Pymablock: an algorithm and a package for quasi-degenerate perturbation theory

A common technique in the study of complex quantum-mechanical systems is to reduce the number of degrees of freedom in the Hamiltonian by using quasi-degenerate perturbation theory. While the Schrieffer--Wolff transformation achieves this and constructs an effective Hamiltonian, its scaling is suboptimal, and implementing it efficiently is both challenging and error-prone. We introduce an algorithm for constructing an equivalent effective Hamiltonian as well as a Python package, Pymablock, that implements it. Our algorithm combines an optimal asymptotic scaling with a range of other improvements. The package supports numerical and analytical calculations of any order and it is designed to be interoperable with any other packages for specifying the Hamiltonian. We demonstrate how the package handles constructing a k.p model, analyses a superconducting qubit, and computes the low-energy spectrum of a large tight-binding model. We also compare its performance with reference calculations and demonstrate its efficiency.Comment: 21 pages, 5 figure

Lift Response of a Stalled Wing to Pulsatile Disturbances

The transient lift response of a low-Reynolds-number wing subjected to small amplitude pulsatile disturbances is investigated. The wing has a small aspect ratio and a semicircular planform, and it is fully stalled at a 20 deg angle of attack. Microvalve actuators distributed along the leading edge of the wing produce the transient disturbance. It is shown that the lift response to a single pulse increases with increasing actuator supply pressure and that the lift response curves are similar to each other when scaled by the total impulse. Furthermore, for fixed actuator supply pressure, the amplitude and total impulse of the transient lift response curve increases with increasing external flow speed. In this case, the lift response curves are similar when scaled by the dynamic pressure. The lift response to a single pulse can be treated as a filter kernel, and it can be used to predict the lift time history for the arbitrary actuator input signals. The kernel is similar in shape to transient measurements obtained by other investigators on two-dimensional wings and flaps. Comparisons between the model predictions and the experiments using multiple pulse inputs and square-wave modulated input signals at low frequencies are presented

Adjuvancy and reactogenicity of N-acetylglycosaminyl-N-acetylmuramyl-dipeptide (GMDP) orally administered just prior to trivalent influenza subunit vaccine. A double-blind placebo-controlled study in nursing home residents.

One hundred and fifty-three nursing home residents received 0, 5, 25 or 50 mg N-acetylglucosaminyl-N-acetylmuramyl-dipeptide (GMDP) orally, and trivalent influenza subunit vaccine intramuscularly. One day after intervention, there was a strong increase of total leucocytes, monocytes and neutrophils in the groups receiving 25 or 50 mg GMDP. A GMDP dose dependent increase in systemic, but not in local, vaccine side-effects was observed. No significant differences in post-vaccination haemagglutination inhibiting serum antibody titres were observed between the four groups, indicating that oral administration of GMDP together with influenza vaccination, does not lead to a higher vaccine efficacy

Biophysical and enzymatic properties of aminoglycoside adenylyltransferase AadA6 from Pseudomonas aeruginosa

AbstractThe gene coding for the aminoglycoside adenylyltransferase (aadA6) from a clinical isolate of Pseudomonas aeruginosa was cloned and expressed in Escherichia coli strain BL21(DE3)pLysS. The overexpressed enzyme (AadA6, 281 amino-acid residues) and a carboxy-terminal truncated variant molecule ([1-264]AadA6) were purified to near homogeneity and characterized. Light scattering experiments conducted under low ionic strength supported equilibrium between monomeric and homodimeric arrangements of the enzyme subunits. Circular Dichroism spectropolarimetry indicated a close structural relation to adenylate kinases. Both forms modified covalently the aminoglycosides streptomycin and spectinomycin. The enzyme required at least 5mM MgCl2 for normal Michaelis–Menten kinetics. Streptomycin exhibited a strong substrate inhibition effect at 1mM MgCl2. The truncated 17 residues at the C-terminus have little influence on protein folding, whereas they have a positive effect on the enzymic activity and stabilize dimers at high protein concentrations (>100μM). Homology modelling and docking based on known crystal structures yielded models of the central ternary complex of monomeric AadA6 with ATP and streptomycin or spectinomycin