Fractional photon-assisted tunneling in an optical superlattice: large contribution to particle transfer

Fractional photon-assisted tunneling is investigated both analytically and numerically for few interacting ultra-cold atoms in the double-wells of an optical superlattice. This can be realized experimentally by adding periodic shaking to an existing experimental setup [Phys. Rev. Lett. 101, 090404 (2008)]. Photon-assisted tunneling is visible in the particle transfer between the wells of the individual double wells. In order to understand the physics of the photon-assisted tunneling, an effective model based on the rotating wave approximation is introduced. The validity of this effective approach is tested for wide parameter ranges which are accessible to experiments in double-well lattices. The effective model goes well beyond previous perturbation theory approaches and is useful to investigate in particular the fractional photon-assisted tunneling resonances. Analytic results on the level of the experimentally realizable two-particle quantum dynamics show very good agreement with the numerical solution of the time-dependent Schr\"odinger equation. Far from being a small effect, both the one-half-photon and the one-third-photon resonance are shown to have large effects on the particle transfer.Comment: 9 pages, 11 png-figure

Visualizing the emergence of the pseudogap state and the evolution to superconductivity in a lightly hole-doped Mott insulator

Superconductivity emerges from the cuprate antiferromagnetic Mott state with hole doping. The resulting electronic structure is not understood, although changes in the state of oxygen atoms appear paramount. Hole doping first destroys the Mott state yielding a weak insulator where electrons localize only at low temperatures without a full energy gap. At higher doping, the 'pseudogap', a weakly conducting state with an anisotropic energy gap and intra-unit-cell breaking of 90\degree-rotational (C4v) symmetry appears. However, a direct visualization of the emergence of these phenomena with increasing hole density has never been achieved. Here we report atomic-scale imaging of electronic structure evolution from the weak-insulator through the emergence of the pseudogap to the superconducting state in Ca2-xNaxCuO2Cl2. The spectral signature of the pseudogap emerges at lowest doping from a weakly insulating but C4v-symmetric matrix exhibiting a distinct spectral shape. At slightly higher hole-density, nanoscale regions exhibiting pseudogap spectra and 180\degree-rotational (C2v) symmetry form unidirectional clusters within the C4v-symmetric matrix. Thus, hole-doping proceeds by the appearance of nanoscale clusters of localized holes within which the broken-symmetry pseudogap state is stabilized. A fundamentally two-component electronic structure11 then exists in Ca2-xNaxCuO2Cl2 until the C2v-symmetric clusters touch at higher doping, and the long-range superconductivity appears.Comment: See the Nature Physics website for the published version available at http://dx.doi.org/10.1038/Nphys232

Evolution of oligomeric state through allosteric pathways that mimic ligand binding.

Evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. We showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. In this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the PyrR family of pyrimidine operon attenuators. In this family, a perfectly sequence-conserved helix that forms a tetrameric interface is exposed as solvent-accessible surface in dimeric orthologs. This means that mutations must be acting from a distance to destabilize the interface. We identified 11 key mutations controlling oligomeric state, all distant from the interfaces and outside ligand-binding pockets. Finally, we show that the key mutations introduce conformational changes equivalent to the conformational shift between the free versus nucleotide-bound conformations of the proteins.This is the accepted manuscript. The final version is available from AAAS at http://www.sciencemag.org/content/346/6216/1254346.abstract

Numerical Schemes for Rough Parabolic Equations

This paper is devoted to the study of numerical approximation schemes for a class of parabolic equations on (0, 1) perturbed by a non-linear rough signal. It is the continuation of [8, 7], where the existence and uniqueness of a solution has been established. The approach combines rough paths methods with standard considerations on discretizing stochastic PDEs. The results apply to a geometric 2-rough path, which covers the case of the multidimensional fractional Brownian motion with Hurst index H \textgreater{} 1/3.Comment: Applied Mathematics and Optimization, 201

Gate-Controlled Ionization and Screening of Cobalt Adatoms on a Graphene Surface

We describe scanning tunneling spectroscopy (STS) measurements performed on individual cobalt (Co) atoms deposited onto backgated graphene devices. We find that Co adatoms on graphene can be ionized by either the application of a global backgate voltage or by the application of a local electric field from a scanning tunneling microscope (STM) tip. Large screening clouds are observed to form around Co adatoms ionized in this way, and we observe that some intrinsic graphene defects display a similar behavior. Our results provide new insight into charged impurity scattering in graphene, as well as the possibility of using graphene devices as chemical sensors.Comment: 19 pages, 4 figure

A Case Report of Malignant Perivascular Epithelioid Cell Tumors of the Uterus and Literature Review

