting the appropriate model, click on the "Assign Coefficients (s, D, etc)" button to assign values to the model's parameter list.
If you chose a non-interacting system, you will be prompted with a dialogue for entering partial concentration, "s", "D" and concentration dependency parameters sigma and delta. If you click on the "Simulate s and D" button, you will be able to assign the sedimentation and diffusion coefficient by modeling a molecule in the module called Model s, D and f from Molecular Weight for 4 basic shapes. Selecting any one of the check buttons for sphere, prolate, oblate or long rod model will substitute the appropriate s and D coefficients for the selected shape into the dialogue.
If you have selected to model more than one component, clicking on the "Next" button will cycle through the list of selected components, presenting coefficient dialogues for each component. After entering the last component's parameters, click on the "OK" button to be returned to the Model Selection dialogue.
If you choose an equilibrating system, an information message will be displayed informing you that one of the four possible parameters "s" and "D" can be left blank (assigned to zero) because of the molecular weight constraints for the second component. The Svedberg relationship allows three parameters to be specified, while the fourth can then be automatically calculated. The coefficient dialogue for equilibrating systems will display a single screen for both components, While it is possible to assign values for all parameters, you should always leave one of the four parameters set to zero so it can be more accurately assigned by the program itself.
After entering all model parameters, you have the opportunity to save the newly defined model. A file dialogue will appear which allows you to save the model to a file. You will be prompted to enter a short description for your model to facilitate later identification. Once saved, the model can be retrieved at a later time with the "Load existing Model" button from the main finite element simulation panel.
This document is part of the UltraScan Software Documentation
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Last modified on January 12, 2003