Rule-based parameterization

More recently, the Landis group" has used valence bond concepts to derive new angular potential energy functions and to develop rules for parameterization. The VALBOND force field angular energy function is based on Pauling s hybrid orbital nonorthogonality functions and can be derived for any arbitrary combination of s, p, d, and f orbitals. 

The UFF force field represents still another type of force field in that it is neither parameterized in the classical way nor based on ab initio quantum chemical calculations. Instead, the parameters in UFF are evaluated from general rules based on the elements, their hybridization and connectivity. The reason for this choice of parameterization scheme is that the goal of the UFF force field is to extend the calculations to the entire periodic table, making the large number of parameters required for such a task untenable by traditional prescriptions. 

Universal. The parameters in the Universal force field (UFF) [14-16] are calculated using general rules based only upon the element, its hybridization, and its connectivity. For this reason, the UFF has broad applicability but is inherently less accurate than extensively parameterized force fields such as COMPASS. Bond-stretching terms in the UFF are either harmonic or Morse functions. The anglebending and torsion terms are described by a small cosine Fourier expansion. For nonbonded terms, the LJ 6-12 potential and Coulombic terms are used for steric and electrostatic terms, respectively. 

RNA structure prediction models that predominantly rely upon molecular mechanics techniques such as molecular dynamics (MD) are referred to here as physics-based (PB) models. These models are based on the classical all-atom MD simulation technique, which employs a parameterized force field, a set of energy rules, to emulate atom interactions. In order to decrease computational expense from the all-atom representation, CG models group multiple atoms into beads or pseudoatoms. In a similar sense, the all-atom MD force field must be converted to depict feasible interactions between these pseudoatoms. 

These classification methods use different principles and rules for learning and prediction of class membership, but wiU usually produce a comparable result. Some comparisons of the methods have been given (i.e., Kotsiantis, 2007 Rani et al., 2006). Although the modem methods such as SVM have demonstrated very good performance, the drawback is that the model becomes an incomprehensible black-box that removes the explanatory information provided by, for example, a logistic regression model. However, classification performance usually outweighs the need for a comprehensible model. PCA has been used for classification based on bioimpedance measurements. Technically, PCA is not a method for classification but rather a method of data reduction, more suitable as a parameterization step before the classification analysis. 

The parameterizations of 7i and 0 can be made based on both classical statistical and Bayesian principles of inference. The major difference between these two is that the Bayesian framework treat parameters as random variables, while the classical statistical regard them as fixed. Probabilities under the Bayesian framework are subjective and express the assessor s degree of belief Bayesian inference follows by assigning prior distribution to n and 0 expressing one s state of knowledge before observing the data. Bayes rule is then applied to update the beliefs into posterior distribution. 

Lever has described S the electrochemical parameterization of metal complex redox couples based upon a Ru(III)/Ru(II) couple to generate an electrochemical series of ligands. Values of the parameter, El(L), defined as one sixth of the value of the Ru(IID/Ru(II) potential for [RuLe] in acetonitrile, were presented for over 200 ligands, and additional parameters Sm and 7m/ which depend upon the metal and redox couple, as well as spin state and stereochemistry, were also tabulated. The calculated redox potential of a M(n)/M(n-1) couple was defined as Sm[2 El(L)] + Im and the model tested over a range of complexes, largely restricted to examples where an electron was added to, or removed from, the t2g subset in octahedral systems. The approach has proved to be useful both in prediction of electrochemical properties and as an aid in the interpretation of experimental data.53... 

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