Parametrized Stochastic Grammars for RNA Secondary Structure Prediction

We propose a two-level stochastic context-free grammar (SCFG) architecture for parametrized stochastic modeling of a family of RNA sequences, including their secondary structure. A stochastic model of this type can be used for maximum a posteriori estimation of the secondary structure of any new sequence in the family. The proposed SCFG architecture models RNA subsequences comprising paired bases as stochastically weighted Dyck-language words, i.e., as weighted balanced-parenthesis expressions. The length of each run of unpaired bases, forming a loop or a bulge, is taken to have a phase-type distribution: that of the hitting time in a finite-state Markov chain. Without loss of generality, each such Markov chain can be taken to have a bounded complexity. The scheme yields an overall family SCFG with a manageable number of parameters.Comment: 5 pages, submitted to the 2007 Information Theory and Applications Workshop (ITA 2007

Extensions of the Classical Transformations of 3F2

It is shown that the classical quadratic and cubic transformation identities satisfied by the hypergeometric function ${}_3F_2$ can be extended to include additional parameter pairs, which differ by integers. In the extended identities, which involve hypergeometric functions of arbitrarily high order, the added parameters are nonlinearly constrained: in the quadratic case, they are the negated roots of certain orthogonal polynomials of a discrete argument (dual Hahn and Racah ones). Specializations and applications of the extended identities are given, including an extension of Whipple's identity relating very well poised ${}_7F_6(1)$ series and balanced ${}_4F_3(1)$ series, and extensions of other summation identities.Comment: 22 pages, expanded version, to appear in Advances in Applied Mathematic

Associated Legendre Functions and Spherical Harmonics of Fractional Degree and Order

Trigonometric formulas are derived for certain families of associated Legendre functions of fractional degree and order, for use in approximation theory. These functions are algebraic, and when viewed as Gauss hypergeometric functions, belong to types classified by Schwarz, with dihedral, tetrahedral, or octahedral monodromy. The dihedral Legendre functions are expressed in terms of Jacobi polynomials. For the last two monodromy types, an underlying `octahedral' polynomial, indexed by the degree and order and having a non-classical kind of orthogonality, is identified, and recurrences for it are worked out. It is a (generalized) Heun polynomial, not a hypergeometric one. For each of these families of algebraic associated Legendre functions, a representation of the rank-2 Lie algebra so(5,C) is generated by the ladder operators that shift the degree and order of the corresponding solid harmonics. All such representations of so(5,C) are shown to have a common value for each of its two Casimir invariants. The Dirac singleton representations of so(3,2) are included.Comment: 44 pages, final version, to appear in Constructive Approximatio

A Theory of Magnetization Reversal in Nanowires

Magnetization reversal in a ferromagnetic nanowire which is much narrower than the exchange length is believed to be accomplished through the thermally activated growth of a spatially localized nucleus, which initially occupies a small fraction of the total volume. To date, the most detailed theoretical treatments of reversal as a field-induced but noise-activated process have focused on the case of a very long ferromagnetic nanowire, i.e., a highly elongated cylindrical particle, and have yielded a reversal rate per unit length, due to an underlying assumption that the nucleus may form anywhere along the wire. But in a bounded-length (though long) cylindrical particle with flat ends, it is energetically favored for nucleation to begin at either end. We indicate how to compute analytically the energy of the critical nucleus associated with either end, i.e., the activation barrier to magnetization reversal, which governs the reversal rate in the low-temperature (Kramers) limit. Our treatment employs elliptic functions, and is partly analytic rather than numerical. We also comment on the Kramers prefactor, which for this reversal pathway does not scale linearly as the particle length increases, and tends to a constant in the low-temperature limit.Comment: 11 pages, presented at Fluctuations and Noise 200