Richard D. Berlin
Center for Cell Analysis & Modeling

CCAM Educational References

Virtual Cell Curricular Exercises

Biochemistry II

This homework is preceeded by a lecture that highlights the relationship between quantitative studies of cellular behaviors e.g. PIP2 concentrations in relation to IP3 production and affects of fluorescent indicators on cellular biochemistry. This exercise is specifically designed to have students become familiar with the Virtual Cell and highlight significance of cellular locations on dynamic behavior of species.

 

Virtual Cell Homework Assignment

Created by Instructor: Les Loew

1. Establish an account on the Virtual Cell website (http://Vcell.org). Make your username easily identifiable by the instructor (e.g. first_name_last_name).
2. Go through the FRAP Binding Tutorial and create the corresponding Virtual Cell model
3. Elaborate the model by
   1. adding an extracellular compartment
   2. adding passive fluxes for r and rf across the nuclear membrane: (J_flux1 = k1*(r_cytosol-r_nucleus); J_flux2=k2*(rf_cytosol - rf_nucleus))
   3. create a new application with the geometry N1E_for_PIP2 (it is under the collection of geometries labeled 'les')
   4. put the binding sites in a 5µm X 5µm square within the nucleus
   5. use a circle as the bleaching spot to fill as much of the nucleus as you can
   6. Run a 30s simulation using 0.001 as the timestep and keep every 1000 timepoints
4. Save and close the model. Share the model by adding the instructors account name to the access control list.

Evaluation

Homework is evaluated on the following criteria:

1. Creating a model that completes a simulation run
2. Obtaining the correct simulation result for the example