A Hyperstable Miniprotein: Additive Effects of D- and L-Ala Substitutions

The effects of alanine substitutions in each helical segment of the structure, and Gly to D-Ala mutations at sites where glycines have positive phi angles in the Trp-cage miniprotein are reported. The effects of the stabilizing mutation were additive, yielding a 20-residue construct (Tm = 83^o^C). Gly to L-Ala substitutions were uniformly destabilizing ([DELTA][DELTA]G~F~ > 11 kJ/mol): the preference for a D-Ala can be as large as 16 kJ/mol. Glycine to D-Ala mutations are validated as a strategy for the design of hyperstable miniprotein scaffolds suitable for stereospecific pharmacophore display

Spin susceptibility of underdoped cuprates: the case of Ortho-II YBa_2Cu_3O_{6.5}

Recent inelastic neutron scattering measurements found that the spin susceptibility of detwinned and highly ordered ortho-II YBa_2Cu_3O_{6.5} exhibits, in both the normal and superconducting states, one-dimensional incommensurate modulations at low energies which were interpreted as a signature of dynamic stripes. We propose an alternative model based on quasiparticle transitions between the arcs of a truncated Fermi surface. Such transitions are resonantly enhanced by scattering to the triplet spin resonance. We show that the anisotropy in the experimental spin response is consistent with this model if the gap at the saddle points is anisotropic.Comment: 5 fives, 3 postscript figure

First-principle Wannier functions and effective lattice fermion models for narrow-band compounds

We propose a systematic procedure for constructing effective lattice fermion models for narrow-band compounds on the basis of first-principles electronic structure calculations. The method is illustrated for the series of transition-metal (TM) oxides: SrVO$_3$, YTiO$_3$, V$_2$O$_3$, and Y$_2$Mo$_2$O$_7$. It consists of three parts, starting from LDA. (i) construction of the kinetic energy Hamiltonian using downfolding method. (ii) solution of an inverse problem and construction of the Wannier functions (WFs) for the given kinetic energy Hamiltonian. (iii) calculation of screened Coulomb interactions in the basis of \textit{auxiliary} WFs, for which the kinetic-energy term is set to be zero. The last step is necessary in order to avoid the double counting of the kinetic-energy term, which is included explicitly into the model. The screened Coulomb interactions are calculated in a hybrid scheme. First, we evaluate the screening caused by the change of occupation numbers and the relaxation of the LMTO basis functions, using the conventional constraint-LDA approach, where all matrix elements of hybridization involving the TM $d$ orbitals are set to be zero. Then, we switch on the hybridization and evaluate the screening associated with the change of this hybridization in RPA. The second channel of screening is very important, and results in a relatively small value of the effective Coulomb interaction for isolated $t_{2g}$ bands. We discuss details of this screening and consider its band-filling dependence, frequency dependence, influence of the lattice distortion, proximity of other bands, and the dimensionality of the model Hamiltonian.Comment: 35 pages, 25 figure

Role for the fission yeast RecQ helicase in DNA repair in G2.

Members of the RecQ helicase subfamily are mutated in several human genomic instability syndromes, such as Bloom, Werner, and Rothmund-Thomson syndromes. We show that Rqh1, the single Schizosaccharomyces pombe homologue, is a 3'-to-5' helicase and exists with Top3 in a high-molecular-weight complex. top3 deletion is inviable, and this is suppressed by concomitant loss of rqh1 helicase activity or loss of recombination functions. This is consistent with RecQ helicases in other systems. By using epistasis analysis of the UV radiation sensitivity and by analyzing the kinetics of Rhp51 (Rad51 homologue), Rqh1, and Top3 focus formation in response to UV in synchronized cells, we identify the first evidence of a function for Rqh1 and Top3 in the repair of UV-induced DNA damage in G(2). Our data provide evidence that Rqh1 functions after Rad51 focus formation during DNA repair. We also identify a function for Rqh1 upstream of recombination in an Rhp18-dependent (Rad18 homologue) pathway. The model that these data allow us to propose helps to reconcile different interpretations of RecQ family helicase function that have arisen between work based on the S. pombe system and models based on studies of Saccharomyces cerevisiae SGS1 suggesting that RecQ helicases act before Rad51

Phase transition in a spring-block model of surface fracture

A simple and robust spring-block model obeying threshold dynamics is introduced to study surface fracture of an overlayer subject to stress induced by adhesion to a substrate. We find a novel phase transition in the crack morphology and fragment-size statistics when the strain and the substrate coupling are varied. Across the transition, the cracks display in succession short-range, power-law and long-range correlations. The study of stress release prior to cracking yields useful information on the cracking process.Comment: RevTeX, 4 pages, 4 Postscript figures included using epsfi

Threshold detachment of negative ions by electron impact

The description of threshold fragmentation under long range repulsive forces is presented. The dominant energy dependence near threshold is isolated by decomposing the cross section into a product of a back ground part and a barrier penetration probability resulting from the repulsive Coulomb interaction. This tunneling probability contains the dominant energy variation and it can be calculated analytically based on the same principles as Wannier's description for threshold ionization under attractive forces. Good agreement is found with the available experimental cross sections on detachment by electron impact from $D^{-}$, $O^{-}$ and $B^{-}$.Comment: 4 pages, 4 figures (EPS), to appear in Phys.Rev.Lett, Feb. 22nd, 199

The Structure of Barium in the hcp Phase Under High Pressure

Recent experimental results on two hcp phases of barium under high pressure show interesting variation of the lattice parameters. They are here interpreted in terms of electronic structure calculation by using the LMTO method and generalized pseudopotential theory (GPT) with a NFE-TBB approach. In phase II the dramatic drop in c/a is an instability analogous to that in the group II metals but with the transfer of s to d electrons playing a crucial role in Ba. Meanwhile in phase V, the instability decrease a lot due to the core repulsion at very high pressure. PACS numbers: 62.50+p, 61.66Bi, 71.15.Ap, 71.15Hx, 71.15LaComment: 29 pages, 8 figure

Electronic structure of spin 1/2 Heisenberg antiferromagnetic systems: Ba_2Cu(PO_4)_2 and Sr_2Cu(PO_4)_2

We have employed first principles calculations to study the electronic structure and magnetic properties of the low-dimensional phosphates, Ba2Cu(PO4)2 and Sr2Cu(PO4)2. Using the self-consistent tight-binding lin- earized muffin-tin orbital method and the Nth order muffin-tin orbital method, we have calculated the various intrachain as well as the interchain hopping parameters between the magnetic ions Cu2+ for both the com- pounds. We find that the nearest-neighbor intrachain hopping t is the dominant interaction suggesting the compounds to be indeed one dimensional. Our analysis of the band dispersion, orbital projected band struc- tures, and the hopping parameters confirms that the Cu2+-Cu2+ super-super exchange interaction takes place along the crystallographic b direction mediated by O-P-O. We have also analyzed in detail the origin of short-range exchange interaction for these systems. Our ab initio estimate of the ratio of the exchange inter- action of Sr2Cu(PO4)2 to that of Ba2Cu(PO4)2 compares excellently with available experimental results.Comment: 6 pages, 4 figure