Electroweak Absorptive Parts in NRQCD Matching Conditions

Electroweak corrections associated with the instability of the top quark to the next-to-next-to-leading logarithmic (NNLL) total top pair threshold cross section in e+e- annihilation are determined. Our method is based on absorptive parts in electroweak matching conditions of the NRQCD operators and the optical theorem. The corrections lead to ultraviolet phase space divergences that have to be renormalized and lead to NLL mixing effects. Numerically, the corrections can amount to several percent and are comparable to the known NNLL QCD corrections.Comment: 17 pages, revtex4, 4 postscript figures included; minor changes in text and references, title modified in printed versio

Investigating the concept of accessibility for predicting novel RNA-RNA interactions

State-of-the-art methods for predicting novel trans RNA-RNA interactions use the so-called accessibility as key concept. It estimates whether a region in a given RNA sequence is accessible for forming trans interactions, using a thermodynamic model which quantifies its secondary structure features. RNA-RNA interactions are then predicted by finding the minimum free energy base pairing between the two transcripts, taking into account the accessibility as energy penalty. We investigated the underlying assumptions of this approach using the two methods RNAPLEX and INTARNA on two datasets, containing sRNA-mRNA and snoRNA-rRNA interactions, respectively. We find that (1) known trans RNA-RNA interactions frequently overlap regions containing RNA structure features, (2) the estimated accessibility reflects sRNA structures fairly well, but often disagrees with structures of longer transcripts, (3) the prediction performance of RNA-RNA interaction prediction methods is independent of the quality of the estimated accessibility profiles, and (4) one important overall effect of accessibility profiles is to prevent the thermodynamic model from predicting too long interactions. Based on our findings, we conclude that the accessibility concept to the minimum free energy approach to predicting novel RNA-RNA interactions has conceptual limitations and discuss potential ways of improving the field in the future

3D Hydrophobic Moment Vectors as a Tool to Characterize the Surface Polarity of Amphiphilic Peptides

AbstractThe interaction of membranes with peptides and proteins is largely determined by their amphiphilic character. Hydrophobic moments of helical segments are commonly derived from their two-dimensional helical wheel projections, and the same is true for β-sheets. However, to the best of our knowledge, there exists no method to describe structures in three dimensions or molecules with irregular shape. Here, we define the hydrophobic moment of a molecule as a vector in three dimensions by evaluating the surface distribution of all hydrophilic and lipophilic regions over any given shape. The electrostatic potential on the molecular surface is calculated based on the atomic point charges. The resulting hydrophobic moment vector is specific for the instantaneous conformation, and it takes into account all structural characteristics of the molecule, e.g., partial unfolding, bending, and side-chain torsion angles. Extended all-atom molecular dynamics simulations are then used to calculate the equilibrium hydrophobic moments for two antimicrobial peptides, gramicidin S and PGLa, under different conditions. We show that their effective hydrophobic moment vectors reflect the distribution of polar and nonpolar patches on the molecular surface and the calculated electrostatic surface potential. A comparison of simulations in solution and in lipid membranes shows how the peptides undergo internal conformational rearrangement upon binding to the bilayer surface. A good correlation with solid-state NMR data indicates that the hydrophobic moment vector can be used to predict the membrane binding geometry of peptides. This method is available as a web application on http://www.ibg.kit.edu/HM/

Phase Space Matching and Finite Lifetime Effects for Top-Pair Production Close to Threshold

The top-pair $t\bar t$ production cross section close to threshold in $e^+e^-$ collisions is strongly affected by the small lifetime of the top quark. Since the cross section is defined through final states containing the top decay products, a consistent definition of the cross section depends on prescriptions how these final states are accounted for the cross section. Experimentally, these prescriptions are implemented for example through cuts on kinematic quantities such as the reconstructed top quark invariant masses. As long as these cuts do not reject final states that can arise from the decay of a top and an anti-top quark with a small off-shellness compatible with the nonrelativistic power-counting, they can be implemented through imaginary phase space matching conditions in NRQCD. The prescription-dependent cross section can then be determined from the optical theorem using the $e^+e^-$ forward scattering amplitude. We compute the phase space matching conditions associated to cuts on the top and anti-top invariant masses at next-to-next-to-leading logarithmic (NNLL) order and partially at next-to-next-to-next-to-leading logarithmic (N${}^3$LL) order in the nonrelativistic expansion and, together with finite lifetime and electroweak effects known from previous work, analyze their numerical impact on the $t\bar t$ cross section. We show that the phase space matching contributions are essential to make reliable NRQCD predictions, particularly for energies below the peak region, where the cross section is small. We find that irreducible background contributions associated to final states that do not come from top decays are strongly suppressed and can be neglected for the theoretical predictions.Comment: 62 pages, 21 figure

On Electroweak Matching Conditions for Top Pair Production at Threshold

We determine the real parts of electroweak matching conditions relevant for top quark pair production close to threshold in e+e- annihilation at next-to-next-to-leading logarithmic (NNLL) order. Numerically the corrections are comparable to the NNLL QCD corrections.Comment: 12 pages, revtex4, 1 postscript figure included; minor changes in text and references, version published in Phys. Rev.

Structure of the Membrane Anchor of Pestivirus Glycoprotein Erns, a Long Tilted Amphipathic Helix

Erns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells. Its unusual C-terminus plays multiple roles, as the amphiphilic helix acts as a membrane anchor, as a signal peptidase cleavage site, and as a retention/secretion signal. We analyzed the structure and membrane binding properties of this sequence to gain a better understanding of the underlying mechanisms. CD spectroscopy in different setups, as well as Monte Carlo and molecular dynamics simulations confirmed the helical folding and showed that the helix is accommodated in the amphiphilic region of the lipid bilayer with a slight tilt rather than lying parallel to the surface. This model was confirmed by NMR analyses that also identified a central stretch of 15 residues within the helix that is fully shielded from the aqueous layer, which is C-terminally followed by a putative hairpin structure. These findings explain the strong membrane binding of the protein and provide clues to establishing the Erns membrane contact, processing and secretion

O(alpha_s^2) corrections to fermionic Higgs decays in the MSSM

We compute the two-loop corrections of O(alpha_s^2) to the Yukawa couplings in the framework of the Minimal Supersymmetric Standard Model (MSSM). The calculation is performed using the effective Lagrangian approach under the approximation of neglecting the Higgs boson mass with respect to the top quark, gluino and all squark flavour masses. As an application we derive the O(alpha_s^2) corrections to the partial decay width of the lightest Higgs boson to a bottom quark pair. We find that the two-loop corrections are sizable for large values of tan_beta and low CP-odd Higgs boson mass. With our calculation of the O(alpha_s^2) corrections the remaining theoretical uncertainties reduce below a few percent.Comment: 22 pages, 10 figure

Ein System zur Interpretation einer Äußerung: Methode

Kuhn T, Kunzmann S, Kummert F, et al. Ein System zur Interpretation einer Äußerung: Methode. In: Fortschritte der Akustik. Plenarvorträge und Kurzreferate der 17. Gemeinschaftstagung der Deutschen Arbeitsgemeinschaft für Akustik, DAGA '91. Vol Teil B. Bochum; 1991: 1081-1084