Voltage-flux-characteristics of asymmetric dc SQUIDs

We present a detailed analysis of voltage-flux V(Phi)-characteristics for asymmetric dc SQUIDs with various kinds of asymmetries. For finite asymmetry alpha_I in the critical currents of the two Josephson junctions, the minima in the V(Phi)-characteristics for bias currents of opposite polarity are shifted along the flux axis by Delta_Phi = (alpha_I)*(beta_L) relative to each other; beta_L is the screening parameter. This simple relation allows the determination of alpha_I in our experiments on YBa_2Cu_3O_(7-x} dc SQUIDs and comparison with theory. Extensive numerical simulations within a wide range of beta_L and noise parameter Gamma reveal a systematic dependence of the transfer function V_Phi on alpha_I and alpha_R (junction resistance asymmetry). As for the symmetric dc SQUID, V_Phi factorizes into g(Gamma*beta_L)*f(alpha_I,beta_L), where now f also depends on alpha_I. For \beta_L below five we find mostly a decrease of V_Phi with increasing alpha_I, which however can only partially account for the frequently observed discrepancy in V_Phi between theory and experiment for high-T_c dc SQUIDs.Comment: 4 pages, 7 figures, Applied Superconductivity Conference 2000, to be published in IEEE Trans. Appl. Supercon

Commensurability effects in superconducting Nb films with quasiperiodic pinning arrays

We study experimentally the critical depinning current Ic versus applied magnetic field B in Nb thin films which contain 2D arrays of circular antidots placed on the nodes of quasiperiodic (QP) fivefold Penrose lattices. Close to the transition temperature Tc we observe matching of the vortex lattice with the QP pinning array, confirming essential features in the Ic(B) patterns as predicted by Misko et al. [Phys. Rev. Lett, vol.95, 177007 (2005)]. We find a significant enhancement in Ic(B) for QP pinning arrays in comparison to Ic in samples with randomly distributed antidots or no antidots.Comment: 4 pages, 3 figure

Multigrid reduction-in-time convergence for advection problems: A Fourier analysis perspective

A long-standing issue in the parallel-in-time community is the poor convergence of standard iterative parallel-in-time methods for hyperbolic partial differential equations (PDEs), and for advection-dominated PDEs more broadly. Here, a local Fourier analysis (LFA) convergence theory is derived for the two-level variant of the iterative parallel-in-time method of multigrid reduction-in-time (MGRIT). This closed-form theory allows for new insights into the poor convergence of MGRIT for advection-dominated PDEs when using the standard approach of rediscretizing the fine-grid problem on the coarse grid. Specifically, we show that this poor convergence arises, at least in part, from inadequate coarse-grid correction of certain smooth Fourier modes known as characteristic components, which was previously identified as causing poor convergence of classical spatial multigrid on steady-state advection-dominated PDEs. We apply this convergence theory to show that, for certain semi-Lagrangian discretizations of advection problems, MGRIT convergence using rediscretized coarse-grid operators cannot be robust with respect to CFL number or coarsening factor. A consequence of this analysis is that techniques developed for improving convergence in the spatial multigrid context can be re-purposed in the MGRIT context to develop more robust parallel-in-time solvers. This strategy has been used in recent work to great effect; here, we provide further theoretical evidence supporting the effectiveness of this approach

Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting

Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity inPinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. MakingP. sylvestrisan even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation

The multiple gene duplication problem revisited

Motivation: Deciphering the location of gene duplications and multiple gene duplication episodes on the Tree of Life is fundamental to understanding the way gene families and genomes evolve. The multiple gene duplication problem provides a framework for placing gene duplication events onto nodes of a given species tree, and detecting episodes of multiple gene duplication. One version of the multiple gene duplication problem was defined by Guigó et al. in 1996. Several heuristic solutions have since been proposed for this problem, but no exact algorithms were known

Reducing quantum control for spin-spin entanglement distribution

We present a protocol that sets maximum stationary entanglement between remote spins through scattering of mobile mediators without initialization, post-selection or feedback of the mediators' state. No time-resolved tuning is needed and, counterintuitively, the protocol generates two-qubit singlet states even when classical mediators are used. The mechanism responsible for such effect is resilient against non-optimal coupling strengths and dephasing affecting the spins. The scheme uses itinerant particles and scattering centres and can be implemented in various settings. When quantum dots and photons are used a striking result is found: injection of classical mediators, rather than quantum ones, improves the scheme efficiency.Comment: 7 pages, 5 figures, replaced with published versio

Functional classification of protein toxins as a basis for bioinformatic screening

Proteins are fundamental to life and exhibit a wide diversity of activities, some of which are toxic. Therefore, assessing whether a specific protein is safe for consumption in foods and feeds is critical. Simple BLAST searches may reveal homology to a known toxin, when in fact the protein may pose no real danger. Another challenge to answer this question is the lack of curated databases with a representative set of experimentally validated toxins. Here we have systematically analyzed over 10,000 manually curated toxin sequences using sequence clustering, network analysis, and protein domain classification. We also developed a functional sequence signature method to distinguish toxic from non-toxic proteins. The current database, combined with motif analysis, can be used by researchers and regulators in a hazard screening capacity to assess the potential of a protein to be toxic at early stages of development. Identifying key signatures of toxicity can also aid in redesigning proteins, so as to maintain their desirable functions while reducing the risk of potential health hazards

Does shade improve light interception efficiency? A comparison among seedlings from shade-tolerant and -intolerant temperate deciduous tree species

• Here, we tested two hypotheses: shading increases light interception efficiency (LIE) of broadleaved tree seedlings, and shade-tolerant species exhibit larger LIEs than do shade-intolerant ones. The impact of seedling size was taken into account to detect potential size-independent effects on LIE. LIE was defined as the ratio of mean light intercepted by leaves to light intercepted by a horizontal surface of equal area. • Seedlings from five species differing in shade tolerance (Acer saccharum, Betula alleghaniensis, A. pseudoplatanus, B. pendula, Fagus sylvatica) were grown under neutral shading nets providing 36, 16 and 4% of external irradiance. Seedlings (1- and 2-year-old) were three-dimensionally digitized, allowing calculation of LIE. • Shading induced dramatic reduction in total leaf area, which was lowest in shade-tolerant species in all irradiance regimes. Irradiance reduced LIE through increasing leaf overlap with increasing leaf area. There was very little evidence of significant size-independent plasticity of LIE. • No relationship was found between the known shade tolerance of species and LIE at equivalent size and irradiance