Three-body monopole corrections to the realistic interactions

It is shown that a very simple three-body monopole term can solve practically all the spectroscopic problems--in the $p$, $sd$ and $pf$ shells--that were hitherto assumed to need drastic revisions of the realistic potentials.Comment: 4 pages, 5figure

Isobaric multiplet yrast energies and isospin non-conserving forces

The isovector and isotensor energy differences between yrast states of isobaric multiplets in the lower half of the $pf$ region are quantitatively reproduced in a shell model context. The isospin non-conserving nuclear interactions are found to be at least as important as the Coulomb potential. Their isovector and isotensor channels are dominated by J=2 and J=0 pairing terms, respectively. The results are sensitive to the radii of the states, whose evolution along the yrast band can be accurately followed.Comment: 4 pages, 4 figures. Superseeds second part of nucl-th/010404

RNA denaturation: excluded volume, pseudoknots and transition scenarios

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.Comment: 4 pages 3 figure

Calculated corrections to superallowed Fermi beta decay: New evaluation of the nuclear-structure-dependent terms

The measured $ft$-values for superallowed $0^{+} \to 0^{+}$ nuclear $\beta$-decay can be used to obtain the value of the vector coupling constant and thus to test the unitarity of the Cabibbo-Kobayashi-Maskawa matrix. An essential requirement for this test is accurate calculations for the radiative and isospin symmetry-breaking corrections that must be applied to the experimental data. We present a new and consistent set of calculations for the nuclear-structure-dependent components of these corrections. These new results do not alter the current status of the unitarity test -- it still fails by more than two standard deviations -- but they provide calculated corrections for eleven new superallowed transitions that are likely to become accessible to precise measurements in the future. The reliability of all calculated corrections is explored and an experimental method indicated by which the structure-dependent corrections can be tested and, if necessary, improved.Comment: Revtex4, one figur

Glassy transition in a disordered model for the RNA secondary structure

We numerically study a disordered model for the RNA secondary structure and we find that it undergoes a phase transition, with a breaking of the replica symmetry in the low temperature region (like in spin glasses). Our results are based on the exact evaluation of the partition function.Comment: 4 pages, 3 figure

Freiburg RNA Tools: a web server integrating IntaRNA, ExpaRNA and LocARNA

The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA–RNA interaction, exact RNA matching and alignment of RNA, respectively. The Freiburg RNA tools web server and the software packages of the stand-alone tools are freely accessible at http://rna.informatik.uni-freiburg.de

RNA secondary structure formation: a solvable model of heteropolymer folding

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the transition between the native and molten phase of the RNA as a function of temperature. The transition is driven by a competition between the energy gained from the polymer's overlap with the native structure and the entropic gain of forming random contacts. A simplified Go-like model is proposed and solved exactly. The predicted critical behavior is verified via exact numerical enumeration of a large ensemble of similarly designed sequences.Comment: 4 pages including 2 figure

Sorting live stem cells based on Sox2 mRNA expression.

PMCID: PMC3507951This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.While cell sorting usually relies on cell-surface protein markers, molecular beacons (MBs) offer the potential to sort cells based on the presence of any expressed mRNA and in principle could be extremely useful to sort rare cell populations from primary isolates. We show here how stem cells can be purified from mixed cell populations by sorting based on MBs. Specifically, we designed molecular beacons targeting Sox2, a well-known stem cell marker for murine embryonic (mES) and neural stem cells (NSC). One of our designed molecular beacons displayed an increase in fluorescence compared to a nonspecific molecular beacon both in vitro and in vivo when tested in mES and NSCs. We sorted Sox2-MB(+)SSEA1(+) cells from a mixed population of 4-day retinoic acid-treated mES cells and effectively isolated live undifferentiated stem cells. Additionally, Sox2-MB(+) cells isolated from primary mouse brains were sorted and generated neurospheres with higher efficiency than Sox2-MB(-) cells. These results demonstrate the utility of MBs for stem cell sorting in an mRNA-specific manner

Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences. Results: The sequence/folding energy (FE) relationship was studied by statistical, bioinformatic methods in 90 CDS containing 26,370 codons. I found that the FE (dG) associated with coding sequences is significant and negative (407 kcal/1000 bases, mean +/- S.E.M.) indicating that these sequences are able to form structures. However, the FE has only a small free component, less than 10% of the total. The contribution of the 1st and 3rd codon bases to the FE is larger than the contribution of the 2nd (central) bases. It is possible to achieve a ~ 4-fold change in FE by altering the wobble bases in synonymous codons. The sequence/FE relationship can be described with a simple algorithm, and the total FE can be predicted solely from the sequence composition of the nucleic acid. The contributions of different synonymous codons to the FE are additive and one codon cannot replace another. The accumulated contributions of synonymous codons of an amino acid to the total folding energy of an mRNA is strongly correlated to the relative amount of that amino acid in the translated protein. Conclusion: Synonymous codons are not interchangable with regard to their role in determining the mRNA FE and the relative amounts of amino acids in the translated protein, even if they are indistinguishable in respect of amino acid coding.Comment: 14 pages including 6 figures and 1 tabl

Missing and Quenched Gamow Teller Strength

Gamow-Teller strength functions in full $(pf)^{8}$ spaces are calculated with sufficient accuracy to ensure that all the states in the resonance region have been populated. Many of the resulting peaks are weak enough to become unobservable. The quenching factor necessary to bring into agreement the low lying observed states with shell model predictions is shown to be due to nuclear correlations. To within experimental uncertainties it is the same that is found in one particle transfer and (e,e') reactions. Perfect consistency between the observed $^{48}Ca(p,n)^{48}Sc$ peaks and the calculation is achieved by assuming an observation threshold of 0.75\% of the total strength, a value that seems typical in several experimentsComment: 11 pages, 6 figures avalaible upon request, RevTeX, FTUAM-94/0