0-pi oscillations in nanostructured Nb/Fe/Nb Josephson junctions

The physics of the $\pi$ phase shift in ferromagnetic Josephson junctions may enable a range of applications for spin-electronic devices and quantum computing. We investigate transitions from ``0'' to ``$\pi$'' states in Nb/Fe/Nb Josephson junctions by varying the Fe barrier thickness from 0.5 nm to 5.5 nm. From magnetic measurements we estimate for Fe a magnetic dead layer of about 1.1 nm. By fitting the characteristic voltage oscillations with existing theoretical models we extrapolate an exchange energy of 256 meV, a Fermi velocity of $1.98 \times 10^5$ m/s and an electron mean free path of 6.2 nm, in agreement with other reported values. From the temperature dependence of the $I_CR_N$ product we show that its decay rate exhibits a nonmonotonic oscillatory behavior with the Fe barrier thickness.Comment: 7 pages, 5 figures, accepted for publication in Eur. Phys. J.

Electron Production and Collective Field Generation in Intense Particle Beams

Electron cloud effects (ECEs) are increasingly recognized as important, but incompletely understood, dynamical phenomena, which can severely limit the performance of present electron colliders, the next generation of high-intensity rings, such as PEP-II upgrade, LHC, and the SNS, the SIS 100/200, or future high-intensity heavy ion accelerators such as envisioned in Heavy Ion Inertial Fusion (HIF). Deleterious effects include ion-electron instabilities, emittance growth, particle loss, increase in vacuum pressure, added heat load at the vacuum chamber walls, and interference with certain beam diagnostics. Extrapolation of present experience to significantly higher beam intensities is uncertain given the present level of understanding. With coordinated LDRD projects at LLNL and LBNL, we undertook a comprehensive R&D program including experiments, theory and simulations to better understand the phenomena, establish the essential parameters, and develop mitigating mechanisms. This LDRD project laid the essential groundwork for such a program. We developed insights into the essential processes, modeled the relevant physics, and implemented these models in computational production tools that can be used for self-consistent study of the effect on ion beams. We validated the models and tools through comparison with experimental data, including data from new diagnostics that we developed as part of this work and validated on the High-Current Experiment (HCX) at LBNL. We applied these models to High-Energy Physics (HEP) and other advanced accelerators. This project was highly successful, as evidenced by the two paragraphs above, and six paragraphs following that are taken from our 2003 proposal with minor editing that mostly consisted of changing the tense. Further benchmarks of outstanding performance are: we had 13 publications with 8 of them in refereed journals, our work was recognized by the accelerator and plasma physics communities by 8 invited papers and we have 5 additional invitations for invited papers at upcoming conferences, we attracted collaborators who had SBIR funding, we are collaborating with scientists at CERN and GSI Darmstadt on gas desorption physics for submission to Physical Review Letters, and another PRL on absolute measurements of electron cloud density and Phys. Rev. ST-AB on electron emission physics are also being readied for submission

Beam Interaction Measurements with a Retarding Field Analyzer in a High-Current High-Vacuum Positively-Charged Particle Accelerator

A Retarding Field Analyzer (RFA) was inserted in a drift region of a magnetic transport section of the high-current experiment (HCX) that is at high-vacuum to measure ions and electrons resulting from beam interaction with background gas and walls. The ions are expelled during the beam by the space-charge potential and the electrons are expelled mainly at the end of the beam, when the beam potential decays. The ion energy distribution shows the beam potential of {approx} 2100 V and the beam-background gas total cross-section of 1.6x10{sup -20} m{sup 2}. The electron energy distribution reveals that the expelled electrons are mainly desorbed from the walls and gain {approx} 22 eV from the beam potential decaying with time before entering the RFA. Details of the RFA design and of the measured energy distributions are presented and discussed

Mitochondrial Pseudogenes in the Nuclear Genomes of Drosophila

Mitochondrial pseudogenes in nuclear chromosomes (numts) have been detected in the genomes of a diverse range of eukaryotic species. However, the numt content of different genomes and their properties is not uniform, and study of these differences provides insight into the mechanisms and dynamics of genome evolution in different organisms. In the genus Drosophila, numts have previously only been identified on a genome-wide scale in the melanogaster subgroup. The present study extends the identification to 11 species of the Drosophila genus. We identify a total of 302 numts and show that the numt complement is highly variable in Drosophilids, ranging from just 4 in D. melanogaster to 67 in D. willistoni, broadly correlating with genome size. Many numts have undergone large-scale rearrangements in the nucleus, including interruptions, inversions, deletions and duplications of sequence of variable size. Estimating the age of the numts in the nucleus by phylogenetic tree reconstruction reveals the vast majority of numts to be recent gains, 90% having arisen on terminal branches of the species tree. By identifying paralogs and counting duplications among the extant numts we estimate that 23% of extant numts arose through post-insertion duplications. We estimate genus average rates of insertion of 0.75 per million years, and a duplication rate of 0.010 duplications per numt per million years

Heavy-Ion-Induced Electronic Desorption of Gas from Metals

During heavy-ion operation in several particle accelerators worldwide, dynamic pressure rises of orders of magnitude were triggered by lost beam ions that bombarded the vacuum chamber walls. This ion-induced molecular desorption, observed at CERN, GSI, and BNL, can seriously limit the ion beam lifetime and intensity of the accelerator. From dedicated test stand experiments we have discovered that heavy-ion-induced gas desorption scales with the electronic energy loss (dEe/dx) of the ions slowing down in matter; but it varies only little with the ion impact angle, unlike electronic sputtering

