Scientific Visualization

Initially the entire backbone is shown; as the simulated annealing process begins, only the switch is shown. The color changes indirectly indicate the change in temperature for this short clip. At the conclusion of the process, both the initial and final configurations of the switch are shown for comparison.

One reference for this study can be found at:
Todd J. Minehardt, Roger Cooke, Edward Pate, and Peter Kollman, A molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd, Biophys. J. 80, 1151-1168 (2001).