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 and Snigirev, EPJC 45 (2006) 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., PRC 74 (2006) 064901; PRC 77 (2008) 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.
Program title: HYDJET++, version 2
Catalogue identifier: AECR_v1_0
Program summary URL:
http://cpc.cs.qub.ac.uk/summaries/AECR_v1_0.html
Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland
Licensing provisions: Standard CPC licence,
http://cpc.cs.qub.ac.uk/licence/licence.html
No. of lines in distributed program, including test data, etc.: 100 387
No. of bytes in distributed program, including test data, etc.: 797 019
Distribution format: tar.gz
Programming language: C++ (however there is a Fortran-written part which is included in the generator structure as a separate directory)
Computer: Hardware independent (both C++ and Fortran compilers and ROOT environment 1 (
http://root.cern.ch/) should be installed)
Operating system: Linux (Scientific Linux, Red Hat Enterprise, FEDORA, etc.)
RAM: 50 MBytes (determined by ROOT requirements)
Classification: 11.2
External routines: ROOT 1 (
http://root.cern.ch/)
Nature of problem: The experimental and phenomenological study of multi-particle production in relativistic heavy ion collisions is expected to provide valuable information on the dynamical behavior of strongly-interacting matter in the form of quark–gluon plasma (QGP) 2–4, as predicted by lattice Quantum Chromodynamics (QCD) calculations. Ongoing and future experimental studies in a wide range of heavy ion beam energies require the development of new Monte Carlo (MC) event generators and improvement of existing ones. Especially for experiments at the CERN Large Hadron Collider (LHC), implying very high parton and hadron multiplicities, one needs fast (but realistic) MC tools for heavy ion event simulations 5–7. The main advantage of MC technique for the simulation of high-multiplicity hadroproduction is that it allows a visual comparison of theory and data, including if necessary the detailed detector acceptances, responses and resolutions. The realistic MC event generator has to include maximum possible number of observable physical effects, which are important to determine the event topology: from the bulk properties of soft hadroproduction (domain of low transverse momenta
p
T
≲
1
GeV
/
c
) such as collective flows, to hard multi-parton production in hot and dense QCD-matter, which reveals itself in the spectra of high-
p
T
particles and hadronic jets. Moreover, the role of hard and semi-hard particle production at LHC can be significant even for the bulk properties of created matter, and hard probes of QGP became clearly observable in various new channels 8–11. In the majority of the available MC heavy ion event generators, the simultaneous treatment of collective flow effects for soft hadroproduction and hard multi-parton in-medium production (medium-induced partonic rescattering and energy loss, so-called “jet quenching”) is lacking. Thus, in order to analyze existing data on low and high-
p
T
hadron production, test the sensitivity of physical observables at the upcoming LHC experiments (and other future heavy ion facilities) to the QGP formation, and study the experimental capabilities of constructed detectors, the development of adequate and fast MC models for simultaneous collective flow and jet quenching simulations is necessary. HYDJET++ event generator includes detailed treatment of soft hadroproduction as well as hard multi-parton production, and takes into account known medium effects.
Solution method: A heavy ion event in HYDJET++ is a superposition of the soft, hydro-type state and the hard state resulting from multi-parton fragmentation. Both states are treated independently. HYDJET++ is the development and continuation of HYDJET MC model 12. The main program is written in the object-oriented C++ language under the ROOT environment 1. The hard part of HYDJET++ is identical to the hard part of Fortran-written HYDJET 13 (version 1.5) and is included in the generator structure as a separate directory. The routine for generation of single hard NN collision, generator PYQUEN 12,14, modifies the “standard” jet event obtained with the generator PYTHIA 6.4 15. The event-by-event simulation procedure in PYQUEN includes
1.
generation of initial parton spectra with PYTHIA and production vertexes at given impact parameter;
2.
rescattering-by-rescattering simulation of the parton path in a dense zone and its radiative and collisional energy loss;
3.
final hadronization according to the Lund string model for hard partons and in-medium emitted gluons.
