Terminal contributions for duplex oligonucleotide thermodynamic properties in the context of nearest neighbor models.

Additive physical properties of DNA polymer duplexes have been expanded in terms of eight irreducible parameters that ultimately lead to consistency relations among the corresponding 10 duplex dimer contributions. End parameters are often added to allow for oligomer analysis which would add four extra degrees of freedom to the aforementioned parameters. Analysis of sufficient experimental data on oligomer duplexes allows for the unambiguous recovery of irreducible parameters.

The role played by exons in genomic DNA sequence correlations.

The codon structure inside exons imposes a strong modulation with period-3 for genomic composition correlations. A new formalism for calculating nucleotide correlations along DNA sequences in terms of an irreducible set of six correlation functions is presented. New procedures to extract the corresponding period-3 modulations are also developed.

Irreducible representation for nucleotide sequence physical properties and self-consistency of nearest-neighbor dimer sets.

A compact representation of usual DNA/RNA four-nucleotide sets based on molecular affinity classes is proposed. In a geometrical correspondence to this formulation, it follows that intrinsic tetrahedral symmetry correlates nucleotide properties. This representation also leads to a proper decomposition frame for any sequence-dependent physical expectation.

Scattering from dilute ferrofluid suspensions in soft polymer gels.

Small angle neutron and x-ray scattering methods are used to investigate the structure of dilute suspensions of two different ferrofluid systems dispersed in soft polyacrylamide hydrogels. It is found that the particles in the fluid are fractal aggregates composed of smaller particles of radius ca. 5 nm.