A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins

Bacteriocins are peptide-derived molecules produced by bacteria, whose recently-discovered functions include virulence factors and signalling molecules as well as their better known roles as antibiotics. To date, close to five hundred bacteriocins have been identified and classified. Recent discoveries have shown that bacteriocins are highly diverse and widely distributed among bacterial species. Given the heterogeneity of bacteriocin compounds, many tools struggle with identifying novel bacteriocins due to their vast sequence and structural diversity. Many bacteriocins undergo post-translational processing or modifications necessary for the biosynthesis of the final mature form. Enzymatic modification of bacteriocins as well as their export is achieved by proteins whose genes are often located in a discrete gene cluster proximal to the bacteriocin precursor gene, referred to as \textit{context genes} in this study. Although bacteriocins themselves are structurally diverse, context genes have been shown to be largely conserved across unrelated species. Using this knowledge, we set out to identify new candidates for context genes which may clarify how bacteriocins are synthesized, and identify new candidates for bacteriocins that bear no sequence similarity to known toxins. To achieve these goals, we have developed a software tool, Bacteriocin Operon and gene block Associator (BOA) that can identify homologous bacteriocin associated gene clusters and predict novel ones. We discover that several phyla have a strong preference for bactericon genes, suggesting distinct functions for this group of molecules. Availability: https://github.com/idoerg/BOAComment: Accepted for publication in BMC Bioinformatic

Three-dimensional massive gravity and the bigravity black hole

We study three-dimensional massive gravity formulated as a theory with two dynamical metrics, like the f-g theories of Isham-Salam and Strathdee. The action is parity preserving and has no higher derivative terms. The spectrum contains a single massive graviton. This theory has several features discussed recently in TMG and NMG. We find warped black holes, a critical point, and generalized Brown-Henneaux boundary conditions.Comment: 8 pages, Revtex. Minor change. References adde

Interacting electrons on trilayer honeycomb lattices

Few-layer graphene systems come in various stacking orders. Considering tight-binding models for electrons on stacked honeycomb layers, this gives rise to a variety of low-energy band structures near the charge neutrality point. Depending on the stacking order these band structures enhance or reduce the role of electron-electron interactions. Here, we investigate the instabilities of interacting electrons on honeycomb multilayers with a focus on trilayers with ABA and ABC stackings theoretically by means of the functional renormalization group. We find different types of competing instabilities and identify the leading ordering tendencies in the different regions of the phase diagram for a range of local and non-local short-ranged interactions. The dominant instabilities turn out to be toward an antiferromagnetic spin-density wave (SDW), a charge density wave and toward quantum spin Hall (QSH) order. Ab-initio values for the interaction parameters put the systems at the border between SDW and QSH regimes. Furthermore, we discuss the energy scales for the interaction-induced gaps of this model study and put them into context with the scales for single-layer and Bernal-stacked bilayer honeycomb lattices. This yields a comprehensive picture of the possible interaction-induced ground states of few-layer graphene.Comment: 12 pages, 12 figure

Quantum Antiferromagnetism in Quasicrystals

The antiferromagnetic Heisenberg model is studied on a two-dimensional bipartite quasiperiodic lattice. The distribution of local staggered magnetic moments is determined on finite square approximants with up to 1393 sites, using the Stochastic Series Expansion Quantum Monte Carlo method. A non-trivial inhomogeneous ground state is found. For a given local coordination number, the values of the magnetic moments are spread out, reflecting the fact that no two sites in a quasicrystal are identical. A hierarchical structure in the values of the moments is observed which arises from the self-similarity of the quasiperiodic lattice. Furthermore, the computed spin structure factor shows antiferromagnetic modulations that can be measured in neutron scattering and nuclear magnetic resonance experiments. This generic model is a first step towards understanding magnetic quasicrystals such as the recently discovered Zn-Mg-Ho icosahedral structure.Comment: RevTex, 4 pages with 5 figure