Then the PYQUEN multi-jets generated according to the binomial distribution are included in the hard part of the event. The mean number of jets produced in an AA event is the product of the number of binary NN subcollisions at a given impact parameter and the integral cross section of the hard process in
NN collisions with the minimum transverse momentum transfer
p
T
min
. In order to take into account the effect of nuclear shadowing on parton distribution functions, the impact parameter dependent parameterization obtained in the framework of Glauber–Gribov theory 16 is used. 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 (the adapted C++ code FAST MC 17,18). Hadron multiplicities are calculated using the effective thermal volume approximation and Poisson multiplicity distribution around its mean value, which is supposed to be proportional to the number of participating nucleons at a given impact parameter of AA collision. The fast soft hadron simulation procedure includes
1.
generation of the 4-momentum of a hadron in the rest frame of a liquid element in accordance with the equilibrium distribution function;
2.
generation of the spatial position of a liquid element and its local 4-velocity in accordance with phase space and the character of motion of the fluid;
3.
the standard von Neumann rejection/acceptance procedure to account for the difference between the true and generated probabilities;
4.
boost of the hadron 4-momentum in the center mass frame of the event;
5.
the two- and three-body decays of resonances with branching ratios taken from the SHARE particle decay table 19.
The high generation speed in HYDJET++ is achieved due to almost 100% generation efficiency of the “soft” part because of the nearly uniform residual invariant weights which appear in the freeze-out momentum and coordinate simulation. Although HYDJET++ is optimized for very high energies of RHIC and LHC colliders (c.m.s. energies of heavy ion beams
s
=
200
and 5500 GeV per nucleon pair, respectively), in practice it can also be used for studying the particle production in a wider energy range down to
s
∼
10
GeV
per nucleon pair at other heavy ion experimental facilities. As one moves from very high to moderately high energies, the contribution of the hard part of the event becomes smaller, while the soft part turns into just a multi-parameter fit to the data.
Restrictions: HYDJET++ is only applicable for symmetric AA collisions of heavy (
A
≳
40
) ions at high energies (c.m.s. energy
s
≳
10
GeV
per nucleon pair). The results obtained for very peripheral collisions (with the impact parameter of the order of two nucleus radii,
b
∼
2
R
A
) and very forward rapidities may be not adequate.
Additional comments: Accessibility
http://cern.ch/lokhtin/hydjet++
Running time: The generation of 100 central (0–5%) Au+Au events at
s
=
200
A
GeV
(Pb+Pb events at
s
=
5500
A
GeV
) with default input parameters takes about 7 (85) minutes on a PC 64 bit Intel Core Duo CPU @ 3 GHz with 8 GB of RAM memory under Red Hat Enterprise.
References:
1 I.P. Lokhtin, A.M. Snigirev, Eur. Phys. J. C 46 (2006) 211.
2 N.S. Amelin, R. Lednicky, T.A. Pocheptsov, I.P. Lokhtin, L.V. Malinina, A.M. Snigirev, Iu.A. Karpenko, Yu.M. Sinyukov, Phys. Rev. C 74 (2006) 064901.
3 N.S. Amelin, I. Arsene, L. Bravina, Iu.A. Karpenko, R. Lednicky, I.P. Lokhtin, L.V. Malinina, A.M. Snigirev, Yu.M. Sinyukov, Phys. Rev. C 77 (2008) 014903.
RNA silencing (also known as RNA interference) is a conserved biological response to double-stranded RNA that regulates gene expression, and has evolved in plants as a defence against viruses. The ...response is mediated by small interfering RNAs (siRNAs), which guide the sequence-specific degradation of cognate messenger RNAs. As a counter-defence, many viruses encode proteins that specifically inhibit the silencing machinery. The p19 protein from the tombusvirus is such a viral suppressor of RNA silencing and has been shown to bind specifically to siRNA. Here, we report the 1.85-Å crystal structure of p19 bound to a 21-nucleotide siRNA, where the 19-base-pair RNA duplex is cradled within the concave face of a continuous eight-stranded β-sheet, formed across the p19 homodimer interface. Direct and water-mediated intermolecular contacts are restricted to the backbone phosphates and sugar 2′-OH groups, consistent with sequence-independent p19-siRNA recognition. Two α-helical 'reading heads' project from opposite ends of the p19 homodimer and position pairs of tryptophans for stacking over the terminal base pairs, thereby measuring and bracketing both ends of the siRNA duplex. Our structure provides an illustration of siRNA sequestering by a viral protein.
The phase structure of planar and channel, un-annealed and annealed proton exchanged waveguides made in benzoic acid and benzoic acid + lithium benzoate melts on Z cut of congruent lithium niobate ...crystal was investigated using mode spectroscopy, IR spectroscopy, XRD, SEM, AFM, microindentation, and wet etching techniques. In un-annealed waveguides, three layers (probably β
2
, β
1
, and κ
2
phases) can be distinguished. At least two different structural layers are present in annealed channel waveguides. Proton exchange (225
o
C, 28 h) in benzoic acid + 3 mol.% of lithium benzoate leads to formation of κ
2
phase and a thin layer of α phase.
Fluctuations of anisotropic flow in lead-lead collisions at LHC energies arising in HYDJET++model are studied. It is shown that intrinsic fluctuations of the flow which appear mainly because of the ...fluctuations of particle multiplicity, momenta and coordinates are insufficient to match the measured experimental data, provided the eccentricity of the freeze-out hypersurface is fixed at any given impact parameter b. However, when the variations of the eccentricity in HYDJET++ are taken into account, the agreement between the model results and the data is drastically improved. Both model calculations and the data are filtered through the unfolding procedure. This procedure eliminates the non-flow fluctuations to a higher degree, thus indicating a dynamical origin of the flow fluctuations in HYDJET++ event generator.
Physical observables in relativistic heavy ion collisions are determined by various multi-particle production mechanisms. The simultaneous model treatment of different collective nuclear effects at ...high energies (such as a hard multi-parton fragmentation in hot QCD-matter, thermal resonance production, hydrodynamical flows, etc.) is actually a rather complicated task. We discuss the simulation of the above effects by means of the Monte-Carlo model HYDJET++.
The accelerated cell death 11 (acd11) mutant of Arabidopsis provides a genetic model for studying immune response activation and localized cellular suicide that halt pathogen spread during infection ...in plants. Here, we elucidate ACD11 structure and function and show that acd11 disruption dramatically alters the in vivo balance of sphingolipid mediators that regulate eukaryotic-programmed cell death. In acd11 mutants, normally low ceramide-1-phosphate (C1P) levels become elevated, but the relatively abundant cell death inducer phytoceramide rises acutely. ACD11 exhibits selective intermembrane transfer of C1P and phyto-C1P. Crystal structures establish C1P binding via a surface-localized, phosphate headgroup recognition center connected to an interior hydrophobic pocket that adaptively ensheaths lipid chains via a cleft-like gating mechanism. Point mutation mapping confirms functional involvement of binding site residues. A π helix (π bulge) near the lipid binding cleft distinguishes apo-ACD11 from other GLTP folds. The global two-layer, α-helically dominated, “sandwich” topology displaying C1P-selective binding identifies ACD11 as the plant prototype of a GLTP fold subfamily.
Display omitted
•The acd11 mutant of Arabidopsis provides a genetic model for cell suicide in plants•ACD11 forms a GLTP fold and functions as a ceramide-1-phosphate transfer protein•apo-ACD11 is a unique GLTP fold because of a π bulge located near the lipid binding site•In acd11 mutants, ceramide-1-phosphate increases, but phytoceramide rises acutely
Plant immune response activation and localized cellular suicide halt pathogen spread during infection. The Arabidopsis accelerated cell death 11 (acd11) null mutant provides a genetic model of these processes. acd11 plants are found to have moderately elevated ceramide-1-phosphate but dramatically elevated phyto-ceramide, a potent programmed cell death (PCD) inducer. Using structure-function analyses, Mundy, Patel, Brown, and colleagues show that ACD11 protein forms a GLTP fold that binds and transfers ceramide-1-phosphate (and its phyto derivative), but not glycosphingolipid or ceramide, during membrane interaction. Thus, ACD11 helps maintain a proper balance between anti- and pro-PCD sphingolipid inducers in plants.
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