Weak localization effect on thermomagnetic phenomena

The quantum transport equation (QTE) is extended to study weak localization (WL) effects on galvanomagnetic and thermomagnetic phenomena. QTE has many advantages over the linear response method (LRM): (i) particle-hole asymmetry which is necessary for the Hall effect is taken into account by the nonequilibrium distribution function, while LRM requires expansion near the Fermi surface, (ii) when calculating response to the temperature gradient, the problem of WL correction to the heat current operator is avoided, (iii) magnetic field is directly introduced to QTE, while the LRM deals with the vector potential and and special attention should be paid to maintain gauge invariance, e.g. when calculating the Nernst effect the heat current operator should be modified to include the external magnetic field. We reproduce in a very compact form known results for the conductivity, the Hall and the thermoelectric effects and then we study our main problem, WL correction to the Nernst coefficient (transverse thermopower).Comment: 20 pages 2 figure

Computational and Experimental Characterization of RNA Cubic Nanoscaffolds

The fast-developing field of RNA nanotechnology requires the adoption and development of novel and faster computational approaches to modeling and characterization of RNA-based nano-objects. We report the first application of Elastic Network Modeling (ENM), a structure-based dynamics model, to RNA nanotechnology. With the use of an Anisotropic Network Model (ANM), a type of ENM, we characterize the dynamic behavior of non-compact, multi-stranded RNA-based nanocubes that can be used as nano-scale scaffolds carrying different functionalities. Modeling the nanocubes with our tool NanoTiler and exploring the dynamic characteristics of the models with ANM suggested relatively minor but important structural modifications that enhanced the assembly properties and thermodynamic stabilities. In silico and in vitro, we compared nanocubes having different numbers of base pairs per side, showing with both methods that the 10 bp-long helix design leads to more efficient assembly, as predicted computationally. We also explored the impact of different numbers of single-stranded nucleotide stretches at each of the cube corners and showed that cube flexibility simulations help explain the differences in the experimental assembly yields, as well as the measured nanomolecule sizes and melting temperatures. This original work paves the way for detailed computational analysis of the dynamic behavior of artificially designed multi-stranded RNA nanoparticles

Linear square-mass trajectories of radially and orbitally excited hadrons in holographic QCD

We consider a new approach towards constructing approximate holographic duals of QCD from experimental hadron properties. This framework allows us to derive a gravity dual which reproduces the empirically found linear square-mass trajectories of universal slope for radially and orbitally excited hadrons. Conformal symmetry breaking in the bulk is exclusively due to infrared deformations of the anti-de Sitter metric and governed by one free mass scale proportional to Lambda_QCD. The resulting background geometry exhibits dual signatures of confinement and provides the first examples of holographically generated linear trajectories in the baryon sector. The predictions for the light hadron spectrum include new relations between trajectory slopes and ground state masses and are in good overall agreement with experiment.Comment: 33 pages, 5 figures, updated to the extended version published in JHEP, vector meson bulk potential and metric corrected, comments and references added, phenomenology and conclusions unchange

Closure properties and complexity of rational sets of regular languages

This work received funding in part by the National Research Network RiSE on Rigorous Systems Engineering (Austrian Science Fund (FWF): S11403-N23), by the Vienna Science and Technology Fund (WWTF) through grant PROSEED, by an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), and by the European Research Council under the European Community's Seventh Framework Programme (FP7/2007–2013)/ERC grant agreement DIADEM no. 246858

Defining the Rhizobium leguminosarum Species Complex

Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains

Defining the Rhizobium leguminosarum Species Complex

Bacteria currently included in Rhizobium leguminosarum are too diverse to be considered a single species, so we can refer to this as a species complex (the Rlc). We have found 429 publicly available genome sequences that fall within the Rlc and these show that the Rlc is a distinct entity, well separated from other species in the genus. Its sister taxon is R. anhuiense. We constructed a phylogeny based on concatenated sequences of 120 universal (core) genes, and calculated pairwise average nucleotide identity (ANI) between all genomes. From these analyses, we concluded that the Rlc includes 18 distinct genospecies, plus 7 unique strains that are not placed in these genospecies. Each genospecies is separated by a distinct gap in ANI values, usually at approximately 96% ANI, implying that it is a ‘natural’ unit. Five of the genospecies include the type strains of named species: R. laguerreae, R. sophorae, R. ruizarguesonis, “R. indicum” and R. leguminosarum itself. The 16S ribosomal RNA sequence is remarkably diverse within the Rlc, but does not distinguish the genospecies. Partial sequences of housekeeping genes, which have frequently been used to characterize isolate collections, can mostly be assigned unambiguously to a genospecies, but alleles within a genospecies do not always form a clade, so single genes are not a reliable guide to the true phylogeny of the strains. We conclude that access to a large number of genome sequences is a powerful tool for characterizing the diversity of bacteria, and that taxonomic conclusions should be based on all available genome sequences, not just those of type strains

Glueballs, Hybrids, Multiquarks. Experimental facts versus QCD inspired concepts

The spectroscopy of light and heavy mesons is reviewed with emphasis on glueballs, hybrids, and tetraquarks.Comment: 266 pages, 117 figures, 39 tables. to be published in Physics Report

Computational and Experimental Characterization of RNA Cubic Nanoscaffolds

The fast-developing field of RNA nanotechnology requires the adoption and development of novel and faster computational approaches to modeling and characterization of RNA-based nano-objects. We report the first application of Elastic Network Modeling (ENM), a structure-based dynamics model, to RNA nanotechnology. With the use of an Anisotropic Network Model (ANM), a type of ENM, we characterize the dynamic behavior of non-compact, multi-stranded RNA-based nanocubes that can be used as nano-scale scaffolds carrying different functionalities. Modeling the nanocubes with our tool NanoTiler and exploring the dynamic characteristics of the models with ANM suggested relatively minor but important structural modifications that enhanced the assembly properties and thermodynamic stabilities. In silico and in vitro, we compared nanocubes having different numbers of base pairs per side, showing with both methods that the 10 bp-long helix design leads to more efficient assembly, as predicted computationally. We also explored the impact of different numbers of single-stranded nucleotide stretches at each of the cube corners and showed that cube flexibility simulations help explain the differences in the experimental assembly yields, as well as the measured nanomolecule sizes and melting temperatures. This original work paves the way for detailed computational analysis of the dynamic behavior of artificially designed multi-stranded RNA nanoparticles.This is a manuscript of an article published as Afonin, Kirill A., Wojciech Kasprzak, Eckart Bindewald, Praneet S. Puppala, Alex R. Diehl, Kenneth T. Hall, Tae Jin Kim et al. "Computational and experimental characterization of RNA cubic nanoscaffolds." Methods 67, no. 2 (2014): 256-265. 10.1016/j.ymeth.2013.10.013. Posted with permission.</p