Daifeng Hu,1,* Mengyue Miao,1,* Hui Zhou,1 Xia Gu,1,2 Xuedan Wang,3 Alexander Tobias Teichmann,1 Qin Wang,1 Youzhe Yang1,2 1Sichuan Provincial Center for Gynaecology and Breast Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, People’s Republic of China; 2Academician (Expert) Workstation of Sichuan Province, Luzhou, 646000, People’s Republic of China; 3Department of Pathology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, People’s Republic of China*These authors contributed equally to this workCorrespondence: Qin Wang; Youzhe Yang, The Affiliated Hospital of Southwest Medical University, NO. 25 Taiping Street, Jiangyang District, Luzhou, 646000, People’s Republic of China, Email [email protected]; [email protected]: Perivascular epithelioid cell tumors (PEComas) are rare mesenchymal tumors originating from perivascular epithelioid cells. In gynecological system, the uterus is one of the most common sites affected by PEComas. Most PEComas are benign, and patients usually have a good prognosis. However, malignant uterus PEComa is rare, and better comprehensive epidemiological investigations are needed. To date, there are a few reported cases of uterus PEComa. We herein report a rare case of malignant PEComa occurred in the uterine corpus and cervix, possibly accompanied by pulmonary lymphangioleiomyomatosis (PLAM). In addition, 55 cases of malignant uterus PEComa were picked out and collected in the data base of PubMed and Medline. On the one hand, the age of onset, population distribution, clinical manifestations, metastatic sites and routes of metastasis were analysed. On the other hand, a summary of the epidemiology, pathogenesis, diagnosis, and treatments of uterus PEComa was given.Keywords: perivascular epithelioid cell tumors, uterus, malignant, rare case, cervi

Origin of Co-Expression Patterns in E.coli and S.cerevisiae Emerging from Reverse Engineering Algorithms

BACKGROUND: The concept of reverse engineering a gene network, i.e., of inferring a genome-wide graph of putative gene-gene interactions from compendia of high throughput microarray data has been extensively used in the last few years to deduce/integrate/validate various types of "physical" networks of interactions among genes or gene products. RESULTS: This paper gives a comprehensive overview of which of these networks emerge significantly when reverse engineering large collections of gene expression data for two model organisms, E. coli and S. cerevisiae, without any prior information. For the first organism the pattern of co-expression is shown to reflect in fine detail both the operonal structure of the DNA and the regulatory effects exerted by the gene products when co-participating in a protein complex. For the second organism we find that direct transcriptional control (e.g., transcription factor-binding site interactions) has little statistical significance in comparison to the other regulatory mechanisms (such as co-sharing a protein complex, co-localization on a metabolic pathway or compartment), which are however resolved at a lower level of detail than in E. coli. CONCLUSION: The gene co-expression patterns deduced from compendia of profiling experiments tend to unveil functional categories that are mainly associated to stable bindings rather than transient interactions. The inference power of this systematic analysis is substantially reduced when passing from E. coli to S. cerevisiae. This extensive analysis provides a way to describe the different complexity between the two organisms and discusses the critical limitations affecting this type of methodologies

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information

Gene duplication is common in all three domains of life, especially in eukaryotic genomes. The duplicates provide new material for the action of evolutionary forces such as selection or genetic drift. Here we describe a sophisticated procedure to extract duplicated genes (paralogs) from 26 available eukaryotic genomes, to pre-calculate several evolutionary indexes (evolutionary rate, synonymous distance/clock, transition redundant exchange clock, etc.) based on the paralog family, and to identify block or segmental duplications (paralogons). We also constructed an internet-accessible Eukaryotic Paralog Group Database (EPGD; http://epgd.biosino.org/EPGD/). The database is gene-centered and organized by paralog family. It focuses on paralogs and evolutionary duplication events. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website as plain text files. The database will be very useful for both experimentalists and bioinformaticians interested in the study of duplication events or paralog families

Transcriptional Autoregulatory Loops Are Highly Conserved in Vertebrate Evolution

BACKGROUND: Feedback loops are the simplest building blocks of transcriptional regulatory networks and therefore their behavior in the course of evolution is of prime interest. METHODOLOGY: We address the question of enrichment of the number of autoregulatory feedback loops in higher organisms. First, based on predicted autoregulatory binding sites we count the number of autoregulatory loops. We compare it to estimates obtained either by assuming that each (conserved) gene has the same chance to be a target of a given factor or by assuming that each conserved sequence position has an equal chance to be a binding site of the factor. CONCLUSIONS: We demonstrate that the numbers of putative autoregulatory loops conserved between human and fugu, danio or chicken are significantly higher than expected. Moreover we show, that conserved autoregulatory binding sites cluster close to the factors' starts of transcription. We conclude, that transcriptional autoregulatory feedback loops constitute a core transcriptional network motif and their conservation has been maintained in higher vertebrate organism evolution

Ribosomal oxygenases are structurally conserved from prokaryotes to humans

2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components1,2 and in the hydroxylation of transcription factors3 and splicing factor proteins4. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA5,6,7 and ribosomal proteins8 have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy9,10,11,12. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans8 raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone Nε-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. This coordination flexibility has probably contributed to the evolution of the wide range of reactions catalysed by oxygenases