Folding of a donor–acceptor polyrotaxane by using noncovalent bonding interactions

Mechanically interlocked compounds, such as bistable catenanes and bistable rotaxanes, have been used to bring about actuation in nanoelectromechanical systems (NEMS) and molecular electronic devices (MEDs). The elaboration of the structural features of such rotaxanes into macromolecular materials might allow the utilization of molecular motion to impact their bulk properties. We report here the synthesis and characterization of polymers that contain π electron-donating 1,5-dioxynaphthalene (DNP) units encircled by cyclobis(paraquat-p-phenylene) (CBPQT4+), a π electron-accepting tetracationic cyclophane, synthesized by using the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The polyrotaxanes adopt a well defined “folded” secondary structure by virtue of the judicious design of two DNP-containing monomers with different binding affinities for CBPQT4+. This efficient approach to the preparation of polyrotaxanes, taken alongside the initial investigations of their chemical properties, sets the stage for the preparation of a previously undescribed class of macromolecular architectures

Spin Wave Instability of Itinerant Ferromagnet

We show variationally that instability of the ferromagnetic state in the Hubbard model is largely controlled by softening of a long-wavelength spin-wave excitation, except in the over-doped strong-coupling region where the individual-particle excitation becomes unstable first. A similar conclusion is drawn also for the double exchange ferromagnet. Generally the spin-wave instability may be regarded as a precursor of the metal-insulator transition.Comment: 11 pages, 8 figure

Variational Monte Carlo Study of Spin-Gapped Normal State and BCS-BEC Crossover in Two-Dimensional Attractive Hubbard Model

We study properties of normal, superconducting (SC) and CDW states for an attractive Hubbard model on the square lattice, using a variational Monte Carlo method. In trial wave functions, we introduce an interspinon binding factor, indispensable to induce a spin-gap transition in the normal state, in addition to the onsite attractive and intersite repulsive factors. It is found that, in the normal state, as the interaction strength $|U|/t$ increases, a first-order spin-gap transition arises at $|U_{\rm c}|\sim W$ ($W$: band width) from a Fermi liquid to a spin-gapped state, which is conductive through hopping of doublons. In the SC state, we confirm by analysis of various quantities that the mechanism of superconductivity undergoes a smooth crossover at around |U_{\ma{co}}|\sim |U_{\rm c}| from a BCS type to a Bose-Einstein condensation (BEC) type, as $|U|/t$ increases. For |U|<|U_{\ma{co}}|, quantities such as the condensation energy, a SC correlation function and the condensate fraction of onsite pairs exhibit behavior of $\sim \exp(-t/|U|)$, as expected from the BCS theory. For |U|>|U_{\ma{co}}|, quantities such as the energy gain in the SC transition and superfluid stiffness, which is related to the cost of phase coherence, behave as $\sim t^2/|U|\propto T_{\rm c}$, as expected in a bosonic scheme. In this regime, the SC transition is induced by a gain in kinetic energy, in contrast with the BCS theory. We refer to the relevance to the pseudogap in cuprate superconductors.Comment: 14 pages, 22 figures, submitted to Journal of the Physical Society of Japa

Dispersion of Ordered Stripe Phases in the Cuprates

A phase separation model is presented for the stripe phase of the cuprates, which allows the doping dependence of the photoemission spectra to be calculated. The idealized limit of a well-ordered array of magnetic and charged stripes is analyzed, including effects of long-range Coulomb repulsion. Remarkably, down to the limit of two-cell wide stripes, the dispersion can be interpreted as essentially a superposition of the two end-phase dispersions, with superposed minigaps associated with the lattice periodicity. The largest minigap falls near the Fermi level; it can be enhanced by proximity to a (bulk) Van Hove singularity. The calculated spectra are dominated by two features -- this charge stripe minigap plus the magnetic stripe Hubbard gap. There is a strong correlation between these two features and the experimental photoemission results of a two-peak dispersion in La$_{2-x}$Sr$_x$CuO$_4$, and the peak-dip-hump spectra in Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$. The differences are suggestive of the role of increasing stripe fluctuations. The 1/8 anomaly is associated with a quantum critical point, here expressed as a percolation-like crossover. A model is proposed for the limiting minority magnetic phase as an isolated two-leg ladder.Comment: 24 pages, 26 PS figure

Bias and Evolution of the Mutationally Accessible Phenotypic Space in a Developmental System

