Quantum Field Kinetics

Using the general framework of quantum field theory, we derive basic equations of quantum field kinetics. The main goal of this approach is to compute the observables associated with a quark-gluon plasma at different stages of its evolution. We start by rewriting the integral equations for the field correlators in different forms, depending on the relevant dynamical features at each different stage. Next, two versions of perturbation expansion are considered. The first is best suited for the calculation of electromagnetic emission from chaotic, but not equilibrated, strongly interacting matter. The second version allows one to derive evolution equations, which are generalizations of the familiar QCD evolution equations, and provide a basis for the calculation of the initial quark and gluon distributions after the first hard interaction of the heavy ions.Comment: 13 pages, REVTeX, 2 postscript figures appende

Stable vortex and dipole vector solitons in a saturable nonlinear medium

We study both analytically and numerically the existence, uniqueness, and stability of vortex and dipole vector solitons in a saturable nonlinear medium in (2+1) dimensions. We construct perturbation series expansions for the vortex and dipole vector solitons near the bifurcation point where the vortex and dipole components are small. We show that both solutions uniquely bifurcate from the same bifurcation point. We also prove that both vortex and dipole vector solitons are linearly stable in the neighborhood of the bifurcation point. Far from the bifurcation point, the family of vortex solitons becomes linearly unstable via oscillatory instabilities, while the family of dipole solitons remains stable in the entire domain of existence. In addition, we show that an unstable vortex soliton breaks up either into a rotating dipole soliton or into two rotating fundamental solitons.Comment: To appear in Phys. Rev.

Towards Reliable Automatic Protein Structure Alignment

A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based on local structure similarity. In this work, we propose a method to incorporate global information in obtaining optimal alignments and superpositions. Our method, when applied to optimizing the TM-score and the GDT score, produces significantly better results than current state-of-the-art protein structure alignment tools. Specifically, if the highest TM-score found by TMalign is lower than (0.6) and the highest TM-score found by one of the tested methods is higher than (0.5), there is a probability of (42%) that TMalign failed to find TM-scores higher than (0.5), while the same probability is reduced to (2%) if our method is used. This could significantly improve the accuracy of fold detection if the cutoff TM-score of (0.5) is used. In addition, existing structure alignment algorithms focus on structure similarity alone and simply ignore other important similarities, such as sequence similarity. Our approach has the capacity to incorporate multiple similarities into the scoring function. Results show that sequence similarity aids in finding high quality protein structure alignments that are more consistent with eye-examined alignments in HOMSTRAD. Even when structure similarity itself fails to find alignments with any consistency with eye-examined alignments, our method remains capable of finding alignments highly similar to, or even identical to, eye-examined alignments.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Finite-temperature correlations in the one-dimensional trapped and untrapped Bose gases

We calculate the dynamic single-particle and many-particle correlation functions at non-zero temperature in one-dimensional trapped repulsive Bose gases. The decay for increasing distance between the points of these correlation functions is governed by a scaling exponent that has a universal expression in terms of observed quantities. This expression is valid in the weak-interaction Gross-Pitaevskii as well as in the strong-interaction Girardeau-Tonks limit, but the observed quantities involved depend on the interaction strength. The confining trap introduces a weak center-of-mass dependence in the scaling exponent. We also conjecture results for the density-density correlation function.Comment: 18 pages, Latex, Revtex

Heavy Quarks and Heavy Quarkonia as Tests of Thermalization

We present here a brief summary of new results on heavy quarks and heavy quarkonia from the PHENIX experiment as presented at the "Quark Gluon Plasma Thermalization" Workshop in Vienna, Austria in August 2005, directly following the International Quark Matter Conference in Hungary.Comment: 8 pages, 5 figures, Quark Gluon Plasma Thermalization Workshop (Vienna August 2005) Proceeding