Numt-Mediated Double-Strand Break Repair Mitigates Deletions during Primate Genome Evolution

Non-homologous end joining (NHEJ) is the major mechanism of double-strand break repair (DSBR) in mammalian cells. NHEJ has traditionally been inferred from experimental systems involving induced double strand breaks (DSBs). Whether or not the spectrum of repair events observed in experimental NHEJ reflects the repair of natural breaks by NHEJ during chromosomal evolution is an unresolved issue. In primate phylogeny, nuclear DNA sequences of mitochondrial origin, numts, are inserted into naturally occurring chromosomal breaks via NHEJ. Thus, numt integration sites harbor evidence for the mechanisms that act on the genome over evolutionary timescales. We have identified 35 and 55 lineage-specific numts in the human and chimpanzee genomes, respectively, using the rhesus monkey genome as an outgroup. One hundred and fifty two numt-chromosome fusion points were classified based on their repair patterns. Repair involving microhomology and repair leading to nucleotide additions were detected. These repair patterns are within the experimentally determined spectrum of classical NHEJ, suggesting that information from experimental systems is representative of broader genetic loci and end configurations. However, in incompatible DSBR events, small deletions always occur, whereas in 54% of numt integration events examined, no deletions were detected. Numts show a statistically significant reduction in deletion frequency, even in comparison to DSBR involving filler DNA. Therefore, numts show a unique mechanism of integration via NHEJ. Since the deletion frequency during numt insertion is low, native overhangs of chromosome breaks are preserved, allowing us to determine that 24% of the analyzed breaks are cohesive with overhangs of up to 11 bases. These data represent, to the best of our knowledge, the most comprehensive description of the structure of naturally occurring DSBs. We suggest a model in which the sealing of DSBs by numts, and probably by other filler DNA, prevents nuclear processing of DSBs that could result in deleterious repair

HIGH CURRENT BEAM EXTRACTION FROM THE 88-INCH CYCLOTRON AT LBNL

Abstract The low energy beam transport system and the inflector of the 88-Inch Cyclotron have been improved to provide more intense heavy-ion beams, especially for experiments requiring 48 Ca beams. In addition to a new spiral inflector [1] and increased injection voltage, the injection line beam transport and beam orbit dynamics in the cyclotron have been analyzed, new diagnostics have been developed, and extensive measurements have been performed to improve the transmission efficiency. By coupling diagnostics, such as emittance scanners in the injection line and a radially-adjustable beam viewing scintillator within the cyclotron, with computer simulations we have been able to identify loss mechanisms. The diagnostics used and their findings will be presented. We will discuss the solutions we have employed to address losses, such as changing our approach to tuning VENUS and running the cyclotron's central trim coil asymmetrically

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

The natural transfer of DNA from mitochondria to the nucleus generates nuclear copies of mitochondrial DNA (numts) and is an ongoing evolutionary process, as genome sequences attest. In humans, five different numts cause genetic disease and a dozen human loci are polymorphic for the presence of numts, underscoring the rapid rate at which mitochondrial sequences reach the nucleus over evolutionary time. In the laboratory and in nature, numts enter the nuclear DNA via non-homolgous end joining (NHEJ) at double-strand breaks (DSBs). The frequency of numt insertions among 85 sequenced eukaryotic genomes reveal that numt content is strongly correlated with genome size, suggesting that the numt insertion rate might be limited by DSB frequency. Polymorphic numts in humans link maternally inherited mitochondrial genotypes to nuclear DNA haplotypes during the past, offering new opportunities to associate nuclear markers with mitochondrial markers back in time

New experimental measurements of electron clouds in ion beams with large tune depression

We study electron clouds in high perveance beams (K = 8E-4) with a large tune depression of 0.2 (defined as the ratio of a single particle oscillation response to the applied focusing fields, with and without space charge). These 1 MeV, 180 mA, K+ beams have a beam potential of +2 kV when electron clouds are minimized. Simulation results are discussed in a companion paper [J-L. Vay, this Conference]. We have developed the first diagnostics that quantitatively measure the accumulation of electrons in a beam [1]. This, together with measurements of electron sources, will enable the electron particle balance to be measured, and electron-trapping efficiencies determined. We, along with colleagues from GSI and CERN, have also measured the scaling of gas desorption with beam energy and dE/dx [2]. Experiments where the heavy-ion beam is transported with solenoid magnetic fields, rather than with quadrupole magnetic or electrostatic fields, are being initiated. We will discuss initial results from experiments using electrode sets (in the middle and at the ends of magnets) to either expel or to trap electrons within the magnets. We observe electron oscillations in the last quadrupole magnet when we flood the beam with electrons from an end wall. These oscillations, of order 10 MHz, are observed to grow from the center of the magnet while drifting upstream against the beam, in good agreement with simulations

Absolute Measurement of Electron Cloud Density

Beam interaction with background gas and walls produces ubiquitous clouds of stray electrons that frequently limit the performance of particle accelerator and storage rings. Counterintuitively we obtained the electron cloud accumulation by measuring the expelled ions that are originated from the beam-background gas interaction, rather than by measuring electrons that reach the walls. The kinetic ion energy measured with a retarding field analyzer (RFA) maps the depressed beam space-charge potential and provides the dynamic electron cloud density. Clearing electrode current measurements give the static electron cloud background that complements and corroborates with the RFA measurements, providing an absolute measurement of electron cloud density during a 5 {micro}s duration beam pulse in a drift region of the magnetic transport section of the High-Current Experiment (HCX) at LBNL