A Microscopic Derivation of the SO(5)-Symmetric Landau-Ginzburg Potential

We construct a microscopic model of electron interactions which gives rise to both superconductivity and antiferromagnetism, and which admits an approximate SO(5) symmetry that relates these two phases. The symmetry can be exact, or it may exist only in the long-wavelength limit, depending on the detailed form of the interactions. We compute the macroscopic Landau-Ginzburg free energy for this model as a function of temperature and doping, by explicitly integrating out the fermions. We find that the resulting phase diagram can resemble that observed for the cuprates, with the antiferromagnetism realized as a spin density wave, whose wavelength might be incommensurate with the lattice spacing away from half filling.Comment: 29 pp., plain TeX, 7 figures, uses macros.tex (included) and epsf.tex; added subject clas

Photoluminescence Stokes shift and exciton fine structure in CdTe nanocrystals

The photoluminescence spectra of spherical CdTe nanocrystals with zincblende structure are studied by size-selective spectroscopic techniques. We observe a resonant Stokes shift of 15 meV when the excitation laser energy is tuned to the red side of the absorption band at 2.236 eV. The experimental data are analyzed within a symmetry-based tight-binding theory of the exciton spectrum, which is first shown to account for the size dependence of the fundamental gap reported previously in the literature. The theoretical Stokes shift presented as a function of the gap shows a good agreement with the experimental data, indicating that the measured Stokes shift indeed arises from the electron-hole exchange interaction.Comment: 8 pages, 4 figures, LaTe

Photon echoes from (In,Ga)As quantum dots embedded in a Tamm-plasmon microcavity

We acknowledge the financial support by the Deutsche Forschungsgemeinschaft through the Collaborative Research Centre TRR 142 and the International Collaborative Research Centre 160. S.V.P. and Yu.V.K. thank the Russian Foundation of Basic Research for partial financial support (contracts no. ofi_m 16-29-03115 and no. 15-52-12016NNIO_a). M.B. acknowledges partial financial support from the Russian Ministry of Science and Education (contract no. 14.Z50.31.0021). Yu.V.K. acknowledges Saint Petersburg State University for a research grant 11.42.993.2016. The project SPANGL4Q acknowledges financial support from the Future and Emerging Technologies (FET) programme within the Seventh Framework Programme for Research of the European Commission, under FET-Open grant no. FP7-284743.We report on the coherent optical response from an ensemble of (In,Ga)As quantum dots (QDs) embedded in a planar Tamm-plasmon microcavity with a quality factor of approx. 100. Significant enhancement of the light-matter interaction is demonstrated under selective laser excitation of those quantum dots which are in resonance with the cavity mode. The enhancement is manifested through Rabi oscillations of the photon echo, demonstrating coherent control of excitons with picosecond pulses at intensity levels more than an order of magnitude smaller as compared with bare quantum dots. The decay of the photon echo transients is weakly changed by the resonator indicating a small decrease of the coherence time T2 which we attribute to the interaction with the electron plasma in the metal layer located close (40 nm) to the QD layer. Simultaneously we see a reduction of the population lifetime T1, inferred from the stimulated photon echo, due to an enhancement of the spontaneous emission by a factor of 2, which is attributed to the Purcell effect, while non-radiative processes are negligible as confirmed from time-resolved photoluminescence.PostprintPeer reviewe

Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome

Transposable elements (TEs) have no longer been totally considered as “junk DNA” for quite a time since the continual discoveries of their multifunctional roles in eukaryote genomes. As one of the most important and abundant TEs that still active in human genome, Alu, a SINE family, has demonstrated its indispensable regulatory functions at sequence level, but its spatial roles are still unclear. Technologies based on 3C(chromosomeconformation capture) have revealed the mysterious three-dimensional structure of chromatin, and make it possible to study the distal chromatin interaction in the genome. To find the role TE playing in distal regulation in human genome, we compiled the new released Hi-C data, TE annotation, histone marker annotations, and the genome-wide methylation data to operate correlation analysis, and found that the density of Alu elements showed a strong positive correlation with the level of chromatin interactions (hESC: r=0.9, P<2.2×1016; IMR90 fibroblasts: r = 0.94, P < 2.2 × 1016) and also have a significant positive correlation withsomeremote functional DNA elements like enhancers and promoters (Enhancer: hESC: r=0.997, P=2.3×10−4; IMR90: r=0.934, P=2×10−2; Promoter: hESC: r = 0.995, P = 3.8 × 10−4; IMR90: r = 0.996, P = 3.2 × 10−4). Further investigation involving GC content and methylation status showed the GC content of Alu covered sequences shared a similar pattern with that of the overall sequence, suggesting that Alu elements also function as the GC nucleotide and CpG site provider. In all, our results suggest that the Alu elements may act as an alternative parameter to evaluate the Hi-C data, which is confirmed by the correlation analysis of Alu elements and histone markers. Moreover, the GC-rich Alu sequence can bring high GC content and methylation flexibility to the regions with more distal chromatin contact, regulating the transcription of tissue-specific genes

