Nearest neighbor free energy parameters

Qualitative form of the surface roughness as a function of temperature for a crystal bonded by simple nearest neighbor pair interactions. The roughness is measured by the parameter S equal to the number of free bonds parallel to the surface per surface site, (p is the nearest neighbor bond energy. Note the precipitous increase in S as kT approaches (p due to cooperative effects. 

Recall that the secondary-structure model for RNA is a model - and a crude one at that. It neglects pseudo knots and other tertiary interactions, does not take deviations from the additive nearest neighbor energy model into account, and is based on thermodynamic parameters extracted from melting experiments by means of multidimensional fitting procedures. Thus, you cannot expect perfect predictions for each individual sequence. Rather, the accuracy is on the order of 50% of the base pairs for the minimum free energy structure. 

Doshi, K., Cannone, J., Cobaugh, C., and Gutell, R. (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction. BMC Bioinformatics 5, 105. 

Peek and Hill [1950] used a close-packed lattice with zo = 12 and nearest-neighbor distance fl. The Amolecules were distributed between B lattice sites hence, the volume fraction occupied was y = N/B, and the holes fraction h = l —y. The interaction energy was introduced via the quasichemical equation. Unfortunately, the /i-fraction did not enter explicitly either the partition function or derived from it free energy. Instead, the authors introduced an expandable lattice parameter a = where [Pg.235]

Here, f is the energy coefficient, b the force constant, o is the finite distance at which the potential is zero and the cutoff distances r and Tc are free parameters. The functional form of the l/gxci interactions is defined by a combination of Eq. 16.15 terms between the backbone and base sites within a DNA strand and on the opposite strands, except for the nearest neighbors (see Figure 16.2 (B.l)). The lack of angular component on this potential allows for ssDNA to be highly flexible. 

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