Dynamical shift condition for unequal mass black hole binaries

Certain numerical frameworks used for the evolution of binary black holes make use of a gamma driver, which includes a damping factor. Such simulations typically use a constant value for damping. However, it has been found that very specific values of the damping factor are needed for the calculation of unequal mass binaries. We examine carefully the role this damping plays, and provide two explicit, non-constant forms for the damping to be used with mass-ratios further from one. Our analysis of the resultant waveforms compares well against the constant damping case.Comment: 10 pages, 14 figure

Simulations of black-hole binaries with unequal masses or non-precessing spins: accuracy, physical properties, and comparison with post-Newtonian results

We present gravitational waveforms for the last orbits and merger of black-hole-binary (BBH) systems along two branches of the BBH parameter space: equal-mass binaries with equal non-precessing spins, and nonspinning unequal-mass binaries. The waveforms are calculated from numerical solutions of Einstein's equations for black-hole binaries that complete between six and ten orbits before merger. Along the equal-mass spinning branch, the spin parameter of each BH is $\chi_i = S_i/M_i^2 \in [-0.85,0.85]$, and along the unequal-mass branch the mass ratio is $q =M_2/M_1 \in [1,4]$. We discuss the construction of low-eccentricity puncture initial data for these cases, the properties of the final merged BH, and compare the last 8-10 GW cycles up to $M\omega = 0.1$ with the phase and amplitude predicted by standard post-Newtonian (PN) approximants. As in previous studies, we find that the phase from the 3.5PN TaylorT4 approximant is most accurate for nonspinning binaries. For equal-mass spinning binaries the 3.5PN TaylorT1 approximant (including spin terms up to only 2.5PN order) gives the most robust performance, but it is possible to treat TaylorT4 in such a way that it gives the best accuracy for spins $\chi_i > -0.75$. When high-order amplitude corrections are included, the PN amplitude of the $(\ell=2,m=\pm2)$ modes is larger than the NR amplitude by between 2-4%.Comment: 21 pages, 9 figures, 6 tables. Version accepted by PR

Orthophosphate binding at the dimer interface of Corynebacterium callunae starch phosphorylase: mutational analysis of its role for activity and stability of the enzyme

<p>Abstract</p> <p>Background</p> <p>Orthophosphate recognition at allosteric binding sites is a key feature for the regulation of enzyme activity in mammalian glycogen phosphorylases. Protein residues co-ordinating orthophosphate in three binding sites distributed across the dimer interface of a non-regulated bacterial starch phosphorylase (from <it>Corynebacterium callunae</it>) were individually replaced by Ala to interrogate their unknown function for activity and stability of this enzyme.</p> <p>Results</p> <p>While the mutations affected neither content of pyridoxal 5'-phosphate cofactor nor specific activity in phosphorylase preparations as isolated, they disrupted (Thr²⁸→Ala, Arg¹⁴¹→Ala) or decreased (Lys³¹→Ala, Ser¹⁷⁴→Ala) the unusually strong protective effect of orthophosphate (10 or 100 mM) against inactivation at 45°C and subunit dissociation enforced by imidazole, as compared to wild-type enzyme. Loss of stability in the mutated phosphorylases appeared to be largely due to weakened affinity for orthophosphate binding. Binding of sulphate mimicking the crystallographically observed "non-covalent phosphorylation" of the phosphorylase at the dimer interface did not have an allosteric effect on the enzyme activity.</p> <p>Conclusions</p> <p>The phosphate sites at the subunit-subunit interface of <it>C. callunae </it>starch phosphorylase appear to be cooperatively functional in conferring extra kinetic stability to the native dimer structure of the active enzyme. The molecular strategy exploited for quaternary structure stabilization is to our knowledge novel among dimeric proteins. It can be distinguished clearly from the co-solute effect of orthophosphate on protein thermostability resulting from (relatively weak) interactions of the ligand with protein surface residues.</p

Plant Transcription Factors @ uni-potsdam.de

We present the Plant Transcription Factor Database (PlnTFDB), and the putative complete set of TFs in the algae _Chlamydomonas reinhardtii_, _Ostreococcus tauri_ and the vascular plants _Oryza sativa_ and _Arabidopsis thaliana_

A highly efficient pipeline for protein expression in Leishmania tarentolae using infrared fluorescence protein as marker

Background: Leishmania tarentolae, a unicellular eukaryotic protozoan, has been established as a novel host for recombinant protein production in recent years. Current protocols for protein expression in Leishmania are, however, time consuming and require extensive lab work in order to identify well-expressing cell lines. Here we established an alternative protein expression work-flow that employs recently engineered infrared fluorescence protein (IFP) as a suitable and easy-to-handle reporter protein for recombinant protein expression in Leishmania. As model proteins we tested three proteins from the plant Arabidopsis thaliana, including a NAC and a type-B ARR transcription factor. Results: IFP and IFP fusion proteins were expressed in Leishmania and rapidly detected in cells by deconvolution microscopy and in culture by infrared imaging of 96-well microtiter plates using small cell culture volumes (2 mu L - 100 mu L). Motility, shape and growth of Leishmania cells were not impaired by intracellular accumulation of IFP. In-cell detection of IFP and IFP fusion proteins was straightforward already at the beginning of the expression pipeline and thus allowed early pre-selection of well-expressing Leishmania clones. Furthermore, IFP fusion proteins retained infrared fluorescence after electrophoresis in denaturing SDS-polyacrylamide gels, allowing direct in-gel detection without the need to disassemble cast protein gels. Thus, parameters for scaling up protein production and streamlining purification routes can be easily optimized when employing IFP as reporter. Conclusions: Using IFP as biosensor we devised a protocol for rapid and convenient protein expression in Leishmania tarentolae. Our expression pipeline is superior to previously established methods in that it significantly reduces the hands-on-time and work load required for identifying well-expressing clones, refining protein production parameters and establishing purification protocols. The facile in-cell and in-gel detection tools built on IFP make Leishmania amenable for high-throughput expression of proteins from plant and animal sources

Collapse of Nonlinear Gravitational Waves in Moving-Puncture Coordinates

We study numerical evolutions of nonlinear gravitational waves in moving-puncture coordinates. We adopt two different types of initial data -- Brill and Teukolsky waves -- and evolve them with two independent codes producing consistent results. We find that Brill data fail to produce long-term evolutions for common choices of coordinates and parameters, unless the initial amplitude is small, while Teukolsky wave initial data lead to stable evolutions, at least for amplitudes sufficiently far from criticality. The critical amplitude separates initial data whose evolutions leave behind flat space from those that lead to a black hole. For the latter we follow the interaction of the wave, the formation of a horizon, and the settling down into a time-independent trumpet geometry. We explore the differences between Brill and Teukolsky data and show that for less common choices of the parameters -- in particular negative amplitudes -- Brill data can be evolved with moving-puncture coordinates, and behave similarly to Teukolsky waves