Genetic and developmental architecture may bias the mutationally available phenotypic spectrum. Although such asymmetries in the introduction of variation may influence possible evolutionary trajectories, we lack quantitative characterization of biases in mutationally inducible phenotypic variation, their genotype-dependence, and their underlying molecular and developmental causes. Here we quantify the mutationally accessible phenotypic spectrum of the vulval developmental system using mutation accumulation (MA) lines derived from four wild isolates of the nematodes Caenorhabditis elegans and C. briggsae. The results confirm that on average, spontaneous mutations degrade developmental precision, with MA lines showing a low, yet consistently increased, proportion of developmental defects and variants. This result indicates strong purifying selection acting to maintain an invariant vulval phenotype. Both developmental system and genotype significantly bias the spectrum of mutationally inducible phenotypic variants. First, irrespective of genotype, there is a developmental bias, such that certain phenotypic variants are commonly induced by MA, while others are very rarely or never induced. Second, we found that both the degree and spectrum of mutationally accessible phenotypic variation are genotype-dependent. Overall, C. briggsae MA lines exhibited a two-fold higher decline in precision than the C. elegans MA lines. Moreover, the propensity to generate specific developmental variants depended on the genetic background. We show that such genotype-specific developmental biases are likely due to cryptic quantitative variation in activities of underlying molecular cascades. This analysis allowed us to identify the mutationally most sensitive elements of the vulval developmental system, which may indicate axes of potential evolutionary variation. Consistent with this scenario, we found that evolutionary trends in the vulval system concern the phenotypic characters that are most easily affected by mutation. This study provides an empirical assessment of developmental bias and the evolution of mutationally accessible phenotypes and supports the notion that such bias may influence the directions of evolutionary change

Evolution of Susceptibility to Ingested Double-Stranded RNAs in Caenorhabditis Nematodes

International audienceBACKGROUND: The nematode Caenorhabditis elegans is able to take up external double-stranded RNAs (dsRNAs) and mount an RNA interference response, leading to the inactivation of specific gene expression. The uptake of ingested dsRNAs into intestinal cells has been shown to require the SID-2 transmembrane protein in C. elegans. By contrast, C. briggsae was shown to be naturally insensitive to ingested dsRNAs, yet could be rendered sensitive by transgenesis with the C. elegans sid-2 gene. Here we aimed to elucidate the evolution of the susceptibility to external RNAi in the Caenorhabditis genus. PRINCIPAL FINDINGS: We study the sensitivity of many new species of Caenorhabditis to ingested dsRNAs matching a conserved actin gene sequence from the nematode Oscheius tipulae. We find ample variation in the Caenorhabditis genus in the ability to mount an RNAi response. We map this sensitivity onto a phylogenetic tree, and show that sensitivity or insensitivity have evolved convergently several times. We uncover several evolutionary losses in sensitivity, which may have occurred through distinct mechanisms. We could render C. remanei and C. briggsae sensitive to ingested dsRNAs by transgenesis of the Cel-sid-2 gene. We thus provide tools for RNA interference studies in these species. We also show that transgenesis by injection is possible in many Caenorhabditis species. CONCLUSIONS: The ability of animals to take up dsRNAs or to respond to them by gene inactivation is under rapid evolution in the Caenorhabditis genus. This study provides a framework and tools to use RNA interference and transgenesis in various Caenorhabditis species for further comparative and evolutionary studies

A Developmental Systems Perspective on Epistasis: Computational Exploration of Mutational Interactions in Model Developmental Regulatory Networks

The way in which the information contained in genotypes is translated into complex phenotypic traits (i.e. embryonic expression patterns) depends on its decoding by a multilayered hierarchy of biomolecular systems (regulatory networks). Each layer of this hierarchy displays its own regulatory schemes (i.e. operational rules such as +/− feedback) and associated control parameters, resulting in characteristic variational constraints. This process can be conceptualized as a mapping issue, and in the context of highly-dimensional genotype-phenotype mappings (GPMs) epistatic events have been shown to be ubiquitous, manifested in non-linear correspondences between changes in the genotype and their phenotypic effects. In this study I concentrate on epistatic phenomena pervading levels of biological organization above the genetic material, more specifically the realm of molecular networks. At this level, systems approaches to studying GPMs are specially suitable to shed light on the mechanistic basis of epistatic phenomena. To this aim, I constructed and analyzed ensembles of highly-modular (fully interconnected) networks with distinctive topologies, each displaying dynamic behaviors that were categorized as either arbitrary or functional according to early patterning processes in the Drosophila embryo. Spatio-temporal expression trajectories in virtual syncytial embryos were simulated via reaction-diffusion models. My in silico mutational experiments show that: 1) the average fitness decay tendency to successively accumulated mutations in ensembles of functional networks indicates the prevalence of positive epistasis, whereas in ensembles of arbitrary networks negative epistasis is the dominant tendency; and 2) the evaluation of epistatic coefficients of diverse interaction orders indicates that, both positive and negative epistasis are more prevalent in functional networks than in arbitrary ones. Overall, I conclude that the phenotypic and fitness effects of multiple perturbations are strongly conditioned by both the regulatory architecture (i.e. pattern of coupled feedback structures) and the dynamic nature of the spatio-temporal expression trajectories displayed by the simulated networks