Index | Bifurcations analysis | Reference of the study and remarks | Competition |
---|---|---|---|
(A) | Hopf bifurcation | Analytic: Lewis (2003) [41] citing Glass&Mackey (1988) [5] Experimental: Swinburne et al. (2008) [42] | - |
(B) | Hopf bifurcation | Analytic: Widder et al. (2007) [43]. The minimum Hill exponent to make oscillations possible is n = 3. | - |
(C) | - | Experimental: Atkinson et al. (2003) [6]: The notation 2 + 2 refers to the fact that the DNA loops operate when 2 DNA-bound dimers form a tetramer. It is still not clear if the design functions with competition or not, and this is the reason for employing the 2 + 2 notation instead of the arrows. | Probable |
(D) | - | Numeric: Scott et al. (2006) [44] on the Atkinson oscillator. | No |
(E) | SNIC bifurcation | Numeric: Guantes&Poyatos (2006) [18] associate their Design I to the Atkinson experimental context. The oscillators they propose due their oscillations to the time-scale difference between activator and repressor life-time. Otherwise, higher multimers than dimers are needed. | Yes |
(F) | Hopf bifurcation | Numeric: Hasty et al. (2002) [45] Experimental: Stricker et a. (2008) [7] | No |
(G) | Hopf bifurcation | Numeric: Smolen et al. (1998) [46]. The activator needs to be at least a dimer for the existence of the oscillations. | Yes |
(H) | - | Experimental and numeric: Elowitz&Liebler (2000) [4]: n = 2 from Figure (1) above makes reference to the value employed by Elowitz&Leibler in their model. See also the discussion in the Supporting Information from Buchler et al. (2005) [47]. | Â |
 | Hopf bifurcation | Analytic: Mueller et al. (2006) [48]: a general case. | - |