Shell-model phenomenology of low-momentum interactions

The first detailed comparison of the low-momentum interaction V_{low k} with G matrices is presented. We use overlaps to measure quantitatively the similarity of shell-model matrix elements for different cutoffs and oscillator frequencies. Over a wide range, all sets of V_{low k} matrix elements can be approximately obtained from a universal set by a simple scaling. In an oscillator mean-field approach, V_{low k} reproduces satisfactorily many features of the single-particle and single-hole spectra on closed-shell nuclei, in particular through remarkably good splittings between spin-orbit partners on top of harmonic oscillator closures. The main deficiencies of pure two-nucleon interactions are associated with binding energies and with the failure to ensure magicity for the extruder-intruder closures. Here, calculations including three-nucleon interactions are most needed. V_{low k} makes it possible to define directly a meaningful unperturbed monopole Hamiltonian, for which the inclusion of three-nucleon forces is tractable.Comment: 5 pages, 4 figures, minor additions, to appear as Rapid Comm. in Phys. Rev.

Low-momentum interactions for nuclei

We show how the renormalization group is used to construct a low-momentum nucleon-nucleon interaction V_{low k}, which unifies all potential models used in nuclear structure calculations. V_{low k} can be directly applied to the nuclear shell model or to nucleonic matter without a G matrix resummation. It is argued that V_{low k} parameterizes a high-order chiral effective field theory two-nucleon force. We use cutoff dependence as a tool to assess the error in the truncation of nuclear forces to two-nucleon interactions and introduce a low-momentum three-nucleon force, which regulates A=3,4 binding energies. The adjusted three-nucleon interaction is perturbative for small cutoffs. In contrast to other precision interactions, the error due to missing many-body forces can be estimated, when V_{low k} and the corresponding three-nucleon force are used in nuclear structure calculations and the cutoff is varied.Comment: 10 pages, 5 figures, talk at INT workshop on Nuclear Forces and the Quantum Many-Body Problem, Seattle, October 200

Expression, maturation and turnover of DrrS, an unusually stable, DosR regulated small RNA in Mycobacterium tuberculosis

Mycobacterium tuberculosis depends on the ability to adjust to stresses encountered in a range of host environments, adjustments that require significant changes in gene expression. Small RNAs (sRNAs) play an important role as post-transcriptional regulators of prokaryotic gene expression, where they are associated with stress responses and, in the case of pathogens, adaptation to the host environment. In spite of this, the understanding of M. tuberculosis RNA biology remains limited. Here we have used a DosR-associated sRNA as an example to investigate multiple aspects of mycobacterial RNA biology that are likely to apply to other M. tuberculosis sRNAs and mRNAs. We have found that accumulation of this particular sRNA is slow but robust as cells enter stationary phase. Using reporter gene assays, we find that the sRNA core promoter is activated by DosR, and we have renamed the sRNA DrrS for DosR Regulated sRNA. Moreover, we show that DrrS is transcribed as a longer precursor, DrrS+, which is rapidly processed to the mature and highly stable DrrS. We characterise, for the first time in mycobacteria, an RNA structural determinant involved in this extraordinary stability and we show how the addition of a few nucleotides can lead to acute destabilisation. Finally, we show how this RNA element can enhance expression of a heterologous gene. Thus, the element, as well as its destabilising derivatives may be employed to post-transcriptionally regulate gene expression in mycobacteria in combination with different promoter variants. Moreover, our findings will facilitate further investigations into the severely understudied topic of mycobacterial RNA biology and into the role that regulatory RNA plays in M. tuberculosis pathogenesis

The topology of evolutionary biology

Central notions in evolutionary biology are intrinsically topological. This claim is maybe most obvious for the discontinuities associated with punctuated equilibria. Recently, a mathematical framework has been developed that derives the concepts of phenotypic characters and homology from the topological structure of the phenotype space. This structure in turn is determined by the genetic operators and their interplay with the properties of the genotype-phenotype map