Table 3 Potential parameters used in the PBD model
From: Nonlinear physics opens a new paradigm for accurate transcription start site prediction
Potential V | D | \(\alpha\) | b | c | d | |
|---|---|---|---|---|---|---|
AT base pair | \(0.09075\;\)eV | \(3.0\;\)Å\(^{-1}\) | \(4.00\;\)eV | \(0.74\;\)Å\(^{-1}\) | \(0.20\;\) | |
GC base pair | \(0.09900\;\)eV | \(3.4\;\)Å\(^{-1}\) | \(6.00\;\)eV | \(0.74\;\)Å\(^{-1}\) | \(0.20\;\) |
Potential W | \(\rho\) | \(\delta\) | ||||
|---|---|---|---|---|---|---|
25 | 0.8Å\(^{-1}\) | |||||
Dimer | A–T | A–A | T–T | G–T | A–C | T–A |
|---|---|---|---|---|---|---|
\(K\;\)(eV Å\(^{-3}\)) | 0.00176 | 0.00418 | 0.00418 | 0.00480 | 0.00462 | 0.00506 |
Dimer | G–A | T–C | C–C | G–G | G–C | C–T |
|---|---|---|---|---|---|---|
\(K\;\)(eV Å\(^{-3}\)) | 0.00546 | 0.00546 | 0.00810 | 0.00810 | 0.00865 | 0.00865 |
Dimer | A–G | C–A | T–G | C–G | ||
|---|---|---|---|---|---|---|
\(K\;\)(eV Å\(^{-3}\)) | 0.00865 | 0.01140 | 0.01140 | 0.01690 |