The Kagome Antiferromagnet with Defects: Satisfaction, Frustration, and Spin Folding in a Random Spin System

It is shown that site disorder induces noncoplanar states, competing with the thermal selection of coplanar states, in the nearest neighbor, classical kagome Heisenberg antiferromagnet (AFM). For weak disorder, it is found that the ground state energy is the sum of energies of separately satisfied triangles of spins. This implies that disorder does not induce conventional spin glass behavior. A transformation is presented, mapping ground state spin configurations onto a folded triangular sheet (a new kind of ``spin origami'') which has conformations similar to those of tethered membranes.Comment: REVTEX, 11 pages + 3 pictures upon reques

Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4

The genome of bacteriophage T4 encodes three polynucleotide ligases, which seal the backbone of nucleic acids during infection of host bacteria. The T4Dnl (T4 DNA ligase) and two RNA ligases [T4Rnl1 (T4 RNA ligase 1) and T4Rnl2] join a diverse array of substrates, including nicks that are present in double-stranded nucleic acids, albeit with different efficiencies. To unravel the biochemical and functional relationship between these proteins, a systematic analysis of their substrate specificity was performed using recombinant proteins. The ability of each protein to ligate 20 bp double-stranded oligonucleotides containing a single-strand break was determined. Between 4 and 37 °C, all proteins ligated substrates containing various combinations of DNA and RNA. The RNA ligases ligated a more diverse set of substrates than T4Dnl and, generally, T4Rnl1 had 50-1000-fold lower activity than T4Rnl2. In assays using identical conditions, optimal ligation of all substrates was at pH 8 for T4Dnl and T4Rnl1 and pH 7 for T4Rnl2, demonstrating that the protein dictates the pH optimum for ligation. All proteins ligated a substrate containing DNA as the unbroken strand, with the nucleotides at the nick of the broken strand being RNA at the 3'-hydroxy group and DNA at the 5'-phosphate. Since this RNA-DNA hybrid was joined at a similar maximal rate by T4Dnl and T4Rnl2 at 37 °C, we consider the possibility that this could be an unexpected physiological substrate used during some pathways of 'DNA repair'

Key determinants of target DNA recognition by retroviral intasomes

BACKGROUND: Retroviral integration favors weakly conserved palindrome sequences at the sites of viral DNA joining and generates a short (4–6 bp) duplication of host DNA flanking the provirus. We previously determined two key parameters that underlie the target DNA preference for prototype foamy virus (PFV) and human immunodeficiency virus type 1 (HIV-1) integration: flexible pyrimidine (Y)/purine (R) dinucleotide steps at the centers of the integration sites, and base contacts with specific integrase residues, such as Ala188 in PFV integrase and Ser119 in HIV-1 integrase. Here we examined the dinucleotide preference profiles of a range of retroviruses and correlated these findings with respect to length of target site duplication (TSD). RESULTS: Integration datasets covering six viral genera and the three lengths of TSD were accessed from the literature or generated in this work. All viruses exhibited significant enrichments of flexible YR and/or selection against rigid RY dinucleotide steps at the centers of integration sites, and the magnitude of this enrichment inversely correlated with TSD length. The DNA sequence environments of in vivo-generated HIV-1 and PFV sites were consistent with integration into nucleosomes, however, the local sequence preferences were largely independent of target DNA chromatinization. Integration sites derived from cells infected with the gammaretrovirus reticuloendotheliosis virus strain A (Rev-A), which yields a 5 bp TSD, revealed the targeting of global chromatin features most similar to those of Moloney murine leukemia virus, which yields a 4 bp duplication. In vitro assays revealed that Rev-A integrase interacts with and is catalytically stimulated by cellular bromodomain containing 4 protein. CONCLUSIONS: Retroviral integrases have likely evolved to bend target DNA to fit scissile phosphodiester bonds into two active sites for integration, and viruses that cut target DNA with a 6 bp stagger may not need to bend DNA as sharply as viruses that cleave with 4 bp or 5 bp staggers. For PFV and HIV-1, the selection of signature bases and central flexibility at sites of integration is largely independent of chromatin structure. Furthermore, global Rev-A integration is likely directed to chromatin features by bromodomain and extraterminal domain proteins. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12977-015-0167-3) contains supplementary material, which is available to authorized users

