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.     

Composite boson dominance in many-fermion systems

I recently proposed a method of bosonization based on the use of coherent states of fermion composites, whose validity was restricted to smooth structure functions. In the present paper I remove this limitation and derive results which hold for arbitrary interactions and structure functions. The method respects all symmetries and in particular fermion number conservation. It reproduces exactly the results of the pairing model of atomic nuclei and of the BCS model of superconductivity in the number conserving form of the quasi-chemical equilibrium theory.     

Structural analysis of base mispairing in DNA containing oxidative guanine lesion

Classical molecular dynamics methods were used to analyze the importance of 8-oxoguanine (8-oxoG) pairing with other DNA bases in order to determine the impact of oxidative guanine lesions on DNA structure. Six lesioned molecules, each containing 8-oxoG mispaired with one of the four normal bases on the the opposite strand at the center of 40-mer DNA, and one non-damaged DNA molecule, were simulated for 2 nanoseconds of real time. The 8-oxoG lesioned bases were found to incorporate opposite all normal bases. There are observed conformational and energetical differences among these parings. 8-oxoG in anti-form creates firm hydrogen bonds with cytosine and this bonding has a strong attractive electrostatic interaction energy similar to that of a native base pair-guanine to cytosine. Meanwhile, it does not form a stable base pair with purine bases (adenine and guanine) nor with the pyrimidine base thymine. On the other hand, the 8-oxoG in syn-form was found to pair with adenine.      

Determinantal Resolution of the Universal Subscheme in $$\mathcal{S}{\text{ }} \times {\text{ }}H_{d + 1} $$

We construct a determinantal resolution of singularities for the universal subscheme in and prove that it is isomorphic to the variety of total pairs .     

圆射流中拟序涡配对的数值模拟

用三维涡丝法结合涡丝的增加与合并技术,对不可压圆射流场,数值模拟了在扰动中加入次谐波后流场拟序涡的配对,配对情况与实验结果一致,通过对不同时刻涡量图的比较与分析,给出了次谐波初始强度对涡配对的影响,初始强度越大,涡配对出现越早,涡配对位置越往上游移动;同时还得到了基波与次谐波初始相位差和涡配对的关系,没有相位差时,次谐波增长最快,相位差增加时,涡配对的速度降低。说明控制次谐波的初始强度和基波与次谐波的相位差,能起到控制圆射流剪切层乃至控制整个射流场的目的。     

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     

Confinement effects on the spin potential of first row transition metal cations

Abstract

By using a spherical confinement method, the behaviour of spin potential and pairing energy is studied and compared to the free ion limit for a representative sample of first row transition metal cations. The study was carried out using three approximations within the Kohn–Sham model; exchange-only, exchange plus correlation contribution and correcting the self-interaction error. For the three approaches, the spin potential shows a close connection with the capability of a system to perform a spin-flip process. Namely, in accordance with Hund’s rule, the spin potential increases from low d occupation up to maximum for the half filled configurations; and it decreases from that point on, as d occupation grows. Such a conclusion is reached for confined and non-confined cations, even under extreme confinement conditions. In addition, two important observations are obtained: (a) In contrast to the neutral atoms situation, in the case of cations no eigenvalue crossings are observed under confinement conditions for the whole sample of ions tested. (b) The self-interaction error found in many exchange–correlation functionals does not affect the pairing energy over confined atoms, even when this error has an important contribution on a single eigenvalue. Therefore, pairing energy predicted by exchange–correlation functionals non-corrected by the self-interaction error can be made safely on transition metal cations under high pressures.