Relativistic heavy ion collisions with realistic non-equilibrium mean fields

We study the influence of non-equilibrium phase space effects on the dynamics of heavy ion reactions within the relativistic BUU approach. We use realistic Dirac-Brueckner-Hartree-Fock (DBHF) mean fields determined for two-Fermi-ellipsoid configurations, i.e. for colliding nuclear matter, in a local phase space configuration approximation (LCA). We compare to DBHF mean fields in the local density approximation (LDA) and to the non-linear Walecka model. The results are further compared to flow data of the reaction $Au$ on $Au$ at 400 MeV per nucleon measured by the FOPI collaboration. We find that the DBHF fields reproduce the experiment if the configuration dependence is taken into account. This has also implications on the determination of the equation of state from heavy ion collisions.Comment: Physics Letters B in press; 10 pages, Postscript file replaced by Latex file and 3 Postscript figure

Turbulent thermal diffusion in a multi-fan turbulence generator with the imposed mean temperature gradient

We studied experimentally the effect of turbulent thermal diffusion in a multi-fan turbulence generator which produces a nearly homogeneous and isotropic flow with a small mean velocity. Using Particle Image Velocimetry and Image Processing techniques we showed that in a turbulent flow with an imposed mean vertical temperature gradient (stably stratified flow) particles accumulate in the regions with the mean temperature minimum. These experiments detected the effect of turbulent thermal diffusion in a multi-fan turbulence generator for relatively high Reynolds numbers. The experimental results are in compliance with the results of the previous experimental studies of turbulent thermal diffusion in oscillating grids turbulence (Buchholz et al. 2004; Eidelman et al. 2004). We demonstrated that turbulent thermal diffusion is an universal phenomenon. It occurs independently of the method of turbulence generation, and the qualitative behavior of particle spatial distribution in these very different turbulent flows is similar. Competition between turbulent fluxes caused by turbulent thermal diffusion and turbulent diffusion determines the formation of particle inhomogeneities.Comment: 9 pages, 9 figure, REVTEX4, Experiments in Fluids, in pres

Large Oligomeric Complex Structures Can Be Computationally Assembled by Efficiently Combining Docked Interfaces

Macromolecular oligomeric assemblies are involved in many biochemical processes of living organisms. The benefits of such assemblies in crowded cellular environments include increased reaction rates, efficient feedback regulation, cooperativity and protective functions. However, an atom‐level structural determination of large assemblies is challenging due to the size of the complex and the difference in binding affinities of the involved proteins. In this study, we propose a novel combinatorial greedy algorithm for assembling large oligomeric complexes from information on the approximate position of interaction interfaces of pairs of monomers in the complex. Prior information on complex symmetry is not required but rather the symmetry is inferred during assembly. We implement an efficient geometric score, the transformation match score, that bypasses the model ranking problems of state‐of‐the‐art scoring functions by scoring the similarity between the inferred dimers of the same monomer simultaneously with different binding partners in a (sub)complex with a set of pregenerated docking poses. We compiled a diverse benchmark set of 308 homo and heteromeric complexes containing 6 to 60 monomers. To explore the applicability of the method, we considered 48 sets of parameters and selected those three sets of parameters, for which the algorithm can correctly reconstruct the maximum number, namely 252 complexes (81.8%) in, at least one of the respective three runs. The crossvalidation coverage, that is, the mean fraction of correctly reconstructed benchmark complexes during crossvalidation, was 78.1%, which demonstrates the ability of the presented method to correctly reconstruct topology of a large variety of biological complexes. Proteins 2015; 83:1887–1899. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc

An Introductory Guide to Aligning Networks Using SANA, the Simulated Annealing Network Aligner.

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological networks holds similar promise. Biological networks generally model interactions between biomolecules such as proteins, genes, metabolites, or mRNAs. There is strong evidence that the network topology-the "structure" of the network-is correlated with the functions performed, so that network topology can be used to help predict or understand function. However, unlike sequence comparison and alignment-which is an essentially solved problem-network comparison and alignment is an NP-complete problem for which heuristic algorithms must be used.Here we introduce SANA, the Simulated Annealing Network Aligner. SANA is one of many algorithms proposed for the arena of biological network alignment. In the context of global network alignment, SANA stands out for its speed, memory efficiency, ease-of-use, and flexibility in the arena of producing alignments between two or more networks. SANA produces better alignments in minutes on a laptop than most other algorithms can produce in hours or days of CPU time on large server-class machines. We walk the user through how to use SANA for several types of biomolecular networks

