Algorithm for coding DNA sequences into "spectrum-like" and "zigzag" representations

An algorithm for encoding long strings of building blocks, like 4 DNA bases (adenine-A, cytosine-C, thymine-T, and guanidine-G), 20 natural amino acids (from Alanine Ala to Valine-Val, plus the stop triplet), or all 64 possible base triplets (from AAA to TTT), into "zigzag" or "spectrum-like" representations is suggested. The new encoding scheme can be derived in the 3-, 2-, or 1-dimensional form depending on the user's wishes. The only information, besides the string for which the "spectrum-like" representation is sought, is the initial positioning of the complete set of units from which the string is composed, i.e., four positions for A, C, G, and T, or 20 positions for natural amino acids plus stop, etc. This initial positioning can be initialized in either the 3-, 2-, or 1-D form. As an illustration of the suggested encoding scheme of the visual and chemometric comparison of the first 10 exon strings of the beta globin gene of 10 different species, each string consisting of about 100 basic amino acids long is shown.     

Scars of the Wigner Function

We propose a picture of Wigner function scars as a sequence of concentric rings along a two-dimensional surface inside a periodic orbit. This is verified for a two-dimensional plane that contains a classical hyperbolic orbit of a Hamiltonian system with 2 degrees of freedom. The stationary wave functions are the familiar mixture of scarred and random waves, but the spectral average of the Wigner functions in part of the plane is nearly that of a harmonic oscillator and individual states are also remarkably regular. These results are interpreted in terms of the semiclassical picture of chords and centers.     

Balance of mass, momentum, and energy in splintering central collisions for 40Ar up to 115 MeV /Nucleon

For central collisions of (17-115)A MeV 40Ar+Cu, Ag, Au, an overall balance is determined for the average mass, energy, and longitudinal momentum. Light charged particles and fragments are separated into forward-focused and isotropic components in the frame of the heaviest fragment. Energy removal by the isotropic component reaches 1-2 GeV. For such high deposition energies, statistical multifragmentation models predict much more extensive nuclear disassembly than is observed.     

Gamow-teller strengths of the inverse beta transition 176Yb-->176Lu for spectroscopy of proton-proton and other sub-MeV solar neutrinos

Discrete Gamow-Teller (GT) transitions 176Yb-->176Lu at low excitation energies have been measured via the ( 3He,t) reaction at 450 MeV and at 0 degrees. For 176Yb, two low-lying states are observed, setting low thresholds Q(nu) = 301 and 445 keV for neutrino ( nu) capture. Capture rates estimated from the measured GT strengths, the simple two-state excitation structure, and the low Q(nu) in Yb-Lu indicate that Yb-based nu detectors are well suited for a direct measurement of the sub-MeV solar electron-neutrino ( nu(e)) spectrum including pp neutrinos.     

Self-injection length in La0.7Ca0.3MnO3-YBa2Cu3O7-δ ferromagnet-superconductor multilayer thin films

We have carried out extensive studies on the self-injection problem in barrierless heterojunctions between La_0.7Ca_0.3MnO₃ (LCMO) and YBa₂Cu₃O_7-δ (YBCO) thin films. The heterojunctions were formed in situ by sequentially growing LCMO and YBCO films on 〈100〉 LaAlO₃ (LAO) substrate using a pulsed laser deposition (PLD) system. YBCO micro-bridges with 64 μm width were patterned both on the LAO (control) and LCMO side of the substrate. Critical current, I _c, was measured at 77 K on both the control side as well as the LCMO side for different YBCO film thickness. It was observed that while the control side showed a J _c of ∼ 2 × 10⁶ A/cm², the LCMO side showed about half the value for the same thickness (1800 ?). The difference in J _c indicates that a certain thickness of YBCO has become ‘effectively’ normal due to self-injection. From the measurement of J _c at two different thicknesses (1800 ? and 1500 ?) of YBCO films both on the LAO as well as the LCMO side, the value of self-injection length (at 77 K) was estimated to be ∼ 900 ?. To the authors’ best knowledge, this is the first time that self-injection length has been quantified. A control experiment carried out with LaNiO₃ deposited by PLD on YBCO did not show any evidence of self-injection.     

A chemical test of the principle of critical point universality: the solubility of nickel (II) oxide in isobutyric acid + water near the consolute point

A mixture of isobutyric acid + water has an upper consolute point at 38.8 mass?% isobutyric acid and temperature near 26?°C. Nickel (II) oxide dissolves in this mixture by reacting with the acid to produce water and nickel isobutyrate. The solubility of nickel (II) oxide in isobutyric acid + water has been measured as a function of temperature at compositions, 25, 38.8, and 60 mass?% isobutyric acid. For values of the temperature, T, which were at least 2 K in excess of the liquid-liquid phase transition temperature, the measured values of the solubility, s, lie on a straight line when plotted in van't Hoff form with ln?s versus 1∕T. The slope, (?ln?s∕?(1∕T)), of the line is negative indicating that the dissolution reaction is endothermic. When the temperature was within 2 K of the phase transition temperature, however, (?ln?s∕?(1∕T)) diverged toward negative infinity. The principle of critical point universality predicts that when excess solid nickel (II) oxide is in dissolution equilibrium with liquid isobutyric acid + water, (?ln?s∕?(1∕T)) should diverge upon approaching the consolute point along the critical isopleth at 38.8 mass?% isobutyric acid. As determined by the sign of the enthalpy of solution, the sign of this divergence is expected to be negative. Not only do our experiments confirm these predictions, but they also show that identical behavior can be observed at both 25 and 60 mass?% isobustyric acid, compositions which lie substantially to either side of the critical composition.     

Applying the conjugated circuits method to Clar structures of [n]phenylenes for determining resonance energies

We consider the aromaticity of biphenylene and structurally related linear or angular [n]phenylenes for which the direct application of the model of conjugated circuits does not offer valid expressions for resonance energy and aromaticity. We located the cause of this problem as being due to Kekulé valence structures in which neighboring benzenoid rings are connected by two CC double bonds. By restricting the selection of Kekulé valence structures to those that contribute to Clar structures of such systems, we were able to show that linear and angular [n]phenylenes have approximately similar resonance energies, with angular [n]phenylenes being slightly more stable due to second order contributions arising from disjoint conjugated circuits. Expressions for resonance energies of [n]phenylenes up to n = 8 are listed and recursion expressions for higher n values are outlined.     

Effect of quantum entanglement on Aharonov-Bohm oscillations, spin-polarized transport and current magnification effect

We present a simple model of transmission across a metallic mesoscopic ring. In one of its arm an electron interacts with a single magnetic impurity via an exchange coupling. We show that entanglement between electron and spin impurity states leads to reduction of Aharonov-Bohm oscillations in the transmission coefficient. The spin-conductance is asymmetric in the flux reversal as opposed to the two-probe electrical conductance which is symmetric. In the same model, in contradiction to the naive expectation of a current magnification effect, we observe enhancement as well as suppression of this effect depending on the system parameters. The limitations of this model to the general notion of dephasing or decoherence in quantum systems are pointed out.