Structure of a rare non-standard sequence k-turn bound by L7Ae protein

Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D and H/ACA small nucleolar RNAs and U4 small nuclear RNA. We have solved the crystal structure of T. solenopsae Kt-23 RNA bound to Archeoglobus fulgidus L7Ae protein at a resolution of 2.95 Å. The protein binds in the major groove displayed on the outer face of the k-turn, in a manner similar to complexes with standard k-turn structures. The k-turn adopts a standard N3 class conformation, with a single hydrogen bond from A2b N6 to A2n N3. This contrasts with the structure of the same sequence located in the SAM-I riboswitch, where it adopts an N1 structure, showing the inherent plasticity of k-turn structure. This potentially can affect any tertiary interactions in which the RNA participates

Higgs-Yukawa model on the lattice

We present results from two projects on lattice calculations for the Higgs-Yukawa model. First we report progress on the search of first-order thermal phase transitions in the presence of a dimension-six operator, with the choices of bare couplings that lead to viable phenomenological predictions. In this project the simulations are performed using overlap fermions to implement the required chiral symmetry. Secondly, our study for applying finite-size scaling techniques near the Gaussian fixed point of the Higgs-Yukawa model is presented. We discuss the analytical formulae for the Higgs Yukawa model and show results for a first numerical study in the pure $O(4)$ scalar sector of the theory.Comment: 8 pages, 4 figures; Contribution to the proceedings of the 35th International Symposium on Lattice Field Theory, 18 - 24 June 2017, Granada, Spai

A Two-Dimensional Carbon Semiconductor

We show that patterned defects can be used to disrupt the sub-lattice symmetry of graphene so as to open up a band gap. This way of modifying graphene's electronic structure does not rely on external agencies, the addition of new elements or special boundaries. The method is used to predict a planar, low energy, graphene allotrope with a band gap of 1.2 eV. This defect engineering also allows semiconducting ribbons of carbon to be fabricated within graphene. Linear arrangements of defects lead to naturally embedded ribbons of the semiconducting material in graphene, offering the prospect of two-dimensional circuit logic composed entirely of carbon.Comment: 4 pages, 5 figure

A lattice study of a chirally invariant Higgs-Yukawa model including a higher dimensional Φ6\Phi^6-term

We discuss the non-thermal phase structure of a chirally invariant Higgs-Yukawa model on the lattice in the presence of a higher dimensional $\Phi^6$-term. For the exploration of the phase diagram we use analytical, lattice perturbative calculations of the constraint effectice potential as well as numerical simulations. We also present first results of the effects of the $\Phi^6$-term on the lower Higgs boson mass bounds

The Yang-Mills gradient flow and SU(3) gauge theory with 12 massless fundamental fermions in a colour-twisted box

We perform the step-scaling investigation of the running coupling constant, using the gradient-flow scheme, in SU(3) gauge theory with twelve massless fermions in the fundamental representation. The Wilson plaquette gauge action and massless unimproved staggered fermions are used in the simulations. Our lattice data are prepared at high accuracy, such that the statistical error for the renormalised coupling, g_GF, is at the subpercentage level. To investigate the reliability of the continuum extrapolation, we employ two different lattice discretisations to obtain g_GF. For our simulation setting, the corresponding gauge-field averaging radius in the gradient flow has to be almost half of the lattice size, in order to have this extrapolation under control. We can determine the renormalisation group evolution of the coupling up to g^2_GF ~ 6, before the onset of the bulk phase structure. In this infrared regime, the running of the coupling is significantly slower than the two-loop perturbative prediction, although we cannot draw definite conclusion regarding possible infrared conformality of this theory. Furthermore, we comment on the issue regarding the continuum extrapolation near an infrared fixed point. In addition to adopting the fit ansatz a'la Symanzik for performing this task, we discuss a possible alternative procedure inspired by properties derived from low-energy scale invariance at strong coupling. Based on this procedure, we propose a finite-size scaling method for the renormalised coupling as a means to search for infrared fixed point. Using this method, it can be shown that the behaviour of the theory around g^2_GF ~ 6 is still not governed by possible infrared conformality.Comment: 24 pages, 6 figures; Published version; Appendix A added for tabulating data; One reference included; Typos correcte

Differential expression of three galaxin-related genes during settlement and metamorphosis in the scleractinian coral Acropora millepora

BACKGROUND: The coral skeleton consists of CaCO3 deposited upon an organic matrix primarily as aragonite. Currently galaxin, from Galaxea fascicularis, is the only soluble protein component of the organic matrix that has been characterized from a coral. Three genes related to galaxin were identified in the coral Acropora millepora. RESULTS: One of the Acropora genes (Amgalaxin) encodes a clear galaxin ortholog, while the others (Amgalaxin-like 1 and Amgalaxin-like 2) encode larger and more divergent proteins. All three proteins are predicted to be extracellular and share common structural features, most notably the presence of repetitive motifs containing dicysteine residues. In situ hybridization reveals distinct, but partially overlapping, spatial expression of the genes in patterns consistent with distinct roles in calcification. Both of the Amgalaxin-like genes are expressed exclusively in the early stages of calcification, while Amgalaxin continues to be expressed in the adult, consistent with the situation in the coral Galaxea. CONCLUSION: Comparisons with molluscs suggest functional convergence in the two groups; lustrin A/pearlin proteins may be the mollusc counterparts of galaxin, whereas the galaxin-like proteins combine characteristics of two distinct proteins involved in mollusc calcification. Database searches indicate that, although sequences with high similarity to the galaxins are restricted to the Scleractinia, more divergent members of this protein family are present in other cnidarians and some other metazoans. We suggest that ancestral galaxins may have been secondarily recruited to roles in calcification in the Triassic, when the Scleractinia first appeared. Understanding the evolution of the broader galaxin family will require wider sampling and expression analysis in a range of cnidarians and other animals

Investigation of the 1+1 dimensional Thirring model using the method of matrix product states

We present preliminary results of a study on the non-thermal phase structure of the (1+1) dimensional massive Thirring model, employing the method of matrix product states. Through investigating the entanglement entropy, the fermion correlators and the chiral condensate, it is found that this approach enables us to observe numerical evidence of a Kosterlitz-Thouless phase transition in the model.Comment: 7 pages, 4 figures; contribution to the proceedings of Lattice 2018 conferenc

The k-junction motif in RNA structure

The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP riboswitch contains a related k-junction, and analysis of >11 000 sequences shows that the structure is common to these riboswitches. The k-junction exhibits all the key features of an N1-class k-turn, including the standard cross-strand hydrogen bonds. The third helix of the junction is coaxially aligned with the C (canonical) helix, while the k-turn loop forms the turn into the NC (non-canonical) helix. Analysis of ligand binding by ITC and global folding by gel electrophoresis demonstrates the importance of the k-turn nucleotides. Clearly the basic elements of k-turn structure are structurally well suited to generate a three-way helical junction, retaining all the key features and interactions of the k-turn