Bending instability in galactic discs. Advocacy of the linear theory

We demonstrate that in N-body simulations of isolated disc galaxies there is numerical vertical heating which slowly increases the vertical velocity dispersion and the disc thickness. Even for models with over a million particles in a disc, this heating can be significant. Such an effect is just the same as in numerical experiments by Sellwood (2013). We also show that in a stellar disc, outside a boxy/peanut bulge, if it presents, the saturation level of the bending instability is rather close to the value predicted by the linear theory. We pay attention to the fact that the bending instability develops and decays very fast, so it couldn't play any role in secular vertical heating. However the bending instability defines the minimal value of the ratio between the vertical and radial velocity dispersions $\sigma_z / \sigma_R \approx 0.3$ (so indirectly the minimal thickness) which could have stellar discs in real galaxies. We demonstrate that observations confirm last statement.Comment: 8 pages, 8 figures, accepted for publication in MNRA

Metallicity-dependendent kinematics and morphology of the Milky Way bulge

We use N-body chemo-dynamic simulations to study the coupling between morphology, kinematics and metallicity of the bar/bulge region of our Galaxy. We make qualitative comparisons of our results with available observations and find very good agreement. We conclude that this region is complex, since it comprises several stellar components with different properties -- i.e. a boxy/peanut bulge, thin and thick disc components, and, to lesser extents, a disky pseudobulge, a stellar halo and a small classical bulge -- all cohabiting in dynamical equilibrium. Our models show strong links between kinematics and metallicity, or morphology and metallicity, as already suggested by a number of recent observations. We discuss and explain these links.Comment: 5 pages, 4 figures, accepted for publication in MNRAS Letter

Forming disc galaxies in major mergers: III. The effect of angular momentum on the radial density profiles of disc galaxies

We study the effect of angular momentum on the surface density profiles of disc galaxies, using high resolution simulations of major mergers whose remnants have downbending radial density profiles (type II). As described in the previous papers of this series, in this scenario, most of the disc mass is acquired after the collision via accretion from a hot gaseous halo. We find that the inner and outer disc scalelengths, as well as the break radius, correlate with the total angular momentum of the initial merging system, and are larger for high angular momentum systems. We follow the angular momentum redistribution in our simulated galaxies, and find that, like the mass, the disc angular momentum is acquired via accretion, i.e. to the detriment of the gaseous halo. Furthermore, high angular momentum systems give more angular momentum to their discs, which affects directly their radial density profile. Adding simulations of isolated galaxies to our sample, we find that the correlations are valid also for disc galaxies evolved in isolation. We show that the outer part of the disc at the end of the simulation is populated mainly by inside-out stellar migration, and that in galaxies with higher angular momentum, stars travel radially further out. This, however, does not mean that outer disc stars (in type II discs) were mostly born in the inner disc. Indeed, generally the break radius increases over time, and not taking this into account leads to overestimating the number of stars born in the inner disc.Comment: 12 pages, 13 figures, accepted for publication in MNRA

Bar formation and evolution in disc galaxies with gas and a triaxial halo: Morphology, bar strength and halo properties

We follow the formation and evolution of bars in N-body simulations of disc galaxies with gas and/or a triaxial halo. We find that both the relative gas fraction and the halo shape play a major role in the formation and evolution of the bar. In gas-rich simulations, the disc stays near-axisymmetric much longer than in gas-poor ones, and, when the bar starts growing, it does so at a much slower rate. Due to these two effects combined, large-scale bars form much later in gas-rich than in gas-poor discs. This can explain the observation that bars are in place earlier in massive red disc galaxies than in blue spirals. We also find that the morphological characteristics in the bar region are strongly influenced by the gas fraction. In particular, the bar at the end of the simulation is much weaker in gas-rich cases. In no case did we witness bar destruction. Halo triaxiality has a dual influence on bar strength. In the very early stages of the simulation it induces bar formation to start earlier. On the other hand, during the later, secular evolution phase, triaxial haloes lead to considerably less increase of the bar strength than spherical ones. The shape of the halo evolves considerably with time. The inner halo parts may become more elongated, or more spherical, depending on the bar strength. The main body of initially triaxial haloes evolves towards sphericity, but in initially strongly triaxial cases it stops well short of becoming spherical. Part of the angular momentum absorbed by the halo generates considerable rotation of the halo particles that stay located relatively near the disc for long periods of time. Another part generates halo bulk rotation, which, contrary to that of the bar, increases with time but stays small.Comment: 21 pages, 16 figures, accepted for publication in MNRAS. A high resolution version is at http://195.221.212.246:4780/dynam/paper/amr12/rm_3axhalo_gas.pd

