Polaron cross-overs and d-wave superconductivity in Hubbard-Holstein model

We present a theoretical study of superconductivity of polarons in the Hubbard-Holstein model. A residual kinematic interaction proportional to the square of the polaron hopping energy between polarons and phonons provides a pairing field for the polarons. We find that superconducting instability in the d-wave channel is possible with small transition temperatures which is maximum in the large to small polaron cross-over region. An s-wave instability is found to be not possible when the effective on-site interaction between polarons is repulsive

The Effect of Large Amplitude Fluctuations in the Ginzburg-Landau Phase Transition

The lattice Ginzburg-Landau model in d=3 and d=2 is simulated, for different values of the coherence length $\xi$ in units of the lattice spacing $a$, using a Monte Carlo method. The energy, specific heat, vortex density $v$, helicity modulus $\Gamma_\mu$ and mean square amplitude are measured to map the phase diagram on the plane $T-\xi$. When amplitude fluctuations, controlled by the parameter $\xi$, become large ($\xi \sim 1$) a proliferation of vortex excitations occurs changing the phase transition from continuous to first order.Comment: 4 pages, 5 postscript (eps) figure

Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells

RNA interference and the microRNA (miRNA) pathway can induce sequence-specific mRNA degradation and/or translational repression. The human genome encodes hundreds of miRNAs that can post-transcriptionally repress thousands of genes. Using reporter constructs, we observed that degradation of mRNAs bearing sites imperfectly complementary to the endogenous let-7 miRNA is considerably stronger in human HEK293 than HeLa cells. The degradation did not result from the Ago2-mediated endonucleolytic cleavage but it was Dicer- and Ago2-dependent. We used this feature of HEK293 to address the size of a pool of transcripts regulated by RNA silencing in a single cell type. We generated HEK293 cell lines depleted of Dicer or individual Ago proteins. The cell lines were used for microarray analyses to obtain a comprehensive picture of RNA silencing. The 3'-untranslated region sequences of a few hundred transcripts that were commonly up-regulated upon Ago2 and Dicer knock-downs showed a significant enrichment of putative miRNA-binding sites. The up-regulation upon Ago2 and Dicer knock-downs was moderate and we found no evidence, at the mRNA level, for activation of silenced genes. Taken together, our data suggest that, independent of the effect on translation, miRNAs affect levels of a few hundred mRNAs in HEK293 cells

Superconductivity in the Three-Fold Charge-Ordered Metal of the Triangular-Lattice Extended Hubbard Model

The quarter-filling extended Hubbard model on the triangular lattice is studied to explore pairing instability in the three-fold charge-ordered (CO) metal. We derive a second-order strong-coupling effective Hamiltonian of doped carriers into the three-fold CO insulator at electron density of $n=2/3$, and then study the $f$- and $d_{xy}$-wave superconductivities down to $n=1/2$ by using the BCS mean-field approximation. It is found that the triplet $f$-wave pairing is more stable than the $d_{xy}$-wave one. We also point out that this coexisting state of the charge ordering and superconductivity is possible to have critical temperature $T_c \sim 0.01 t$.Comment: 4 pages, 7 figure

Phase Transitions Driven by Vortices in 2D Superfluids and Superconductors: From Kosterlitz-Thouless to 1st Order

The Landau-Ginzburg-Wilson hamiltonian is studied for different values of the parameter $\lambda$ which multiplies the quartic term (it turns out that this is equivalent to consider different values of the coherence length $\xi$ in units of the lattice spacing $a$). It is observed that amplitude fluctuations can change dramatically the nature of the phase transition: for small values of $\lambda$ ($\xi/a > 0.7$), instead of the smooth Kosterlitz-Thouless transition there is a {\em first order} transition with a discontinuous jump in the vortex density $v$ and a larger non-universal drop in the helicity modulus. In particular, for $\lambda$ sufficiently small ($\xi/a \cong 1$), the density of bound pairs of vortex-antivortex below $T_c$ is so low that, $v$ drops to zero almost for all temperature $T<Tc$.Comment: 8 pages, 5 .eps figure

