NMR study of slowly exchanging protons in yeast tRNAAsp

We have monitored the exchange of imino and amino protons by NMR after quick transfer of yeast tRNAAsp in 2H2O solvent. When the concentration of exchange-catalyzing buffer is not too high, one imino proton exchanges considerably more slowly than any other (e.g., 100 hr versus 4 hr for the second-slowest imino proton at 18°C in 15 mM Mg). This provides excellent conditions for identification, by the nuclear Overhauser effect, of the slowest exchanging proton, which we show to be the imino proton of the U-8. A-14 reverse Hoogsteen tertiary-structure base pair; other slowly exchanging protons are identified as imino protons from A.U-11 and G.ψ-13. In preliminary experiments, we find that the exchange of these protons is catalyzed by cacodylate or Tris buffer. The lifetimes of two other imino protons, ca. 10 min at 28°C, are buffer independent. Slowly exchanging amino protons have also been observed. Correlation with the exchange of the uracil-8 imino proton suggests that they may be from adenine-14

Density of States and Energy Gap in Andreev Billiards

We present numerical results for the local density of states in semiclassical Andreev billiards. We show that the energy gap near the Fermi energy develops in a chaotic billiard. Using the same method no gap is found in similar square and circular billiards.Comment: 9 pages, 6 Postscript figure

Hydrodynamic Synchronisation of Model Microswimmers

We define a model microswimmer with a variable cycle time, thus allowing the possibility of phase locking driven by hydrodynamic interactions between swimmers. We find that, for extensile or contractile swimmers, phase locking does occur, with the relative phase of the two swimmers being, in general, close to 0 or pi, depending on their relative position and orientation. We show that, as expected on grounds of symmetry, self T-dual swimmers, which are time-reversal covariant, do not phase-lock. We also discuss the phase behaviour of a line of tethered swimmers, or pumps. These show oscillations in their relative phases reminiscent of the metachronal waves of cilia.Comment: 17 pages, 8 figure

Anomalous Behavior near T_c and Synchronization of Andreev Reflection in Two-Dimensional Arrays of SNS Junctions

We have investigated low-temperature transport properties of two-dimensional arrays of superconductor--normal-metal--superconductor (SNS) junctions. It has been found that in two-dimensional arrays of SNS junctions (i) a change in the energy spectrum within an interval of the order of the Thouless energy is observed even when the thermal broadening far exceeds the Thouless energy for a single SNS junction; (ii) the manifestation of the subharmonic energy gap structure (SGS) with high harmonic numbers is possible even if the energy relaxation length is smaller than that required for the realization of a multiple Andreev reflection in a single SNS junction. These results point to the synchronization of a great number of SNS junctions. A mechanism of the SGS origin in two-dimensional arrays of SNS junctions, involving the processes of conventional and crossed Andreev reflection, is proposed.Comment: 5 pages, 5 figure

Generic flow profiles induced by a beating cilium

We describe a multipole expansion for the low Reynolds number fluid flows generated by a localized source embedded in a plane with a no-slip boundary condition. It contains 3 independent terms that fall quadratically with the distance and 6 terms that fall with the third power. Within this framework we discuss the flows induced by a beating cilium described in different ways: a small particle circling on an elliptical trajectory, a thin rod and a general ciliary beating pattern. We identify the flow modes present based on the symmetry properties of the ciliary beat.Comment: 12 pages, 6 figures, to appear in EPJ

Electron spin relaxation by nuclei in semiconductor quantum dots

We have studied theoretically the electron spin relaxation in semiconductor quantum dots via interaction with nuclear spins. The relaxation is shown to be determined by three processes: (i) -- the precession of the electron spin in the hyperfine field of the frozen fluctuation of the nuclear spins; (ii) -- the precession of the nuclear spins in the hyperfine field of the electron; and (iii) -- the precession of the nuclear spin in the dipole field of its nuclear neighbors. In external magnetic fields the relaxation of electron spins directed along the magnetic field is suppressed. Electron spins directed transverse to the magnetic field relax completely in a time on the order of the precession period of its spin in the field of the frozen fluctuation of the nuclear spins. Comparison with experiment shows that the hyperfine interaction with nuclei may be the dominant mechanism of electron spin relaxation in quantum dots

A Look at the Generalized Heron Problem through the Lens of Majorization-Minimization

In a recent issue of this journal, Mordukhovich et al.\ pose and solve an interesting non-differentiable generalization of the Heron problem in the framework of modern convex analysis. In the generalized Heron problem one is given $k+1$ closed convex sets in \Real^d equipped with its Euclidean norm and asked to find the point in the last set such that the sum of the distances to the first $k$ sets is minimal. In later work the authors generalize the Heron problem even further, relax its convexity assumptions, study its theoretical properties, and pursue subgradient algorithms for solving the convex case. Here, we revisit the original problem solely from the numerical perspective. By exploiting the majorization-minimization (MM) principle of computational statistics and rudimentary techniques from differential calculus, we are able to construct a very fast algorithm for solving the Euclidean version of the generalized Heron problem.Comment: 21 pages, 3 figure

Propulsion in a viscoelastic fluid

Flagella beating in complex fluids are significantly influenced by viscoelastic stresses. Relevant examples include the ciliary transport of respiratory airway mucus and the motion of spermatozoa in the mucus-filled female reproductive tract. We consider the simplest model of such propulsion and transport in a complex fluid, a waving sheet of small amplitude free to move in a polymeric fluid with a single relaxation time. We show that, compared to self-propulsion in a Newtonian fluid occurring at a velocity U_N, the sheet swims (or transports fluid) with velocity U / U_N = [1+De^2 (eta_s)/(eta) ]/[1+De^2], where eta_s is the viscosity of the Newtonian solvent, eta is the zero-shear-rate viscosity of the polymeric fluid, and De is the Deborah number for the wave motion, product of the wave frequency by the fluid relaxation time. Similar expressions are derived for the rate of work of the sheet and the mechanical efficiency of the motion. These results are shown to be independent of the particular nonlinear constitutive equations chosen for the fluid, and are valid for both waves of tangential and normal motion. The generalization to more than one relaxation time is also provided. In stark contrast with the Newtonian case, these calculations suggest that transport and locomotion in a non-Newtonian fluid can be conveniently tuned without having to modify the waving gait of the sheet but instead by passively modulating the material properties of the liquid.Comment: 21 pages, 1 figur