BMC Systems Biology

Table 1 Copy number and association rate for subsystems when we use the DNA size ratio method

From: System size reduction in stochastic simulations of the facilitated diffusion mechanism

DNA size		lacI			$k_{λ}^{assoc} s^{- 1}$
4.6 Mbp	1000	100	10		2400
$2.3 Mbp$	496	50	5	172.28	169.09	168.75
1.0 Mbp	216	22	2	50.78	49.79	49.68
460 Kbp	99	10	1	20.60	20.19	20.15
230 Kbp	50	5	-	9.81	9.61	9.59
100 Kbp	22	2	-	4.15	4.07	4.06
46 Kbp	10	1	-	1.89	1.85	1.85

The full system consists of (i) 1000, (ii) 100 and (iii) 10 lacI molecules. When computing $k_{λ}^{assoc}$ , we assumed that, for the full system, the time spent on the DNA is: i) 〈f₁₀〉≈0.923, (ii) 〈f₁₀₀〉≈0.922 and (iii) 〈f₁₀₀₀〉≈0.921.

Back to article page

ISSN: 1752-0509

Contact us

General enquiries: ORSupport@springernature.com