On leading order gravitational backreactions in de Sitter spacetime

Backreactions are considered in a de Sitter spacetime whose cosmological constant is generated by the potential of scalar field. The leading order gravitational effect of nonlinear matter fluctuations is analyzed and it is found that the initial value problem for the perturbed Einstein equations possesses linearization instabilities. We show that these linearization instabilities can be avoided by assuming strict de Sitter invariance of the quantum states of the linearized fluctuations. We furthermore show that quantum anomalies do not block the invariance requirement. This invariance constraint applies to the entire spectrum of states, from the vacuum to the excited states (should they exist), and is in that sense much stronger than the usual Poincare invariance requirement of the Minkowski vacuum alone. Thus to leading order in their effect on the gravitational field, the quantum states of the matter and metric fluctuations must be de Sitter invariant.Comment: 12 pages, no figures, typos corrected and some clarifying comments added, version accepted by Phys. Rev.

Partitioning of a polymer chain between a confining cavity and a gel

A lattice field theory approach to the statistical mechanics of charged polymers in electrolyte solutions [S. Tsonchev, R. D. Coalson, and A. Duncan, Phys. Rev. E 60, 4257, (1999)] is applied to the study of a polymer chain contained in a spherical cavity but able to diffuse into a surrounding gel. The distribution of the polymer chain between the cavity and the gel is described by its partition coefficient, which is computed as a function of the number of monomers in the chain, the monomer charge, and the ion concentrations in the solution.Comment: 17 pages, 6 figure

An Algorithmic Test for Diagonalizability of Finite-Dimensional PT-Invariant Systems

A non-Hermitean operator does not necessarily have a complete set of eigenstates, contrary to a Hermitean one. An algorithm is presented which allows one to decide whether the eigenstates of a given PT-invariant operator on a finite-dimensional space are complete or not. In other words, the algorithm checks whether a given PT-symmetric matrix is diagonalizable. The procedure neither requires to calculate any single eigenvalue nor any numerical approximation.Comment: 13 pages, 1 figur

Template assisted surface micro microstructuring of flowable dental composites and its effect on the microbial adhesion properties

Despite their various advantages, such as good esthetic properties, absence of mercury and adhesive bonding to teeth, modern dental composites still have some drawbacks, e.g., a relatively high rate of secondary caries on teeth filled with composite materials. Recent research suggests that microstructured biomaterials surfaces may reduce microbial adhesion to materials due to unfavorable physical material–microbe interactions. The objectives of this study were, therefore, to test the hypotheses that (i) different surface microstructures can be created on composites by a novel straightforward approach potentially suitable for clinical application and (ii) that these surface structures have a statistically significant effect on microbial adhesion properties.Peer ReviewedPostprint (author's final draft

Van der Waals interaction and spontaneous decay of an excited atom in a superlens-type geometry

Within the framework of macroscopic quantum electrodynamics, the resonant van der Waals potential experienced by an excited two-level atom near a planar magneto-electric two-layer system consisting of a slab of left-handed material and a perfect mirror is studied. It is shown that disregarding of material absorption leads to unphysical results, with divergent values for the potential away from the surface. Under appropriate conditions, the setup is found to feature a barrier near the surface which can be employed to levitate particles or used as a trapping or cooling mechanism. Finally, the problem of spontaneous decay [J. K\"{a}stel and M. Fleischhauer, Phys. Rev. A \textbf{68}, 011804(R) (2005)] is revisited. Disregarding of absorption is shown to drastically falsify the dependence on the atomic position of the decay rate.Comment: 10 Pages, 6 figure

Decoherence of encoded quantum registers

In order to eliminate disturbing effects of decoherence, encoding of quantum information in decoherence-free subspaces has been suggested. We analyze the benefits of this concept for a quantum register that is realized in a spin chain in contact with a common bosonic bath. Within a dissipation-less model we provide explicit analytical results for the average fidelity of plain and encoded quantum registers. For the investigation of dissipative spin-boson couplings we employ a master equation of Bloch-Redfield type.Comment: 13 pages, 9 figure