Single Electrons from Heavy Flavor Decays in p+p Collisions at sqrt(s) = 200 GeV

The invariant differential cross section for inclusive electron production in p+p collisions at sqrt(s) = 200 GeV has been measured by the PHENIX experiment at the Relativistic Heavy Ion Collider over the transverse momentum range $0.4 <= p_T <= 5.0 GeV/c at midrapidity (eta <= 0.35). The contribution to the inclusive electron spectrum from semileptonic decays of hadrons carrying heavy flavor, i.e. charm quarks or, at high p_T, bottom quarks, is determined via three independent methods. The resulting electron spectrum from heavy flavor decays is compared to recent leading and next-to-leading order perturbative QCD calculations. The total cross section of charm quark-antiquark pair production is determined as sigma_(c c^bar) = 0.92 +/- 0.15 (stat.) +- 0.54 (sys.) mb.Comment: 329 authors, 6 pages text, 3 figures. Submitted to Phys. Rev. Lett. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Nuclear Modification of Electron Spectra and Implications for Heavy Quark Energy Loss in Au+Au Collisions at sqrt(s_NN)=200 GeV

The PHENIX experiment has measured mid-rapidity transverse momentum spectra (0.4 < p_T < 5.0 GeV/c) of electrons as a function of centrality in Au+Au collisions at sqrt(s_NN)=200 GeV. Contributions from photon conversions and from light hadron decays, mainly Dalitz decays of pi^0 and eta mesons, were removed. The resulting non-photonic electron spectra are primarily due to the semi-leptonic decays of hadrons carrying heavy quarks. Nuclear modification factors were determined by comparison to non-photonic electrons in p+p collisions. A significant suppression of electrons at high p_T is observed in central Au+Au collisions, indicating substantial energy loss of heavy quarks.Comment: 330 authors, 6 pages text, 3 figures. Submitted to Phys. Rev. Lett. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Measurement of Bottom versus Charm as a Function of Transverse Momentum with Electron-Hadron Correlations in p+p Collisions at sqrt(s)=200 GeV

The momentum distribution of electrons from semi-leptonic decays of charm and bottom for mid-rapidity |y|<0.35 in p+p collisions at sqrt(s)=200 GeV is measured by the PHENIX experiment at the Relativistic Heavy Ion Collider (RHIC) over the transverse momentum range 2 < p_T < 7 GeV/c. The ratio of the yield of electrons from bottom to that from charm is presented. The ratio is determined using partial D/D^bar --> e^{+/-} K^{-/+} X (K unidentified) reconstruction. It is found that the yield of electrons from bottom becomes significant above 4 GeV/c in p_T. A fixed-order-plus-next-to-leading-log (FONLL) perturbative quantum chromodynamics (pQCD) calculation agrees with the data within the theoretical and experimental uncertainties. The extracted total bottom production cross section at this energy is \sigma_{b\b^bar}= 3.2 ^{+1.2}_{-1.1}(stat) ^{+1.4}_{-1.3}(syst) micro b.Comment: 432 authors, 6 pages text, 3 figures. Submitted to Phys. Rev. Lett. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Measurement of Transverse Single-Spin Asymmetries for Mid-rapidity Production of Neutral Pions and Charged Hadrons in Polarized p+p Collisions at sqrt(s) = 200 GeV

The transverse single-spin asymmetries of neutral pions and non-identified charged hadrons have been measured at mid-rapidity in polarized proton-proton collisions at sqrt(s) = 200 GeV. The data cover a transverse momentum (p_T) range 0.5-5.0 GeV/c for charged hadrons and 1.0-5.0 GeV/c for neutral pions, at a Feynman-x (x_F) value of approximately zero. The asymmetries seen in this previously unexplored kinematic region are consistent with zero within statistical errors of a few percent. In addition, the inclusive charged hadron cross section at mid-rapidity from 0.5 < p_T < 7.0 GeV/c is presented and compared to NLO pQCD calculations. Successful description of the unpolarized cross section above ~2 GeV/c using NLO pQCD suggests that pQCD is applicable in the interpretation of the asymmetry results in the relevant kinematic range.Comment: 331 authors, 6 pages text, 2 figures, 3 tables. Submitted to Phys. Rev. Lett. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm