Tuning Monte Carlo Generators: The Perugia Tunes

We present 9 new tunes of the pT-ordered shower and underlying-event model in PYTHIA 6.4. These "Perugia" tunes update and supersede the older "S0" family. The data sets used to constrain the models include hadronic Z0 decays at LEP, Tevatron minimum-bias data at 630, 1800, and 1960 GeV, Tevatron Drell-Yan data at 1800 and 1960 GeV, and SPS min-bias data at 200, 546, and 900 GeV. In addition to the central parameter set, called "Perugia 0", we introduce a set of 8 related "Perugia Variations" that attempt to systematically explore soft, hard, parton density, and colour structure variations in the theoretical parameters. Based on these variations, a best-guess prediction of the charged track multiplicity in inelastic, nondiffractive minimum-bias events at the LHC is made. Note that these tunes can only be used with PYTHIA 6, not with PYTHIA 8. Note: this report was updated in March 2011 with a new set of variations, collectively labeled "Perugia 2011", that are optimized for matching applications and which also take into account some lessons from the early LHC data. In order not to break the original text, these are described separately in Appendix B. Note 2: a subsequent "Perugia 2012" update is described in Appendix C.Comment: 46 page

High-throughput sequencing reveals a simple model of nucleosome energetics

We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of finite-size particles in an arbitrary external potential and arrays of DNA-bound histone octamers. We derive an analytical solution to infer free energies of nucleosome formation directly from nucleosome occupancies measured in high-throughput experiments. The sequence-specific part of free energies is then captured by fitting them to a sum of energies assigned to individual nucleotide motifs. We have developed hierarchical models of increasing complexity and spatial resolution, establishing that nucleosome occupancies can be explained by systematic differences in mono- and dinucleotide content between nucleosomal and linker DNA sequences, with periodic dinucleotide distributions and longer sequence motifs playing a secondary role. Furthermore, similar sequence signatures are exhibited by control experiments in which genomic DNA is either sonicated or digested with micrococcal nuclease in the absence of nucleosomes, making it possible that current predictions based on high-throughput nucleosome positioning maps are biased by experimental artifacts.Comment: 36 pages, 13 figure

Corrections to the Central Limit Theorem for Heavy-Tailed Probability Densities

Classical Edgeworth expansions provide asymptotic correction terms to the Central Limit Theorem (CLT) up to an order that depends on the number of moments available. In this paper, we provide subsequent correction terms beyond those given by a standard Edgeworth expansion in the general case of regularly varying distributions with diverging moments (beyond the second). The subsequent terms can be expressed in a simple closed form in terms of certain special functions (Dawson's integral and parabolic cylinder functions), and there are qualitative differences depending on whether the number of moments available is even, odd or not an integer, and whether the distributions are symmetric or not. If the increments have an even number of moments, then additional logarithmic corrections must also be incorporated in the expansion parameter. An interesting feature of our correction terms for the CLT is that they become dominant outside the central region and blend naturally with known large-deviation asymptotics when these are applied formally to the spatial scales of the CLT

Cross-Correlation Studies between CMB Temperature Anisotropies and 21 cm Fluctuations

During the transition from a neutral to a fully reionized universe, scattering of cosmic microwave background (CMB) photons via free-electrons leads to a new anisotropy contribution to the temperature distribution. If the reionization process is inhomogeneous and patchy, the era of reionization is also visible via brightness temperature fluctuations in the redshifted 21 cm line emission from neutral Hydrogen. Since regions containing electrons and neutral Hydrogen are expected to trace the same underlying density field, the two are (anti) correlated and this is expected to be reflected in the anisotropy maps via a correlation between arcminute-scale CMB temperature and the 21 cm background. In terms of the angular cross-power spectrum, unfortunately, this correlation is insignificant due to a geometric cancellation associated with second order CMB anisotropies. The same cross-correlation between ionized and neutral regions, however, can be studied using a bispectrum involving large scale velocity field of ionized regions from the Doppler effect, arcminute scale CMB anisotropies during reionization, and the 21 cm background. While the geometric cancellation is partly avoided, the signal-to-noise ratio related to this bispectrum is reduced due to the large cosmic variance related to velocity fluctuations traced by the Doppler effect. Unless the velocity field during reionization can be independently established, it is unlikely that the correlation information related to the relative distribution of ionized electrons and regions containing neutral Hydrogen can be obtained with a combined study involving CMB and 21 cm fluctuations.Comment: 10 pages, 3 figure

