Structural, electronic, vibrational and dielectric properties of LaBGeO5_5 from first principles

Structural, electronic, vibrational and dielectric properties of LaBGeO$_5$ with the stillwellite structure are determined based on \textit{ab initio} density functional theory. The theoretically relaxed structure is found to agree well with the existing experimental data with a deviation of less than $0.2\%$. Both the density of states and the electronic band structure are calculated, showing five distinct groups of valence bands. Furthermore, the Born effective charge, the dielectric permittivity tensors, and the vibrational frequencies at the center of the Brillouin zone are all obtained. Compared to existing model calculations, the vibrational frequencies are found in much better agreement with the published experimental infrared and Raman data, with absolute and relative rms values of 6.04 cm$^{-1}$, and $1.81\%$, respectively. Consequently, numerical values for both the parallel and perpendicular components of the permittivity tensor are established as 3.55 and 3.71 (10.34 and 12.28), respectively, for the high-(low-)frequency limit

Laser-driven quantum magnonics and THz dynamics of the order parameter in antiferromagnets

The impulsive generation of two-magnon modes in antiferromagnets by femtosecond optical pulses, so-called femto-nanomagnons, leads to coherent longitudinal oscillations of the antiferromagnetic order parameter that cannot be described by a thermodynamic Landau-Lifshitz approach. We argue that this dynamics is triggered as a result of a laser-induced modification of the exchange interaction. In order to describe the oscillations we have formulated a quantum mechanical description in terms of magnon pair operators and coherent states. Such an approach allowed us to} derive an effective macroscopic equation of motion for the temporal evolution of the antiferromagnetic order parameter. An implication of the latter is that the photo-induced spin dynamics represents a macroscopic entanglement of pairs of magnons with femtosecond period and nanometer wavelength. By performing magneto-optical pump-probe experiments with 10 femtosecond resolution in the cubic KNiF$_3$ and the uniaxial K$_2$NiF$_4$ collinear Heisenberg antiferromagnets, we observed coherent oscillations at the frequency of 22 THz and 16 THz, respectively. The detected frequencies as a function of the temperature ideally fit the two-magnon excitation up to the N\'eel point. The experimental signals are described as dynamics of magnetic linear dichroism due to longitudinal oscillations of the antiferromagnetic vector.Comment: 25 pages, 10 figure

Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes.

BackgroundGeneral translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate to control translation rates are not well understood.ResultsHere, we show that these sequence features specify 42-81% of the variance in translation rates in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Mus musculus, and Homo sapiens. We establish that control by RNA secondary structure is chiefly mediated by highly folded 25-60 nucleotide segments within mRNA 5' regions, that changes in tri-nucleotide frequencies between highly and poorly translated 5' regions are correlated between all species, and that control by distinct biochemical processes is extensively correlated as is regulation by a single process acting in different parts of the same mRNA.ConclusionsOur work shows that general features control a much larger fraction of the variance in translation rates than previously realized. We provide a more detailed and accurate understanding of the aspects of RNA structure that directs translation in diverse eukaryotes. In addition, we note that the strongly correlated regulation between and within cis-control features will cause more even densities of translational complexes along each mRNA and therefore more efficient use of the translation machinery by the cell

On the choice of heavy baryon currents in the relativistic three-quark model

We test the sensitivity of bottom baryon observables with regard to the choice of the interpolating three-quark currents within the relativistic three-quark model. We have found that the semileptonic decay rates are clearly affected by the choice of currents, whereas the asymmetry parameters show only a very weak dependence on the choice of current.Comment: revtex, 9 page

