Characterisation of the mycobacterial NER system reveals novel functions of uvrD1 helicase

In this study, we investigated the role of the nucleotide excision repair (NER) pathway in mycobacterial DNA repair. Mycobacterium smegmatis lacking the NER excinuclease component uvrB, the helicase uvrD1 and a double knock-out lacking both proteins were constructed and their sensitivity to a series of DNA damaging agents wa analysed. As anticipated, the mycobacterial NER system was shown to be involved in the processing of bulky DNA adducts and inter-strand cross-links. In addition, it could be shown to exert a protective effect against oxidising and nitrosating agents. Interestingly, inactivation of uvrB and uvrD1 significantly increased marker integration frequencies in gene conversion assays. This implies that in mycobacteria, which lack the postreplicative mismatch repair system, NER, and particularly the UvrD1 helicase, is involved in the processing of a subset of recombination-associated mismatches

Water resources simulation in the Rio Grande basin using coupled models

Regional assessments of water resources under global climate change require models that can resolve management, land use, and climate effects. Los Alamos National Laboratory is developing a coupled model of water resources that places a river basin in its global context. The upper Rio Grande basin above El Paso, Texas is the testbed for this model. The model structure and computational approach are emphasize and issues such as nonlinear feedback between components and spatial and temporal scaling of processes are discussed. Using simulations of regional meteorology, the effects of high spatial resolution simulations on the distribution of precipitation are demonstrated

Solar Physics

Abstract Relative magnetic helicity, as a conserved quantity of ideal magnetohydrodynamics, has been highlighted as an important quantity to study in plasma physics. Due to its non-local nature, its estimation is not straightforward in both observational and numerical data. In the present study we derive expressions for the practical computation of the gauge-independent relative magnetic helicity in three-dimensional finite domains. The derived expressions are easy to implement and rapid to compute. They are derived in Cartesian coordinates, but can be easily written in other coordinate systems. We apply our method to a numerical model of a force-free equilibrium containing a flux rope, and compare the results with those obtained employing known half-space equations. We find that our method requires a much smaller volume than half-space expressions to derive the full helicity content. Additionally, we prove that values of relative magnetic helicity of different magnetic fields can be compared with each other in the same sense as free-energy values can. Therefore, relative magnetic helicity can be meaningfully and directly compared between different datasets, such as those from different active regions, but also the same dataset at different times. Typical applications of our formulae include the helicity computation in threedimensional models of the solar atmosphere, e.g. coronal-field reconstructions by force-free extrapolation and discretized magnetic fields of numerical simulations

Thermodynamic properties and structural stability of thorium dioxide

Using density functional theory (DFT) calculations, we have systematically investigated the thermodynamic properties and structural stabilities of thorium dioxide (ThO$_2$). Based on the calculated phonon dispersion curves, we calculate the thermal expansion coefficient, bulk modulus, and heat capacities at different temperatures for ThO$_2$ under the quasi-harmonic approximation. All the results are in good agreement with corresponding experiments proving the validity of our methods. Our theoretical studies can help people more clearly understand the thermodynamic behaviors of ThO$_2$ at different temperatures. In addition, we have also studied possible defect formations and diffusion behaviors of helium in ThO$_2$, to discuss its structural stability. It is found that in intrinsic ThO$_2$ without any Fermi energy shifts, the interstitial Th$_i^{4+}$ defect other than oxygen or thorium vacancies, interstitial oxygen, and any kinds of Frenkel pairs, is most probable to form with an energy release of 1.74 eV. However, after upshifting the Fermi energy, the formation of the other defects also becomes possible. For helium diffusion, we find that only through the thorium vacancy can it happen with the small energy barrier of 0.52 eV. Otherwise, helium atoms can hardly incorporate or diffuse in ThO$_2$. Our results indicate that people should prevent upshifts of the Fermi energy of ThO$_2$ to avoid the formation of thorium vacancies and so as to prevent helium caused damages.Comment: 11 pages, 11 figure

Hyperon Nonleptonic Decays in Chiral Perturbation Theory Reexamined

We recalculate the leading nonanalytic contributions to the amplitudes for hyperon nonleptonic decays in chiral perturbation theory. Our results partially disagree with those calculated before, and include new terms previously omitted in the P-wave amplitudes. Although these modifications are numerically significant, they do not change the well-known fact that good agreement with experiment cannot be simultaneously achieved using one-loop S- and P-wave amplitudes.Comment: 14 pages, latex, 3 figures, uses axodraw.sty, minor additions, to appear in Phys. Rev.

Steinberg modules and Donkin pairs

We prove that in positive characteristic a module with good filtration for a group of type E6 restricts to a module with good filtration for a subgroup of type F4. (Recall that a filtration of a module for a semisimple algebraic group is called good if its layers are dual Weyl modules.) Our result confirms a conjecture of Brundan for one more case. The method relies on the canonical Frobenius splittings of Mathieu. Next we settle the remaining cases, in characteristic not 2, with a computer-aided variation on the old method of Donkin.Comment: 16 pages; proof of Brundan's conjecture adde

Genus Two Partition and Correlation Functions for Fermionic Vertex Operator Superalgebras I

We define the partition and $n$-point correlation functions for a vertex operator superalgebra on a genus two Riemann surface formed by sewing two tori together. For the free fermion vertex operator superalgebra we obtain a closed formula for the genus two continuous orbifold partition function in terms of an infinite dimensional determinant with entries arising from torus Szeg\"o kernels. We prove that the partition function is holomorphic in the sewing parameters on a given suitable domain and describe its modular properties. Using the bosonized formalism, a new genus two Jacobi product identity is described for the Riemann theta series. We compute and discuss the modular properties of the generating function for all $n$-point functions in terms of a genus two Szeg\"o kernel determinant. We also show that the Virasoro vector one point function satisfies a genus two Ward identity.Comment: A number of typos have been corrected, 39 pages. To appear in Commun. Math. Phy

Effective Lagrangians and Parity-Conserving Time-Reversal Violation at Low Energies

Using effective Lagrangians, we argue that any time-reversal-violating but parity-conserving effects are too small to be observed in flavor-conserving nuclear processes without dramatic improvement in experimental accuracy. In the process we discuss other arguments that have appeared in the literature.Comment: Revised manuscript, 11 pages, RevTex, epsf.st

Resonant Auger spectroscopy at the L2,3 shake-up thresholds as a probe of electron correlation effects in nickel

The excitation energy dependence of the three-hole satellites in the L3-M4,5M4,5 and L2-M4,5M4,5 Auger spectra of nickel metal has been measured using synchrotron radiation. The satellite behavior in the non-radiative emission spectra at the L3 and L2 thresholds is compared and the influence of the Coster-Kronig channel explored. The three-hole satellite intensity at the L3 Auger emission line reveals a peak structure at 5 eV above the L3 threshold attributed to resonant processes at the 2p53d9 shake-up threshold. This is discussed in connection with the 6-eV feature in the x-ray absorption spectrum.Comment: 8 pages, 4 figures; http://prb.aps.org/abstract/PRB/v58/i7/p3677_