GenoMass ‐ a computer software for automated identification of oligonucleotide DNA adducts from LC‐MS analysis of DNA digests

In the investigation of oligonucleotides, DNA and their adducts by LC‐MS, a myriad of data are generated that make manual data processing quite difficult. This paper describes a ‘reversed pseudo‐combinatorial’ approach for fragment identification and the software implementation of this approach. Combinatorial isomer libraries are generated in silico to represent the digestion products of oligonucleotides, DNA or DNA adducts of various sizes. The software automatically calculates ion masses of each isomeric segment of the library, searches for them in complicated LC‐MS data, lists their intensities and plots extracted ion chromatograms (EIC). This customized new data analysis tool has enabled a study of the enzymatic behavior of a nuclease system in the digestion of normal and adducted DNA, and in the recognition of oligomers containing a carcinogen bound to a nucleobase. The software program potentially can be further expanded to postulate unknown DNA sequences and recognize the adduction sites. Copyright © 2008 John Wiley & Sons, Ltd.     

T = 0 versusT = 1 pairing in 0(36) limit of IBM-4 for heavyN = Z nuclei

In theO(36) limit of the interacting boson model including spin-isospin degrees of freedom (IBM-4), starting with a group chain that preservess andd boson spins and isospins together with a simple mixing hamiltonian, it is shown that the model generates, for heavyN =Z nuclei, even-even to odd-odd staggering in the number ofT = 0 pairs in the ground states for moderate difference in the basicT = 0 andT = 1s-boson pair energies; the staggering disappears when the energy difference is large.     

Phase transitions in electron systems with short-range pairing interactions: Ground state

We propose a real-space, tight-binding model of electrons with short-range pairing interactions. The model involves a competition between the ordinary single particle hoppingt and an attractive interactionV between the singlet electronic pairs formed on neighboring lattice sites. The Hamiltonian effectively describes a mechanism for pair formation. We study the ground-state properties of its onedimensional version using numerically exact finite chain calculations for up toN= 10 sites. The ground-state wave functions, the energy spectrum, and various ground-state correlation functions are calculated with the help of an exactly equivalent system of two coupledS=1/2 spin chains. The results indicate the existence of a transition between the band and the localized pairs situation. The transition takes place forV/t= 1.4–0.1 and appears to be of essential singularity type. Comparison with other models used for pairing phenomena, like the negativeU-Hubbard model is made.     

Prime spectra of non-commutative generalizations of MV-algebras

Non-commutative generalizations of MV-algebras were introduced by G. Georgescu and A. Iorgulesco as well as by the author; the generalizations are equivalent and are called GMV-algebras. We show that GMV-algebras can be considered as special cases of Grishin algebras. As MV-algebras are algebraic models of the Łukasiewicz logic and Grishin algebras have the analogous role for the classical bilinear logic, GMV-algebras correspond to a non-commutative logic between the above logics. Further, by A. Dvurečenskij, any GMV-algebra is isomorphic to an interval of an l-group, which in general is not commutative. This generalizes D. Mundici's representation of MV-algebras by means of intervals of abelian l-groups. In the paper (using this representation) we describe the properties of prime ideal spectra of GMV-algebras and of their factor algebras and ideals and prove that the spectrum of closed ideals of any GMV-algebra is homeomorphic to that of a completely distributive GMV-algebra. Received January 4, 2001; accepted in final form May 2, 2002.     

On the invertibility of time series models

A generalized definition of invertibility is proposed and applied to linear, non-linear and bilinear models. It is shown that some recently studied non-linear models are not invertible, but conditions for invertibility can be achieved for the other models.     

On a multivariate central limit theorem for stationary bilinear processes

In 1957, Parzen proved a central limit theorem for a class of scalar processes which he called multilinear processes. In the present paper only stationary bilinear processes are considered, but the theory is generalized to the multivariate case.     

Pairing mechanism in the doped Hubbard antiferromagnet: the 4×4 model as a test case

We introduce a local formalism, in terms of eigenstates of number operators, having well defined point symmetry, to solve the Hubbard model at weak coupling on a N × N square lattice (for even N). The key concept is that of W = 0 states, that are the many-body eigenstates of the kinetic energy with vanishing Hubbard repulsion. At half filling, the wave function demonstrates an antiferromagnetic order, a lattice step translation being equivalent to a spin flip. Further, we state a general theorem which allows to find all the W = 0 pairs (two-body W = 0 singlet states). We show that, in special cases, this assigns the ground state symmetries at least in the weak coupling regime. The N = 4 case is discussed in detail. To study the doped half filled system, we enhance the group theory analysis of the 4×4 Hubbard model introducing an Optimal Group which explains all the degeneracies in the one-body and many-body spectra. We use the Optimal Group to predict the possible ground state symmetries of the 4×4 doped antiferromagnet by means of our general theorem and the results are in agreement with exact diagonalization data. Then we create W = 0 electron pairs over the antiferromagnetic state. We show analitycally that the effective interaction between the electrons of the pairs is attractive and forms bound states. Computing the corresponding binding energy we are able to definitely predict the exact ground state symmetry. Received 24 October 2000     

Interplay between spin-density-wave and superconducting states in quasi-one-dimensional conductors

The interference between spin-density-wave and superconducting instabilities in quasi-one-dimensional correlated metals is analyzed using the renormalization group method. At the one-loop level, we show how the interference leads to a continuous crossover from a spin-density-wave state to unconventional superconductivity when deviations from perfect nesting of the Fermi surface exceed a critical value. Singlet pairing between electrons on neighboring stacks is found to be the most favorable symmetry for superconductivity. The consequences of non uniform spin-density-wave pairing on the structure of phase diagram within the crossover region is also discussed. Received 3 January 2001 and Received in final form 1st March 2001     

Accessibility of the matrix Riccati differential equation

A known result on the classification of transitive Lie group actions on complex Grassmann manifolds is exploited to derive a necessary and sufficient accessibility criterion for the complex matrix differential Riccati equation. We treat both cases, the symmetric as well as the non-symmetric Riccati equation. Corresponding accessibility results for the real Riccati equation are also available, but not stated here. An application to the accessibility of generalized double bracket flows is given. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)