Calculating the Secrets of Life Contributions of the Mathematical Sciences to Molecular Biology (1995) / Chapter Skim
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Pages 187-191
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From page 187... ...
Combining these contributions (and allowing the interstranc3 twisting to equilibrate with the residual superhelicity) , the free energy G of a state is found to depend on three parameters: the number ~ of separates} base pairs, the number HAT Of these that are A Ts, and the number r of runs of separation: GO ~2~ 2 CK ~ 2 n, 7 7 + _J + ar + bATnAT + bGC (n nAT)
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From page 188... ...
values are computed for all parameters of interest. These may include the expected torsional deformation of the strand-separated regions, expected numbers of separated base pairs, of separated A T pairs, and of runs of separation, the ensemble average free energy G
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From page 189... ...
- G (7.9) Base pairs that require incremental free energy to separate at equilibrium have G(x)
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From page 190... ...
First, growth conditions are found for Z(n,r) , the contribution to the partition function from all states having n total separated base pairs in r runs.
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From page 191... ...
for the series ratios p and ¢ occur at reasonably small cutoffs (r ~ 8, n ~ 150 for a molecule of N = 5,000 base pairs under reasonable environmental conditions)
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