Characteristics of transposable element exonization within human and mouse

Insertion of transposed elements within mammalian genes is thought to be an important contributor to mammalian evolution and speciation. Insertion of transposed elements into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Elucidation of the evolutionary constraints that have shaped fixation of transposed elements within human and mouse protein coding genes and subsequent exonization is important for understanding of how the exonization process has affected transcriptome and proteome complexities. Here we show that exonization of transposed elements is biased towards the beginning of the coding sequence in both human and mouse genes. Analysis of single nucleotide polymorphisms (SNPs) revealed that exonization of transposed elements can be population-specific, implying that exonizations may enhance divergence and lead to speciation. SNP density analysis revealed differences between Alu and other transposed elements. Finally, we identified cases of primate-specific Alu elements that depend on RNA editing for their exonization. These results shed light on TE fixation and the exonization process within human and mouse genes.Comment: 11 pages, 4 figure

Photon echo transients from an inhomogeneous ensemble of semiconductor quantum dots

We acknowledge the financial support by the Deutsche Forschungsgemeinschaft, Project ICRC TRR 160 and the Russian Foundation of Basic Research (RFBR) in the frame of the Project No. 15-52-12016 NNIO_a. The project SPANGL4Q acknowledges financial support from the Future and Emerging Technologies (FET) programme within the Seventh Framework Programme for Research of the European Commission, under FET-Open Grant No. FP7-284743. S.V.P. thanks the RFBR for partial financial support (Project No. 14-02-31735 mol_a). S.V.P. and I.A.Yu. acknowledge partial financial support from the Ministry of Education and Science of the Russian Federation (Grant No. 11.G34.31.0067) and St-Petersburg State University (SPbU) (Grant No. 11.38.213.2014). M.B. acknowledges support from the Ministry of Education and Science of the Russian Federation (Grant No. 14.Z50.31.0021).An ensemble of quantum dot excitons may be used for coherent information manipulation. Due to the ensemble inhomogeneity any optical information retrieval occurs in form of a photon echo. We show that the inhomogeneity can lead to a significant deviation from the conventional echo timing sequence. Variation of the area of the initial rotation pulse, which generates excitons in a dot subensemble only, reveals this complex picture of photon echo formation. We observe a retarded echo for π/2 pulses, while for 3π/2 the echo is advanced in time as evidenced through monitoring the Rabi oscillations in the time-resolved photon echo amplitude from (In,Ga)As/GaAs self-assembled quantum dot structures and confirmed by detailed calculations.PostprintPeer reviewe

The \u3cem\u3eChlamydomonas\u3c/em\u3e Genome Reveals the Evolution of Key Animal and Plant Functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella

Sub-nanosecond Pulse Generation from a Two-section Laser-thyristor: Theoretical Analysis

We have developed a theoretical model of a two-section laser-thyristor. It is shown that using a 4 µm weakly doped p-base can increase blocking voltage up to 50 V, which makes it possible to generate 2 ns 10 A current pulses. It is demonstrated that the proposed device utilizes passive Q switching to generate high-power short optical pulses that account for up to 80% of output power. By picking the optimal passive section length, we have achieved optical pulses of ∼30 ps full width at half maximum (FWHM) and ∼100 W peak power. &nbsp; &nbsp; Keywords: pulsed laser, semiconductor N-p-N-i-P heterostructure, laser-thyristor, dynamic model of pulsed lase