Impulsive Fermi magnon-phonon resonance in antiferromagnetic CoF2CoF_{2}

Understanding spin-lattice interactions in antiferromagnets is one of the most fundamental issues at the core of the recently emerging and booming fields of antiferromagnetic spintronics and magnonics. Recently, coherent nonlinear spin-lattice coupling was discovered in an antiferromagnet which opened the possibility to control the nonlinear coupling strength and thus showing a novel pathway to coherently control magnon-phonon dynamics. Here, utilizing intense narrow band terahertz (THz) pulses and tunable magnetic fields up to 7 T, we experimentally realize the conditions of the Fermi magnon-phonon resonance in antiferromagnetic $CoF_{2}$. These conditions imply that both the spin and the lattice anharmonicities harvest energy transfer between the subsystems, if the magnon eigenfrequency $f_{m}$ is twice lower than the frequency of the phonon $2f_{m}=f_{ph}$. Performing THz pump-infrared probe spectroscopy in conjunction with simulations, we explore the coupled magnon-phonon dynamics in the vicinity of the Fermi-resonance and reveal the corresponding fingerprints of an impulsive THz-induced response. This study focuses on the role of nonlinearity in spin-lattice interactions, providing insights into the control of coherent magnon-phonon energy exchange

Spin-induced optical second harmonic generation in the centrosymmetric magnetic semiconductors EuTe and EuSe

Spectroscopy of the centrosymmetric magnetic semiconductors EuTe and EuSe reveals spin-induced optical second harmonic generation (SHG) in the band gap vicinity at 2.1-2.4eV. The magnetic field and temperature dependence demonstrates that the SHG arises from the bulk of the materials due to a novel type of nonlinear optical susceptibility caused by the magnetic dipole contribution combined with spontaneous or induced magnetization. This spin-induced susceptibility opens access to a wide class of centrosymmetric systems by harmonics generation spectroscopy.Comment: 5 pages, 3 figures, submitted to PR

A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA

Genomic RNA of primate lentiviruses serves both as an mRNA that encodes Gag and Gag-Pol polyproteins and as a propagated genome. Translation of this RNA is initiated by standard cap dependant mechanism or by internal entry of the ribosome. Two regions of the genomic RNA are able to attract initiation complexes, the 5′ untranslated region and the gag coding region itself. Relying on probing data and a phylogenetic study, we have modelled the secondary structure of HIV-1, HIV-2 and SIVMac coding region. This approach brings to light conserved secondary-structure elements that were shown by mutations to be required for internal entry of the ribosome. No structural homologies with other described viral or cellular IRES can be identified and lentiviral IRESes show many peculiar properties. Most notably, the IRES present in HIV-2 gag coding region is endowed with the unique ability to recruit up to three initiation complexes on a single RNA molecule. The structural and functional properties of gag coding sequence define a new type of IRES. Although its precise role is unknown, the conservation of the IRES among fast evolving lentiviruses suggests an important physiological role

Determinants of Initiation Codon Selection during Translation in Mammalian Cells

Factors affecting translation of mRNA contribute to the complexity of eukaryotic proteomes. In some cases, translation of a particular mRNA can generate multiple proteins. However, the factors that determine whether ribosomes initiate translation from the first AUG codon in the transcript, from a downstream codon, or from multiple sites are not completely understood. Various mRNA properties, including AUG codon-accessibility and 5′ leader length have been proposed as potential determinants that affect where ribosomes initiate translation. To explore this issue, we performed studies using synthetic mRNAs with two in-frame AUG codons−both in excellent context. Open reading frames initiating at AUG1 and AUG2 encode large and small isoforms of a reporter protein, respectively. Translation of such an mRNA in COS-7 cells was shown to be 5′ cap-dependent and to occur efficiently from both AUG codons. AUG codon-accessibility was modified by using two different elements: an antisense locked nucleic acid oligonucleotide and an exon-junction complex. When either element was used to mask AUG1, the ratio of the proteins synthesized changed, favoring the smaller (AUG2-initiated) protein. In addition, we observed that increased leader length by itself changed the ratio of the proteins and favored initiation at AUG1. These observations demonstrate that initiation codon selection is affected by various factors, including AUG codon-accessibility and 5′ leader length, and is not necessarily determined by the order of AUG codons (5′→3′). The modulation of AUG codon accessibility may provide a powerful means of translation regulation in eukaryotic cells

Gene expression changes and community turnover differentially shape the global ocean metatranscriptome

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms