Breakdown of adiabatic invariance in spherical tokamaks

Thermal ions in spherical tokamaks have two adiabatic invariants: the magnetic moment and the longitudinal invariant. For hot ions, variations in magnetic-field strength over a gyro period can become sufficiently large to cause breakdown of the adiabatic invariance. The magnetic moment is more sensitive to perturbations than the longitudinal invariant and there exists an intermediate regime, super-adiabaticity, where the longitudinal invariant remains adiabatic, but the magnetic moment does not. The motion of super-adiabatic ions remains integrable and confinement is thus preserved. However, above a threshold energy, the longitudinal invariant becomes non-adiabatic too, and confinement is lost as the motion becomes chaotic. We predict beam ions in present-day spherical tokamaks to be super-adiabatic but fusion alphas in proposed burning-plasma spherical tokamaks to be non-adiabatic.Comment: 6 pages, 8 figure

First-principles study of high conductance DNA sequencing with carbon nanotube electrodes

Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nano-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore both reduce conformational fluctuations and significantly improve the conductance. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several $\mu$A. Below 1 V the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second-largest, cytosine the third and finally thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations. Based on these results we propose a DNA sequencing protocol combining three possible data analysis strategies.Comment: 12 pages, 17 figures, 3 table

Dissociation spectrum of H2+_2^+ from a short, intense infrared laser pulse: vibration structure and focal volume effects

The dissociation spectrum of the hydrogen molecular ion by short intense pulses of infrared light is calculated. The time-dependent Schr\"odinger equation is discretized and integrated in position and momentum space. For few-cycle pulses one can resolve vibrational structure that commonly arises in the experimental preparation of the molecular ion from the neutral molecule. We calculate the corresponding energy spectrum and analyze the dependence on the pulse time-delay, pulse length, and intensity of the laser for $\lambda \sim 790$nm. We conclude that the proton spectrum is a both a sensitive probe of the vibrational dynamics and the laser pulse. Finally we compare our results with recent measurements of the proton spectrum for 55 fs pulses using a Ti:Sapphire laser ($\lambda \sim 790$nm). Integrating over the laser focal volume, for the intensity $I \sim 3 \times 10^{15}$W cm$^{-2}$, we find our results are in excellent agreement with these experiments.Comment: 17 pages, 8 figures, preprin

Atlas Toolkit: Fast registration of 3D morphological datasets in the absence of landmarks

Image registration is a gateway technology for Developmental Systems Biology, enabling computational analysis of related datasets within a shared coordinate system. Many registration tools rely on landmarks to ensure that datasets are correctly aligned; yet suitable landmarks are not present in many datasets. Atlas Toolkit is a Fiji/ImageJ plugin collection offering elastic group-wise registration of 3D morphological datasets, guided by segmentation of the interesting morphology. We demonstrate the method by combinatorial mapping of cell signalling events in the developing eyes of chick embryos, and use the integrated datasets to predictively enumerate Gene Regulatory Network states

A Methodology for the Diagnostic of Aircraft Engine Based on Indicators Aggregation

Aircraft engine manufacturers collect large amount of engine related data during flights. These data are used to detect anomalies in the engines in order to help companies optimize their maintenance costs. This article introduces and studies a generic methodology that allows one to build automatic early signs of anomaly detection in a way that is understandable by human operators who make the final maintenance decision. The main idea of the method is to generate a very large number of binary indicators based on parametric anomaly scores designed by experts, complemented by simple aggregations of those scores. The best indicators are selected via a classical forward scheme, leading to a much reduced number of indicators that are tuned to a data set. We illustrate the interest of the method on simulated data which contain realistic early signs of anomalies.Comment: Proceedings of the 14th Industrial Conference, ICDM 2014, St. Petersburg : Russian Federation (2014

Quantum and classical resonant escapes of a strongly-driven Josephson junction

The properties of phase escape in a dc SQUID at 25 mK, which is well below quantum-to-classical crossover temperature $T_{cr}$, in the presence of strong resonant ac driving have been investigated. The SQUID contains two Nb/Al-AlO$_{x}$/Nb tunnel junctions with Josephson inductance much larger than the loop inductance so it can be viewed as a single junction having adjustable critical current. We find that with increasing microwave power $W$ and at certain frequencies $\nu$ and $\nu$/2, the single primary peak in the switching current distribution, \textrm{which is the result of macroscopic quantum tunneling of the phase across the junction}, first shifts toward lower bias current $I$ and then a resonant peak develops. These results are explained by quantum resonant phase escape involving single and two photons with microwave-suppressed potential barrier. As $W$ further increases, the primary peak gradually disappears and the resonant peak grows into a single one while shifting further to lower $I$. At certain $W$, a second resonant peak appears, which can locate at very low $I$ depending on the value of $\nu$. Analysis based on the classical equation of motion shows that such resonant peak can arise from the resonant escape of the phase particle with extremely large oscillation amplitude resulting from bifurcation of the nonlinear system. Our experimental result and theoretical analysis demonstrate that at $T\ll T_{cr}$, escape of the phase particle could be dominated by classical process, such as dynamical bifurcation of nonlinear systems under strong ac driving.Comment: 10 pages, 9 figures, 1 tabl

Velocity Statistics in the Two-Dimensional Granular Turbulence

We studied the macroscopic statistical properties on the freely evolving quasi-elastic hard disk (granular) system by performing a large-scale (up to a few million particles) event-driven molecular dynamics systematically and found that remarkably analogous to an enstrophy cascade process in the decaying two-dimensional fluid turbulence. There are four typical stages in the freely evolving inelastic hard disk system, which are homogeneous, shearing (vortex), clustering and final state. In the shearing stage, the self-organized macroscopic coherent vortices become dominant. In the clustering stage, the energy spectra are close to the expectation of Kraichnan-Batchelor theory and the squared two-particle separation strictly obeys Richardson law.Comment: 4 pages, 4 figures, to be published in PR

Infrared luminosities of galaxies in the Local Volume

Near-infrared properties of 451 galaxies with distances D \leq 10 Mpc are considered basing on the all-sky two micron survey (2MASS). A luminosity function of the galaxies in the K-band is derived within [-25,-11] mag. The local (D < 8 Mpc) luminosity density is estimated to be 6.8*10^8 L_sun/Mpc^3 that exceeds (1.5+-0.1) times the global cosmic density in the K-band. Virial mass-to-K-luminosity ratios are determined for nearby groups and clusters. In the luminosity range of (5*10^{10} - 2*10^{13})L_sun, the groups and clusters follow the relation \lg(M/L_K) propto (0.27+-0.03) lg(L_K) with a scatter of \~0.1 comparable to errors of the observables. The mean ratio ~= (20-25) M_sun/L_sun for the galaxy systems turns out to be significantly lower than the global ratio, (80-90)M_sun/L_sun, expected in the standard cosmological model with the matter density of Omega_m =0.27. This discrepancy can be resolved if most of dark matter in the universe is not associated with galaxies and their systems.Comment: 15 pages, 7 figures. Astronomy Letters, submitte

High-pressure phase and transition phenomena in ammonia borane NH3BH3 from X-ray diffraction, Landau theory, and ab initio calculations

Structural evolution of a prospective hydrogen storage material, ammonia borane NH3BH3, has been studied at high pressures up to 12 GPa and at low temperatures by synchrotron powder diffraction. At 293 K and above 1.1 GPa a disordered I4mm structure reversibly transforms into a new ordered phase. Its Cmc21 structure was solved from the diffraction data, the positions of N and B atoms and the orientation of NH3 and BH3 groups were finally assigned with the help of density functional theory calculations. Group-theoretical analysis identifies a single two-component order parameter, combining ordering and atomic displacement mechanisms, which link an orientationally disordered parent phase I4mm with ordered distorted Cmc21, Pmn21 and P21 structures. We propose a generic phase diagram for NH3BH3, mapping three experimentally found and one predicted (P21) phases as a function of temperature and pressure, along with the evolution of the corresponding structural distortions. Ammonia borane belongs to the class of improper ferroelastics and we show that both temperature- and pressure-induced phase transitions can be driven to be of the second order. The role of N-H...H-B dihydrogen bonds and other intermolecular interactions in the stability of NH3BH3 polymorphs is examined.Comment: 23 pages, 7 figure

Double exchange-driven spin pairing at the (001) surface of manganites

The (001) surface of La_{1-x}Ca_xMnO_3 system in various magnetic orderings is studied by first principle calculations. A general occurrence is that z^2 dangling bond charge -- which is ``invisible'' in the formal valence picture -- is promoted to the bulk gap/Fermi level region. This drives a double-exchange-like process that serves to align the surface Mn spin with its subsurface neighbor, regardless of the bulk magnetic order. For heavy doping, the locally ``ferromagnetic'' coupling is very strong and the moment enhanced by as much as 30% over the bulk value.Comment: 6 pages, 4 figure