Theory of the Diamagnetism Above the Critical Temperature for Cuprates

Recently experiments on high critical temperature superconductors has shown that the doping levels and the superconducting gap are usually not uniform properties but strongly dependent on their positions inside a given sample. Local superconducting regions develop at the pseudogap temperature ($T^*$) and upon cooling, grow continuously. As one of the consequences a large diamagnetic signal above the critical temperature ($T_c$) has been measured by different groups. Here we apply a critical-state model for the magnetic response to the local superconducting domains between $T^*$ and $T_c$ and show that the resulting diamagnetic signal is in agreement with the experimental results.Comment: published versio

Fluctuating diamagnetism in underdoped high temperature superconductors

The fluctuation induced diamagnetism of underdoped high temperature superconductors is studied in the framework of the Lawrence-Doniach model. By taking into account the fluctuations of the phase of the order parameter only, the latter reduces to a layered XY-model describing a liquid of vortices which can be either thermally excited or induced by the external magnetic field. The diamagnetic response is given by a current-current correlation function which is evaluated using the Coulomb gas analogy. Our results are then applied to recent measurements of fluctuation diamagnetism in underdoped YBCO. They allow to understand both the observed anomalous temperature dependence of the zero-field susceptibility and the two distinct regimes appearing in the magnetic field dependence of the magnetization.Comment: 12 pages, 4 figures included, accepted for publication in PR

Jahn-Teller polarons and their superconductivity in a molecular conductor

We present a theoretical study of a possibility of superconductivity in a three dimensional molecular conductor in which the interaction between electrons in doubly degenerate molecular orbitals and an {\em intra}molecular vibration mode is large enough to lead to the formation of $E\otimes \beta$ Jahn-Teller small polarons. We argue that the effective polaron-polaron interaction can be attractive for material parameters realizable in molecular conductors. This interaction is the source of superconductivity in our model. On analyzing superconducting instability in the weak and strong coupling regimes of this attractive interaction, we find that superconducting transition temperatures up to 100 K are achievable in molecular conductors within this mechanism. We also find, for two particles per molecular site, a novel Mott insulating state in which a polaron singlet occupies one of the doubly degenerate orbitals on each site. Relevance of this study in the search for new molecular superconductors is pointed out.Comment: Submitted to Phys. Rev.

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

Ab initio identification of human microRNAs based on structure motifs

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are short, non-coding RNA molecules that are directly involved in post-transcriptional regulation of gene expression. The mature miRNA sequence binds to more or less specific target sites on the mRNA. Both their small size and sequence specificity make the detection of completely new miRNAs a challenging task. This cannot be based on sequence information alone, but requires structure information about the miRNA precursor. Unlike comparative genomics approaches, <it>ab initio </it>approaches are able to discover species-specific miRNAs without known sequence homology.</p> <p>Results</p> <p>MiRPred is a novel method for <it>ab initio </it>prediction of miRNAs by genome scanning that only relies on (predicted) secondary structure to distinguish miRNA precursors from other similar-sized segments of the human genome. We apply a machine learning technique, called linear genetic programming, to develop special classifier programs which include multiple regular expressions (motifs) matched against the secondary structure sequence. Special attention is paid to scanning issues. The classifiers are trained on fixed-length sequences as these occur when shifting a window in regular steps over a genome region. Various statistical and empirical evidence is collected to validate the correctness of and increase confidence in the predicted structures. Among other things, we propose a new criterion to select miRNA candidates with a higher stability of folding that is based on the number of matching windows around their genome location. An ensemble of 16 motif-based classifiers achieves 99.9 percent specificity with sensitivity remaining on an acceptable high level when requiring all classifiers to agree on a positive decision. A low false positive rate is considered more important than a low false negative rate, when searching larger genome regions for unknown miRNAs. 117 new miRNAs have been predicted close to known miRNAs on human chromosome 19. All candidate structures match the free energy distribution of miRNA precursors which is significantly shifted towards lower free energies. We employed a human EST library and found that around 75 percent of the candidate sequences are likely to be transcribed, with around 35 percent located in introns.</p> <p>Conclusion</p> <p>Our motif finding method is at least competitive to state-of-the-art feature-based methods for <it>ab initio </it>miRNA discovery. In doing so, it requires less previous knowledge about miRNA precursor structures while programs and motifs allow a more straightforward interpretation and extraction of the acquired knowledge.</p