Heavy ion event generator HYDJET++ (HYDrodynamics plus JETs)

HYDJET++ is a Monte-Carlo event generator for simulation of relativistic heavy ion AA collisions considered as a superposition of the soft, hydro-type state and the hard state resulting from multi-parton fragmentation. This model is the development and continuation of HYDJET event generator (Lokhtin & Snigirev, 2006, EPJC, 45, 211). The main program is written in the object-oriented C++ language under the ROOT environment. The hard part of HYDJET++ is identical to the hard part of Fortran-written HYDJET and it is included in the generator structure as a separate directory. The soft part of HYDJET++ event is the "thermal" hadronic state generated on the chemical and thermal freeze-out hypersurfaces obtained from the parameterization of relativistic hydrodynamics with preset freeze-out conditions. It includes the longitudinal, radial and elliptic flow effects and the decays of hadronic resonances. The corresponding fast Monte-Carlo simulation procedure, C++ code FAST MC (Amelin et al., 2006, PRC, 74, 064901; 2008, PRC, 77, 014903) is adapted to HYDJET++. It is designed for studying the multi-particle production in a wide energy range of heavy ion experimental facilities: from FAIR and NICA to RHIC and LHC.Comment: 44 pages including 6 figures as EPS-files; prepared using LaTeX package for publication in Computer Physics Communication

Explanation of the RHIC HBT Puzzle by a Granular Source of Quark-Gluon Plasma Droplets

We present a review on the explanation of the RHIC HBT puzzle by a granular pion-emitting source of quark-gluon plasma droplets. The evolution of the droplet is described by relativistic hydrodynamics with an equation of state suggested by lattice gauge results. The granular source evolution is obtained by superposing all of the evolutions of individual droplets. Pions are assumed to be emitted thermally from the droplets at the freeze-out configuration characterized by a freeze-out temperature $T_f$. We find that the average particle emission time scales with the initial radius of the droplet. Pions will be emitted earlier if the droplet radius is smaller. An earlier emission time will lead to a smaller extracted HBT radius $R_{\rm out}$, while the extracted HBT radius $R_{\rm side}$ is determined by the scale of the distribution of the droplet centers. However, a collective expansion of the droplets can further decrease $R_{\rm out}$. As a result, the value of $R_{\rm out}/R_{\rm side}$ can be close to, or even less than 1 for theComment: 8 pages, 4 figures, invited talk presented at the XI International Workshop on Correlation and Fluctuation in Multiparticle Production, Nov. 21-24, 2006, Hangzhou, Chin

DRAGON: Monte Carlo generator of particle production from a fragmented fireball in ultrarelativistic nuclear collisions

A Monte Carlo generator of the final state of hadrons emitted from an ultrarelativistic nuclear collision is introduced. An important feature of the generator is a possible fragmentation of the fireball and emission of the hadrons from fragments. Phase space distribution of the fragments is based on the blast wave model extended to azimuthally non-symmetric fireballs. Parameters of the model can be tuned and this allows to generate final states from various kinds of fireballs. A facultative output in the OSCAR1999A format allows for a comprehensive analysis of phase-space distributions and/or use as an input for an afterburner.Comment: name of the model changed from QuaG to DRAGON in the new version, otherwise only cosmetic changes, uses elsart.cls, the software package described here can be downloaded from http://www.fpv.umb.sk/~tomasik/soft.htm

The prominent role of the heaviest fragment in multifragmentation and phase transition for hot nuclei

The role played by the heaviest fragment in partitions of multifragmenting hot nuclei is emphasized. Its size/charge distribution (mean value, fluctuations and shape) gives information on properties of fragmenting nuclei and on the associated phase transition.Comment: 11 pages, Proceedings of IWND09, August 23-25, Shanghai (China

Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum

BACKGROUND: Stagonospora nodorum, a fungal ascomycete in the class dothideomycetes, is a damaging pathogen of wheat. It is a model for necrotrophic fungi that cause necrotic symptoms via the interaction of multiple effector proteins with cultivar-specific receptors. A draft genome sequence and annotation was published in 2007. A second-pass gene prediction using a training set of 795 fully EST-supported genes predicted a total of 10762 version 2 nuclear-encoded genes, with an additional 5354 less reliable version 1 genes also retained. RESULTS: In this study, we subjected soluble mycelial proteins to proteolysis followed by 2D LC MALDI-MS/MS. Comparison of the detected peptides with the gene models validated 2134 genes. 62% of these genes (1324) were not supported by prior EST evidence. Of the 2134 validated genes, all but 188 were version 2 annotations. Statistical analysis of the validated gene models revealed a preponderance of cytoplasmic and nuclear localised proteins, and proteins with intracellularassociated GO terms. These statistical associations are consistent with the source of the peptides used in the study. Comparison with a 6-frame translation of the S. nodorum genome assembly confirmed 905 existing gene annotations (including 119 not previously confirmed) and provided evidence supporting 144 genes with coding exon frameshift modifications, 604 genes with extensions of coding exons into annotated introns or untranslated regions (UTRs), 3 new gene annotations which were supported by tblastn to NR, and 44 potential new genes residing within un-assembled regions of the genome. CONCLUSION: We conclude that 2D LC MALDI-MS/MS is a powerful, rapid and economical tool to aid in the annotation of fungal genomic assemblies

Modelling primary proteolysis in cheddar cheese in commercial cool stores : a thesis presented in partial fulfilment of the requirements for the degree of Master of Technology in Bioprocess Engineering at Massey University

One issue identified as a possible problem during the manufacture of cheddar cheese is the possibility of producing a non-uniform product. It was proposed that a pallet of cheese experiencing different time-temperature histories, depending on the position within the pallet, could cause the heterogeneity. This work involved the investigation of that issue. The level of primary proteolysis observed in cheese was measured over time in cheeses of different compositions, stored at different temperatures. The remaining intact α s ₁casein was measured using reverse phase high performance liquid chromatography. Several trends were observed during maturation. High temperatures caused a faster rate of disappearance of α s ₁casein. The temperature relationship followed Arrhenius law. High moisture content caused a faster rate of the disappearance of α s ₁casein. The level of rennet added to the milk during production had a directly proportional effect on the rate of the disappearance of α s ₁casein. Salt had no observable effect in the range investigated here. From the data a kinetic model was developed that described the rate of disappearance of α s ₁casein in terms of the temperature, the moisture content, and the level of rennet in the cheese. The heat transfer occurring in the commercial pallet of cheese was mathematically modelled and solved numerically. The heat transfer model was then applied to produce data describing the time-temperature profile throughout a pallet of cheese for a variety of possible industrial storage conditions. The kinetic model developed was then used to predict the extent of proteolysis in each case. It was found that there would be significantly different levels of proteolysis within a pallet of cheese that had undergone chilling. A 10% difference in the level of proteolysis between the surface and the centre was observed after chilling for 40 days. During freezing the difference in the level of proteolysis after freezing was complete ranged from 10-25%. It was found that the heterogeneity was reduced during the thawing process and that the greatest reduction in non-uniformity was observed when thawed at lower temperatures

Dynamical freeze-out condition in ultrarelativistic heavy ion collisions

We determine the decoupling surfaces for the hydrodynamic description of heavy ion collisions at RHIC and LHC by comparing the local hydrodynamic expansion rate with the microscopic pion-pion scattering rate. The pion $p_T$ spectra for nuclear collisions at RHIC and LHC are computed by applying the Cooper-Frye procedure on the dynamical-decoupling surfaces, and compared with those obtained from the constant-temperature freeze-out surfaces. Comparison with RHIC data shows that the system indeed decouples when the expansion rate becomes comparable with the pion scattering rate. The dynamical decoupling based on the rates comparison also suggests that the effective decoupling temperature in central heavy ion collisions remains practically unchanged from RHIC to LHC.Comment: 7 pages, 9 figure

Advanced Transport Operating System (ATOPS) color displays software description: MicroVAX system

This document describes the software created for the Display MicroVAX computer used for the Advanced Transport Operating Systems (ATOPS) project on the Transport Systems Research Vehicle (TSRV). The software delivery of February 27, 1991, known as the 'baseline display system', is the one described in this document. Throughout this publication, module descriptions are presented in a standardized format which contains module purpose, calling sequence, detailed description, and global references. The global references section includes subroutines, functions, and common variables referenced by a particular module. The system described supports the Research Flight Deck (RFD) of the TSRV. The RFD contains eight Cathode Ray Tubes (CRTs) which depict a Primary Flight Display, Navigation Display, System Warning Display, Takeoff Performance Monitoring System Display, and Engine Display