Algorithmic computation of knot polynomials of secondary structure elements of proteins

The classification of protein structures is an important and still outstanding problem. The purpose of this paper is threefold. First, we utilize a relation between the Tutte and homfly polynomial to show that the Alexander-Conway polynomial can be algorithmically computed for a given planar graph. Second, as special cases of planar graphs, we use polymer graphs of protein structures. More precisely, we use three building blocks of the three-dimensional protein structure-alpha-helix, antiparallel beta-sheet, and parallel beta-sheet-and calculate, for their corresponding polymer graphs, the Tutte polynomials analytically by providing recurrence equations for all three secondary structure elements. Third, we present numerical results comparing the results from our analytical calculations with the numerical results of our algorithm-not only to test consistency, but also to demonstrate that all assigned polynomials are unique labels of the secondary structure elements. This paves the way for an automatic classification of protein structures.

Semiring induced valuation algebras: Exact and approximate local computation algorithms

Local computation in join trees or acyclic hypertrees has been shown to be linked to a particular algebraic structure, called valuation algebra.There are many models of this algebraic structure ranging from probability theory to numerical analysis, relational databases and various classical and non-classical logics. It turns out that many interesting models of valuation algebras may be derived from semiring valued mappings. In this paper we study how valuation algebras are induced by semirings and how the structure of the valuation algebra is related to the algebraic structure of the semiring. In particular, c-semirings with idempotent multiplication induce idempotent valuation algebras and therefore permit particularly efficient architectures for local computation. Also important are semirings whose multiplicative semigroup is embedded in a union of groups. They induce valuation algebras with a partially defined division. For these valuation algebras, the well-known architectures for Bayesian networks apply. We also extend the general computational framework to allow derivation of bounds and approximations, for when exact computation is not feasible.

Ixaru's Extended Frequency Dependent Quadrature Rules for Slater Integrals: Parallel Computation Issues

We describe recent progress of an ongoing research programme aimed at producing computational science software that can exploit high performance architectures in the atomic physics application domain. We examine the computational bottleneck of matrix construction in a suite of two-dimensional R-matrix propagation programs, 2DRMP, that are aimed at creating virtual electron collision experiments on HPC architectures. We build on Ixaru's extended frequency dependent quadrature rules (EFDQR) for Slater integrals and examine the challenge of constructing Hamiltonian matrices in parallel across an m-processor compute node in a block cyclic distribution for subsequent diagonalization by ScaLAPACK.