3-D Simulations of Protostellar Jets in Stratified Ambient Media

We present fully three-dimensional hydrodynamical simulations of radiative cooling jets propagating into stratified isothermal ambient media with power-law density and pressure distributions. The parameters used are mainly suitable for protostellar jets but results applicable to extragalactic jets are also presented. Comparisons are made with previous simulations of jets through homogeneous media. We find that for radiative cooling jets propagating into regions where the ambient medium has an increasing density (and pressure) gradient, the ambient gas tends to compress the cold, low-pressure cocoon of shocked material that surrounds the beam and destroy the bow shock-like structure at the head. The compressing medium collimates the jet and promotes the development of Kelvin-Helmholtz instabilities which cause beam focusing, wiggling and the formation of internal traveling shocks, $close$ $to$ $the$ $head$, via pinching along the beam. This remarkably resembles the structure of some observed systems (e.g. Haro 6-5B northern and HH 24G jets). These effects are larger for jets with smaller density ratio between jet and environment $\eta$ (tested for $\eta$=1, 3, and 10) and larger Mach number $M_a=v_j/c_a$ (tested for $M_a=$12 and 24, where $v_j$ is the jet velocity and $c_a$ the ambient sound speed). In an ambient medium of decreasing density (and pressure), the beam is poorly collimated and relaxes, becoming faint. This could explain ''invisible'' jet sections, like the gap between the parent source and collimated beam (e.g., in HH30 jet). Although, on average, jets propagating into an increasing (decreasing) density environment are decelerated (accelerated) by the increasing (decreasing) ram pressure of the ambient medium, we find that their propagation velocities have an oscillating pattern.Comment: 33 pp, LaTeX file, 13 figures upon request. To appear in the Astrophys. J., vol 471, nov. 10t

Correlation between nucleotide composition and folding energy of coding sequences with special attention to wobble bases

Background: The secondary structure and complexity of mRNA influences its accessibility to regulatory molecules (proteins, micro-RNAs), its stability and its level of expression. The mobile elements of the RNA sequence, the wobble bases, are expected to regulate the formation of structures encompassing coding sequences. Results: The sequence/folding energy (FE) relationship was studied by statistical, bioinformatic methods in 90 CDS containing 26,370 codons. I found that the FE (dG) associated with coding sequences is significant and negative (407 kcal/1000 bases, mean +/- S.E.M.) indicating that these sequences are able to form structures. However, the FE has only a small free component, less than 10% of the total. The contribution of the 1st and 3rd codon bases to the FE is larger than the contribution of the 2nd (central) bases. It is possible to achieve a ~ 4-fold change in FE by altering the wobble bases in synonymous codons. The sequence/FE relationship can be described with a simple algorithm, and the total FE can be predicted solely from the sequence composition of the nucleic acid. The contributions of different synonymous codons to the FE are additive and one codon cannot replace another. The accumulated contributions of synonymous codons of an amino acid to the total folding energy of an mRNA is strongly correlated to the relative amount of that amino acid in the translated protein. Conclusion: Synonymous codons are not interchangable with regard to their role in determining the mRNA FE and the relative amounts of amino acids in the translated protein, even if they are indistinguishable in respect of amino acid coding.Comment: 14 pages including 6 figures and 1 tabl

Mathematics of complexity in experimental high energy physics

Mathematical ideas and approaches common in complexity-related fields have been fruitfully applied in experimental high energy physics also. We briefly review some of the cross-pollination that is occurring.Comment: 7 pages, 3 figs, latex; Second International Conference on Frontier Science: A Nonlinear World: The Real World, Pavia, Italy, 8-12 September 200

Thermalization algorithms for classical gauge theories

I propose a method, based on a set of Langevin equations, for bringing classical gauge theories to thermal equilibrium while respecting the set of Gauss' constraints exactly. The algorithm is described in detail for the SU(2) gauge theory with or without the Higgs doublet. As an example of application, canonical average of the maximal Lyapunov exponent is computed for the SU(2) Yang-Mills theory.Comment: 20 pages, plain LaTeX, figures part of the LaTeX sourc

Lack of experience-based stratification in homing pigeon leadership hierarchies

In societies that make collective decisions through leadership, a fundamental question concerns the individual attributes that allow certain group members to assume leadership roles over others. Homing pigeons form transitive leadership hierarchies during flock flights, where flock members are ranked according to the average time differences with which they lead or follow others' movement. Here, we test systematically whether leadership ranks in navigational hierarchies are correlated with prior experience of a homing task. We constructed experimental flocks of pigeons with mixed navigational experience: half of the birds within each flock had been familiarized with a specific release site through multiple previous releases, while the other half had never been released from the same site. We measured the birds' hierarchical leadership ranks, then switched the same birds' roles at a second site to test whether the relative hierarchical positions of the birds in the two subsets would reverse in response to the reversal in levels of experience. We found that while across all releases the top hierarchical positions were occupied by experienced birds significantly more often than by inexperienced ones, the remaining experienced birds were not consistently clustered in the top half—in other words, the network did not become stratified. We discuss our results in light of the adaptive value of structuring leadership hierarchies according to ‘merit’ (here, navigational experience)

String Percolation and the Glasma

We compare string percolation phenomenology to Glasma results on particle rapidity densities, effective string or flux tube intrinsic correlations, the ridge phenomena and long range forward-backward correlations. Effective strings may be a tool to extend the Glasma to the low density QCD regime. A good example is given by the minimum of the negative binomial distribution parameter k expected to occur at low energy/centrality.Comment: Submitted to Phys. Lett

Percolation of color sources and critical temperature

We argue that clustering of color sources, leading to the percolation transition, may be the way to achieve deconfinement in heavy ion collisions. The critical density for percolation is related to the effective critical temperature of the thermal bath asociated to the presence of strong color fields inside the percolating cluster. We find that the temperature is rapidity, centrality and energy dependent. We emphasize the similarities of percolation of strings with color glass condensate.Comment: LaTeX, 9 page

Schwinger Model and String Percolation in Hadron-Hadron and Heavy Ion Collisions

In the framework of the Schwinger Model for percolating strings we establish a general relation between multiplicity and transverse momentum square distributions in hadron-hadron and heavy ion collisions. Some of our results agree with the Colour Glass Condensate model.Comment: 7 pages, 1 figur

Density saturation and the decrease of the normalised width of the multiplicity distribution in high energy pp collisions

It is experimentally observed that the width of the KNO multiplicity distribution --or the negative binomial parameter 1/k-- for pp collisions, in the energy region 10 to 1800 GeV, is an increasing function of the energy. We argue that in models with parton or string saturation such trend will necessary change: at some energy the distribution will start to become narrower. In the framework of percolating strings, we have estimated the change to occur at an energy of the order of 5--10 TeV.Comment: 10 pages, 4 figures, uses elsart and amsmath; comparison with some other models was added; version accepted by PL

Limiting temperature from a parton gas with power-law tailed distribution

We combine Tsallis distributed massless partons to an effective thermal prehadron spectrum by folding. A limiting temperature and a mass spectrum combined of three exponentials emerge from this procedure. Meson and baryon resonance spectra have different polynomial prefactors.Comment: 4 pages, 2 figures, revtex4 style, v2 more reference