Forming disk galaxies in wet major mergers. I. Three fiducial examples

Using three fiducial Nbody+SPH simulations, we follow the merging of two disk galaxies with a hot gaseous halo component each, and examine whether the merger remnant can be a spiral galaxy. The stellar progenitor disks are destroyed by violent relaxation during the merging and most of their stars form a classical bulge, while the remaining form a thick disk and its bar. A new stellar disk forms subsequently and gradually in the remnant from the gas accreted mainly from the halo. It is vertically thin and well extended in its equatorial plane. A bar starts forming before the disk is fully in place, contrary to what is assumed in idealised simulations of isolated bar-forming galaxies. It has morphological features such as ansae and boxy/peanut bulges. Stars of different ages populate different parts of the box/peanut. A disky pseudobulge forms also, so that by the end of the simulation, all three types of bulges coexist. The oldest stars are found in the classical bulge, followed by those of the thick disk, then by those in the thin disk. The youngest stars are in the spiral arms and the disky pseudobulge. The disk surface density profiles are of type II (exponential with downbending), and the circular velocity curves are flat and show that the disks are submaximum in these examples: two clearly so and one near-borderline between maximum and submaximum. On average, only roughly between 10 and 20% of the stellar mass is in the classical bulge of the final models, i.e. much less than in previous simulations.Comment: 17 pages, 8 figures, accepted for publication in ApJ. V2: replaced Figure 4 with correct versio

RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach

RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept of a cluster of co-regulated orthologous operons allows the user to distribute the analysis of large regulons and to perform the comparative analysis of multiple clusters independently. Two major workflows currently implemented in RegPredict are: (i) regulon reconstruction for a known regulatory motif and (ii) ab initio inference of a novel regulon using several scenarios for the generation of starting gene sets. RegPredict provides a comprehensive collection of manually curated positional weight matrices of regulatory motifs. It is based on genomic sequences, ortholog and operon predictions from the MicrobesOnline. An interactive web interface of RegPredict integrates and presents diverse genomic and functional information about the candidate regulon members from several web resources. RegPredict is freely accessible at http://regpredict.lbl.gov

Towards a Maximal Mass Model

We investigate the possibility to construct a generalization of the Standard Model, which we call the Maximal Mass Model because it contains a limiting mass $M$ for its fundamental constituents. The parameter $M$ is considered as a new universal physical constant of Nature and therefore is called the fundamental mass. It is introduced in a purely geometrical way, like the velocity of light as a maximal velocity in the special relativity. If one chooses the Euclidean formulation of quantum field theory, the adequate realization of the limiting mass hypothesis is reduced to the choice of the de Sitter geometry as the geometry of the 4-momentum space. All fields, defined in de Sitter p-space in configurational space obey five dimensional Klein-Gordon type equation with fundamental mass $M$ as a mass parameter. The role of dynamical field variables is played by the Cauchy initial conditions given at $x_5 = 0$, guarantying the locality and gauge invariance principles. The corresponding to the geometrical requirements formulation of the theory of scalar, vector and spinor fields is considered in some detail. On a simple example it is demonstrated that the spontaneously symmetry breaking mechanism leads to renormalization of the fundamental mass $M$. A new geometrical concept of the chirality of the fermion fields is introduced. It would be responsible for new measurable effects at high energies $E \geq M$. Interaction terms of a new type, due to the existence of the Higgs boson are revealed. The most intriguing prediction of the new approach is the possible existence of exotic fermions with no analogues in the SM, which may be candidate for dark matter constituents.Comment: 28 page

Transcriptional regulation of carbohydrate utilization pathways in the Bifidobacterium genus

Bifidobacteria, which represent common commensals of mammalian gut, are believed to have positive effects on human health. The influence of certain non-digestible carbohydrates (and their use as so-called prebiotics) on growth and metabolic activity of bifidobacteria is of increasing interest; however, mechanisms of transcriptional control of carbohydrate metabolism are poorly understood in these species. We used a comparative genomics approach to reconstruct carbohydrate utilization pathways and transcriptional regulons in 10 Bifidobacterium genomes. Analysis of regulatory gene regions revealed candidate DNA motifs and reconstructed regulons for 268 transcription factors from the LacI, ROK, DeoR, AraC, GntR, and TetR families that form 64 orthologous groups of regulators. Most of the reconstructed regulons are local and control specific catabolic pathways for host- and diet-derived glycans and monosaccharides. Mosaic distributions of many of these local regulators across Bifidobacterium species correlate with distribution of corresponding catabolic pathways. In contrast, the maltose, galactose, sucrose, and fructose regulons, as well as a novel global LacI-family regulator that is predicted to control the central carbohydrate metabolism and arabinose catabolism genes, are universally present in all 10 studied bifidobacteria. A novel group of TetR-family regulators presumably controls the glucoside and galactoside utilization pathways. Paralogs of the ribose repressor RbsR control the pyrimidine nucleoside utilization genes. Multiple paralogs of the maltose regulator MalR co-regulate large sets of genes involved in maltodextrin utilization. The inferred metabolic regulons provide new insights on diverse carbohydrate utilization networks in bifidobacteria that can be employed in metabolic modeling, phenotype prediction and the rational development of novel prebiotics