Structural features of highly stable reproducible C₆₀ fullerene aqueous colloid solution probed by various techniques

The method of preparation of highly stable reproducible C₆₀ fullerene aqueous colloid solution is described. The structural organization of C₆₀ fullerenes in aqueous solution was studied and analyzed in detail using various techniques such as chemical analysis, UV/VIS spectroscopy, atomic force and scanning tunneling microscopy, dynamic light scattering, and zeta potential method

Bond-disordered spin systems: Theory and application to doped high-Tc compounds

We examine the stability of magnetic order in a classical Heisenberg model with quenched random exchange couplings. This system represents the spin degrees of freedom in high-$T_\textrm{c}$ compounds with immobile dopants. Starting from a replica representation of the nonlinear $\sigma$-model, we perform a renormalization-group analysis. The importance of cumulants of the disorder distribution to arbitrarily high orders necessitates a functional renormalization scheme. From the renormalization flow equations we determine the magnetic correlation length numerically as a function of the impurity concentration and of temperature. From our analysis follows that two-dimensional layers can be magnetically ordered for arbitrarily strong but sufficiently diluted defects. We further consider the dimensional crossover in a stack of weakly coupled layers. The resulting phase diagram is compared with experimental data for La$_{2-x}$Sr$_x$CuO$_4$.Comment: 12 pages, 5 figure

TOF-Brho Mass Measurements of Very Exotic Nuclides for Astrophysical Calculations at the NSCL

Atomic masses play a crucial role in many nuclear astrophysics calculations. The lack of experimental values for relevant exotic nuclides triggered a rapid development of new mass measurement devices around the world. The Time-of-Flight (TOF) mass measurements offer a complementary technique to the most precise one, Penning trap measurements, the latter being limited by the rate and half-lives of the ions of interest. The NSCL facility provides a well-suited infrastructure for TOF mass measurements of very exotic nuclei. At this facility, we have recently implemented a TOF-Brho technique and performed mass measurements of neutron-rich nuclides in the Fe region, important for r-process calculations and for calculations of processes occurring in the crust of accreting neutron stars.Comment: 8 pages, 4 figures, submitted to Journal of Physics G, proceedings of Nuclear Physics in Astrophysics II

Critical temperature for the nuclear liquid-gas phase transition (from multifragmentation and fission)

Critical temperature Tc for the nuclear liquid-gas phase transition is stimated both from the multifragmentation and fission data. In the first case,the critical temperature is obtained by analysis of the IMF yields in p(8.1 GeV)+Au collisions within the statistical model of multifragmentation (SMM). In the second case, the experimental fission probability for excited 188Os is compared with the calculated one with Tc as a free parameter. It is concluded for both cases that the critical temperature is higher than 16 MeV.Comment: 15 pages, 8 figure

Equistrong Tower Design

The September 11, 2001 events attracted the attention of civil engineers of the world to the problem of safety of towers and skyscrapers. According to recent studies, the WTC collapse was caused by man-made explosions on a critical floor located much lower than the floors hit by terrorist planes which supports the wide-spread rumor in the U.S. that MASAD agents used the aftermath mess-up after the crush of the planes, put some explosives in the critical floor and detonated them in a while. These or any other possible calamities must be technically treated which can be achieved by drastic increase of safety factor of tower design. In the present paper a new approach to the optimal design of towers is advanced based on the principle of equistrength. Introductive Section 1 provides a short overview of the theory of equistrong structures given in the book by Cherepanov and Ershov (1977). In Section 2, a continuum model is used for the design of equistrong towers. The same problem is studied in Section 3 with an account of the discrete, floor-by-floor structure of equistrong towers. Conclusion emphasizes that the equistrong tower designs allow developers to achieve the maximum possible safety factor. Current designs of skyscrapers including WTC towers are as primitive as the Tower of Babylon