Off shell behaviour of the in medium nucleon-nucleon cross section

The properties of nucleon-nucleon scattering inside dense nuclear matter are investigated. We use the relativistic Brueckner-Hartree-Fock model to determine on-shell and half off-shell in-medium transition amplitudes and cross sections. At finite densities the on-shell cross sections are generally suppressed. This reduction is, however, less pronounced than found in previous works. In the case that the outgoing momenta are allowed to be off energy shell the amplitudes show a strong variation with momentum. This description allows to determine in-medium cross sections beyond the quasi-particle approximation accounting thereby for the finite width which nucleons acquire in the dense nuclear medium. For reasonable choices of the in-medium nuclear spectral width, i.e. $\Gamma\leq 40$ MeV, the resulting total cross sections are, however, reduced by not more than about 25% compared to the on-shell values. Off-shell effect are generally more pronounced at large nuclear matter densities.Comment: 31 pages Revtex, 12 figures, typos corrected, to appear in Phys. Rev.

Momentum-Dependent Mean Field Based Upon the Dirac-Brueckner Approach for Nuclear Matter

A momentum-dependent mean field potential, suitable for application in the transport-model description of nucleus-nucleus collisions, is derived in a microscopic way. The derivation is based upon the Bonn meson-exchange model for the nucleon-nucleon interaction and the Dirac-Brueckner approach for nuclear matter. The properties of the microscopic mean field are examined and compared with phenomenological parametrizations which are commonly used in transport-model calculations.Comment: 15 pages text (RevTex) and 4 figures (postscript in a separate uuencoded file), UI-NTH-930

Heavy ion collisions with non-equilibrium Dirac-Brueckner mean fields

The influence of realistic interactions on the reaction dynamics in intermediate energy heavy ion collisions is investigated. The mean field in relativistic transport calculations is derived from microscopic Dirac-Brueckner (DB) self-energies, taking non-equilibrium effects, in particular the anisotropy of the local phase space configurations, into account. Thus this approach goes beyond the local density approximation. A detailed analysis of various in-plane and out-of-plane flow observables is presented for Au on Au reactions at incident energies ranging from 250 to 800 A.MeV and the results are compared to recent measurements of the FOPI collaboration. An overall good agreement with in-plane flow data and a reasonable description of the out-of-plane emission is achieved. For these results the intrinsic momentum dependence of the non-equilibrium mean fields is important. On the other hand, the local density approximation with the same underlying DB forces as well as a standard non-linear version of the $\sigma\omega$ model are less successful in describing the present data. This gives evidence of the applicability of self energies derived from the DB approach to nuclear matter also far from saturation and equilibrium.Comment: 63 pages Latex, using Elsevier style, 20 ps-figures, to appear in Nucl. Phys.

Crystallization and Preliminary Analysis of Crystals of the 24-Meric Hemocyanin of the Emperor Scorpion (Pandinus imperator)

Hemocyanins are giant oxygen transport proteins found in the hemolymph of several invertebrate phyla. They constitute giant multimeric molecules whose size range up to that of cell organelles such as ribosomes or even small viruses. Oxygen is reversibly bound by hemocyanins at binuclear copper centers. Subunit interactions within the multisubunit hemocyanin complex lead to diverse allosteric effects such as the highest cooperativity for oxygen binding found in nature. Crystal structures of a native hemocyanin oligomer larger than a hexameric substructure have not been published until now. We report for the first time growth and preliminary analysis of crystals of the 24-meric hemocyanin (MW = 1.8 MDa) of emperor scorpion (Pandinus imperator), which diffract to a resolution of 6.5 Å. The crystals are monoclinc with space group C 1 2 1 and cell dimensions a = 311.61 Å, b = 246.58 Å and c = 251.10 Å (α = 90.00°, β = 90.02°, γ = 90.00°). The asymmetric unit contains one molecule of the 24-meric hemocyanin and the solvent content of the crystals is 56%. A preliminary analysis of the hemocyanin structure reveals that emperor scorpion hemocyanin crystallizes in the same oxygenated conformation, which is also present in solution as previously shown by cryo-EM reconstruction and small angle x-ray scattering experiments