Figure 8

Simulated folding kinetics of the c-di-GMP riboswitch of the tfoX gene from C. desulforudis audaxviator MP104C. The calculation is based on the 100 best ${\pi }_h^{\mathit{\text{SN}}}$hishapes, and we used the stable helix ([25.5]) of the aptamer as the initial population. We show the results for the 25 best hishapes plus hishape [25.5]. The simulation took 24 hours using 64 cores of a 4x AMD Opteron 6282SE machine with 512 GB RAM running under openSuSE 12.2. This figure was generated using. '/HiKinetics.rb -i Input/c_di_GMP_riboswitch.seq -o Output/c_di_GMP_riboswitch_SN -k 100 -t 4 -s -p [25.5]’.