Next to leading order spin-orbit effects in the motion of inspiralling compact binaries

Using effective field theory (EFT) techniques we calculate the next-to-leading order (NLO) spin-orbit contributions to the gravitational potential of inspiralling compact binaries. We use the covariant spin supplementarity condition (SSC), and explicitly prove the equivalence with previous results by Faye et al. in arXiv:gr-qc/0605139. We also show that the direct application of the Newton-Wigner SSC at the level of the action leads to the correct dynamics using a canonical (Dirac) algebra. This paper then completes the calculation of the necessary spin dynamics within the EFT formalism that will be used in a separate paper to compute the spin contributions to the energy flux and phase evolution to NLO.Comment: 25 pages, 4 figures, revtex4. v2: minor changes, refs. added. To appear in Class. Quant. Gra

Uncertainties of the Inclusive Higgs Production Cross Section at the Tevatron and the LHC

We study uncertainties of the predicted inclusive Higgs production cross section due to the uncertainties of parton distribution functions (PDF). Particular attention is given to bbH Yukawa coupling enhanced production mechanisms in beyond SM scenarios, such as MSSM. The PDF uncertainties are determined by the robust Lagrange Multiplier method within the CTEQ global analysis framework. We show that PDF uncertainties dominate over theoretical uncertainties of the perturbative calculation (usually estimated by the scale dependence of the calculated cross sections), except for low Higgs masses at LHC. Thus for the proper interpretation of any Higgs signal, and for better understanding of the underlying electroweak symmetry breaking mechanism, it is important to gain better control of the uncertainties of the PDFs.Comment: LaTeX, JHEP, 19 pages, 14 figure

Spin and Rotations in Galois Field Quantum Mechanics

We discuss the properties of Galois Field Quantum Mechanics constructed on a vector space over the finite Galois field GF(q). In particular, we look at 2-level systems analogous to spin, and discuss how SO(3) rotations could be embodied in such a system. We also consider two-particle `spin' correlations and show that the Clauser-Horne-Shimony-Holt (CHSH) inequality is nonetheless not violated in this model.Comment: 21 pages, 11 pdf figures, LaTeX. Uses iopart.cls. Revised introduction. Additional reference

Experiments on Multidimensional Solitons

This article presents an overview of experimental efforts in recent years related to multidimensional solitons in Bose-Einstein condensates. We discuss the techniques used to generate and observe multidimensional nonlinear waves in Bose-Einstein condensates with repulsive interactions. We further summarize observations of planar soliton fronts undergoing the snake instability, the formation of vortex rings, and the emergence of hybrid structures.Comment: review paper, to appear as Chapter 5b in "Emergent Nonlinear Phenomena in Bose-Einstein Condensates: Theory and Experiment," edited by P. G. Kevrekidis, D. J. Frantzeskakis, and R. Carretero-Gonzalez (Springer-Verlag

Structure of a bacterial cell surface decaheme electron conduit

Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along “nanowire” appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split ß-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface

A bio-inspired image coder with temporal scalability

We present a novel bio-inspired and dynamic coding scheme for static images. Our coder aims at reproducing the main steps of the visual stimulus processing in the mammalian retina taking into account its time behavior. The main novelty of this work is to show how to exploit the time behavior of the retina cells to ensure, in a simple way, scalability and bit allocation. To do so, our main source of inspiration will be the biologically plausible retina model called Virtual Retina. Following a similar structure, our model has two stages. The first stage is an image transform which is performed by the outer layers in the retina. Here it is modelled by filtering the image with a bank of difference of Gaussians with time-delays. The second stage is a time-dependent analog-to-digital conversion which is performed by the inner layers in the retina. Thanks to its conception, our coder enables scalability and bit allocation across time. Also, our decoded images do not show annoying artefacts such as ringing and block effects. As a whole, this article shows how to capture the main properties of a biological system, here the retina, in order to design a new efficient coder.Comment: 12 pages; Advanced Concepts for Intelligent Vision Systems (ACIVS 2011