Ancient horizontal gene transfer and the last common ancestors

Background The genomic history of prokaryotic organismal lineages is marked by extensive horizontal gene transfer (HGT) between groups of organisms at all taxonomic levels. These HGT events have played an essential role in the origin and distribution of biological innovations. Analyses of ancient gene families show that HGT existed in the distant past, even at the time of the organismal last universal common ancestor (LUCA). Most gene transfers originated in lineages that have since gone extinct. Therefore, one cannot assume that the last common ancestors of each gene were all present in the same cell representing the cellular ancestor of all extant life. Results Organisms existing as part of a diverse ecosystem at the time of LUCA likely shared genetic material between lineages. If these other lineages persisted for some time, HGT with the descendants of LUCA could have continued into the bacterial and archaeal lineages. Phylogenetic analyses of aminoacyl-tRNA synthetase protein families support the hypothesis that the molecular common ancestors of the most ancient gene families did not all coincide in space and time. This is most apparent in the evolutionary histories of seryl-tRNA synthetase and threonyl-tRNA synthetase protein families, each containing highly divergent “rare” forms, as well as the sparse phylogenetic distributions of pyrrolysyl-tRNA synthetase, and the bacterial heterodimeric form of glycyl-tRNA synthetase. These topologies and phyletic distributions are consistent with horizontal transfers from ancient, likely extinct branches of the tree of life. Conclusions Of all the organisms that may have existed at the time of LUCA, by definition only one lineage is survived by known progeny; however, this lineage retains a genomic record of heterogeneous genetic origins. The evolutionary histories of aminoacyl-tRNA synthetases (aaRS) are especially informative in detecting this signal, as they perform primordial biological functions, have undergone several ancient HGT events, and contain many sites with low substitution rates allowing deep phylogenetic reconstruction. We conclude that some aaRS families contain groups that diverge before LUCA. We propose that these ancient gene variants be described by the term “hypnologs”, reflecting their ancient, reticulate origin from a time in life history that has been all but erased”.National Science Foundation (U.S.) (Grant DEB 0830024)Exobiology Program (U.S.) (Grant NNX10AR85G)United States. National Aeronautics and Space Administration (Postdoctoral Program

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal speciesFilamentous fungi produce a diverse array of secondary metabolites (SMs) critical for defense, virulence, and communication. The metabolic pathways that produce SMs are found in contiguous gene clusters in fungal genomes, an atypical arrangement for metabolic pathways in other eukaryotes. Comparative studies of filamentous fungal species have shown that SM gene clusters are often either highly divergent or uniquely present in one or a handful of species, hampering efforts to determine the genetic basis and evolutionary drivers of SM gene cluster divergence. Here, we examined SM variation in 66 cosmopolitan strains of a single species, the opportunistic human pathogen Aspergillus fumigatus. Investigation of genome-wide within-species variation revealed 5 general types of variation in SM gene clusters: nonfunctional gene polymorphisms; gene gain and loss polymorphisms; whole cluster gain and loss polymorphisms; allelic polymorphisms, in which different alleles corresponded to distinct, nonhomologous clusters; and location polymorphisms, in which a cluster was found to differ in its genomic location across strains. These polymorphisms affect the function of representative A. fumigatus SM gene clusters, such as those involved in the production of gliotoxin, fumigaclavine, and helvolic acid as well as the function of clusters with undefined products. In addition to enabling the identification of polymorphisms, the detection of which requires extensive genome-wide synteny conservation (e.g., mobile gene clusters and nonhomologous cluster alleles), our approach also implicated multiple underlying genetic drivers, including point mutations, recombination, and genomic deletion and insertion events as well as horizontal gene transfer from distant fungi. Finally, most of the variants that we uncover within A. fumigatus have been previously hypothesized to contribute to SM gene cluster diversity across entire fungal classes and phyla. We suggest that the drivers of genetic diversity operating within a fungal species shown here are sufficient to explain SM cluster macroevolutionary patterns.National Science Foundation (grant number DEB-1442113). Received by AR. U.S. National Library of Medicine training grant (grant number 2T15LM007450). Received by ALL. Conselho Nacional de Desenvolvimento Cientı´fico e 573 Tecnológico. Northern Portugal Regional Operational Programme (grant number NORTE-01- 0145-FEDER-000013). Received by FR. Fundação de Amparo à Pesquisa do 572 Estado de São Paulo. Received by GHG. National Institutes of Health (grant number R01 AI065728-01). Received by NPK. National Science Foundation (grant number IOS-1401682). Received by JHW. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio