Table 1 Parameter specifications for the WTC model
From: Efficient design of synthetic gene circuits under cell-to-cell variability
Name | Description | Units | Fixed value | Cell-specific | |
|---|---|---|---|---|---|
Fixed parameters | |||||
\(k_{Tet}\) | Max production rate of TetR | nM min\(^{-1}\) | 1.12 | Yes | |
\(k_{Tup}\) | Max production rate of TetR-Tup1 | nM min\(^{-1}\) | 0.79 | Yes | |
\(k_{C}\) | Max production rate of Citrine | nM min\(^{-1}\) | 0.84 | Yes | |
\(d_{Tup}\) | Degradation constant of TetR-Tup1 | min\(^{-1}\) | 1.28 | Yes | |
n | Hill coefficient for promoter repression by TetR | (–) | 1.57 | No | |
\(K_a\) | Association constant for TetR and TetR-Tup1 binding to aTc | nM\(^{-1}\) | 144.37 | No | |
\(U^{nM}_{sc}\) | Scaling constant: nM per tdh3 producing unit (see [4]) | nM \(\cdot\) unit\(^{-1}\) | 0.76 | No | |
Name | Description | Units | Bounds | Explored in log space | Cell-specific |
|---|---|---|---|---|---|
Sampled parameters | |||||
\(d_{Tet}\) | Degradation constant of TetR | min\(^{-1}\) | [\(3 \cdot 10^{-3}\) 0.1] | Yes | Yes |
\(d_{C}\) | Degradation constant of Citrine | min\(^{-1}\) | [\(3 \cdot 10^{-3}\) 0.1] | Yes | Yes |
\(\theta _{Tet}\) | Repression coefficient TetR | nM | [\(10^{-3}\) \(10^{6}\)] | Yes | No |
\(\theta _{Tup}\) | Repression coefficient TetR-Tup1 | nM | [\(10^{-6}\) 20] | Yes | No |